a score=385837.000000 s dm6.chr2R 24342861 29 + 25286936 GT--TTATTAGGTATTTGCACGCCATCTGAA s droSec1.super_23 109407 29 + 989336 GT--TTATTAGGTATTTGCACGCCATCTGAA s droYak3.chr2R 20198385 29 + 21139217 GT--TTATTAGGTATTTGCACGCCATCTGAA s droEre2.scaffold_4845 21596318 29 + 22589142 GT--TTATTAGGTATTTGCACGCCATCTGAA s droBia2.KB462602 788115 29 + 3129309 GT--TTATTAGGTATTTGCACGCCATCTGAG s droSuz1.KI419649 12033159 29 - 14502029 GT--TTATTAGGTATTTGTACGCCATCTGAG s droAna3.scaffold_13266 5704524 27 - 19884421 ----TTATTTTTTATTTGCACGCCATCTGAA s droBip2.KB464407 1953211 27 + 2915140 ----ttattttttatttgcacgCCATCTGAA s droEug2.KB465067 593688 29 + 1515531 tt--tcatttaatagtTACACGCCATCTGAA s droEle2.KB458573 513578 29 - 5320397 GT--TTATTAGGCATTTGCACGCCATCTGAA s droKik2.KB459527 268548 29 - 1234237 GT--TTATTAGGTGATTGCACGCCATCTGAA s droTak2.KB461535 133255 29 - 669855 TT--TTAAAACACTTTTGCACGCCATCTGAG s droRho2.KB449310 26812 29 - 65043 GT--TTATTAGGTATTTGCACGCCATCTGAA s droFic2.KB457177 73764 29 + 995874 tt--ttattaggtATTTGCACGCCATCTGAA s droPse3.chr3 1342092 29 - 19787792 GT--TTATTAAGTATTTTGCAGCCATCTGAA s droPer1.super_34 530932 29 - 916997 GT--TTATTAAGTATTTTGCAGCCATCTGAA s droMir2.chr3 1383168 29 - 20862834 GT--TTATTAAGTATTTTGCAGCCATCTGAA s droWil2.CH963894 1298778 29 + 2843958 GT--TTATTAGGTATTTGCACGCCATCTGAA s droVir3.scaffold_12875 7343533 31 + 20611582 TTTGTTATTAGGTATTTGCACGCCATCTGAA s droMoj3.scaffold_6496 26138254 31 + 26866924 TTTGTTATTAGGTATTTGCACGCCATCTGAA s droAlb1.JH854640 302295 31 + 406291 TTTGTTATTAGGTATTTGCACGCCATCTGAA s droGri2.scaffold_15245 891077 31 + 18325388 TTTGTTATTAGGTATTTGCACGCCATCTGAA a score=333003.000000 s dm6.chr2R 24342890 36 + 25286936 GAACAACGAACGCCAGCTATCGAT------CGC--AAG--------------------T-TTAGC s droSim1.chr2R 18689695 36 + 19596830 GAACAACGAACGCCAGCTATCGAT------CGC--AAG--------------------T-TTAGC s droSec1.super_23 109436 36 + 989336 GAACAACGAACGCCAGCTATCGAT------CGC--AAG--------------------T-TTAGC s droYak3.chr2R 20198414 42 + 21139217 GAACAACGAACGCCAGCTATCGATCGCAAGCGC--AAG--------------------T-TTAGA s droEre2.scaffold_4845 21596347 42 + 22589142 GAACAACGAACGCCAGCTATCGATCGCAAGCGC--AAG--------------------T-TTAGC s droBia2.KB462602 788144 44 + 3129309 CAACAACG-TTGCCAGCCATCGAT------CGC--AAG-----------TTAGCTCAGT-TTAGC s droSuz1.KI419649 12033188 45 - 14502029 CAACAACG-TTGCCAGCCATCGAT------CGC--AAG----------TTTAGCTCAGT-TTAGA s droAna3.scaffold_13266 5704551 32 - 19884421 GCACAACG----CCATCATTCGAT------CGC--AAG--------------------T-TTAGC s droBip2.KB464407 1953238 32 + 2915140 GCACAACG----CCATCATTCGAT------CGC--AAG--------------------T-TTAGC s droEug2.KB465067 593717 22 + 1515531 --------------GCACATCGAT------CGC--AAG--------------------T-TTAGC s droEle2.KB458573 513607 32 - 5320397 GCACAACG----TCAGCCATCGAT------CGC--AAG--------------------T-TTAGC s droKik2.KB459527 268577 32 - 1234237 GCACAACG----CCAGCCATCGAT------CGC--TAG--------------------T-TTAGC s droTak2.KB461535 133284 55 - 669855 CAACAACG-TTGCCAGCCATCGAT------CGC--AAgtttagctctgtttagctctgt-ttagc s droRho2.KB449310 26841 32 - 65043 GCACAACG----TCAGCCATCGAT------CGC--AAG--------------------T-TTAGC s droFic2.KB457177 73793 26 + 995874 GCACAACG----CCAGCCGTCGAT------CGC--AAG--------------------------- s droPse3.chr3 1342121 36 - 19787792 GCACAACG-GAGGCAACGATCGAT------CGC--AAG--------------------TCTCAGC s droPer1.super_34 530961 36 - 916997 GCACAACG-GAGGCAACGATCGAT------CGC--AAG--------------------TCTCAGC s droMir2.chr3 1383197 36 - 20862834 GCACAACG-GAGGCAACGATCGAT------CGC--AAG--------------------TCTCAGC s droWil2.CH963894 1298807 34 + 2843958 GCACAACG-AAGGCAACAATCGAT------CGCAAAAG--------------------T-TT--- s droVir3.scaffold_12875 7343564 35 + 20611582 GCACAACG-AAGGCAACAATCGAT------CGC--AAA--------------------G-TTAGC s droMoj3.scaffold_6496 26138285 35 + 26866924 GCACAACG-AAGGCAACAATCGAT------CGC--AAA--------------------G-TTAGC s droAlb1.JH854640 302326 35 + 406291 GCACAACG-AAGGCAACAATCGAT------CGC--AAA--------------------G-TTAGC s droGri2.scaffold_15245 891108 35 + 18325388 GCACAACG-AAGGCAACAATCGAT------CGC--AAA--------------------G-TTAGC a score=-25467.000000 s dm6.chr2R 24342926 3 + 25286936 CC--------------------------G s droSim1.chr2R 18689731 3 + 19596830 CC--------------------------G s droSec1.super_23 109472 3 + 989336 CC--------------------------G s droYak3.chr2R 20198456 3 + 21139217 CC--------------------------G s droEre2.scaffold_4845 21596389 3 + 22589142 CC--------------------------G s droBia2.KB462602 788188 3 + 3129309 CC--------------------------G s droSuz1.KI419649 12033233 3 - 14502029 CC--------------------------G s droAna3.scaffold_13266 5704593 3 - 19884421 TC--------------------------G s droBip2.KB464407 1953280 3 + 2915140 TC--------------------------G s droEug2.KB465067 593739 3 + 1515531 CC--------------------------G s droEle2.KB458573 513639 3 - 5320397 TC--------------------------G s droKik2.KB459527 268609 2 - 1234237 CC--------------------------- s droTak2.KB461535 133339 3 - 669855 CC--------------------------G s droRho2.KB449310 26873 3 - 65043 TC--------------------------G s droPse3.chr3 1342157 29 - 19787792 CCTGCTCCCGACCAAATCCAAATACAAAA s droPer1.super_34 530997 29 - 916997 CCAGCTCCCGACCAAATCCAAATACAAAA s droMir2.chr3 1383233 29 - 20862834 CCTGCTCCCGACCAAATCCAAATACAAAA s droWil2.CH963894 1298841 3 + 2843958 TC--------------------------A s droVir3.scaffold_12875 7343599 3 + 20611582 TC--------------------------G s droAlb1.JH854640 302361 3 + 406291 TC--------------------------G s droGri2.scaffold_15245 891143 3 + 18325388 TC--------------------------G a score=837338.000000 s dm6.chr2R 24342929 162 + 25286936 TCGAATC----------------------------GT------TTCGA-ATTCGTATTTGG-----AATGAACCACAATAAAAT------CGCCACAAATAAAGTAAA---CAGTCC--AAACAAGTGCC----------------TAGCGACAAAT-------AAGC---AAAC-------------------CAACTGCAACGCATACGGA-------ACAAACAAAA--------------ACACAAATAT--TTCCCATAAC-------TGCA---CTAAATCTACG s droSim1.chr2R 18689734 162 + 19596830 TCGAATC----------------------------GT------TTCGA-ATTCGTATTGGG-----AATGAACCACAATAAAAT------CGCCACAAATAAAGTAAA---CAGTCC--AAACAAGTGCC----------------TAGCGACAAAT-------AAGC---AAAC-------------------CAACTGCAACGCATACGGA-------ACAAACAAAA--------------ACACAAATAT--TTCCCATAAC-------TGCA---ATAAATCCACG s droSec1.super_23 109475 162 + 989336 TCGAATC----------------------------GT------TTCGA-ATTCGTATTTGG-----AATGAACCACAATAAAAT------CGCCACAAATAAAGTAAA---CAGTCC--AAACAAGTGCC----------------TAGCGACAAAT-------AAGC---AAAC-------------------CAACTGCAACGCATACGGA-------ACAAACAAAA--------------ACACAAATAT--TTCCCATAAC-------TGCA---CTAAATCCACG s droYak3.chr2R 20198459 162 + 21139217 TCGAATC----------------------------GT------TTCGA-ATTCGTATTTGG-----AATGAACCACAATAAAAT------CGCCACAAATAAAGTAAA---CAGTCC--AAACAAGTGCC----------------TAGCGACAAAT-------AAGC---AAAG-------------------CAACTGCAACGCATAcgga-------acaaacaaaa--------------acacaaatat--ttcccatAAC-------TGCA---CCAAATCCACG s droEre2.scaffold_4845 21596392 162 + 22589142 TCGAATC----------------------------GT------TTCGA-ATTCGTATTTGG-----AATGAACCACAATAAAAT------CGCCACAAATAAAGTAAA---CAGTCC--AAACAAGTGCC----------------TAGCGACAAAT-------AAGC---AAAC-------------------CAACTGCAACGCATACGGA-------ACAAACAAAA--------------ACACAAATAT--TTCCCATAAC-------TGCA---CTAAATCCGCG s droBia2.KB462602 788191 168 + 3129309 TCGAATC----------------------------GT------TTCGA-A-TCGTATTTGG-----AATGAACCACAATAAAAT------CGCCACAAATAAAGCAAA---CGGTCC--AAACAAGTGCC----------------TAGCGACAAATAAGCGATAAGC---AAAC-------------------TAAATGCAACGCATTCGGA-------ACAAACAAAA--------------GCGCAAATAC--TTCCCATAGC-------CGCA---CGGAAACAACG s droSuz1.KI419649 12033236 168 - 14502029 TCGAATC----------------------------GT------TTCGA-A-TCGTATTTGG-----AATGAACCACAATAAAAT------CGCCACAAATAAAGTAAA---CAGTCC--AAACAAGTGCC----------------TAGCGACAAATAAGCAACAAGC---AAAC-------------------TAAATGCAACGCATACGGA-------ACAAACAAAA--------------GCACAAATAT--TTCCCATAAC-------TGCA---CGGAAACaacg s droAna3.scaffold_13266 5704596 160 - 19884421 CCGCCTC----------------------------GA------TCCGATACTCGTATTTGG-----AATGAACAACAATAAAAT------CGCCACAAATAAAGTAAA---CGGTCC--AAACAAGTGCC---------------AGAGTGACAAAT-------AAGT---CGCC-------------------TAAATGCAGCCGCCACAGA-------TGAATCAAAT------------------AATTTT--TGTCAATAAC-------TAAG---CGAAACAAGCG s droBip2.KB464407 1953283 161 + 2915140 CCGCCTC----------------------------GA------TCCGATATTCGTATTTGG-----AATGAACAACAATAAAAT------CGCCACAAATAAAGTAAA---CGGTCC--AAACAAGTGCC---------------ACAGTGACAAAT-------AAGT---CGCC-------------------TAAATCCAGCCGATACAGA-------Tgaatcaaat-----------------caatttt--tgtcaATAAC-------TAAA---CAAAACAAGCG s droEug2.KB465067 593742 143 + 1515531 TCC----------------------------------------------CGTCGTATTTGG-----AATGATCCACAATAAAGT------CGCCACAAATAAAGTAAA---CAGCCC--AAACAAGTGCC----------------TAGCGACAAAT-------AAGC---CGAC-------------------TAAATGCAGCGCATTCGGA-------ACTCGCAAAA---------------CACAAATAC--TTCCCATAAC-------Tgat---cgaa------- s droEle2.KB458573 513642 163 - 5320397 TCG---------------------------------T------TTCGA-A-TCGTATTTGG-----AATTAACCACAATAAAAT------CGCCACAAATAAAGTAAA---CAGTCC--AAACAAGTGCC----------------TAGCGACAAAT-------AAGC---AAAC-------------------TTAATGCAGCGCATACGGA-------ACAAACAAACCACACAAATATTTcccataaatat--ttcccaTAAC-------TGCA---CGGC------- s droKik2.KB459527 268611 196 - 1234237 TCAGCTC---------TCTgtattttccgt-----tt------tccga-A-TCGTATTTGG-----AATGAACCACAATAAAAT------CGCCACAAATAAAGCAAACAGCAGTCC--AAACAAGTGCCGC----------CGAGCGACGACAAAT-------AAGCT--AAAC-------------------TAAATGCAACACATTCGGAGAGCAGCGCCAACAAAT--------------ATccaaatataatttctataataaCCGCGCACa---cgaaaa----- s droTak2.KB461535 133342 173 - 669855 TCGAATC----------------------------GTA-TCGCCTCGA-A-TCGTATTTGG-----ATTGAACCACAATAAAAT------CGCCACAAATAAAGTAAA---CAGTCC--AAACAAGTGCC----------------TAGCGACAAATAAGCGACCAGC---AAAC-------------------TAAATGCAACGCATAcgga-------acaaacaaaa--------------acacaaatat--ttccCATAAC-------TGCA---CGGAATCAACG s droRho2.KB449310 26876 162 - 65043 TC---------------------------------GT------TTCGA-A-TCGTATTTGG-----AATGAACCACAATAAAAT------CGCCACAAATAAAGTAAA---CAGTCC--AAACAAGTGCC----------------TAGCGACAAAT-------AAGC---AAAC-------------------TAAATGCAACGCATAcgga-------acaaacaaaa-acacaagtaTTTCCCATAAATAT--TTCCCATAAC-------TGCA---CGAT------- s droFic2.KB457177 73819 140 + 995874 -----------------------------------TT--------------TCGTATTTGG-----AAAGAACCACAATAAAAT------CGCCACAAATAAAGTTAA---CAGTCC--AAACAAGTGCC----------------TAGCGACAAAT-------AAGC----AAC-------------------TAAATGCAACGCATAAGGA-------ACAAGCagaa--------------acacaaatat--tttccataac-------tGCA---CGAa------- s droPse3.chr3 1342186 186 - 19787792 CCGAATCGCACACGCACCTACTCGTTGCGTACGTCGC------TGCGG-A-TCGTATTAGGcattaaattaaacacaatCAAAT------CGCCACAAATAAAGCCAACAACAGTCC--AAACAAGTGCCACAGCAAACAAATGCCGAGCGACAAAT-------AAGT-----------------------------------CACACAGAAC-------ACAGGCGAGA--------------------------TTTccaaaat-------taga---aaataaa---- s droPer1.super_34 531026 200 - 916997 CCGAATCGCACACGCACCTACTCGCTGCGTACGTCGC------TGCGG-A-TCGTATTAGGCATTAAATTAAACACAATCAAAT------CGCCACAAATAAAGCCAACAACAGTCC--AAACAAGTGCCACAGCAAACAAATGCCGAGCGACAAAT-------AAGTC--AACT-------------------GAACTGCAACACACAGAAC-------ACAGGCGAGA--------------------------TTTCCAAAAT-------TAGA---AAATAAA---- s droMir2.chr3 1383262 194 - 20862834 CCGAATCGCACACGCACCTACTCGCTGCGTACGTCGC------TGCGG-A-TCGTATTAGGCATTGAATTAAACACAATCAAAT------CGCCACAAATAAAGCCAACAACAGTCC--AAACAAGtgccacagcaaacaaatgccGAGCGACAAAT-------AAGT---------------------------CACTgcaacacacagaac-------acaggcGAGA--------------------------TTTccaaaat-------taga---aaataaa---- s droWil2.CH963894 1298844 151 + 2843958 TCGATCC----------------------------GTATTTACGTCGT-TTTCGTATTAGG-----CATTAACCacaataaaat------caacacaaataaagtaaa---aagtccaaaaacaagtgca----------------aagctacaaat-------aagtcaaaact-------------------taaattc--------caaa-------acaaacaaaa--------------aaaaaaaaaa---------aaa-------taaa---agaa------- s droAlb1.JH854640 302369 134 + 406291 -------------------------------------------------------------------GCCAGACGCACCAAATATaacaactacatctacaacaacaa---cagcag--cgacaa---------------------caacaacacca-------atac--------------------------caacaacagcagcagcagc-------aacggcaaac--------------aCTCACGCGC--AGTTCACAAC--------GCAATTCGAATTTGGCA s droGri2.scaffold_15245 891146 136 + 18325388 ------------------------------------------------------------------------ACACACCAAaaa-------------tacaaaaaaag---aaaaaa--aaagaa---------------------aaacaacatat-------atat---atatatatatatatatatatatacaaaagcagcagcagcaac-------aacaacaaca--------------ataagaacac--acaccaaaac--------GCG---CAACGTTCGCA a score=-3759.000000 s dm6.chr2R 24343091 2 + 25286936 A-A s droSim1.chr2R 18689896 2 + 19596830 A-A s droSec1.super_23 109637 2 + 989336 A-A s droYak3.chr2R 20198621 2 + 21139217 A-A s droEre2.scaffold_4845 21596554 2 + 22589142 A-A s droBia2.KB462602 788359 2 + 3129309 A-A s droSuz1.KI419649 12033404 2 - 14502029 a-a s droAna3.scaffold_13266 5704756 2 - 19884421 AT- s droBip2.KB464407 1953444 1 + 2915140 A-- s droTak2.KB461535 133515 2 - 669855 A-A s droGri2.scaffold_15245 891282 2 + 18325388 A-A a score=-312293.000000 s dm6.chr2R 24343093 81 + 25286936 GTCGAAACAA--------------AGTTAGGCGTA----TTTTTTTTACCA-G--AAACAC--TTA-AA-------------------CAATTTTTACAAAAAACGGATATTA--ATGCAA------------TCA--GT s droSim1.chr2R 18689898 78 + 19596830 GTCGAAACGA--------------AGTTAGGCG------TTTTTTTTACCA-G--AAA-AC--TTG-GA-------------------CAAATTTAACAAAAAACGGATATTA--ATGCAA------------TCA--GT s droSec1.super_23 109639 78 + 989336 GTCGAAACGA--------------AGTTAGGCG------TTTTTTTTACCA-G--AAA-AC--TTA-AA-------------------CAAATTTAACAAAAAACGGATATTA--ATGCAA------------TCA--GT s droYak3.chr2R 20198623 78 + 21139217 GTCGAAACAA--------------agttaaact------tttttttaacga-G--ACA-GC--TTG-Aa-------------------caaattttacaaaaaaCGGATATCA--AAGCAA------------TCA--CT s droEre2.scaffold_4845 21596556 78 + 22589142 GTCGAAACAA--------------AGATAAACG------ATTTTTTTACAA-G--CAA-AC--TTG-AA-------------------CAAATTTTACAAAATACGGATATTA--ATGCAA------------TCA--GT s droBia2.KB462602 788361 58 + 3129309 ATCAAAGcaa--------------tttttaaagga-----tttttttgcaa-a--aac-ac--TTGCGA------------------------------------------TA--AAACAA---------GACTCA---- s droSuz1.KI419649 12033406 82 - 14502029 atcaaaacaa--------------attcaaaagga----ttttttttacaa-a--aag-aC--TTGCGA-------------------TAAGTTtgaagaaaaaaggaaatta--aaacaa---------gactCA---- s droBip2.KB464407 1953445 65 + 2915140 ---------------------------TAACCG------------TTACCA-A--CAA-AC--TAA-AAAGGCTTGAAT--------CCAACTtgaatcaaaatcgaaaccga--aaactt------------------- s droEug2.KB465067 593885 80 + 1515531 atcaaaacaa--------------atttaaaag------gaTTTCCCCAAA-A--CGA-CT--TTG-AA-------------------TTTATTCAAACAAAATCGGAAATTA--AAACGG------------CCATAAA s droEle2.KB458573 513805 64 - 5320397 gttcaaataa--------------atcaaaaaa------ggatttttataaca--aaa-at--ttg-aa-----------------------------gaaaaacggaaatta--aaaaaa------------------- s droKik2.KB459527 268807 109 - 1234237 atcaaaacaaccCGAGTCCGACGCAGCTGAAAAAG----GATTTTCGATAG-ACTCaa-gc--tta-aa----ttaaacaaaataaatcaaacttgACTaaactcgaaataaa--acgaga------------taa---- s droTak2.KB461535 133517 79 - 669855 ATCAAAGCCA--------------ATTTGGAAgga----ttttttgaacaa-a--aag-tC--TTGGAA-------------------TAAATTTGAGGAAAAACGGAAATTA--AAAGAA--------------A--CC s droRho2.KB449310 27038 78 - 65043 ATCcaaacaa--------------atggaaaaagga---tttttcaaataa-a--aat-ac--ttt-aa-----------------aataaatttgaagaaaaacggaaatta--aaaCGA------------------- s droFic2.KB457177 73959 80 + 995874 gtcaaaacaa--------------tttaaaaaagg----atttttttaaaa-g--act-acagtta-aa-------------------------acaacaaaagcggaaaTTAGCAAGCGA----------TATCA--AT s droPse3.chr3 1342372 34 - 19787792 ------------------------------------------------------------------------------------------aaccgcacAAAGCAGgaacaaca--gaaaat----------attta---- s droPer1.super_34 531226 34 - 916997 ------------------------------------------------------------------------------------------AACCGCACAAAGCAGGAACAACA--GAAAAT----------ATTTA---- s droMir2.chr3 1383456 34 - 20862834 ------------------------------------------------------------------------------------------aaccgcaCAAAGCAGGaagaaca--gaaaat----------attta---- s droWil2.CH963894 1298995 51 + 2843958 -----------------------------------------------agag-a--aga-aa--tac-aa-------------------tacaataaatacatagcaaaaattg--ataaaa------------gaa--aa s droGri2.scaffold_15245 891288 72 + 18325388 -----------------------------------TTCGAATTTGGCAGTA-G--CCA-CA--TTA-AA-------------------ACAGCTTTTAAAGCGAAAAAGACCA--AAACAAGTGCCAAACGCATC----- a score=-638244.000000 s dm6.chr2R 24343174 138 + 25286936 TCGA----GACAAGCAGACAGCAAGCGGAAGACTTA---AGGAGA------TAACAA-CTTAT------------AGAGGCCAT---------------AATCAAAGGAATA---AAGCACCATCAGCCAG--CGATGA--GAAGGAACGT---------C--TTCAAT------GATAA------------ACCTTCGAAA------------A-------CTTTTAGAAAAT------------------- s droSim1.chr2R 18689976 138 + 19596830 TCGA----GACAAGGAGACAGCCAGCGGAAGACTTA---AGGAGC------TCAATA-CTTAT------------AGAGGCCAT---------------AATCAAAGAAATA---AAGCACCATCAACCAG--CAGTGA--AAAGGAACGT---------C--TTCAAT------GATAA------------ACCTTCGAAA------------A-------CTTTTAGAAAAT------------------- s droSec1.super_23 109717 138 + 989336 TCGA----GACAAGGAGACAGCAAGCGGAAGACTTA---AGGAAC------TCAATA-CTTAT------------AGAGGCCAT---------------AATCAAAGAAATA---AAGCACCATCAACCAG--CAGTGA--AAAGGAACGT---------C--TTCAAT------GATAA------------ACCTTCGAAA------------A-------CTTTTAGAAAAT------------------- s droYak3.chr2R 20198701 138 + 21139217 TCGC----GACAAGGCGACAACAAGAGGAAGACTCC---AAGATC---CGACACCAA-CTCAC------------AGAGGCCATAAAAGGGACAGCAGGAAGCTAAGGAATAAAGAAGTAGAACCAACCAG------------------------------------AT------GATAA------------ACTTTCGAAA------------A-------CGTttagaaaat------------------- s droEre2.scaffold_4845 21596634 158 + 22589142 TCGA----GACAAGGAGACTACACAAGAAGGACTTC---AAGAGCTGACAACACCAA-TTCAT------------AGAGGCCATAGAAAGGACAGCAGTAATCAAAGGAGCA---AAGCACCATCAACCAG--TTGAGA---AAGGAACGT---------C--TTCAAT------GCGAA------------ACCTTCGAAA------------A-------CTTTTAGAAAAT------------------- s droBia2.KB462602 788419 146 + 3129309 ---------ACAGCAAAACATCAAGAGCTAAGCCTc---aaactt------ataaaa-t----------------aaaagccattAATAGACAAACAGTAATCAAAGG-------AAGTAGCAT-TACGAG--GAAAAACGGATGAAACAT----TAAAAC--GTCAAT------GATAA------------ACTTACAAAA------------A-------cggtttaataat------------------- s droSuz1.KI419649 12033488 147 - 14502029 ---------AGAGGAAATCAACAAGAACAAaacctt---aaattt------aattaa-ttta-------------aaaggccataaaaagacgaaaagcaatcaaagg-------aagcagaat-aaggaa--ataaaa--aaaggaaagt----aaaaac--atcaat------gataa------------acctacaaaa------------a-------cggtcagaacat------------------- s droBip2.KB464407 1953510 137 + 2915140 ---------acgaaggagcaaaaaaaacaatactac---TCTAAA------GTATAA-TCCAA------------AGGAGCA-----------------AATATAAGACAAA---ACACAGTAACACACAA--AAGGAT--CAAGAA-------------C--TTCAA--------ATAA------------AACTCCAAAACAAAGGACTAACA-------CTTTAAGGAAAC------------------- s droEug2.KB465067 593965 108 + 1515531 CCAA----GACAAGGAGACTCCGAGAGGAAGACTTt---aaaacc------tacaaa-ctaa------------------actt---------------aattaaataaaaa---gaccataaaaagacaa--acgaga---------------------a--atcaa--------ataa------------acttacgaaa------------a-------------------------------------- s droEle2.KB458573 513869 147 - 5320397 -------------ggagacACTAAGAGGAAGACTTG---agagct--aaaataaaaa-ttagttaaaaga-----caaagccataaaaagacaaaata-aattaaaggaagg---aagcagcattcaaaaa--tagagg--aataaacaac---------c--ttcaat------gataa--------------cgataaaa------------a------------agaaact------------------- s droKik2.KB459527 268916 97 - 1234237 ------------aggagactttgaataaaaatctac---aaaaat------------------------------aaatctcaa---------------aaacaaataaata---aaaca--------------agcaa--ataaaacatt---------t--ttctataaatcagataa------------a----caata------------a-------------------------------------- s droTak2.KB461535 133596 127 - 669855 ACTG----GAGAGGAAGACATCAAGAGCTAAacgtt---aaaatt------attaaa-tta--------------aaaggccatacaaagaaaaagt--aatcaaaggaagg---a------------cag--taaaaa---------------------c--atcaat------gataa------------acctacaaaa------------a-------cgggcaaaaaat------------------- s droRho2.KB449310 27116 134 - 65043 -------------GGAGACACTTAGAGGAAGACTTC---AAGAGC------TAAtca-tacaattaaataaaaccccaagccataaaaagacgtaaagaaataaaaggaaga---aagcagcatacaaaaa--tagata--------------------------caat------tttaa------------aattttgaca------------a----------------aat------------------- s droFic2.KB457177 74039 148 + 995874 CCGG--------AGCGAAACTTAAGCGGACGACTTC---AAAACT---TTTGATAAA-TTGATACAACTC-----ACaagccataaaaaacaa------cataaagggaagg---aagcaactggatgaag--gataaa--aataaaaaacttaaaagaaa--atcaac------tttaa------------atgaaagaa---------------------------------------------------- s droPse3.chr3 1342406 90 - 19787792 ---------------------------caatactgt---aaaaaa------aaaaca-a----------------aaacgcc-----------------actcaacaataaa---accaaaaatattgcAA--GGAATT--TTTAAACCAC---------T--TGCAAA------ATCAA------------ACGC--------------------------------------------------------- s droPer1.super_34 531260 93 - 916997 ---------------------------CAATACTGTAAAAAAAAA------AAAACA-A----------------AAACGCC-----------------ACTCAACAATAAA---ACCAAAAATATTGCAA--GGAATT--TTTAAACCAC---------T--TGCAAA------ATCAA------------ACGC--------------------------------------------------------- s droMir2.chr3 1383490 91 - 20862834 ---------------------------caatactgt---aaaaac------aaaagaca----------------aaacgcC-----------------ACTCaacaataaa---accaaatatatTACAA--GGAATT--TTTAAACGAC---------T--TGCACA------ATTAA------------ACGC--------------------------------------------------------- s droWil2.CH963894 1299046 159 + 2843958 ttgatattgtaacaacaacaacaacaaaaaggaact---gaaatt------ctatat-ttcc-------------aaagacggcaaaaacaaaa-----aacaaaccgaaca---agcaaaaacCTTTTAG--TGAATT-Gtattaacaat---------t--ttctaa------atcga------------aattaaatca------------aagcaacgcaaggagaaaaa------------------- s droMoj3.scaffold_6496 26138320 142 + 26866924 ------TCGAGACcaaat------atacaaagcaac---agatat------acaaaa-g----------------cagcagcaagagcaa---------cagcaacatcagc---aat-aacgacgacaagaacaacaa--caacaacaac---------aacaacaac------aataaAT----------ACTTACGCGC------------A----GCTCGC------AGTTCGCAT-----------TT s droGri2.scaffold_15245 891360 164 + 18325388 ------TCGA---CAAATAAGTCAACACAAAACAAT---ACCAAA------TCGAAT-C----------------AAACATca-----aa---------cagcaactacagc---aacaaacagcaaccag--cagcaa--caacaacaac---------a--aacagT------TACAAATTCAATGTGCAATTTTTGTAT------------T----GCTCTTACAAAGATTTTGCATAATTTTTCAAATT a score=-35569.000000 s dm6.chr2R 24343312 12 + 25286936 --AGCAAACATCCC s droSim1.chr2R 18690114 12 + 19596830 --AAAAAACATCCC s droSec1.super_23 109855 12 + 989336 --AAAAAACATCCC s droYak3.chr2R 20198839 12 + 21139217 --tacaaacatcct s droEre2.scaffold_4845 21596792 12 + 22589142 --AACAAACATCCT s droBia2.KB462602 788565 12 + 3129309 --aaagataaaCTA s droSuz1.KI419649 12033635 12 - 14502029 --aaaacaaaactt s droEle2.KB458573 514025 12 - 5320397 --aaattaaactta s droKik2.KB459527 269013 12 - 1234237 --attaaagccaGA s droTak2.KB461535 133723 12 - 669855 --aaatcaaaactt s droRho2.KB449310 27250 12 - 65043 --aaaataaaacta s droFic2.KB457177 74190 12 + 995874 --aaacttacttaa s droPse3.chr3 1342496 12 - 19787792 --Aacgcatattta s droPer1.super_34 531353 12 - 916997 --AACGCATATTTA s droMir2.chr3 1383581 12 - 20862834 --GACgcacattta s droWil2.CH963894 1299205 9 + 2843958 -----aaaaattaa s droMoj3.scaffold_6496 26138462 9 + 26866924 GGCA---GTACC-- s droGri2.scaffold_15245 891524 12 + 18325388 AGCGCGCGCACC-- a score=37240.000000 s dm6.chr2R 24343324 4 + 25286936 AATA s droSim1.chr2R 18690126 4 + 19596830 AATA s droSec1.super_23 109867 4 + 989336 AATA s droYak3.chr2R 20198851 4 + 21139217 aata s droEre2.scaffold_4845 21596804 4 + 22589142 AATA s droBia2.KB462602 788577 4 + 3129309 GGTA s droSuz1.KI419649 12033647 4 - 14502029 aata s droEle2.KB458573 514037 4 - 5320397 aata s droKik2.KB459527 269025 4 - 1234237 AACA s droTak2.KB461535 133735 4 - 669855 aata s droRho2.KB449310 27262 4 - 65043 aata s droFic2.KB457177 74202 4 + 995874 attc s droPse3.chr3 1342508 4 - 19787792 aata s droPer1.super_34 531365 4 - 916997 AATA s droMir2.chr3 1383593 4 - 20862834 aata s droWil2.CH963894 1299214 4 + 2843958 aata s droMoj3.scaffold_6496 26138473 4 + 26866924 ATTA s droAlb1.JH854640 302522 4 + 406291 aata s droGri2.scaffold_15245 891547 2 + 18325388 --CG a score=25387.000000 s dm6.chr2R 24343328 11 + 25286936 A--------ACCAC-AACAA s droSim1.chr2R 18690130 11 + 19596830 A--------ACCAC-AACAA s droSec1.super_23 109871 11 + 989336 A--------ACCAC-AACAA s droYak3.chr2R 20198855 11 + 21139217 a--------accac-aaaaa s droEre2.scaffold_4845 21596808 11 + 22589142 A--------AACGC-AAAAA s droBia2.KB462602 788581 11 + 3129309 A--------ACCAC-AAAAA s droSuz1.KI419649 12033651 12 - 14502029 a--------actgcaaaaaa s droEug2.KB465067 594073 7 + 1515531 ------------ac-taaaa s droEle2.KB458573 514041 11 - 5320397 c--------tttaa-aagaa s droKik2.KB459527 269029 7 - 1234237 A--------ACCAC-A---- s droTak2.KB461535 133739 12 - 669855 a--------actacaaaaaa s droRho2.KB449310 27266 11 - 65043 a--------actac-aaaag s droFic2.KB457177 74206 11 + 995874 a--------actac-aaaaa s droPse3.chr3 1342512 19 - 19787792 aatattgtgacaac-aaaaa s droPer1.super_34 531369 19 - 916997 AATAGTGTGACAAC-AAAAA s droMir2.chr3 1383597 19 - 20862834 aatattgtgacaac-aaaaa s droWil2.CH963894 1299218 10 + 2843958 t--------atca--acaaa s droVir3.scaffold_12875 7343670 11 + 20611582 a--------acaac-aacaa s droMoj3.scaffold_6496 26138478 11 + 26866924 A--------ACAAC-AAATA s droGri2.scaffold_15245 891551 11 + 18325388 A--------ACAAC-AACCA a score=-143664.000000 s dm6.chr2R 24343339 27 + 25286936 TTAT-AAAACGCGAGA--------AAGGATTTGGTA s droSim1.chr2R 18690141 27 + 19596830 ATAC-AAGACGCGAGA--------AAGGATTTGGTA s droSec1.super_23 109882 27 + 989336 ATAC-AAGACGCGAGA--------AAGGATTTGGTA s droYak3.chr2R 20198866 28 + 21139217 ttacaaaaacgCGAGA--------AAGGATTTGCTA s droEre2.scaffold_4845 21596819 28 + 22589142 TTACAAAAACGCGAGG--------AAGGATTTGGTA s droBia2.KB462602 788592 8 + 3129309 ACATTGC----------------------------A s droSuz1.KI419649 12033663 28 - 14502029 aCATTGCAACTCGCGG--------AAGAATTTAGTA s droEug2.KB465067 594080 24 + 1515531 g----aaaacttgCGA--------GTGAGTTCAGCA s droEle2.KB458573 514052 24 - 5320397 agacaacagctcgaaa--------aattgatc---- s droKik2.KB459527 269036 24 - 1234237 -TATAAAAGC---AGA--------AAGGAttcatta s droTak2.KB461535 133751 28 - 669855 acatTGCAACTCGTgg--------aagaatttaatt s droRho2.KB449310 27277 13 - 65043 acaa-----------------------aatttaata s droFic2.KB457177 74217 26 + 995874 GTCT-TCGGCGCGCGA--------AA-ACCCTATTA s droPse3.chr3 1342531 18 - 19787792 taaatataacacaaGC--------TA---------- s droPer1.super_34 531388 18 - 916997 TAAATATAACACAAGC--------TA---------- s droMir2.chr3 1383616 18 - 20862834 taaatataacacaAGT--------TA---------- s droWil2.CH963894 1299228 31 + 2843958 atacaagattccggaa-----tttaaaaattaagca s droVir3.scaffold_12875 7343681 27 + 20611582 --------cagcaacaCTCACGCGCAGTTTTCGCT- s droMoj3.scaffold_6496 26138489 18 + 26866924 --------AAGCAAAA---------AGACCAAAAC- s droAlb1.JH854640 302526 19 + 406291 --------aagcaaaa--------aagacCAAAAC- a score=-177776.000000 s dm6.chr2R 24343366 17 + 25286936 AATCAT-----CTAAAAC--------------------CAG-----------------T--------------- s droSim1.chr2R 18690168 17 + 19596830 AATCAT-----CCAAAAC--------------------CAG-----------------T--------------- s droSec1.super_23 109909 17 + 989336 AATCAT-----CCAAAAC--------------------CAG-----------------T--------------- s droYak3.chr2R 20198894 28 + 21139217 AAACAT-----CCGAAACCTAATTAA---------CAGCAG-----------------T--------------- s droEre2.scaffold_4845 21596847 37 + 22589142 AATCAT-----CCAAAACCAAATTAACAGCCTAATCAGCAG-----------------T--------------- s droBia2.KB462602 788600 11 + 3129309 AGATTG-----CTAAG---------------------------------------------------------- s droSuz1.KI419649 12033691 11 - 14502029 AATCTG-----CTCAA---------------------------------------------------------- s droAna3.scaffold_13266 5704758 18 - 19884421 AACCGTTAAGCCCAAAAC-------------------------------------------------------- s droEug2.KB465067 594104 10 + 1515531 --------------------------------AAACAGCAA-----------------C--------------- s droEle2.KB458573 514076 3 - 5320397 ---------------------------------------ag-----------------c--------------- s droKik2.KB459527 269060 7 - 1234237 ------------------------------------atcaa----------------tt--------------- s droRho2.KB449310 27290 21 - 65043 --------------------------------aatcggcgagcgaaata------aaCT--------------- s droFic2.KB457177 74243 14 + 995874 ---------------------------------------------AATGACCAATAGAC--------------- s droVir3.scaffold_12875 7343708 19 + 20611582 -------------------------------------------------------ACGTTTCGAATTTGGCAGT s droMoj3.scaffold_6496 26138507 14 + 26866924 -------------------------------------------------------AAGTGCCGCA-----CATC s droAlb1.JH854640 302545 14 + 406291 -------------------------------------------------------AAGTGCCAAG-----CATC a score=-467580.000000 s dm6.chr2R 24343383 28 + 25286936 ---------------------------TCAACAAAC------------------------------AA---C-------ACATATAGTAAACATT s droSim1.chr2R 18690185 26 + 19596830 ---------------------------TCAACAAACA-------------------------T---AA---C-------AC----AGTAAACATT s droSec1.super_23 109926 30 + 989336 ---------------------------TCAACAAACA-------------------------T---AA---C-------ACATATAGTAAATGTT s droYak3.chr2R 20198922 30 + 21139217 ---------------------------TTGACAAACT-------------------------C---AA---C-------ATTTAtagtaaaaatt s droEre2.scaffold_4845 21596884 30 + 22589142 ---------------------------TCAAAAAGTA-------------------------T---AC---A-------ATTTATAGTAAAGAGT s droBia2.KB462602 788611 25 + 3129309 ----------------------------CAACAAACG------------------------------------------ACTACATCTAAATACA s droSuz1.KI419649 12033702 54 - 14502029 ----------------------------CaaaaaaaGGACTTCAATCAACTTTGAACTAATTT---AA---C-------GCTAtaagaaaattca s droAna3.scaffold_13266 5704776 32 - 19884421 ----------------------------TAAAAAAGG-------------------------CCTGAA---C-------ACCTGAATCAAAAATT s droEug2.KB465067 594114 19 + 1515531 ---------------------------TAAATAAAAG-------------------------T------------------------CAACTGTG s droEle2.KB458573 514079 27 - 5320397 ---------------------------aaaataaaaa-------------------------c---aa---c----------taaactagaggat s droKik2.KB459527 269067 37 - 1234237 ---------------------------ttaataaaaa-------------------------c---aa---ccaAGGAGCTacaaaagaaacatt s droTak2.KB461535 133779 4 - 669855 -------------------------------------------------------------------------------------------aatc s droRho2.KB449310 27311 33 - 65043 ---------------------------TCAATAAAAG-------------------------C---AAATCC-------ACACCAGgatataatg s droFic2.KB457177 74257 29 + 995874 ---------------------------TCTACAAAAG-------------------------C---CA-----------AACTACATCGGGAAGG s droPse3.chr3 1342549 21 - 19787792 --------------------------------------------------------------------------AATCATATTGAAGCAGAACTA s droPer1.super_34 531406 21 - 916997 --------------------------------------------------------------------------AATCATATTGAAGCAGAACTA s droMir2.chr3 1383634 21 - 20862834 --------------------------------------------------------------------------AATCATATTGAAGCAGAACTa s droWil2.CH963894 1299266 15 + 2843958 --------------------------------------------------------------------------------aggaaactttaacca s droVir3.scaffold_12875 7343727 32 + 20611582 ACCACATTAAATCAGCAA----ATAAAGCAAAAAAG----------------------------------------------------------- s droMoj3.scaffold_6496 26138521 28 + 26866924 TCCTCAT----CCAGCGC----AGTTGACAAATAAG----------------------------------------------------------- s droAlb1.JH854640 302559 28 + 406291 TCTCT------CCAGCGC--TAATAAGTcaaatacg----------------------------------------------------------- s droGri2.scaffold_15245 891612 28 + 18325388 -------TTAGCTAGCAGCACAAGTTGTCAGTTTT------------------------------------------------------------ a score=-178088.000000 s dm6.chr2R 24343411 26 + 25286936 AAATATT----AAATCACA-----AGTTTTA-------GAAG-------------- s droSim1.chr2R 18690211 26 + 19596830 AAAAATT----AAATCACA-----AGTTTTA-------AAAC-------------- s droSec1.super_23 109956 26 + 989336 AAATATT----AAATCACA-----AGTTTTA-------GAAC-------------- s droYak3.chr2R 20198952 26 + 21139217 aaataac----acaacaca-----agtttta-------aaaa-------------- s droEre2.scaffold_4845 21596914 26 + 22589142 TAATAAC----ACAACGCA-----AGTTTTA-------AAAA-------------- s droBia2.KB462602 788636 31 + 3129309 AGAAATC----AGGAAGCA-----ACTTTAA--TTTCtaaaa-------------- s droSuz1.KI419649 12033756 33 - 14502029 acaaatC----AGGAAGCa-----acttaaaatttcataaaa-------------- s droAna3.scaffold_13266 5704808 28 - 19884421 GAAAATCTA--AAATCGAA-----AACTTAC-------AAAG-------------- s droEug2.KB465067 594133 26 + 1515531 GACTATT----ccattaat-----aatttta-------aaaa-------------- s droEle2.KB458573 514106 20 - 5320397 aaataaa----aaaaaa-----------tca-------ggaa-------------- s droKik2.KB459527 269104 30 - 1234237 aaaaatacaagaaataact-----aaatttt-------ataa-------------- s droTak2.KB461535 133783 26 - 669855 cgctaaa----taaaaatt-----aatgtag-------caaa-------------- s droRho2.KB449310 27344 31 - 65043 aaataaa----acaaatcaggaagaaactaa-------atcg-------------- s droFic2.KB457177 74286 26 + 995874 ATAGAGT----AAATCAGG-----AAGCCAC-------TAAA-------------- s droPse3.chr3 1342570 27 - 19787792 AAccata----aaaccaaa----caaattaa-------agct-------------- s droPer1.super_34 531427 27 - 916997 AACCATA----AAACCAAA----CAAATTAA-------AGCT-------------- s droMir2.chr3 1383655 27 - 20862834 aaccata----aaatcaaa----aaaattaa-------agct-------------- s droWil2.CH963894 1299281 26 + 2843958 aacaaac----aagacaca-----aaataac-------gtgc-------------- s droVir3.scaffold_12875 7343774 21 + 20611582 -----------------------AAGCATCT-------CTCCAG-----CGCAGCG s droMoj3.scaffold_6496 26138560 15 + 26866924 -----------------------aaatatat-------atata-----------ta s droAlb1.JH854640 302598 26 + 406291 -----------------------aaatccaa-------ataaatcaaaccgcaaca a score=-1147160.000000 s dm6.chr2R 24343437 169 + 25286936 GCAAACAA-----------AGAT-----A---------------A---AAACT----CT-TAACACCAG--tt-------------------aaa-------------------------taaaatatac------taaa--------------aga-actgcaacc------------aa---------------------aaaataaca------------------t-----ac------------aat-taaatgaaatt----aaa--A---------GCCATAAAGAAACT---T----AAAGCCA----------TTGGAAAC--------------AAGC---CATAAAAGCGGTCCAG---AACCTAAATAT--TAAACAC-AAAC---------------------------CAAA s droSim1.chr2R 18690237 188 + 19596830 GCAAATAA-----------AGAT-----A---------------A---GAACT----CT-CAACAACAG--TT-------------------AAA-------------------------TAAAGAATAA------TAAG--------------AGA-ACTGCAAGC------------AA---------------------ACAATAAAC------------------T-----AC------------ATT-TAAATG---------AAA--A---------GCCATAAAGAAACT---T----AAAGCCA----------TTGGAAAC--------------AAGC---CATACAAGCGGTCCAG---AACCTAAAAAT--TAAACAC-AAACCAACCAGCAACTCCACTCTACGCT---CAAA s droSec1.super_23 109982 189 + 989336 GTAAACAA-----------AGAT-----A---------------A---AAACT----CT-CAACATTAG--TT-------------------AAA-------------------------TAAAGAATAA------TAAG--------------AGA-ACTGCAAGC------------AA---------------------ACAATAAAC------------------T-----AC------------ATT-TAAATG---------AAA--A---------GCCATAAAGAAACT---T----AAAGCCA----------TTGGAAACA-------------AAGC---CATACAAGCGGTCCAG---AACCTAAAAAT--TAAACAC-AAACCAACCAGCAACTCCACTCTTCGCT---CAAA s droYak3.chr2R 20198978 190 + 21139217 cgcaacaa-----------attt-----a---------------acataaact----ct-caaaatcag--tt-------------------aaa-------------------------taaaataaaa------taaa--------------tga-actgcaagc------------aa---------------------gcaataaag------------------t-----ag------------att-taaata---------aaa--a---------gccacaaaGAAACT---T----AAAGCCA----------TAGGAAAC--------------CAGC---CATACAATCGATCCAG---AACTCAAAAA---CAAGCAC-AAACCAAACAGCAACTCCACTCTTCGCC---TGAA s droEre2.scaffold_4845 21596940 191 + 22589142 CGCAACAA-----------AGAT-----A---------------AAA-AAACT----CT-CAAAACCAA--TC------------------AAAA-------------------------TAAAATATAA------GAAA--------------AGA-ACTGCGAGC------------AA---------------------ACAATAAAA------------------T-----AG------------ATT-TAAATG---------AAA--A---------GCCACAAAGAAACT---T----AAAGCCA----------TTGGAAAC--------------AAGC---CATATAATCGATCCAG---AACTCAAAAA---GAAACACAAAACCAACCAGCAACTCCACTCTTCGCT---TAAA s droBia2.KB462602 788667 136 + 3129309 caccacaa-----------aaga-----a---------------a---acgg---------aactcaac--tc-------------------aaa-------------------------taaagta----------------------------------------------------aa---------------------ataaataac------------------t-----aa------------gct-aaaaca---------aaa--a---------gccataCAGAAACT--------AAGGCCA----------TACAAC--------------------------------GAACCAG---AACTT--------CAGCCGC-AGAA-----ACCAACTCCACTCTGCGCA-----CA s droSuz1.KI419649 12033789 144 - 14502029 caccacaa-----------atga-----a-------------aga---aaac---------aactctaa--tt-------------------aaa-------------------------tcaaata----------------------------------------------------aa---------------------ataactatt------------------t-----aa------------gtt-aaaaca---------aaa--a---------gccatacagaaact---a----aaagcca----------taaaaaag------------------------------gaTCAAG---AACTT--------TGGCCAC-GAAG-----AAAAACTCCACTTTGcgcc--attaa s droAna3.scaffold_13266 5704836 137 - 19884421 GCGTATCA-----------AGAA-----A---------------A---AAACT----CTACAACTCTA------------------------AAA-------------------------CCATATAATC------CAAA--------------GGA----GCAAAT------------AA---------------------AAAAAGAAT------------------C-----A---------------T-CAAATA---------ACA--G---------CGCACAA--------------------CA----------CACAACAG------------------------------GATTAAG---AACTCCAAAA---AGGACTT-AAGCTTTCAAGGAAAC------------------- s droEug2.KB465067 594159 164 + 1515531 ccat----------------------------------------c---aaact----tt-aaataaca------------------------aag-------------------------caatttatat------tgaa--------------taa-attgcaaat------------ga---------------------gccataaat------------------t-----aa------------ata-taaacg---------aAA--A---------GTCTTAGAGAAACT---TATACATAACCA----------TAATACATA-------------AAGC---CATAAAata-----------------------cacacaa-aaaccaaacaagaaCTTTATTTTCCGCC--ACAAA s droEle2.KB458573 514126 192 - 5320397 gtaaatcg-----------ctta-----a---------------a---atattatacct-gaaacaaag--tt-------------------aaa-------------------------taaataa--a------taaa--------------taa-tcagcatg-------------aa---------------------gcaataaat------------------t-----aa------------att-taaaca---------caa--a---------gcCATATAGAAACT---C----AACGCCA----------TAAATaaagc------------aact---taaacaaacagtcaagcaaaacctacaacttacaacaac-aaac-----aagaacTCTGTATTTTgca--acaaa s droKik2.KB459527 269134 246 - 1234237 ataaatac-----------aaattattaa---------------g---gaact----tt-taaattctt--tttagaatttattaaactttgaaa-------------------------taaactaaaa------ccagtagaaaaccttcttaaa-actacaaaa------------ga---------------------accaaaacttGTTAAGCaaatacctggt-----aa------------atc-tcaata---------aaa--a---------tgaactgaagaactactc----aaaatca----------caaaataaa-------------aaat---catacaa--aacctaa---aaccacagaa---acattaa-aaacacaaTAGTTGCAACATTCAACTTc--ttgaa s droTak2.KB461535 133809 139 - 669855 gaaaatta-----------aatt-----a---------------a---atctc----ca-caaaactaa-----------------------aaa-------------------------aaaaacacaa------cata--------------aaa----------------------aa---------------------gtaaaaaat------------------t-----aa------------atg-taaaca---------aag--a---------gccatacagaaact---a----aaaGCCA----------TAATAAGC-------------------------------AACCAG---AACTT--------TAGCTGC-AAAC-----ACAAACCACA---------------- s droRho2.KB449310 27375 179 - 65043 ctaaataa-----------caga-----a---------------a---aaaga----ag-caaagaaa------------------------aaa-------------------------aaacataatt------taaa--------------aaacactgcatgt------------aa---------------------gcaataaat------------------t-----aa------------att-taaaca---------aaa--a---------gccaTATAGAAACT---C----CAAGCCA----------TAGCTACAGCAACTTGAACAAACAGT---CACACAA--AACCCAC---AACTTATAAA---GAACTCC-CAAA-----ATAAACCAAA---------------- s droFic2.KB457177 74322 183 + 995874 cagaacaa-----------aaaa-----a---------------a---ttaaa----ct-caaTAAAGG-att-------------------aaa-------------------------accaacaaaa------taa---------------caa-GCTGCAAGC------------AA---------------------GCATTAAAT------------------T-----Ac------------act-aaaac----------aaa--a---------gccataaAGAAACT---A----GAAGCCA----------TACTACA---------------AGAA---tataaaagcttaaaat---aaatt--------caaatac-aaaacaaacaagaactTTAATCTCAGCCACACAAA s droPse3.chr3 1342597 188 - 19787792 GAAAATAG-----------AAGA-----A---------------C---AACCA----AT-CGAAGCAGAAATA-------------------AAA-------------------------CCGCACAAAAGACTCCTAGA--------------AGG-CCAGTAAACTCTACCA-----AC---------------------ATAATAAAC------------------C-----AACACAAACGCAACATT-CAAACC---------AAATCA---------TCctttaaaaaaca---a----actgcAA----------CCATAATC--------------AACT---CAAAGGAAAGACACGC---AACGCATATTTTCGAAAGAC-A---------------------------------- s droPer1.super_34 531454 188 - 916997 GAAAATAG-----------AAGA-----G---------------C---AAACA----AT-CGAAGCAGAAATA-------------------AAA-------------------------CCGCACAAAAGACACCTAGA--------------AGG-CCAGTAAACTCTACCA-----AC---------------------ATAATAAAC------------------C-----AACACAAACGCAACATT-CAAACC---------AAATCA---------TCCTTTAAAAAACA---A----ACTGCAA----------CCATAATC--------------AACT---CAAAGGAAAGACACAC---AACGCATATTTTCGAAAGAC-A---------------------------------- s droMir2.chr3 1383682 188 - 20862834 gaaaatag-----------aaga-----a---------------c---aaaaa----at-tgaagcagaaata-------------------aaa-------------------------ccgcacaaaagacacctaaa--------------agG-ACAGTAAACTCTACCA-----AC---------------------ATAATAAAC------------------C-----AACACAAACGCAACATT-CAAACC---------AAATCT---------tcctttaaaaaaca---a----actgcaA----------CCATAATC--------------AACT---CAAAGGAAAGACACAC---AACGCATATTTTCGaaagca-a---------------------------------- s droWil2.CH963894 1299307 181 + 2843958 aaatacaa-----------caat-----a---------------c---aaata----aa-cagcaaaaa--ct-------------------aaacGATTGAGATTTCCAATTATAACTGtaaacttaaa------gaaa--------------aaa-atcgcacac------------ac---------------------acagaaaat------------------t-----aa------------att----------------aaa--a---------ctctCATTGGAAAT---A----AAACTCA--------------------------------AACT---TAATTGTCAAAACTAA---TCCTCgaaat---taattgc-aattaatAAAGCAAA-------------------- s droVir3.scaffold_12875 7343795 171 + 20611582 ----ACAA-----------ATAA-----G-------------TCA---ATACA----AA-ACAAA--AC--CA-------------------AAA-------------------------AAATAAAaac------aaca--------------aca-acaacagcagcagcta-----aa-----------------aacaacaacaaAC------------------AGTTACAA------------ATTACAAATGT--------GCA--ATTCATGAATTGCATTTGCAAACG---C----AACTTAAACGCATTTATCAACATTT--------------TGGCG--CATTTGCATAGCGAA------------------------------------------------------------ s droMoj3.scaffold_6496 26138575 145 + 26866924 ----ataa-----------ataa-----a---------------a---ataCC----AA-ATA---------T-------------------AAA-------------------------ATGcaacagt------aaca--------------gca-acagcagcagcaacta-----aaatagcaacagaagaaacatcaacgataaAC------------------AGTTAGAA------------ATT-TAAATG------------------------TGCTTTGGCGTACG---C----AGCACAA----------CAACATTT--------------TGA-------------AGCGGA------------------------------------------------------------ s droAlb1.JH854640 302624 173 + 406291 ----acaacaacagcaactacaa-----acaGTTATCAGTTTTCA---GTATT----GA-ATATATTGT--Gt-------------------gaa-------------------------taattttatg------aatt--------------gca-tttgcaactgcaacta-----aa-------------------cTCCCATTAGT------------------a-ctgcaa------------att-caaattg--------aca--A------------ATTGACGCGCG---C----AATNCAA----------CTGCAACT--------------AAACTCCCATTAGTACTGCGAA------------------------------------------------------------ s droGri2.scaffold_15245 891686 149 + 18325388 --------------------------------------------G---CGACC----AA-AAAAA---------------------------AAG-------------------------AAATAAAAAG------AAAC--------------GTA-TCGGTGTTTATAATTGTTTTTAA-------------------TAATAATAAGC------------------A----AAT------------ATC-TAAACGATATTAGACGCG--CTCAATTACAGGCTGCAGCGAGTG---C----AGCACAA----------C-GCGTTT--------------GGT----GATTATAACAGCAAA------------------------------------------------------------ a score=145371.000000 s dm6.chr2R 24343606 38 + 25286936 ATT--------CAAATTCC-G-CGC-CAAACGAC-C----AC-AC----------TGCGCAACAC s droSim1.chr2R 18690425 38 + 19596830 ATT--------CAAATTTC-C-CGC-CAAGCGAC-C----AC-AC----------TGCGCAACAC s droSec1.super_23 110171 38 + 989336 ATT--------CAAATTCC-C-CGC-CAAGCGAC-C----AC-AC----------TGCGCAACAC s droYak3.chr2R 20199168 38 + 21139217 ATT--------CAAATTCC-C-CGC-CAAGCGAG-C----AC-AC----------TGCGCAACAC s droEre2.scaffold_4845 21597131 38 + 22589142 ATT--------CAAATTCC-C-CGC-CAAACGAC-C----AC-AC----------TGCGCAACAC s droBia2.KB462602 788803 38 + 3129309 CTT--------CGAATTTG-C-CGC-CAAGCCGC-C----TC-TC----------TTCGCAACAC s droSuz1.KI419649 12033933 38 - 14502029 att--------taaatttg-c-cGC-CAAGCCGC-C----TC-AC----------TTCGCAACAC s droAna3.scaffold_13266 5704973 39 - 19884421 ATT--------TAAATTTG-G-CGC-CCAACCGC-T----GA-GCT---------TTTGCAACAC s droBip2.KB464407 1953647 39 + 2915140 ATT--------CAAATTTG-C-CGC-CCAACCGC-T----GA-GCT---------TTTGCAACAC s droEug2.KB465067 594324 37 + 1515531 -TT--------CAAATTTG-C-CGC-CAAAGCCC-G----CC-AC----------TTCGCAACAC s droEle2.KB458573 514318 38 - 5320397 ttt--------caaattaa-c-cGC-CAAACGAC-T----TT-GC----------TTTGCAACAC s droKik2.KB459527 269380 40 - 1234237 att--------caaattcgaG-CGC-CAAATCAG-C----ACTGC----------TTCGCAACAC s droTak2.KB461535 133960 36 - 669855 ATT--------CAAATTTG-C-CGC-CCAGCCGC-T-------AC----------TTCGCAACAC s droRho2.KB449310 27568 38 - 65043 att--------caaatcta-C-CGC-CAAACCCC-T----TT-GC----------TTTGCAACAC s droFic2.KB457177 74505 39 + 995874 ATT--------CGAACTCG-CGCGC-CCTGCCCC-T----CC-AC----------TTTGCAACAC s droPse3.chr3 1342785 40 - 19787792 ATT--------CAAATTTAAG-CGC-CACATCCCGC----AG-AT----------TATGCAACAC s droPer1.super_34 531642 40 - 916997 ATT--------CAAATTTAAG-CGC-CACATCCCGC----AG-AT----------TATGCAACAC s droMir2.chr3 1383870 40 - 20862834 att--------caaatttagg-CGC-CAAATCCCGC----AG-AT----------TATGCAACAC s droWil2.CH963894 1299502 42 + 2843958 gtt--------taaattta-g-cGC-CAATTGCT-TGTCAAC-AT----------TATGCAACAC s droVir3.scaffold_12875 7343966 43 + 20611582 -TT--------CAAATTTGCG-CGC-GCG------C----AC-ACACACAAATCTTGTGCAACAC s droMoj3.scaffold_6496 26138720 43 + 26866924 -TT--------CAAATAAGCG-CGC-CCA------A----AC-ACAGCCCATTCGTGTGCAACAC s droAlb1.JH854640 302797 51 + 406291 -TTCAAATTGACAAATTGACG-CGC-GCAATT---C----AC-ACGAACCAC---TGCACAACAC s droGri2.scaffold_15245 891835 19 + 18325388 -CG--------GCAAGCAGCG-CACAGCA------------------------------------ a score=210873.000000 s dm6.chr2R 24343644 51 + 25286936 A---CGAGC-------GC-------T--GCATCCCTGG-----------ACTTCAGCCGCATTCCAACACTGCAGGACTGT--------- s droSim1.chr2R 18690463 51 + 19596830 A---CGAGC-------GC-------T--GCATCCCTGG-----------ACTTCCGCCGCATTCCAACACTGCAGGACTGT--------- s droSec1.super_23 110209 51 + 989336 A---CGAGC-------GC-------T--GCATCCCTGG-----------ACTTCCGCCGCATTCCAACACTGCAGGACTGT--------- s droYak3.chr2R 20199206 51 + 21139217 T---CGAGC-------GC-------T--GCATCCCTGG-----------ACTTCCGCCGCATTCCAACACTGCAGGACTGT--------- s droEre2.scaffold_4845 21597169 51 + 22589142 T---CGAGC-------GC-------T--GCATCCCTGG-----------ACTTCCGCCGCATTCCAACACTGCAGGACTGT--------- s droBia2.KB462602 788841 51 + 3129309 T---CGAGC-------GC-------T--GCATCCCTGG-----------CTTTCCGCCACATTCCAACACTGCAGGACTGT--------- s droSuz1.KI419649 12033971 51 - 14502029 T---CGAGC-------GC-------T--GCATCCCTGG-----------CTTTCCGACACATTCCAACACTGCAGGACTGT--------- s droAna3.scaffold_13266 5705012 39 - 19884421 TTTCTGAAC-TTTTTTGC-------T--GCATCCCTGG--------------------------------TAACGGGCTGT--------- s droBip2.KB464407 1953686 40 + 2915140 TTTCTGAACtttttttGC-------T--GCATCCCTGG--------------------------------TTTCGGGCTGT--------- s droEug2.KB465067 594361 51 + 1515531 T---CAGCT-------GC-------T--GCATCCCTGG-----------ATTTCCGCCACATTCCAACACTGCAGGACTGT--------- s droEle2.KB458573 514356 51 - 5320397 T---CGAAC-------GC-------T--GCATCCCTGG-----------ACTTCCGCCACATTCCAACACTGCAGGACTGT--------- s droKik2.KB459527 269420 50 - 1234237 T---CGAGC-------GC-------T--ACATCCCTGG------------TTTCCGCCGCATTCCAACACTGCAGGACTGT--------- s droTak2.KB461535 133996 44 - 669855 T---CGAGC-------GC-------T--TCA------------------AATACAGGGTGATTCCTGCAGCCAGGGGCTGT--------- s droRho2.KB449310 27606 51 - 65043 T---CAGCC-------AC-------G--GCATCCCTGG-----------GTTTCCGCCACATTCCAACACTGCAGGACTGT--------- s droFic2.KB457177 74544 51 + 995874 T---TAGCC-------GC-------T--GTATCCCTGG-----------CTTTCCGCCGCATTCCAACACTGCAGGACTGT--------- s droPse3.chr3 1342825 60 - 19787792 TAGGCAGGC-------GCGAGCCAGT--CCATCCCTGG------------TTTCCACCACATTGCAACACTGTAGGACTGT--------- s droPer1.super_34 531682 60 - 916997 TAGGCAGGC-------GCGAGCCAGT--CCATCCCTGG------------TTTCCACCACATTGCAACACTGTAGGACTGT--------- s droMir2.chr3 1383910 60 - 20862834 TAGGCAGGC-------GCGAGCCAGT--GCATCCCTGG------------TTTCCACCACATTGCAACACTGTAGGACTGT--------- s droWil2.CH963894 1299544 49 + 2843958 T------GC-------GA-------TTAGTAGCCCTGG-----------ATTTGCACCAC-TCACAACACTGCAGGACTGT--------- s droVir3.scaffold_12875 7344010 44 + 20611582 ----------------GC-------G--A--CTGTTAA-----------GCGCCTG--------TTAAGCTGTCTGTTAGTTAGCAGCAG s droMoj3.scaffold_6496 26138764 46 + 26866924 ----------------GC-------G--ACTCTGTTAA-----------GCATCTG--------TTAAACTGGCTGTTAGTTAGCAGCAG s droGri2.scaffold_15245 891855 50 + 18325388 ----------------GC-------A--AAACAGCTGACGGCGACAGCGGCGCCCGC-------TTATTGTGCCtgtgtgtt-------- a score=-427576.000000 s dm6.chr2R 24343695 263 + 25286936 CA----GCTGTCAG-TTTTCC-----------------------------TGTGTGTGTGCGC----------G-CGTAAGTGTGTGC----G-------------------TGC--ACTTAAGAAACTT----AAATT-CGC-------GTT----CTTG--GCCAAAA---AAAAC--CC--GGGTTTTTAATA-------AGTT-----------------------------------ATA-G--------CGTT----------T--TCCTCG-----------ACTGAGAAC-------TT--------------------------GG-CCCCCAG-GCAGACGGGC----AC--AA---AAA--CCGCCCCAGAA-----------------ACG--CGC----CCGCCG-CCGCC----------AAAAAG---GCC---GAA---------AACGCCAGCGAA-----------------------------------------------------------ACGCGCGCGTTGAG----TGTTTT----CTGTGTGGTTTTATTTTTGGAA-----TATAAA-------------GCG------------ATC s droSim1.chr2R 18690514 261 + 19596830 CA----GCTGTCAG-TTTTCC-----------------------------TGTGTGTGTGCGC----------G-CGTGAGTGTGTGC----G-------------------TGC--ACTTAAGAAACTT----AAATT-CGC-------GTT----CTTG--GCC--AA---AAAAC--CC--GGGTTGTTAATA-------AGTT-----------------------------------ATA-G--------CGTT----------T--TCCTCG-----------ACTGAGAAC-------TT--------------------------GG-CCCCCAG-GCAGACGGGC----AC--AA---AAA--CCGCCCTAGAA-----------------ACG--CGC----CCGCCG-CCGTC----------GAAAAG---GCC---GAA---------AACGCCAGCGAA-----------------------------------------------------------ACGCGCGCGTTGAG----TGTTTT----CTGTGTGGTTTTATTTTTGGAA-----TATAAA-------------GCG------------ATC s droSec1.super_23 110260 261 + 989336 CA----GCTGTCAG-TTTTCC-----------------------------TGTGTGTGTGCGC----------G-CGTGAGTGTGTGC----G-------------------TGC--ACTTAAGAAACTT----AAATT-CGC-------GTT----CTTG--GCC--AA---AAAAC--CC--GGGTTGTTAATA-------AGTT-----------------------------------ATA-G--------CGTT----------T--TCCTCG-----------ACTGAGAAC-------TT--------------------------GG-CCCCCAG-GCAGACGGGC----AC--AA---AAA--CCGCCCCAGTA-----------------ACG--CGC----CCGCCG-CCGTC----------GAAAAG---GCC---GAA---------AACGCCAGCGAA-----------------------------------------------------------ACGCGCGCGTTGAG----TGTTTT----CTGTGTGGTTTTATTTTTGGAA-----TATAAA-------------GCG------------ATC s droYak3.chr2R 20199257 263 + 21139217 CA----GCTGTCAG-Ttttcc---------------------------tgtgtgtgtgtgcgc----------g-cgtgagtgtgtgc----g-------------------tgc--acTTAAGAAACTT----AAATT-CGC-------gtt----cttg--gcc--aa---aaaac--cC--GGGTTGTTAATA-------AGTT-----------------------------------ATA-G--------CGTT----------T--CCCTCG-----------ACTGAGAAC-------TT--------------------------GG-CCCCCAG-GCAGCCGGGC----AC--GA---AAA--CCGCCCCAGAA-----------------ACG--CGT----CCGCCG-CAGCC----------GAGAAG---GCC---CAA---------AACGCCAGCGAA-----------------------------------------------------------ACGCGCGCGTTGAG----TGTTTT----CTGtgtggttttatttttggaa-----tataAA-------------GCG------------ATC s droEre2.scaffold_4845 21597220 262 + 22589142 CA----GCTGTCAG-TTTTCC-----------------------------TGTGTGTGTGCGC----------G-CGTGAGTGTGTGC----G-------------------TAC--ACTTAAGAAACTT----AAATTCCGC-------GTT----CTTG--GCC--AA---AAAAT--CC--GGGTTTTTAATA-------AGTT-----------------------------------ATA-G--------CGTG----------T--CCCCCG-----------ACTGAGAAC-------TT--------------------------GG-CCCCCAG-GCAGCCGGGC----AC--AA---AAT--CCGCCCCAGAA-----------------ACG--CGT----CCGCCG-CAGCC----------GAGAAG---GCC---GAA---------AACGCCAGCGAA-----------------------------------------------------------ACGCGCGCGTTGAG----TGTTTT----CTGTGTGGTTTTATTTTTGGAA-----TATAAA-------------GCG------------ATC s droBia2.KB462602 788892 281 + 3129309 CA----GCTGTCAA-Ctctgc-----------------------------tgtgtgtgtgcga----------g-cgtgcgtgtgtgc----gtgttgcAAAACGTCGGCGTTGC--Act--aaaaacttaacaaaaat-CGC-------GTT----CCCG--GCC---G---AAAAC--CC--GGGTTGCTAAC------------------------------------------------------------CGTC----------T--TGCG-G-----------GCTAAGAAC-------TC--------------------------GG-CCCCCAG-GCAGCCGGCC----AC--CA---GAAA-CCGCCCCAGAA-----------------ACG--CG-----CCGTCG-CAGC-----------GAAACG---CCTAGGGAA---------AACGCCAGCGAA-----------------------------------------------------------ACGCGCGCGTTGTG----TGTTTT--C-CTgtgtagttttatttttggaa-----tacaAA-------------GCGAGAGAGA-----ATC s droSuz1.KI419649 12034022 286 - 14502029 CA----GCTGTCAA-CTctcc-------tg------------------tgtgtgtgtgtgcga----------g-tgtgcgtgtgtgc----gtgttgCAAAACGTCGGCGTTGC--ACt--aaaaacttaacaaaaat-CGC-------GTT----CCTG--GCC---G---AAAAC--CC--GGGTTGCTAAC------------------------------------------------------------CGTT----------T--TGCG-G-----------GCTAAGAAC-------TT--------------------------GG-CCCCCAG-GCAGCCGGCC----AC--AA---AAAACCCGCCCCAGAA-----------------ACG--CG-----CCGTCG-CAGCa----------aaaaaa---CCTAAGAAA---------AGCGCCAGCGAA-----------------------------------------------------------ACGCGCGCGTTGTG----TGTTTT--T-CTgtgtagttttatttttggaa-----tataaA-------------GCGAGAGAG------ATC s droAna3.scaffold_13266 5705051 317 - 19884421 CA----GCTGTCAA-TTTTGCCC-CAAGTG------------------GCTGTGTGTTTGTGT----------T-TGTGTGTGCGTGC----GTGTTGCAAAATCGCGGCGTTGC--AGCCAAA----------AAATT-CGC-------GTT-----TCG--CCC----------TC--CG--AAATTGTTAATA-------ATTTTGATAAAGCGGGC----------CAAAAAGACTGCATA-G--------GGTA----------G--CCTGCA-----------ACGGCGGCA-------GC--------------------------AG-CCCCCAG-GCGAACGGCA----AACAGG---CAA--ACGCAGCAG--------------------------------CGGCG-CAGC-----------TAAGCG---GCC-AGCAA---------ATCGACAGAATA--------------GTATCGCGTT---------------------GT------------GTGCGCGCGGTGTG----TGTTTT----GTGTG-----TTATTTTTGGAA-----TTAAGAATCAAATACGGGCGCT------------AGG s droBip2.KB464407 1953726 339 + 2915140 CA----GCTGTCAATTTTTGCCC-CAAGTG------------------GCcaagtgtttgtgt----------t-tgtgtgtgcgtgc----gtgttGCAAAATCGCGGCGTTGC--AGCCaaa----------aaaaC-CGC-------GTT-----TCG--CCC----------TC--Cg--aaattgttaata-------attttgataaaacgGGCGAAAACACTGCAAAAACAAGGAAca-g--------gcct----------g--caggca-----------gcggcggca-------gt--------------------------ag-cccccag-gcaaacggca----ac---g---cag--cagcagcgg--------------------------------cggcg-cagc------------aaacg---gcc-agaagccatcagccagcagcagAGTATCAGAG--------ATATCGCGTt---------------------gt------------gtgcgcgcggtgtg----tgtttt----gtgtg-----ttatttttggaa-----ttaaGAATCAAATACGGGCGCT------------AGG s droEug2.KB465067 594412 282 + 1515531 CA----GCTGTCAA-ttttcc---tgtgtg------------------tgtgtgtgcgtgcga----------g-tgtgtgcgtgtgc----gtgttgCAAAACGTCGGCGTTGC--acttaaaaacctta---aaatt-cGC-------GTT----CCTG--GCC-GAA---AAAAC--CC--GGGTTGTTGGCC-------ACTT-----------------------------------GGT-G--------CGGT----------T--TTTCGG-----------GCTCAGAAC-------TC--------------------------GG-CCCCCAG-GCAGCCGGGC----AT--AA---AAT--CCGCCCCAGAA-----------------ACG--CGA----TCGCCG-CAGC---------------------CA---AAA---------AACGCCAGCGAA-----------------------------------------------------------ACGCGCGCGTTGTG----TGTTTT----GTGcgtagttttatttttggaa-----tataaA-------------GCG------------ATC s droEle2.KB458573 514407 278 - 5320397 CA----GCTGTCAA-Ttttcc-----------------------------tgtgtgtgtgtgt----------g-tgcgtgcgtgtgc----gtgtTGCAAAACGTCGGCgttgc--acttaaa----------aaatt-cGC-------GTT----TCTG--GCC---A---AAAAC--CC--GGGTTGTC---------------------------------------------------------------CGAT----------T--ACCG-G-----------GCCAAAAGC-------GT-------------TA-----------GG-CCCCCAG-GCAACCGGGCCA--AA--GA---AAA--CCGCACGAGAA-----------------ACG--CGC----TCCCCG-TTGCCAGTACATACTCAATAA---GCG---AAA---------AACGCCAGCAAA-----------------------------------------------------------ACGCGCGcgttgtt---ctgtttt--t-gtgtgtagttttatttttggaa-----tatagaag-----------aag------------aaa s droKik2.KB459527 269470 306 - 1234237 CAGCTGGCTGTCAA-TTTGCC----AAGCGAAC---------------CAAGTCTGTGTGCga----------gccgtgtgtgtgtga----gtgttgcaAAACGTCGGCGTTGC--ACT---AAATCTT----AAATT-CGC-------GTTAAATTCTG--GTT--AA---AAGGCGGCC--AATTAGTTGGTT-------ATCT-----------------------------------GGG-G--------GAAT----------A--AACCCG-----------GCTGagcag-------tt-------------ag----------cag-cccccag-gcgg----------ag------------ccagcccagag-----------------cag--cag----cccgcg-c--------------cagcag---gca-gggaa---------aacgccagccagccagca--gccgccGAATCGCGTt-----------------------------------gtgtgcgcggtgtg----tgtttt----gtgtg-----ttatttttggaa----ttaaaga-------------gcg------------atc s droTak2.KB461535 134040 276 - 669855 CA----GCTGTCAT-Ttttcc-----------------------------------------t----------g-tgtgtgtgtgtgc----gcattGCAAAACGTCGGCGTTGC--ACc--gaaaacttaaa-aaagt-cGC-------GTT----CCTG--GCC---G---AAAAC--CC--GGGTTGTTAGCC-------AATT-----------------------------------CGC-G--------TGGT----------T--TTGCGG-----------CCCAAGAAC-------TT--------------------------GG-CCCCCAG-GCAGCCGGGC----ATCGAG---AAA--CCGCCCCAGAA-----------------ACG--CG-----CCGCCG-CAGCC----------CAGAAG---ACG---AGA---------AACGCCTGCGAA-----------------------------------------------------------ACGCGCGCGCTGTG--TCTGTTTTCCC-GTGTGCGGtgttatttttggaa-----tataaa-------------GCGAG----------ATC s droRho2.KB449310 27657 286 - 65043 CA----GCTGTCAA-Ttttcc-----------------------------tgtgtgtgtgtgc----------g-tgcgtgcgtgtgc----gtgtTGCAAAACGTCGGCgttgc--acttaaaaaattaaat-aaaac-caa-------aac-----------ca--aa---aaaac--cc--GGGTTGCTAACA-------ATTT-----------------------------------ACG--------------------------------G-----------GCTAAAGCG-------TT--------------------------AGCCCCCCAG-GCAACCGGGCCA--AA--GA---AAA--CCGCCCGAGAA-----------------ACGCTCGC----GCGTTGTCAGTA----------TACAAG---CGA---AAA---------AACGCCAGCAAA-----------------------------------------------------------ACGCGCGCGTTGTT---CTGTTTT--T-Gtgtgtagttttatttttggaa-----tatagAAAAAACGCCAA--GCG------------AGC s droFic2.KB457177 74595 253 + 995874 CA----GCTGTCAA-CTTCct-----------------------------tgagagtgtgtgt----------g-cgtgcgtgtgtg--------ttgcaAAACGTCGGCGTTGC--ACTTAA-----------AAATT-CGC-------GTT----TCTG--GCC--AG---AAAAC--CC--GGGTTGTTAACA-------AACT-----------------------------------AAACG--------GATT----------T--TCTGGG-----------CCCCAAAAC-------AT--------------------------AG-CCCCCAG-GCAACCGGGC----AA-GGA---AAA--CCGCCCGCAAA-----------------ACG--CGC----TCGCCA-------------------------------GGG---------A---------AA-----------------------------------------------------------ACGCGCgcgttgtg----tgtttt--t-gtgtgtggttttatttttggaa-----tatagaaaGA---------GCG------------ACG s droPse3.chr3 1342885 311 - 19787792 CA----GCTGTCAA-TTTTCT------GCTTgc---------------ggtgtttgtgtgtgt----------g-cgttcgtGCGTGT----TTGTTGCAAAACGACGGCGTTGC--AGCCCAA----------AAATT-CGC-------GTT----TTGA--TCC--GA---AATTC--AA--TTGtagttaatt-------attt-----------------------------------aaa-a--------caat----------tgaGCCACG-----------GCCGGCAGT-------GC-------------CAGCTAGCGCAGGAG-AGCTCAG-CCGAACAGCG----AC------------GCGTCAGGGAA-----------------TCG--TGCAAGAGGGCCA-GCGCC--------------AG---GGC---AAA---------AACGCCATCGAA-----------------TCGCGTT---------------------GTGTG---------CGGCGTGcggtgtg----tgtttt----gtgt-----tttatttttggaa-----ttaaAT-------------ACGGCAGCAGCCCctgcc s droPer1.super_34 531742 311 - 916997 CA----GCTGTCAA-TTTTCT------GCTTGC---------------GGTGTTTGTGTGTGT----------G-CGTTCGTGCGTGT----TTGTTGCAAAACGACGGCGTTGC--AGCCCAA----------AAATT-CGC-------GTT----TTGA--TCC--GA---AATTC--AA--TTGTAGTTAATT-------ATTT-----------------------------------AAA-A--------CAAT----------TGAGCCACG-----------GCCGGCAGT-------GC-------------CAGCTAGCGCAGGAG-AGCTCAG-CCGAACAGCG----AC------------GCGTCAGGGAA-----------------TCG--TGCAAGAGGGCCA-GCGCC--------------AG---GGC---AAA---------AACGCCATCGAA-----------------TCGCGTT---------------------GTGTG---------CGGCGTGCGGTGTG----TGTTTT----GTGT-----TTTATTTTTGGAA-----TTAAAT-------------ACGGCAGCAGCCCCTGCC s droMir2.chr3 1383970 311 - 20862834 CA----GCTGTCAA-TTTTCT------GCTTgc---------------ggtgtttgtgtgtgt----------g-cgtgcgtgcgtgt----ttgttgcAAAACGACGGCGTTGC--AGCCCAA----------AAATT-CGC-------GTT----TTGA--TCC--AA---AATTC--AA--TTGtagttaatt-------attt-----------------------------------aaa-a--------caat----------tgaGCCACG-----------GCCGGCAGT-------GC-------------CAGCTAGCGCAGGAG-AGCTCAG-CCGAACAGCG----AC------------GCGTCAGGGAA-----------------TCG--TGCAAGAGGGCCA-GCGCC--------------AG---GGC---AGA---------AACGCCATCGAA-----------------TCGCGTT---------------------GTGTG---------CGGCGTGcggtgtg----tttttt----gtgt-----tttatttttggaa-----ttaaAT-------------ACGGCAGCAGCCCctgcc s droWil2.CH963894 1299593 318 + 2843958 CA----GCTGTCAG-TTTTTTCTATAAgtgtgcgcgactgtgcatatacgtgagcgtgtgcgt----------g-cgtgtgtgtgtgt----gtgtggt-------------tgc--a----------------AACGC-CGT-------CGT----TTTGCAACC--AA---CAAAA--AC--GCGTTAAAAact-------aaga-----------------------------------ata-a--------taat----------a-------a-----------ttcaatcat-------tt--------------------------aa-acaaaagaacaaaCTGTT----GC--AGCTTCGT--CTgcccaagca-----------------gca--g------cagccg-ccgcg---------------------C---AAT---------AAAGTTAGCAACTACGTC--TGCCCCCTCTCGCGTTCgctc-------tctctgtcactctc---------gCGGCAGcggtgtg----tgtttt--t-gtgtg----tttatttttggaaCGTACCAGAGA-------------GCC------------GTT s droVir3.scaffold_12875 7344054 346 + 20611582 CA----GTTGTCAG-TTTTTC---------------------------T-TGTGTGCTTGCGCC---------G-CGTGTGTGTGTGCGTGCGT--------------GTGCTGCAAACCGAA-----------AGTTT-CGTGaatta-att----gtta--ata--at---aatac--aaatatattattcata------tatta-----------------------------------ttg-t--------tattaataaCAAGCT--GCAGCGCGTGCA-----GCAAACGGC------GTT-----------------------------CGTGTTA-ATAACT--------GC--AG---CGC--CAGCAACGGCAAGCTGCGCAAACAGCTGAcg--gcg----gcggca-gcgac----------ggcggc---ggc---CAC---------A--ACAACAACA---------------CTGCGCGCTCgtgtgtgtgtgtgtgtgtttgtgtgcacttgtgtgcgtgcgtg-tgtttgtgcgtTCT--TAGTGT------TTATTTTTGGAA-----TTAAAAAGCTA--------GC---------------- s droMoj3.scaffold_6496 26138810 368 + 26866924 CA----GTTGTCAG-TTTTTC---------------------------T-TGTGTGCTTGCGCC---------G-CGTGTGTGTGCGC----------------------GCTGCCCACCGAA-----------AGTTT-CGTGAATTA-ATT----GTTA--ATA--ATCGAAATAC--AA--ATATTATTGACA-------ATTG-----------------------------------CTG-T--------CAATAATAACGAG-T--GCAGCGCTTTCG-----GCGAACGGCGTCCGTGTTAACTactgcagtgtcagcaacggccagc-agtgcaa-acagctgaca----gc--gg---cgg--tggcagcggca-----------------gcg--gca----gcggca-gcggc----------agtaat---tgt---cac---------aacacagcaacaaaagcaaagcagcGGCGGCTCGTTCgtttgtgtgtgcgtgcgtgcgtgta---ttg---gtgtgcgtg-tgtttttgtgtttt--t-gtgt------TTATTTTTGGAA-----TTAAAAAGCTA--------GC---------------- s droAlb1.JH854640 302893 377 + 406291 CA----GTTGTCAG-TTTTTC---------------------------T-TGTGTGCTTGCgcc---------g-cgtgtgtgtgtgc----gt-----------taagTGCTGC--AACTAA-----------AG-TT-CGCGGATTATTTT----GTTA--CTA--AT---CATAC--AA--AGattaaacaaatcaatctACCG-----------------------------------TTG-TACGTATCACGCT-GCAGCGCG-G--GCAGCAGACGCGTCTGTGCAAATAAC-----TGTA----------GCGTCGCCAGCGGCAAAC-AGTGCAA-ACAGCTGACGGCCCGc--ta---cag--cgacagcgaca-----------aagccagcg--gta----aaagca-aaggc----------agaggcaaaggc---aaa---------agcaaagcaaaaacagcaacaacgtgcGTGCGCGCCTCTCtgtgtgagcgcgtgtgtgtgt----------gtgtgagtg-tgtt------tttt--t-gtgt------ttatttttggaa-----ttaaAAAGCTA--------GC---------------- s droGri2.scaffold_15245 891905 198 + 18325388 cg----tttgtgtg-tgtgag---------------------------tgtgtgtgtgcgcgcctttgcctgtg-tgtgtgtgtgtgt----gt--------------gtgtTAT---------------------TTT-TGTG------TTT----ATTT--TTG--GA---ATTAA--AT--AAGCTGAGCAAA-------ACTA-----------------------------------AAG-C----------------------T--AAAA-------------TCGAATAAT--------------------------------------CAAAAAA-AAAAAGAAAA----GC--AA---GAA--AAGgaaagaga-------------------g--aga----gagaga-gagag----------gagagt---ggg---aga---------gagagagagaga------------------------------------------------------------------------------------------------------------------------------------------------------- a score=-13736.000000 s dm6.chr2R 24343958 44 + 25286936 TGATCTGA------------------------------------AAAGTGTGCCGCGGC--------------------------CGGATTC------------TAGATATTCAGATT s droSim1.chr2R 18690775 44 + 19596830 TGATCTGA------------------------------------AAAGTGTGCCGCGGC--------------------------CGGATTC------------TAGATATTCAGATT s droSec1.super_23 110521 44 + 989336 TGATCTGA------------------------------------AAACTGTGCCGCGGC--------------------------CGGATTC------------TAGATATTCAGATT s droYak3.chr2R 20199520 44 + 21139217 TGATCTGA------------------------------------AAAGTGTGCCGCGGC--------------------------CGGATTC------------TAGATATTCAGATT s droEre2.scaffold_4845 21597482 44 + 22589142 TGATCTGA------------------------------------AAAGTGTGCCGCGGC--------------------------CGGATTC------------TAGATATTCAGATT s droBia2.KB462602 789173 43 + 3129309 GGATCGGA------------------------------------AAAGTGTGCCGCGGC--------------------------CGGATTTCAG---------TAGATTTTCA---- s droSuz1.KI419649 12034308 43 - 14502029 CGATCGGA------------------------------------AAAGTGTGCCGCGGC--------------------------CGGATTTCAG---------TAGATATTCA---- s droAna3.scaffold_13266 5705368 43 - 19884421 CGGCTGGC------------------------------------AAAGTGTGCCGCGGC--------------------------CGGATTT------------CTGAT-TTCGGATT s droBip2.KB464407 1954065 43 + 2915140 CGGCTGGC------------------------------------AAAGTGTGCCGCGGC--------------------------CGGATTT------------CTGAT-TTCGGATT s droEug2.KB465067 594694 44 + 1515531 TGATCTG-------------------------------------AAAGTGTGCCGCGGC--------------------------CGGATTTT-----------CAGATATTCAGATT s droEle2.KB458573 514685 65 - 5320397 aaagaaga------------------------------------aaagcgATCCGCAGCAATCCGAGGAAAGTAGTACTATAAAGCGAAAGA------------AAAGTGTGC----- s droKik2.KB459527 269776 68 - 1234237 cgatccga--tccgag-gCAGCGCGCAGGAAGGTGGCGGCTGGGAAAGTGTGCCGCGGC--------------------------CGGATCT------------CCTCT--------- s droTak2.KB461535 134316 51 - 669855 TGATCGGA------------------------------------AAAGTGTGCCGCGGC--------------------------CGGATTTCTGTAG-----ATAGATATCTATAAC s droRho2.KB449310 27943 63 - 65043 GGATCCGCAATCCGAGAGGaaagtataacaaaaaaaaaagaaaaaaagtgtGCCGCGGC--------------------------CGG----------------C------------- s droFic2.KB457177 74848 54 + 995874 AGATCtga----------------acagaaaaaagaaa------aaagtgtgCCGCGGC--------------------------CGGATTTT-----------CAGAGGCCC----- s droPse3.chr3 1343196 55 - 19787792 agagcaga---gccagagcagaggagaACAACGGAA--------AAAGTGTGCCGCGGC--------------------------CGGATTT-------------------------- s droPer1.super_34 532053 55 - 916997 AGAGCAGA---GCCAGAGCAGAGGAGAACAACGGAA--------AAAGTGTGCCGCGGC--------------------------CGGATTT-------------------------- s droMir2.chr3 1384281 55 - 20862834 agagcaga---gccagagcagaggagaacaACGGAA--------AAAGTGTGCCGCGGC--------------------------CGGATTT-------------------------- s droWil2.CH963894 1299911 63 + 2843958 TGATCGAA----------------CGGGAAGCGGGG--------AACGCGTAATCCGAC--------------------------AGGGTGTAACGAGGGGTAAAAAGTGTGC----- s droVir3.scaffold_12875 7344410 22 + 20611582 TGAGGCAA------------------------------------AA------CTAAAGC--------------------------TAAAG---------------------------- s droMoj3.scaffold_6496 26139190 28 + 26866924 TGTGGCAA------------------------------------AActaaagctaaagc--------------------------taaag---------------------------- s droGri2.scaffold_15245 892103 25 + 18325388 -gagaAGA------------------------------------AAAGTGTGCCGCAGC--------------------------GGG------------------------------ a score=559800.000000 s dm6.chr2R 24344002 55 + 25286936 CCCAGC-ACCCGAAACCCA---AAC--------------------------------GCAATAATAGACGCGCGCGGTGCCTTGGATC---TCT s droSim1.chr2R 18690819 55 + 19596830 CCCAGC-ACCCGAAACCCA---AAC--------------------------------GCAATAATAGACGCGCGCGGTGCCTTGGATC---TCT s droSec1.super_23 110565 55 + 989336 CCCAGC-ACCCGAAACCCA---AAC--------------------------------GCAATAATAGACGCGCGCGGTGCCTTGGATC---TCT s droYak3.chr2R 20199564 55 + 21139217 CCCAGC-ACCCGAAACCCA---AAC--------------------------------GCAATAATAGACGCGCGCGGTGCCTTGGATC---TCT s droEre2.scaffold_4845 21597526 55 + 22589142 CCCAGC-ACCCGAAACCCA---AAC--------------------------------GCAATAATAGACGCGCGCGGTGCCTTGGATC---TCT s droBia2.KB462602 789216 55 + 3129309 CACAGG-CCAGCAAGCCCA---AAC--------------------------------GCAATAATAGACGCGCGCGGTGCCTTGGATT---TCT s droSuz1.KI419649 12034351 55 - 14502029 CACAGG-CCAGAAAGCCCA---AAC--------------------------------GCAATAATAGACGCGCGCGGTGCCTTGGATT---TCT s droAna3.scaffold_13266 5705411 50 - 19884421 GCTAG------GCAAGGTA---GAC--------------------------------GCAATAATAGACGCGCGCGGTGCCTTGGATT---TCT s droBip2.KB464407 1954108 47 + 2915140 GCTAG------GCAAGGTA--------------------------------------GCAATAATAGACGCGCGCGGTGCCTTGGATT---TCT s droEug2.KB465067 594738 55 + 1515531 TTCAGC-ACCCAAAACCCA---ACA--------------------------------GCAATAATAGACGCGCGCGGTGCCTTGGATT---TCT s droEle2.KB458573 514750 53 - 5320397 CGCAGC-CCCGAAAACCCA---A----------------------------------GCAATAATAGACGCGCGCGGTGCCTTGGATT---TCT s droKik2.KB459527 269844 53 - 1234237 CACAGCTACCGAAAAGGTA--------------------------------------GCAATAATAGACGCGCGCGGTGCCTTGGATT---TCT s droTak2.KB461535 134367 54 - 669855 CC-----ACAAAGAACCCACAAGAC--------------------------------GCAATAATAGACGCGCGCGGTGCCTTGGATT---TCT s droRho2.KB449310 28006 47 - 65043 -------CCCAAAAACCCA---A----------------------------------GCAATAATAGACGCGCGCGGTGCCTTGGATT---TCT s droFic2.KB457177 74902 53 + 995874 CTCGTG-AAAATAACGCCA---A----------------------------------GCAATAATAGACGCGCGCGGTGCCTTGGATT---TTT s droPse3.chr3 1343251 46 - 19787792 CACAGC-------AAGGTA--------------------------------------GCAATAATAGACGCGCGCGGTGCCTTGGATT---TCT s droPer1.super_34 532108 46 - 916997 CACAGC-------AAGGTA--------------------------------------GCAATAATAGACGCGCGCGGTGCCTTGGATT---TCT s droMir2.chr3 1384336 46 - 20862834 CACAGC-------AAGGTA--------------------------------------GCAATAATAGACGCGCGCGGTGCCTTGGATT---TCT s droWil2.CH963894 1299974 46 + 2843958 CACAGA-------AAGGTA--------------------------------------GCAATAATAGACGCGCGCGGTGCCTTGGATT---TCT s droVir3.scaffold_12875 7344432 82 + 20611582 ---------CTAAAACCTA---AAATCGAATCAAACAAAAAAAAGTGTGCCGCAGCGGCAATAATAGACGCGCGTGGTGCCTTGGATTTATTGT s droMoj3.scaffold_6496 26139218 76 + 26866924 ---------ctaaagcCCA---AAATCGAATC------AAAAAAGTGTGCCGCAGCGGCAATAATAGACGCGCGTGGTGCCTTGAATTCACTGT s droAlb1.JH854640 303315 72 + 406291 --------cccaaaatcta---aaatc-----------taaaaaGTGTGCCGCAGCGGCAATAATAGACGCGCGTGGTGCCTTGGATTTATTGT s droGri2.scaffold_15245 892128 36 + 18325388 ----------------------------------------------------------CAATAATAGACGCGCGTGGTGCCTTGGATTTAGTGT a score=701245.000000 s dm6.chr2R 24344057 28 + 25286936 ACGGCTCCACGGTGGAGAACTTTTACCT s droSim1.chr2R 18690874 28 + 19596830 ACGGCTCCACGGTGGAGAACTTTTACCT s droSec1.super_23 110620 28 + 989336 ACGGCTCCACGGTGGAGAACTTTTACCT s droYak3.chr2R 20199619 28 + 21139217 ACGGCTCCACGGTGGAGAACTTTTACCT s droEre2.scaffold_4845 21597581 28 + 22589142 ACGGCTCCACGGTGGAGAACTTTTACCT s droBia2.KB462602 789271 28 + 3129309 ACGGCTCCACGGTGGAGAACTTTTACCT s droSuz1.KI419649 12034406 28 - 14502029 ACGGCTCCACGGTGGAGAACTTTTACCT s droAna3.scaffold_13266 5705461 28 - 19884421 ACGGCTCCACGGTGGAGAACTTTTACCT s droBip2.KB464407 1954155 28 + 2915140 ACGGCTCCACGGTGGAGAACTATTACCT s droEug2.KB465067 594793 28 + 1515531 ACGGCTCCACGGTGGAGAACTTTTACCT s droEle2.KB458573 514803 28 - 5320397 ACGGCTCCACGGTGGAGAACTTTTACCT s droKik2.KB459527 269897 28 - 1234237 ACGGCTCCACGGTGGAGAACTTTTACCT s droTak2.KB461535 134421 28 - 669855 ACGGCTCCACGGTGGAGAACTTTTACCT s droRho2.KB449310 28053 28 - 65043 ACGGCTCCACGGTGGAGAACTTTTACCT s droFic2.KB457177 74955 28 + 995874 ACGGCTCCACGGTGGAGAACTTTTACCT s droPse3.chr3 1343297 28 - 19787792 ACGGCTCCACCGTGGAGAACTTTTACCT s droPer1.super_34 532154 28 - 916997 ACGGCTCCACCGTGGAGAACTTTTACCT s droMir2.chr3 1384382 28 - 20862834 ACGGCTCCACCGTGGAGAACTTTTACCT s droWil2.CH963894 1300020 28 + 2843958 ACGGCTCCACGGTGGAGAACTTTTACCT s droVir3.scaffold_12875 7344514 28 + 20611582 ACGGCTCCACGGTGGATAACTTTTACCT s droMoj3.scaffold_6496 26139294 28 + 26866924 ACGGCTCCACGGTGGAGAACTTTTACCT s droAlb1.JH854640 303387 28 + 406291 ACGGCTCCACGGTGGAGAACTTTTACCT s droGri2.scaffold_15245 892164 28 + 18325388 ACGGCTCCACGGTGGAGAACTTTTACCT s musDom2.KB857237 5261 28 - 101287 ACGGCATCGCGGTGGATAACTTTTACCT a score=19.000000 s dm6.chr2R 24344085 1 + 25286936 C s droSim1.chr2R 18690902 1 + 19596830 C s droSec1.super_23 110648 1 + 989336 C s droYak3.chr2R 20199647 1 + 21139217 C s droEre2.scaffold_4845 21597609 1 + 22589142 C s droBia2.KB462602 789299 1 + 3129309 C s droSuz1.KI419649 12034434 1 - 14502029 C s droAna3.scaffold_13266 5705489 1 - 19884421 C s droBip2.KB464407 1954183 1 + 2915140 C s droEug2.KB465067 594821 1 + 1515531 C s droEle2.KB458573 514831 1 - 5320397 C s droKik2.KB459527 269925 1 - 1234237 C s droTak2.KB461535 134449 1 - 669855 C s droRho2.KB449310 28081 1 - 65043 C s droFic2.KB457177 74983 1 + 995874 C s droPse3.chr3 1343325 1 - 19787792 G s droPer1.super_34 532182 1 - 916997 G s droMir2.chr3 1384410 1 - 20862834 G s droWil2.CH963894 1300048 1 + 2843958 C s droVir3.scaffold_12875 7344542 1 + 20611582 G s droMoj3.scaffold_6496 26139322 1 + 26866924 G s droAlb1.JH854640 303415 1 + 406291 T s droGri2.scaffold_15245 892192 1 + 18325388 G s musDom2.KB857237 5289 1 - 101287 T s triCas2.ChLG1X 6840743 1 + 8109244 C a score=2454295.000000 s dm6.chr2R 24344086 135 + 25286936 AGAATGGATCCGAC--GCGAG-GTGACTCGCGGTACAATCTCAACTACTCGATGAG--TAGCATAGGGCTGAGCCTGGCGGATCCGGCGGACATGTACGGCAACCCG------------GCCCTGGGGGCGGGCCGCCCGCCC---TCCGGTGGC s droSim1.chr2R 18690903 135 + 19596830 AGAATGGATCCGAC--GCGAG-GTGACTCGCGGTACAATCTCAACTACTCGATGAG--TAGCATCGGGCTGAGCCTGGCGGATCCGGCGGACATGTACGGCAAcccg------------gccctgggggcgggccgcccgccc---tccggcggc s droSec1.super_23 110649 135 + 989336 AGAATGGATCCGAC--GCGAG-GTGACTCGCGGTACAATCTCAACTACTCGATGAG--TAGCATCGGGCTGAGCCTGGCGGATCCGGCGGACATGTACGGCAACCCG------------GCCCTGGGGGCGGGCCGTCCGCCA---TCCGGCGGC s droYak3.chr2R 20199648 135 + 21139217 AGAATGGATCCGAC--GCGAG-GTGACTCGCGGTACAATCTCAACTACTCGATGAG--TAGCATCGGGCTGAGCCTGGCGGATCCGGCGGACATGTACGGCAACCCG------------GCCCTGGGGGCGGGCCGTCCGCCC---TCCGGCGGC s droEre2.scaffold_4845 21597610 135 + 22589142 AGAATGGATCCGAC--GCGAG-GTGACTCGCGGTACAACCTCAACTACTCGATGAG--TAGCATCGGGCTGAGCCTGGCGGATCCGGCGGACATGTACGGCAAcccg------------gccctgggggcgggccgcccgccc---tccggcggc s droBia2.KB462602 789300 135 + 3129309 AGAATGGATCCGAC--GCGAG-GTGACTCGCGCTACAATCTCAACTACTCGATGAG--TAGTATTGGGCTGAGTCTGGCGGATCCGGCGGACATGTACGGCAATCCC------------GCCCTGGGCGCGGGTCGCCCGCCC---TCGGGCGGC s droSuz1.KI419649 12034435 135 - 14502029 AGAATGGATCCGAC--GCGAG-GTGACTCGCGCTACAATCTCAACTACTCGATGAG--TAGTATTGGGCTGAGTCTGGCGGATCCGGCGGATATGTACGGTAATCCC------------GCCCTGGGGGCGGGTCGTCCGCCC---TCGGGTGGG s droAna3.scaffold_13266 5705490 141 - 19884421 AGAATGGATCCGAC--GCGGG-GCGACTCGCGCTACAACCTCAACTACTCGATGAG--TAGTATAGGTCTCAGTCTCGCCGACCAGGCGGACATGTACGGCAATCCGGCG---GTGGCCGCCCTGGGTGC---CCGTCCGCCC---TCCGGCGGC s droBip2.KB464407 1954184 141 + 2915140 AGAATGGATCCGAC--GCGGG-GCGACTCGCGCTACAACCTCAACTACTCGATGAG--TAGTATAGGTCTCAGTCTCGCCGATCAGGCGGACATGTACGGCAATCCGGCG---GTGGCCGCCCTGGGTGC---CCGTCCGCCC---TCCGGCGGC s droEug2.KB465067 594822 135 + 1515531 AGAATGGATCCGAC--GCGAG-GTGACTCGCGCTACAACCTCAACTACTCGATGAG--TAGTATCGGGTTAAGCCTGGCGGATCCGGCGGATATGTACGGCAACTCC------------GCCTTGGGGGCGGGTCGTCCGCCC---TCCGGCGGT s droEle2.KB458573 514832 135 - 5320397 AGAATGGATCCGAC--GCGGG-GCGACTCGCGCTACAACCTGAACTACTCGATGAG--TAGTATCGGGTTGAGCCTGACGGATCCGGCGGACATGTACGGCAATGCC------------GCCCTGGGCGGGGCACGccccccc---TCCGGCGGT s droKik2.KB459527 269926 141 - 1234237 AGAATGGATCCGAC--GCGGG-GCGACTCGCGCTACAACCTGAACTACTCGATGAG--TAGTATCGGGCTGAGCCTCTCCGATCCCTCGGACATGTACGGCAACCCGGCG---GTGGCCGCCCTGGGCGC---CCGCCCGCCC---TCCGGCGGC s droTak2.KB461535 134450 135 - 669855 AGAATGGATCCGAC--GCGAG-GTGACTCGCGCTACAATCTCAACTACTCGATGAG--TAGTATTGGGCTGAGTCTGGCGGATCCGGCGGACATGTACGGCAATCCC------------GCCCTGGGGGCGGGTCGTCCGCCC---TCCGGCGGG s droRho2.KB449310 28082 135 - 65043 AGAATGGATCCGAC--GCGGG-GCGACTCGCGCTACAACCTGAACTACTCGATGAG--TAGTATCGGGTTAAGTCTGGCGGATCCGGCGGATATGTACGGCAACGCC------------GCCCTCGGCGGGGCACGCCCACCC---TCGGGCGGT s droFic2.KB457177 74984 138 + 995874 AGAATGGATCCTAC--GCGGG-GCGACTCGCGCTACAACCTGAACTACTCGATGAG--TAGTATCGGGTTGAGTCTGACCGATCCGGCGGATATGTACGGCAGTCCC------------GCCCTGGGGGCGGGCGGTCGGCCCCCGTCGGGGGGC s droPse3.chr3 1343326 141 - 19787792 AGAATGGACCCGAC--GCGAG-GTGACTCGCGCTATAACCTAAACTACTCGATGAG--TAGTATAGGCCTTAGCCTCGCCGACCAGGCCGATATGTACGGCAATCCGGCG---GTGGCGGCCCTGGGCGC---CCGTCCGCCC---AGCGGCGGG s droPer1.super_34 532183 141 - 916997 AGAATGGACCCGAC--GCGAG-GTGACTCGCGCTATAACCTAAACTACTCGATGAG--TAGTATAGGCCTTAGCCTCGCCGACCAGGCCGATATGTACGGCAATCCGGCG---GTGGCGGCCCTGGGCGC---CCGTCCGCCC---AGCGGAGGG s droMir2.chr3 1384411 141 - 20862834 AGAATGGACCCGAC--GCGAG-GTGACTCGCGCTACAACCTAAACTACTCGATGAG--TAGTATAGGCCTCAGCCTCGCCGACCAGGCCGATATGTACGGCAATCCGGCG---GTGGCGGCCCTGGGCGC---CCGTCCGCCC---AGCGGCGGG s droWil2.CH963894 1300049 144 + 2843958 AGAATGGATCCGAC--GCGAG-GTGACTCGCGCTATAATCTAAACTACTCGATGAG--TAGTATTGGATTAAGTCTGGCCGATCAGGCCGATATGTATGGCAATCCGGCG---GTGGCAGCGCTGGGTGGCGGCCGTCCACCG---AGTGGTGGC s droVir3.scaffold_12875 7344543 141 + 20611582 AGAATGGATCCCAC--GCGCG-GTGACGCGCGCTATAACATAAACTACTCAATGAG--TAGTATAGGCTTAAGTCTGGCCGATCAGGCCGACATGTATGGCAATCCCGCG---GTGGCAGCGCTTGGCGG---TCGCCCACCC---AGCGGCGGT s droMoj3.scaffold_6496 26139323 141 + 26866924 AGAATGGATCCCAC--GCGCG-GCGACTCGCGCTACAACCTAAACTACTCGATGAG--TAGCATAGGTCTCAGTCTGGCCGACCAGGCCGACATGTACGGCAATCCCGCC---GTCGCTGCCCTGGGCGC---CCGGCCCCCC---AGCGGCGGC s droAlb1.JH854640 303416 141 + 406291 AGAATGGATCCAGC--GCGCG-GTGACTCGCGCTATAACCTAAACTACTCGATGAG--TAGTATAGGTTTGAGTCTCGCTGATCAGGCGGACATCTACGGCAATCCCGCT---GTGGCGGCGCTTGGCGC---CCGACCACCC---AGCGGCGGC s droGri2.scaffold_15245 892193 141 + 18325388 AGAATGGATCCGAC--GCGCG-GCGATTCGCGCTATAACCTAAACTACTCGATGAG--TAGCATTGGGTTAAGTCTCGCCGATCAGGCCGACATGTATGGCAATCCTGCC---GTTGCGGCACTGGGCGC---CCGCCCGCCC---AGCGGCGGT s musDom2.KB857237 5290 141 - 101287 AGAATGGATCCTTC--GCGAG-GAGACTCGCGGTATAACCTTAACTACTCTATGAG--TAGCATTGGACTTTCGCTAGCCGACCAGGCTGACATGTATGGCAATCCAGCGGCAGTAGCCGCCCTTGG------GCGTCCTCCA---AGCGCTGGT s anoGam1.chr3L 3954404 126 + 41284009 ATAATGGATCCCACCGGTGGGCGCGATTCGCGCTACAATCTGAACTACAGTATGAG--CATGATGAG------------CGAATCGCCAGAGATATACGGCAACCCGAAC---GT----GTCTCTGGCGC-----GCCCACCG---AGCGGTGGT s triCas2.ChLG1X 6840744 123 + 8109244 GAAATGGAACCACCTGGCGGGAGGGATTCCCGATTCAACCTGGGCTACAGCATGAACCTGCTGTCGGG--------GGAGACCCCGCCCGAGATCTACGGCAACCCT------------GGCCTGGG------GCGGCCCTCC---ACCAGC--- a score=433146.000000 s dm6.chr2R 24344221 76 + 25286936 CTGCTCCAGAACATG------GGCGGC---------------------GTTCCGCCGAT---GCAGCGCCCCAATCCC-------------------------GCGGC-----------AGGAGCACCC--CCTGCCCC-------GCAG---T s droSim1.chr2R 18691038 76 + 19596830 cTGCTCCAGAACATG------GGCGGC---------------------GTTCCGCCGAT---GCAGCGCCCCAATCCC-------------------------GCGGC-----------AGGAGCACCC--CCTGCCCC-------CCAA---T s droSec1.super_23 110784 76 + 989336 CTGCTCCAGAACATG------GGAGGC---------------------GTTCCGCCGAT---GCAGCGCCCCAATCCC-------------------------GCGGC-----------AGGAGCACCC--CCTGCCCC-------CCAA---T s droYak3.chr2R 20199783 76 + 21139217 CTGCTCCAGAACATG------GGCGGG---------------------GTTCCGCCGAT---GCAGCGCCCCAATCCC-------------------------GCGGC-----------AGGAGCAccc--cctgcccc-------ccAA---T s droEre2.scaffold_4845 21597745 76 + 22589142 cTGCTCCAGAACATG------GGCGGG---------------------GTTCCGCCGAT---GCAGCGCCCCAATCCC-------------------------GCGGC-----------AGGAGCACCC--CCTGCCCC-------GCAA---T s droBia2.KB462602 789435 82 + 3129309 CTGCTCCAGAACATG------GGCGGT---------------------GTGCCGCCCAT---GCAGCGGCCGAATCCCGC------------------TGGCGGCGGC------------GGGGCACCC--CCTGCCAC-------CCAG---T s droSuz1.KI419649 12034570 85 - 14502029 CTGCTCCAGAATATG------GGCGGT---------------------GTGCCGCCCAT---GCAGCGGGCAAATCCCgc------------------tggcggcggc---------ggaggagcaCCC--CCTGCCAC-------CCAG---T s droAna3.scaffold_13266 5705631 73 - 19884421 CTCCTCCAGAACATG------GGCGGC------------------------CCGTCGAT---GCAGCGACCGAATCCC---------------------GGTGCCGGT------------GGTCCACCC--ACTGGC----------CAG---T s droBip2.KB464407 1954325 73 + 2915140 CTACTCCAGAACATG------GGCGGC------------------------CCGTCGAT---GCAGCGTCCCGGTGCC---------------------GGAGGTGGC------------GGTGCACCC--ACTGGC----------CAA---T s droEug2.KB465067 594957 76 + 1515531 CTGCTGCAGAACATG------GGCGGG---------------------GTGCCGCCAAT---GCAGCGGCCGAACCCC-------------------------GCCTC-----------GGGAGCACCT--CCCTCCAC-------CCAA---T s droEle2.KB458573 514967 88 - 5320397 CTGCTGCAGAACATG------GGCGGC------------------GGTGTGCCGCCCAT---GCAGCGACCAAATCcggcg---------------ggcggcggcggc------------ggagcaCCC--CCCTCCAC-------CCAA---T s droKik2.KB459527 270067 94 - 1234237 CTCCTCCAGAGCATG------ggcggcggcgcaagcggcggcggcggtgtaCCGTCCAT---GCAGCGGCCAAATCCC-------------------------GCCAC-----------AGGAG---CC--acagccgc-------ccag---t s droTak2.KB461535 134585 82 - 669855 CTGCTCCAGAACATG------GGCGGC------------------GGTGTGCCGCCCAT---GCAGCGGGCCAATCCC-------------------------GCCGT--------CGGAGGAGCACCA--CCTGCCAC-------CCAA---T s droRho2.KB449310 28217 82 - 65043 CTGCTCCAGAACATG------GGCGGT------------------GGTGTGCCGCCCAT---GCAGCGGCCAAATCCC---------------------GCGGGCGGC------------GGAGCACCC--CCATCCAC-------CCAA---T s droFic2.KB457177 75122 73 + 995874 TTGCTGCAGAACATG------GGCGGC------------------GGAGTGCCGCCCAT---GCAGCGGCCCA------------------------------CGGGC------------GGAGCGCCT--CCCGCAAC-------CCAG---T s droPse3.chr3 1343467 79 - 19787792 CTCCTGCAGAGcatg------ggcggc---------------ggcggaggcgtgCCCAT---GCAGCGGCCCAATCCC------------------------ACCGGC------------GGTGCAGCT--CCCTCC----------CAG---T s droPer1.super_34 532324 79 - 916997 CTCCTGCAGAGCATG------GGCGGC---------------GGCGGAGGCGTGCCCAT---GCAGCGGCCCAATCCC------------------------ACCGGC------------GGTGCAGCT--CCCTCC----------CAG---T s droMir2.chr3 1384552 79 - 20862834 CTCCTGCAGAGcatg------ggcggc---------------ggcggaggcgtgCCCAT---GCAGCGGCCCAATCCC------------------------ACCGGC------------GGTGCAGCT--CCCTCC----------CAG---T s droWil2.CH963894 1300193 121 + 2843958 CTCTTGCAGAGCAtg------ggtggc---------ggcggcggcggtggcatGCCCAT---ACAGCGGCCTAATCCCCCGGGCGGGGGTGGTgctggtggcggcggc---ggcggaggAGGTGGAGCC--ACAGCTAG-------CCAA---T s droVir3.scaffold_12875 7344684 109 + 20611582 TTGCTCCAAAGCATGggcggcggcggc---------ggcggtggcgcgggcctagccat---gcagcgtcccaatccc-------------------gcggcggtggc-----------agcagcggcggcgcagcagcaacagcaacag---t s droMoj3.scaffold_6496 26139464 103 + 26866924 TTGCTGCAGAGCATG------GGCGGC---------AGCAGTGGCGCGGGCCTGGCGATGCAGCAGCGACCCAATCCG-------------------GCGGCGGCGGC------------gcagcagca--acagcaacagcagcaacag---T s droAlb1.JH854640 303557 115 + 406291 TTGCTGCAGAACAtg---ggcggcggc---------ggcggaggcGTTGGTCTCGCCAT---gcagcggcccaatccg-------------------gcggcagcagcagcggcggtgcagcaacagca--gcagcaacaacagcaacag---t s droGri2.scaffold_15245 892334 109 + 18325388 CTGCTACAGAGCATG---GGCGGCGGC---------GGCGGCGGAGGCGGAGTCACCAT---GCAACGTCCCGTTCca-------------------tcagtagcggc------gcaacaacagcagca--acagcagcagcagcaacag---t s musDom2.KB857237 5431 65 - 101287 TTGTTGCAAAGTATG------GGTGGG--------------------GGAGCTGGTGGT---TCAG-------------------------------GCGTAGGTGGA------------ATAACATCA--CGCTCTTC--------------- s anoGam1.chr3L 3954530 47 + 41284009 TTGGTC--------G------GGCAGG----------------------------TGAT---G-----------TCTC-------------------------GCGGT-----------GGGAACGGTG--GA-------------ACGGGTTT a score=1024765.000000 s dm6.chr2R 24344297 86 + 25286936 GCCAAACGCT-----------------------CCACAGCCCACAGCACGCCTCC------cagcagcagcagcagcaacaaca--gcagcagc-----agcaacaccagcag---cagcaacaa s droSim1.chr2R 18691114 86 + 19596830 GCCAAACGCT-----------------------CCACAGCCCACAGCACGCCTCC------cagcagcagcagcagcagcaaca--acagcagc-----agcagcaacaccag---cagcagcag s droSec1.super_23 110860 86 + 989336 GCCAAACGCT-----------------------CCACAGCCCACAGCACGCCTCC------cagcagcagcagcagcagcaaca--acagcagc-----agcagcaacaccag---cagcagcag s droYak3.chr2R 20199859 92 + 21139217 GCCAAACGCT-----------------------CCACAGCCCACAGCACGCctcccagcagcagcaacagcagcagcagcaaca--acagcagc-----agcagcaacaccag---cagcagcag s droEre2.scaffold_4845 21597821 92 + 22589142 GCCAAACGCT-----------------------CCACAGCCCACAGCACGCCTCCcagcaacagcagcagcagcagcaacaaca--gcagcagc-----agcagcaacaccag---cagcagcag s droBia2.KB462602 789517 77 + 3129309 GCCAGACGCT-----------------------GCACAGCCCACAACACGcctcc------cagcagcagcagcagcagcaaca--gcagcagc-----agcag------------cagcatcag s droSuz1.KI419649 12034655 89 - 14502029 GCCAAACGCT-----------------------CCACAGCCCACAACACGCCtcc------caacagcagcagcagcagcagca--acaacagc-----agcagcaacagcaacatcagcagcag s droAna3.scaffold_13266 5705704 98 - 19884421 GTCAGACCCTGGG--CAACAGTCAGACCTCCCACCACAGCCCCCAGCATGCCTCC---------------cagcagcagcaaca--acaacagc-----agcagcaacaccaa---caacagcag s droBip2.KB464407 1954398 101 + 2915140 GCCAGACCCTGGG--CAACAGTCAGACCTCCCATCacagcccgcagcatgcctcc------------cagcagcagcagcaaca--gcaacagc-----agcagcaacaccaa---cagcaacag s droEug2.KB465067 595033 86 + 1515531 GCCAAACGCT-----------------------CCACAGCCCACAACACGCctcc------cagcaacagcagcagcagcagca--acaacagc-----agcagcaacatcaa---cagcagcag s droEle2.KB458573 515055 86 - 5320397 GCCAAACGCT-----------------------CCACAGCCCACAACACGCctcc------caacagcagcagcagcaacagca--gcaacaac-----aacagcagcagcag---caacatcag s droKik2.KB459527 270161 86 - 1234237 gccagaccct-----------------------acacagcccccagcacgcctcc------caacagcagcagcagcagcaaca--gcaacaac-----agcagcagcagcaa---caccagcag s droTak2.KB461535 134667 77 - 669855 GCCAAACGCT-----------------------CCACAGCCCACAGCACGCctcc------caacagcagcagcagcagcaaca--gcagcagc-----agcaa------------catcagcag s droRho2.KB449310 28299 86 - 65043 GCCAAACGCT-----------------------CCACAGCCCACAACACGCCtcc------caacagcagcagcagcaacagca--gcaacagc-----aacaacagcagcag---caacatcaa s droFic2.KB457177 75195 80 + 995874 GCCAAACGCT-----------------------CCACAGTCCACAACACGCctcc------------cagcagcaacaacagca--gcagcagc-----agcaacaacatcag---cagcaacag s droPse3.chr3 1343546 101 - 19787792 GCCAGACCCTGGG--caacagccagacgca---tcacagtccccagcatgccgcg---------cagcagcaacagcaacaaca--gcagcagc-----agcagcaacaacaa---cagcagcag s droPer1.super_34 532403 98 - 916997 GCCAGACCCTGGG--CAACAGCCAGACGCA---TCACAGTCCCCAGCATGCCGCg---------cagcagcaacagcaacaaca--gcagcagc-----agcag---caacaa---cagcagcag s droMir2.chr3 1384631 98 - 20862834 GCCAGACCCTGGG--caacagccagacgca---tcacagtccccagcatgccgcg---------cagcagcagcaacagcaaca--acagcagc-----agcag---caacaa---cagcagcag s droWil2.CH963894 1300314 104 + 2843958 GTCAGACCTTGGG--CAATAGCCAAACACA---TCACAGTCCacagcatgtgcaa------cagcagcagcagcagcagcaaca--acaacaac-----agcaacaacaacaa---caacagcag s droVir3.scaffold_12875 7344793 89 + 20611582 gCCAAACGCTGGG--------------------CAACAGCCAAACGCACAGTCCg------cagcatcagcagcagcaacagca--gcagcagc-----agcaacagcagcaa---caacaacag s droMoj3.scaffold_6496 26139567 83 + 26866924 GCCAAACGCTGGG--------------------AAACAGCCAAACGCACAGTCCa------cagcaccagcag------cagca--gcaacaac-----agcaacagcagcaa---caacagcag s droAlb1.JH854640 303672 77 + 406291 gccaaactctggg--------------------caacagccaaacgcacagtcct------caacat------------cagca--acaacagc-----agcaacagcaacaa---caacagcag s droGri2.scaffold_15245 892443 92 + 18325388 gccaaacacttagtcca----------------caaca-ccagcaacagcaacaa------cagcagcagcagcaacaacagca--gcaacagc-----agcagcagcaacaa---caacagcaa s musDom2.KB857237 5496 63 - 101287 ---------------------------------CGGTAGTT--------------------TAATGTCAAGTGCA----CAACA--ATGTCAGTCTCTAAGCAATAATTCTGG---AAGTCATGG s anoGam1.chr3L 3954577 81 + 41284009 GATGAACGC------------------------CAATGGTCCACAGTGCgg----------tagtggcggtggtggtggtggtg--gtggtggt-----ggtggaggcggagg---tggtggcgg s apiMel4.Group11 6687583 87 - 14726556 GCCGACCGT------------------------CCACCTCCCAACTTACTTCTCA------AATAAGCCGCGGTGGCGCCACCATGATGGCCGC-----GGCAGCCGCTGCAG---GCGCACCGA a score=5096540.000000 s dm6.chr2R 24344383 293 + 25286936 cagcag-cagcagcaTCCCCAGCAGCAAC------------GCGGCCTTAAG-----CGC-TCCGGCAGCGACTGCTACGAGGAT---CACCAC---------CG---CTCGTCC------GGC------GG------------ACTCACCCTCCAAGGACTGGACAA-----------------------------------CGTGGCCAG------C--------------GG---------AGC---CGTCGAC---GACAGCGTA---------------GA-----CAACTACAACCCGCTGCCCAAC-AAGAAGTCTCCGCCTGCCAACGGCAAAAAGACAAAGGGACGTGTCAAAATCAAAATGGAATACATCGACAATAAGCTGCGTCGCTACACGACCTTCTCCAAGCGCAAGACGGGCATAATGAAGAAGGT s droSim1.chr2R 18691200 293 + 19596830 caacag-cagcagcatccccagcagcaAC------------GCGGCCTCAAG-----CGC-TCCGGCAGCGACTGCTACGAGGAT---CACCAC---------CG---CTCGTCC------GGC------GG------------ACTTACCCTCCAAGGACTGGACAA-----------------------------------CGTGGCCAG------C--------------GG---------AGC---CGTCGAC---GACAGCGTA---------------GA-----CAACTACAACCCGCTGCCCAAC-AAGAAGTCTCCGCCCGCCAACGGCAAAAAGACAAAGGGACGTGTCAAAATCAAAATGGAATACATCGACAACAAGCTGCGTCGCTACACGACCTTCTCCAAGCGCAAGACGGGCATCATGAAGAAGGT s droSec1.super_23 110946 293 + 989336 caacag-cagcagcatccccagcagcagc------------GCGGCCTCAAG-----CGC-TCCGGCAGCGACTGCTACGAGGAT---CACCAC---------CG---CTCGTCC------GGC------GG------------ACTCACCCTCCAAGGACTGGACAA-----------------------------------CGTGGCCAG------C--------------GG---------AGC---CGTCGAC---GACAGCGTA---------------GA-----TAACTACAACCCGCTGCCCAAC-AAGAAGTCTCCGCCCGCCAACGGCAAAAAGACAAAGGGACGTGTTAAAATCAAAATGGAATACATCGACAACAAGCTGCGTCGCTACACGACCTTCTCCAAACGCAAGACGGGCATCATGAAGAAGGT s droYak3.chr2R 20199951 293 + 21139217 caacaa-cagcagcatccccagcagcaac------------GCGGCCTCAAG-----CGC-TCCGGCAGCGACTGCTACGAGGAT---CACCAC---------CG---CTCCTCC------GGC------GG------------CCTCACCCTCCAAGGACTGGACAG-----------------------------------CGTGGCCAG------C--------------GG---------TGC---CGTCGAC---GACAGCGTA---------------GA-----CAACTACAACCCGCTGCCCAAC-AAGAAGTCTCCGCCCGCCAACGGCAAAAAGACAAAGGGACGTGTCAAAATCAAAATGGAATACATCGACAACAAGCTGCGTCGCTACACGACCTTCTCCAAGCGCAAAACGGGCATCATGAAGAAGGT s droEre2.scaffold_4845 21597913 293 + 22589142 caacag-cagcagcatccccagcagcaAC------------GCGGCCTCAAG-----CGC-TCCGGCAGCGACTGCTACGAGGAT---CACCAC---------CG---CTCCTCC------GGC------GG------------ACTCACCCTCCAAGGACTCGACAA-----------------------------------CGTGGCCAG------C--------------GG---------TGC---CGTCGAC---GACAGCGTA---------------GA-----CAACTACAACCCGCTGCCCAAC-AAGAAGTCTCCGCCCGCCAACGGCAAAAAGACAAAGGGACGTGTCAAAATCAAAATGGAATACATCGACAACAAGCTGCGTCGCTACACGACCTTCTCCAAGCGCAAAACGGGCATCATGAAGAAGGT s droBia2.KB462602 789594 302 + 3129309 cagcag-caacagcatccccagcagcagcagcagcag---cggggcCTCAAG-----CGG-TCCGGCAGCGACTGCTACGAGGAC---CACCAC---------CG---GTCCTCC------GGC------GG------------ACTCACCCTGCAGGGACTCGACGG-----------------------------------CGTGGCCGG------C--------------GG---------AGC---CGTGGAC---GACGGCGTG---------------GA-----CAGCTACAACCCACTGCCCAAC-AAGAAGTCGCCACCCGCCAACGGCAAAAAGACAAAGGGACGTgtcaaaatcaaaatggagTACATCGACAACAAGCTGCGTCGCTACACGACCTTCTCCAAGCGCAAGACGGGCATCATGAAGAAGGT s droSuz1.KI419649 12034744 302 - 14502029 cagcag-caacaacatccccaacagcaacagcaacag---aggGGTCTCAAG-----CGA-TCCGGCAGCGATTGCTACGAGGAT---CACCAT---------CG---ATCCTCC------GGC------GG------------ACTCACCCTCCAAGGACTCGATGG-----------------------------------CGTGGCCAG------C--------------GG---------AGC---CGTGGAC---GATGGCGTG---------------GA-----CAGCTACAACCCACTGCCCAAT-AAGAAGTCTCCACCCGCCAACGGCAAAAAGACAAAGGGACGTgtcaaaatcaaaatggaaTACATCGACAACAAGCTGCGTCGCTACACGACCTTCTCCAAGCGCAAAACGGGCATCATGAAGAAGGT s droAna3.scaffold_13266 5705802 299 - 19884421 caacag-caacagc---------------------------GGGGTCTGAAG-----CGA-TCGGGAAGCGACTGCTATGAGGAT---CATCAT---------CG---GTCCGCC---GGAGGT------GG------------ACTCACGCTCCAGGGCCTGGACAACTG------CGGCGCCGCC----------G-GGAGCGTCACCAG------T--------------GC---------CGG---CGTGGAC---GACAACGTC---------------GA-----TGGCTACAACCCGCTGCCGAAC-AAAAAATCTCCGCCCGCCAACGGCAAGAAGACAAAGGGACGTGTCAAAATCAAAATGGAATATATCGACAACAAGCTGCGTCGCTACACGACCTTCTCCAAGCGCAAAACTGGCATCATGAAGAAGGT s droBip2.KB464407 1954499 299 + 2915140 cagcag-caacagc---------------------------gtGGCCTGAAG-----CGA-TCTGGAAGCGACTGCTATGAGGAT---CACCAT---------CG---GTCAGCC---GGTGGT------GG------------ACTCACGCTCCAGGGCCTGGACAACTG------CGGCGCCGCT----------G-GGAGCGTCACCAG------C--------------GC---------CGG---CGTGGAC---GATAACGTG---------------GA-----TGGCTACAATCCgctgccaaac-aaaaaatctccACCCGCCAACGGCAAGAAGACAAAGGGAcgtgtcaaaatcaaaatggaATATATCGACAACAAGCTGCGTCGCTACACGACCTTCTCCAAGCGCAAAACGGGCATCATGAAGAAGGT s droEug2.KB465067 595119 302 + 1515531 cagcag-caacatccccaacagcaacagcagcaacaa---cgcgGGCTCAAG-----CGG-TCCGGCAGCGATTGCTACGAAGAT---CATCAC---------CG---ATCCTCC------GGA------GG------------ACTCACCCTCCAAGGGCTCGACAA-----------------------------------CGTGGCTAG------T--------------GG---------AGC---CGTCGAT---GATAGCGTG---------------GA-----CAACTACAACCCGCTGCCCAAT-AAGAAATCACCGCCCGCCAATGGCAAAAAGACAAAGGGACGtgtcaaaatcaaaatggaaTACATCGACAACAAGCTGCGTCGCTACACGACCTTCTCCAAGCGCAAGACTGGCATCATGAAGAAGGT s droEle2.KB458573 515141 311 - 5320397 cagcaa-caacagcacccccagcagcaacaacaacagcaacgggGACTTAAA-----CGT-TCCGGCAGCGATTGCTACGAGGAT---CACCAT---------CG---CTCCACC---GGCGGA------GG------------ACTCACGCTCCAAGGACTGGACAA-----------------------------------CGTGTCCAG------C--------------GG------TCCAGT---GGTCGAC---GACACCGTG---------------GA-----CAGCTATAACCCACTGCCCAAC-AAGAAATCACCGCCCGCCAATGGCAAAAAGACAAAGGGACGtgtcaaaatcaaaatggaaTATATCGACAACAAGCTGCGTCGCTACACGACCTTCTCCAAGCGCAAAACGGGCATCATGAAGAAGGT s droKik2.KB459527 270247 299 - 1234237 cagcag-caacaacagcagcagcaacatc------------gcgGACTGAAG-----CGA-TCGGGAAGCGATTGCTACGAGGAT---CACCAT---------CG---ATCCGCC------GGC------GG------------ACTGACGCTCCAGGGACTCGACAG-----------------------------------CGTCGCCAGCAGCGCC--------------GG---------CGG---CGTCGAG---GACAACGTG---------------GA-----TGGCTACAACCCGCTGCCCAAC-AAGAAGTCACCGCCCGCCAACGGCAAGAAGACAAAGGGACGTGTCAAAATCAAAATGGAATACATCGACAACAAGCTGCGTCGCTACACGACCTTCTCCAAGCGCAAGACGGGCATCATGAAGAAGGT s droTak2.KB461535 134744 302 - 669855 cagcaa-cagcaacatccccaacagcaacaacagc------gggGCCTCAAG-----CGA-TCCGGCAGCGATTGCTACGAGGAT---CACCAT---------CG---GTCCTCC---GGCGGA------GG------------ACTCACCCTCCAAGGACTCGACAA-----------------------------------TGTGACCAC------T--------------GG---------CAC---CGTGGAC---GACAGCGTG---------------GA-----CAACTACAATCCCTTGCCCAAC-AAGAAGTCGCCGCCCGCCAATGGCAAAAAGACAAAGGGACGtgtcaaaatcaaaatggaaTACATCGACAACAAGCTGCGTCGCTACACGACCTTCTCCAAGCGCAAAACGGGCATCATGAAGAAGGT s droRho2.KB449310 28385 305 - 65043 cagcag-cagcaacacccccagcaacaacaacaac------ggggaCTCAAA-----CGT-TCCGGCAGCGATTGCTACGAGGAT---CACCAT---------CG---CTCCTCC---GGCGGA------GG------------ACTCACCCTCCAAGGACTCGACAG-----------------------------------CGTGTCCAG------C--------------GG---------AGCGGTTGTCGAT---GATGCGGTG---------------GA-----CAGCTATAACCCACTGCCCAAC-AAGAAATCACCGCCCGCCAATGGCAAAAAGACAAAGGGACGTGTCAAAATCAAAATGGAATATATCGACAACAAGCTGCGTCGCTACACGACCTTCTCCAAGCGCAAAACGGGCATCATGAAGAAGGT s droFic2.KB457177 75275 302 + 995874 cagcag-cagcaacacccccagcaacagcagcagcaga---ggggCCTGAAA-----CGT-TCCGGCAGCGACTGCTACGAGGAT---CACCAC---------CG---GTCCTCC------GGA------GG------------ACTCACGCTCCAAGGACTGGACAA-----------------------------------CGTGGCCAC------C--------------AA---------TGC---AGTCGAC---GACTCGGTG---------------GA-----CAACTACAATCCGCTGCCCAAT-AAGAAATCGCCGCCCGCCAATGGGAAGAAGACAAAGGGACGtgtcaaaatcaaaatggaaTACATCGACAACAAGCTGCGTCGCTACACGACCTTCTCCAAACGCAAAACGGGCATCATGAAGAAGGT s droPse3.chr3 1343647 305 - 19787792 caacag-caacagcacc------------------------gcGCCCTTAAG-----CGA-TCCGGCAGCGACTGCTACGAGGAT---CACCAT---------CG---ATCAGCTGGTGGCGGC------GG------------CCTGACGCTCCAGGGCCTGGACAACTG------TGGCGCTGGC----------G-GGAGTGTGGCCAG------C--------------GC---------CGG---CGTCGAC---GACAATGTG---------------GA-----CGGATACAATCCGCTGCCCAAC-AAGAAATCACCGCCCGCCAACGGCAAGAAGACAAAGGGACGTgtcaaaatcaaaatggaatACATTGACAACAAGCTGCGTCGCTACACGACCTTCTCCAAGCGCAAGACGGGCATCATGAAGAAGGT s droPer1.super_34 532501 305 - 916997 caacag-caacagcaCC------------------------GCGCCCTTAAG-----CGA-TCCGGCAGCGACTGCTACGAGGAT---CACCAT---------CG---ATCAGCTGGTGGCGGC------GG------------CCTGACGCTCCAGGGCCTGGACAACTG------TGGCGCTGGC----------G-GGAGTGTGGCCAG------C--------------GC---------CGG---CGTCGAC---GACAATGTG---------------GA-----CGGATACAATCCGCTGCCCAAC-AAGAAATCACCGCCCGCCAACGGCAAGAAGACAAAGGGACGTGTCAAAATCAAAATGGAATACATTGACAACAAGCTGCGTCGCTACACGACCTTCTCCAAGCGCAAGACGGGCATCATGAAGAAGGT s droMir2.chr3 1384729 305 - 20862834 caacag-caacagcacc------------------------gcGCCCTTAAG-----CGA-TCCGGCAGCGACTGCTACGAGGAT---CATCAT---------CG---ATCGGCTGGAGGCGGC------GG------------CCTGACGCTCCAGGGCCTGGACAACTG------TGGCGCTGGC----------G-GGAGTGTGGCCAG------C--------------GC---------CGG---CGTCGAC---GACAATGTG---------------GA-----CGGATACAATCCGCTGCCCAAC-AAGAAATCACCGCCCGCCAACGGCAAGAAGACAAAGGGACGtgtcaaaatcaaaatggaatACATTGACAACAAGCTGCGTCGCTACACGACCTTCTCCAAGCGCAAGACGGGCATCATGAAGAAGGT s droWil2.CH963894 1300418 320 + 2843958 caacaa-caacaacaacacc---------------------gagGACTAAAA-----CGT-TCAGGCAGCGATTGCTATGAggat---catcatcaacagcaacg---ATCAGCC---GGCTCC------GG------------TCTCTCCATGCAGGGCCTGGACAATTGTGCTCCTGGCAGTGTT----------G-GTCCCGTCGGCGG------T--------------GT---------CGA---TGTGGAT---AATAATGTC---------------GA-----TGGCTACAATCCTCTGCCCAAT-AAGAAATCACCACCAGCCAATGGCAAAAAGACAAAAGGCAgggtcaaaatcaaaatggaatACATTGACAACAAGTTGCGTCGCTACACGACCTTCTCAAAACGCAAAACGGGCATCATGAAGAAGGT s droVir3.scaffold_12875 7344882 308 + 20611582 cagcaa-cagcagcagcaacaacagGCGC------------GCGGCTTAAAG-----CGC-AGCGGCAGCGACTGCTACGAGGAT------CAT---------CG---GTCAA------GCGGC------GG------------CATGACGCTTCAGGGTCTGGACAG---------CTGCGCCGCT----------G-GCAGCGTCGCCAG------C--------------GG---------CGG---CGTTGACGTCGACGGCGTC---------------GA-----TAGCTACAACGCGCTGCCCAAT-AAGAAATCACCGCCCGCCAATGGCAAAAAGACAAAGGGACGCGTCAAAATCAAAATGGAGTACATCGACAACAAGCTGCGCCGCTACACGACCTTCTCCAAGCGCAAAACGGGCATCATGAAGAAGGT s droMoj3.scaffold_6496 26139650 302 + 26866924 cagcaa-cag---------caacaATCAC------------GTGGCCTAAAG-----CGC-AGCGGCAGCGACTGCTACGAGGAC------CAT---------CG---CTCTAGT---GGCGGC------GG------------CATGACGCTGCAAGGCCTAGAGAG---------CTGCGCTGCC----------G-GCAGCATAGCCAG------C--------------GG---------CGG---CATCGACGTCGACGGGGTA---------------GA-----CAGCTACAACACGCTGCCCAAT-AAGAAATCACCGCCCGCCAATGGCAAGAAGACAAAGGGACGCGTCAAAATCAAAATGGAGTACATCGACAACAAATTGCGCCGTTACACGACCTTCTCCAAGCGGAAGACTGGCATCATGAAGAAGGT s droAlb1.JH854640 303749 296 + 406291 cag----------------caacaatcgc------------GCGGACTGAAA-----CGC-AGCGGCAGCGATTGCTATGAAGAT------CAC---------CG---ATCAAGC---GGTGGC------GG------------CATGACGTTGCAGGGGTTGGAGAG---------CTGCGCTGCA----------G-GCagcgtcgctgt------t--------------gc---------tgg---cgTCGACGTTGACGGCGTC---------------GA-----TGGCTACAATGCGCTGCCCAAT-AAGAAATCACCGCccgcaaatggcaaaaagacAAAGGGACGcgtcaaaatcaaaatggaaTACATTGACAATAAGCTGCGTCGCTACACAACGTTCTCGAAGCGCAAGACGGGCATCATGAAGAAggt s droGri2.scaffold_15245 892535 320 + 18325388 cagcag-cag---------caacaatcac------------gcggcttaaaa-----cgc-agcggcagcgattgctacGAGGAT------CAT---------CG---TCCCAGC---GGTGGCGGGGGTGG------------TATGACGCTGCAGGGCTTGGAGAG---------CTGTGCCGCCGTT-------G-GCAGCGTTGTCGC------C--------------GGCAGCGTGGCCGG---CGTCGATGTTGATGGTGTC---------------GA-----TGGCTATAATGCGTTGCCCAAT-AAGAAATCACCGCCCGCCAATGGCAAAAAGACAAAGGGACGCGTCAAAATCAAAATGGAGTACATCGACAACAAGCTGCGACGATATACAACGTTCTCCAAGCGCAAAACGGGCATCATGAAGAAGGT s musDom2.KB857237 5559 354 - 101287 AGCCGGACAACAAC---------------------------GTGGTATTAAA-----AGA-TCTGGTTCCGATTGCTACGACGAACCGCACCAT---------CGTGTGCCAAAC---GCCGGC------GGCACTAGTGGATTATCAAGTTTACAAGGCCTCGAAAA---------TTGTGGTGGAGGTGGAGGACA-ACATGGTAgtcaa------caacaaccacaatctAG---------TGG---CTCTGGT---GGCATTGTGACAGAAGTGGTGGATGA-----CAATTATAATTCATTGCAGAGT-AAGAAATCACCGCCTGCAAATGGAAAGAAAACCAAAGGACGCGTCAAAATTAAAATGGAGTACATTGATAACAAACTGAGACGCTACACCACATTTTCTAAACGCAAAACGGGGATCATGAAAAAGGT s anoGam1.chr3L 3954658 282 + 41284009 aggtgg-tggcggCTTGTCTC--------------------GCGGCATAAAG-----CGC-ACCAACTCGGACTGCTACGACGAT---CGGCAA---------CA---GATGGTC------GGG------TC------------GCAGAACATGACCGGTCTCGATGG-----------------------------GTGCACCGTCGGGTC------C--------------GA---------GGT---GGTGGAC---------------------------GA-----CAGCTACACCTCGCTGCAGCCG-AAAAAATCCCCTCCCAGCAATGGAAAGAAGACGAAGGGCCGTGTTAAGATTAAGATGGAATATATCGACAACAAACTACGGCGGTACACGACGTTTTCTAAGCGCAAGACCGGCATCATGAAAAAGGT s apiMel4.Group11 6687670 295 - 14726556 ACGCCG-GCGTGGGATCTGTACAAA----------------GGGGTATCAAGAGGACCAC-TTCGG--ACGTTTGTTACGATGA----CAGCAA---------TG---CACGGCA------AGC------TC------------TTTCGCAACAACAAGGCATGTCAA-------------------------------------TGTCTAC------T--------------GA---------TTG---TGTTCCT---GATAATCTT---------------GAGGAATCATTTACAAGTTTGGGTCAACCGAAAAAGTCACCTCCCTCAAATGGTAAAAAGACCAAAGGACGGgtcaaaattaaaatggagTACATCGATAATAAACTACGAAGGTACACTACCTTCTCCAAGAGGAAAACTGGAATTATGAAGAAGGT s triCas2.ChLG1X 6840867 296 + 8109244 CTGCAG-CAGCTGTCGCCGC-GCCACACC------------ATGGTGTCGAG-----TGCGTGTGGAGGGCGCTCCCTGAAGGGC---GACCTC---------TG---CTACGAC---GACCGC------GG------------CATGCCCCAGCAGGGCATGGGGCT-----------------------------------GGAGGCGTG------C--------------GG---------CGT---CAACGAC---ATCTCCGAA---------------GA-----CACCTACAATGCCCTCCAGCCC-AAGAAGTCGCCGCCGAGTAACGGCAAAAAGACCAAAGGCAGGGTCAAGATCAAGATGGAATACATCGAAAACAAGTTGCGGCGGTACACCACGTTCTCAAAGAGGAAGACTGGCATCATGAAGAAGGT a score=50759.000000 s dm6.chr2R 24344676 2 + 25286936 AA s droSim1.chr2R 18691493 2 + 19596830 AA s droSec1.super_23 111239 2 + 989336 AA s droYak3.chr2R 20200244 2 + 21139217 AA s droEre2.scaffold_4845 21598206 2 + 22589142 AA s droBia2.KB462602 789896 2 + 3129309 AA s droSuz1.KI419649 12035046 2 - 14502029 AA s droAna3.scaffold_13266 5706101 2 - 19884421 AA s droBip2.KB464407 1954798 2 + 2915140 AA s droEug2.KB465067 595421 2 + 1515531 AA s droEle2.KB458573 515452 2 - 5320397 AA s droKik2.KB459527 270546 2 - 1234237 AA s droTak2.KB461535 135046 2 - 669855 AA s droRho2.KB449310 28690 2 - 65043 AA s droFic2.KB457177 75577 2 + 995874 GA s droPse3.chr3 1343952 2 - 19787792 AA s droPer1.super_34 532806 2 - 916997 AA s droMir2.chr3 1385034 2 - 20862834 AA s droWil2.CH963894 1300738 2 + 2843958 AA s droVir3.scaffold_12875 7345190 2 + 20611582 AA s droMoj3.scaffold_6496 26139952 2 + 26866924 AA s droAlb1.JH854640 304045 2 + 406291 aa s droGri2.scaffold_15245 892855 2 + 18325388 AA s musDom2.KB857237 5913 2 - 101287 GA s anoGam1.chr3L 3954940 2 + 41284009 AA s triCas2.ChLG1X 6841163 2 + 8109244 GA a score=30000.000000 s dm6.chr2R 24344678 1 + 25286936 G s droSim1.chr2R 18691495 1 + 19596830 G s droSec1.super_23 111241 1 + 989336 G s droYak3.chr2R 20200246 1 + 21139217 G s droEre2.scaffold_4845 21598208 1 + 22589142 G s droBia2.KB462602 789898 1 + 3129309 G s droSuz1.KI419649 12035048 1 - 14502029 G s droAna3.scaffold_13266 5706103 1 - 19884421 G s droBip2.KB464407 1954800 1 + 2915140 G s droEug2.KB465067 595423 1 + 1515531 G s droEle2.KB458573 515454 1 - 5320397 G s droKik2.KB459527 270548 1 - 1234237 G s droTak2.KB461535 135048 1 - 669855 G s droRho2.KB449310 28692 1 - 65043 G s droFic2.KB457177 75579 1 + 995874 G s droPse3.chr3 1343954 1 - 19787792 G s droPer1.super_34 532808 1 - 916997 G s droMir2.chr3 1385036 1 - 20862834 G s droWil2.CH963894 1300740 1 + 2843958 G s droVir3.scaffold_12875 7345192 1 + 20611582 G s droAlb1.JH854640 304047 1 + 406291 g s droGri2.scaffold_15245 892857 1 + 18325388 G s musDom2.KB857237 5915 1 - 101287 G s anoGam1.chr3L 3954942 1 + 41284009 G s triCas2.ChLG1X 6841165 1 + 8109244 G a score=9096.000000 s dm6.chr2R 24344679 1 + 25286936 A s droSim1.chr2R 18691496 1 + 19596830 A s droSec1.super_23 111242 1 + 989336 A s droYak3.chr2R 20200247 1 + 21139217 A s droEre2.scaffold_4845 21598209 1 + 22589142 A s droBia2.KB462602 789899 1 + 3129309 A s droSuz1.KI419649 12035049 1 - 14502029 A s droAna3.scaffold_13266 5706104 1 - 19884421 A s droBip2.KB464407 1954801 1 + 2915140 A s droEug2.KB465067 595424 1 + 1515531 A s droEle2.KB458573 515455 1 - 5320397 a s droKik2.KB459527 270549 1 - 1234237 C s droTak2.KB461535 135049 1 - 669855 A s droRho2.KB449310 28693 1 - 65043 A s droFic2.KB457177 75580 1 + 995874 A s droAlb1.JH854640 304048 1 + 406291 a s triCas2.ChLG1X 6841166 1 + 8109244 A a score=-60054.000000 s dm6.chr2R 24344680 5 + 25286936 TC------------GCT s droSim1.chr2R 18691497 5 + 19596830 TC------------GCC s droSec1.super_23 111243 5 + 989336 TC------------GCC s droYak3.chr2R 20200248 5 + 21139217 TC------------GCT s droEre2.scaffold_4845 21598210 5 + 22589142 TC------------ACT s droBia2.KB462602 789900 6 + 3129309 TCG-----------GCG s droSuz1.KI419649 12035050 6 - 14502029 TCG-----------GCA s droAna3.scaffold_13266 5706105 5 - 19884421 TC------------GGT s droBip2.KB464407 1954802 5 + 2915140 TC------------GGC s droEug2.KB465067 595425 10 + 1515531 TCGAGA-C------GGA s droEle2.KB458573 515456 2 - 5320397 tc--------------- s droKik2.KB459527 270550 4 - 1234237 TC-------------CT s droTak2.KB461535 135050 6 - 669855 TCG-----------GTT s droRho2.KB449310 28694 5 - 65043 TC------------GCA s droFic2.KB457177 75581 11 + 995874 CCGAGATC------GGG s droWil2.CH963894 1300741 11 + 2843958 ------TCCAGTAAGAG s anoGam1.chr3L 3954944 5 + 41284009 ------------TGGTT s triCas2.ChLG1X 6841167 1 + 8109244 T---------------- a score=-41745.000000 s dm6.chr2R 24344685 18 + 25286936 GGA----GC-Ac------------cc-ctac----gcc-at s droSim1.chr2R 18691502 18 + 19596830 GGA----GC-AC------------CC-CTAC----GCC-AT s droSec1.super_23 111248 18 + 989336 GGA----AC-AC------------CC-CTAC----GCC-AT s droYak3.chr2R 20200253 21 + 21139217 GGAGAACGC-AC------------CC-CTA-----gcc-at s droEre2.scaffold_4845 21598215 18 + 22589142 GGA----GC-AC------------CC-CTAT----GCC-AT s droBia2.KB462602 789906 30 + 3129309 GCA----GC-ACCCTAGTACCATACC-CCAT----ACC-AT s droSuz1.KI419649 12035056 18 - 14502029 GGA----GT-AC------------CC-CTAT----ACC-AT s droAna3.scaffold_13266 5706110 16 - 19884421 ATA----GC-TC------------CT-CCA------GC-GC s droBip2.KB464407 1954807 16 + 2915140 ATG----GT-at------------ct-cct------cc-ac s droEug2.KB465067 595435 19 + 1515531 GGA----GT-AC------------CCACTTT----CCA-AT s droEle2.KB458573 515458 15 - 5320397 -------cc-at------------cc-caat----tcc-at s droKik2.KB459527 270554 10 - 1234237 Aga---------------------tc-cca---------gc s droTak2.KB461535 135056 19 - 669855 GGG----GCTAT------------CC-CCAT----ATT-AT s droRho2.KB449310 28699 11 - 65043 GGA----AT-ac------------cc-------------at s droFic2.KB457177 75592 19 + 995874 GTA----AT-AC------------CC-GAAA----GCTAAT s droWil2.CH963894 1300752 23 + 2843958 GAA----ACGAT------------CC-CTTTCATCGCC-Aa s triCas2.ChLG1X 6841168 16 + 8109244 --A----AC-CT------------CT-CTAC----GTG-AT a score=-91488.000000 s dm6.chr2R 24344703 42 + 25286936 ccccatccccaacgatattttcaa-------cccaaccccgaaaccgaa s droSim1.chr2R 18691520 36 + 19596830 CCCCAT------CGATATTCCCAA-------CCCAACCCCGAAACCGAA s droSec1.super_23 111266 36 + 989336 CCCCAT------CGATATTCCCAA-------CCCAACCCCGAAACCAAA s droYak3.chr2R 20200274 37 + 21139217 ctccat------ccccattcccatcgATGTACCCATTCCTG------GT s droEre2.scaffold_4845 21598233 35 + 22589142 CGCCAT------CGATATTcccat-------cccaaccccgtgtcc-at s droBia2.KB462602 789936 10 + 3129309 TCCTAT-------------------------GCCA-------------- s droSuz1.KI419649 12035074 8 - 14502029 TCCTAT-------------------------AC---------------- s droAna3.scaffold_13266 5706126 16 - 19884421 CTCCAG----------ctcctgct-------cc---------------- s droBip2.KB464407 1954823 7 + 2915140 ctcca--------------------------cc---------------- s droEug2.KB465067 595454 10 + 1515531 CCCTGT-------------------------CCCA-------------- s droEle2.KB458573 515473 8 - 5320397 cccgat-------------------------cc---------------- s droKik2.KB459527 270564 8 - 1234237 tcccag-------------------------ct---------------- s droTak2.KB461535 135075 18 - 669855 CCCCAC-------------------------ACCATACCCACA------ s droRho2.KB449310 28710 8 - 65043 ccccac-------------------------tc---------------- s droFic2.KB457177 75611 15 + 995874 CCCCGT---------------AAA-------CTTAGT------------ s droWil2.CH963894 1300775 4 + 2843958 cccc--------------------------------------------- a score=2113.000000 s dm6.chr2R 24344745 5 + 25286936 atcga s droSim1.chr2R 18691556 5 + 19596830 ATCGA s droSec1.super_23 111302 5 + 989336 ATCGA s droYak3.chr2R 20200311 5 + 21139217 GCCCA s droEre2.scaffold_4845 21598268 5 + 22589142 cccca s droEle2.KB458573 515481 4 - 5320397 -ccaa s droTak2.KB461535 135093 3 - 669855 --CCA s droRho2.KB449310 28718 5 - 65043 accca s droPse3.chr3 1344010 5 - 19787792 ACCTC s droPer1.super_34 532864 5 - 916997 ACCTC s droWil2.CH963894 1300779 1 + 2843958 ----a a score=271405.000000 s dm6.chr2R 24344750 62 + 25286936 tcccca--tcccaatccc------cattcc--AGCCACGATTG-GCGCT---GC------------AATTGGGATG---------TTGAC------ATCG-GGC s droSim1.chr2R 18691561 62 + 19596830 ACCCCA--TCCCAATCCT------CATTCC--AGCCACGATTG-GCGCT---GC------------AATTGGGATG---------TTGAC------ATTG-GGC s droSec1.super_23 111307 62 + 989336 TCCCCA--ACCCAATCCC------TATTCC--AGCCACGATTG-GCGCT---GC------------AATTGGGATG---------TTGAC------ATTG-GGC s droYak3.chr2R 20200316 62 + 21139217 TCCCCt--taccaatccc------aatccc--agccACGATTG-GCGCT---GC------------AATTGGGATG---------TCGAC------ATTG-GGC s droEre2.scaffold_4845 21598273 62 + 22589142 tcccca--tcccaatccc------aattcc--agccACGATTG-GCGCT---GC------------AATTGGGATG---------TTGAC------ATTG-GGC s droBia2.KB462602 789946 56 + 3129309 --------TCCGCATCCC------CATCCC--AGCCACGATTG-GCGCT---GC------------AATTGGGATG---------TTGAC------ATTT-GGC s droSuz1.KI419649 12035082 52 - 14502029 ------------CATCCC------CATCCC--AACCACGATTG-GCGCT---GC------------AATTGGGATG---------TTGAC------ATTT-GGC s droAna3.scaffold_13266 5706142 48 - 19884421 --------------tcct------cctcct----cctcGATTG-GCTGC---GG------------AATTGGGATG---------TCGAC------ATTG-GGC s droBip2.KB464407 1954830 48 + 2915140 --------------tcct------ccatcT----CTTCGATTG-GGTAC---GG------------AATTGGGATG---------TCGAC------ATTG-GGC s droEug2.KB465067 595464 62 + 1515531 -----A--TCCCCACCCC-TATAGCATCCC--AACCACGATTG-CCGGT---GC------------AATTGGGATG---------TTGAC------ATTG-GGC s droEle2.KB458573 515485 73 - 5320397 tccccaacccccaaccccacatacgatccc--aaccaCGATTG-GGATTCTGGC------------AATTGGGATG---------TTGAC------ATTG-GGC s droKik2.KB459527 270572 61 - 1234237 -cccga--TCCCCATTCC------CATATT--GGCCACGATTG-GGCCT---GC------------AATTGGGATG---------TTGAC------ATTG-GGC s droTak2.KB461535 135096 64 - 669855 TCCCCA--TCCGAATCCC------AATCCCTGAGCCACGATTG-GCGCT---GC------------AATTGGGATG---------TTGAC------ATTC-GGC s droRho2.KB449310 28723 70 - 65043 tcccaa--accccaaccc-catacgatccc--aaccaCGATTG-GGATTCTGGC------------AATTGGGATG---------TTGAC------ATTG-GGC s droFic2.KB457177 75626 56 + 995874 --------TGCCAA--CC------GATCCC--GACCACGATTGCTCCCT---GC------------AATTGGGATG---------TTGAC------ATTTCGGC s droPse3.chr3 1344015 66 - 19787792 --------------TCCA------CCTCTC--AACTTGGACTT-GGGCC---ACTgggatc-----ggatgggatgggatgggcatTGAC------ATTG-GAC s droPer1.super_34 532869 66 - 916997 --------------TCCA------CCTCTC--AACTTGGACTT-GGGCC---ACTGGGAGC-----GGATGGGATGGGATGGGCATTGAC------ATTG-GAC s droMir2.chr3 1385102 71 - 20862834 --------------TCCA------CCTCTC--AACTTGGACTT-GGGCC---ACTgggatcggatgggatgggatgggatgggcatTGAC------ATTG-GGC s droWil2.CH963894 1300780 62 + 2843958 --------tccccatccc------catccT--CAACCC-ATCA-CCCAT---AT------------GGATGGGAGA--------ATTGTCTCTCGGATTG-GGA a score=381435.000000 s dm6.chr2R 24344812 78 + 25286936 CACGTTTCCAGCGCATGTGCAATTAATAAATGCTTCAGGGATT-CAGTTGC------------GACG----GAATCCAGCAG-------------TTCCC-------C-CACATC----------T s droSim1.chr2R 18691623 69 + 19596830 CACGTTTCCAGCGCATGTGCAATTAATAAATGCTTCGGGGATT-CAGTCGC------------GACG----GAATCCAG------------------------------CAGAGC----------T s droSec1.super_23 111369 78 + 989336 CACGTTTCCAGCGCATGTGCAATTAATAAATGCTTCGGGGATT-CAGTTGC------------GACG----GAATCCAGCAG-------------TTCCC-------C-CAGAGC----------T s droYak3.chr2R 20200378 78 + 21139217 CACGTTTCCAGCGCATgtgcaattaataaatgcttCGGGGATT-CGGCTGC------------GACG----GAATCCAGAAG-------------TTCCC-------C-CGCAGC----------T s droEre2.scaffold_4845 21598335 78 + 22589142 CACGTTTCCAGCGCATGTGCAATTAATAAATGCTTCGGGGATT-CAGTTGC------------GACG----GAATCCAGAGG-------------CTCCC-------C-CAGAGC----------T s droBia2.KB462602 790002 79 + 3129309 CACGTTTCCAGCGCATGTGCAATTAATAAATGCTTCGGGGATT-CGGTTGC------------GACG----GAATCCAAAGG-------------TTCCC-------CTTAGAAC----------T s droSuz1.KI419649 12035134 79 - 14502029 CACGTTTCCAGCGCatgtgcaattaataaatGCTTCGGGGATT-CGGTTGC------------GACG----GAATCCAAAAG-------------TTCCC-------CTTAGAAC----------T s droAna3.scaffold_13266 5706190 69 - 19884421 CACGTTTCGAGCGCATGTGCAATTAATAAATGCTTCGAGGAGT-CGCATTC------------CC-------AGTCCAAAG-----------------CT-------C-CGAAC------------ s droBip2.KB464407 1954878 70 + 2915140 CACGTTTCGAGCGCATGTGCAATTAATAAATGCTTCGAGGAGT-CGCATTC------------CC-------AGTCCAAAA----------------CCT-------C-CAAAG------------ s droEug2.KB465067 595526 78 + 1515531 CACGTTTCCAGCGCATGTGCAATTAATAAATGCTTGGGGGATT-CAGTTGC------------GACC----GAATCCTAAGG-------------TTCCC-------T-AAGAAC----------T s droEle2.KB458573 515558 57 - 5320397 CACGTTTCCAGCGCATGTGCAATTAATAAATGCTTCGGGGACT-CAGTT------------------------------------------------CCC-------T-AAGAA------------ s droKik2.KB459527 270633 84 - 1234237 CACGTTTCCAGCGCATGTGCAATTAATAAATGCTT---GGGTT-AGACTTC------------GTCG----GAGTCCAAAG--------------CTCCT-------T-GGGAGCAGCAGGGCTGC s droTak2.KB461535 135160 79 - 669855 CACGTTTCCAGCGCATGTGCAATTAATAAATGCTTCGGGGATT-CAGCTGC------------GACG----GAATCCAAAAGC------------TTCTC-------T-TAGAAC----------T s droRho2.KB449310 28793 58 - 65043 CACGTTTCCAGCGCATGTGCAATTAATAAATGCTTCGGGGATT-CAG------------------------------------------------TTCCC-------T-AAGAAC----------- s droFic2.KB457177 75682 74 + 995874 CACGTTTCCAGCGCATGTGCAATTAATAAATGCTTCGGGGACT-CAGTCGC------------ACAG----TCGTTTAG----------------TTCGC-------C-AAGAAA----------- s droPse3.chr3 1344081 95 - 19787792 CACGTTTTGAGCGCATGTGCAATTAATAAATGCTTCTTCGATTCCaactgcagctcctcctctggcA----TTGTCCAGTGCA-GTG--------TCCCT-------C-TTCATC----------T s droPer1.super_34 532935 95 - 916997 CACGTTTTGAGCGCATGTGCAATTAATAAATGCTTCTTCGATTCCAACTGCAGCTCCTCCTCTGGCA----TTGTCCAGTGCA-GTG--------TCCCT-------C-TTCATC----------T s droMir2.chr3 1385173 95 - 20862834 CACGTTTTGAGCGCATGTGCAATTAATAAATGCTTCTTCGATTCcaactgcagctcctcctctggcA----TTGTCCAGTGCA-GTG--------TCCCT-------C-TTCATC----------T s droWil2.CH963894 1300842 73 + 2843958 CACGTTTTGGGCGCatgtgcaattaataaatGCTTC-----TT-CTACTGC---------------------CATCCAAGTCGCCCA--------CTTCC-------C-TTAATC----------T s droVir3.scaffold_12875 7345756 80 + 20611582 CACGTTTTGAGCTCATGTGCAATTAATAAATGCTACCGAATCC-TCAATTC-------ACTCTG-------GAGTCAAGTCAAGTTG--------CTGCG-------C-CT--------------- s droMoj3.scaffold_6496 26140781 93 + 26866924 CACGCTTTGAGCGCATGTGCAATTAATAAATGCTACCGAATCC-GCAATTC-------TCTTTGCCG--TCGATTCGAGTCGAGTCGTTCGAGTCCTGCG-------C-CT--------------- s droGri2.scaffold_15245 893591 96 + 18325388 CACGTTTTGAGCGCATGTGCAATTAATAAATGCTGCCGAATGC-TCAATTC--TCAATTCTTTGTCGTATCAATTCAGG---AGTCC--------CTGCGCGCCTCTC-TT--------------- a score=117151.000000 s dm6.chr2R 24344890 34 + 25286936 CTGGCATTGTTCTGCC------------------TCCG--GAAAGAGCGAGGAT s droSim1.chr2R 18691692 34 + 19596830 CTGGCATTGTTCTGCC------------------TCCG--GAAAGAGCGGGGAT s droSec1.super_23 111447 34 + 989336 CTGGCATTGTTCTGCC------------------TCCA--GAAAGAGCGGCGAT s droYak3.chr2R 20200456 34 + 21139217 CTGGCATTGTTCTGCC------------------TCCG--GAAGGAGCGGGGAT s droEre2.scaffold_4845 21598413 34 + 22589142 CTGGCATTGTTCTGCC------------------TCCG--GAAAGAGCGGGGAT s droBia2.KB462602 790081 34 + 3129309 CTGGCATTGTTCTCCC------------------CGCA--GGCAGAGCGGGCAT s droSuz1.KI419649 12035213 34 - 14502029 CTGGCATTGTTCTCCC------------------TCCA--GTAAGAGCGGGGAT s droAna3.scaffold_13266 5706259 30 - 19884421 CTGGCATTGTTCTGAC----TCTCTCC----GTCTCCA---------------- s droBip2.KB464407 1954948 50 + 2915140 CTGGCATTGTTCTGACTCTTTCTCTCC----GTCTCCAAAGCCGGGGCGGTGGT s droEug2.KB465067 595604 33 + 1515531 CTGGCATTGTTTGGTT------------------TCCA--GTTAGAG-GGGGAT s droEle2.KB458573 515615 40 - 5320397 CTGGCATTGTTCTGAC----CCGCTC--------TCCA--GGAAGAGCGGGGAT s droKik2.KB459527 270717 48 - 1234237 CTGGCATTGTTCTCCG----ACTCTCTTCTAGGCTCTG--CAGAGAGCGGTGCT s droTak2.KB461535 135239 34 - 669855 CTGGCATTGTTCGCCC------------------TCCA--GAAAGAGCGGGGAT s droRho2.KB449310 28851 39 - 65043 -TGGCATTGTTCTGAC----TCTCTC--------TCCA--GGAAGAGCGGGGAC s droFic2.KB457177 75756 40 + 995874 TTGGCATTGTTCTGAC----TCTCTC--------TATA--GGAAGAGCGTGGAG s droPse3.chr3 1344176 29 - 19787792 -Tcccttttctctctt------------------tccc--tctctatcGG---- s droVir3.scaffold_12875 7345836 34 + 20611582 ATGGCATTGTTCGGCG------------------TCTG--CAGACCGCAGTGCT s droMoj3.scaffold_6496 26140874 30 + 26866924 CTTGCATTGTTCTCCG------------------TTTG--AAATGC----TGCT s droGri2.scaffold_15245 893687 20 + 18325388 GTGGCATTGTTTTCTT----------------------------------TGCT a score=243996.000000 s dm6.chr2R 24344924 20 + 25286936 TTATTGTCAATTGGCCATC---G s droSim1.chr2R 18691726 20 + 19596830 TTATTGTCAATTGGCCATC---G s droSec1.super_23 111481 20 + 989336 TTATTGTCAATTGGCCATC---G s droYak3.chr2R 20200490 20 + 21139217 TTATTGCCAATTGGCCATC---G s droEre2.scaffold_4845 21598447 20 + 22589142 TTATTGCCAATTGGCAATC---G s droBia2.KB462602 790115 20 + 3129309 GTATCGTCATCTGGCCATC---G s droSuz1.KI419649 12035247 20 - 14502029 TTATCGTCATCTGGCCATC---G s droAna3.scaffold_13266 5706289 19 - 19884421 -TATCGTCATGTGGCCATC---G s droBip2.KB464407 1954998 20 + 2915140 TTATCGTCATGTGACCATC---G s droEug2.KB465067 595637 20 + 1515531 TTATCGTCATCTGGCCATC---G s droEle2.KB458573 515655 20 - 5320397 TTATCGTCATTTGGCCATC---G s droKik2.KB459527 270765 21 - 1234237 TTATCGTCATGTGGCCATCG--G s droTak2.KB461535 135273 20 - 669855 TTATCGTCATCTGGCCATC---G s droRho2.KB449310 28890 20 - 65043 TTATCGTCATCTGGCCATC---G s droFic2.KB457177 75796 20 + 995874 TTATCGGCATCTGGCCATC---G s droPse3.chr3 1344205 23 - 19787792 CTATCGTTATGTGACCATCGGCG s droPer1.super_34 533059 23 - 916997 CTATCGTTATGTGACCATCGGCG s droMir2.chr3 1385297 23 - 20862834 ctATCGTTATGTGACCATCGGCG s droVir3.scaffold_12875 7345870 20 + 20611582 TTATCGTTGTGTTGCCATC---G s droMoj3.scaffold_6496 26140904 20 + 26866924 TTATCGTTCTGTTGCCATC---G s droGri2.scaffold_15245 893707 20 + 18325388 TTATCGTTGTGCTGCCATC---G a score=140964.000000 s dm6.chr2R 24344944 10 + 25286936 GCACAGTGGT s droSim1.chr2R 18691746 10 + 19596830 GCACAGTGGT s droSec1.super_23 111501 10 + 989336 GCACAGTGGT s droYak3.chr2R 20200510 10 + 21139217 GCACAGTGGT s droEre2.scaffold_4845 21598467 10 + 22589142 GCACAGTGGT s droBia2.KB462602 790135 10 + 3129309 GCACAGTGGT s droSuz1.KI419649 12035267 10 - 14502029 GCACAGTGGT s droAna3.scaffold_13266 5706308 10 - 19884421 GCACAGTGGT s droBip2.KB464407 1955018 10 + 2915140 GTACAGTGGT s droEug2.KB465067 595657 10 + 1515531 GCACAGTGAC s droEle2.KB458573 515675 10 - 5320397 GCACAGTGGT s droKik2.KB459527 270786 10 - 1234237 GCACAGTGGT s droTak2.KB461535 135293 10 - 669855 GCACAGTGGT s droRho2.KB449310 28910 10 - 65043 GCACAGTGGT s droFic2.KB457177 75816 10 + 995874 GCACAGTGGT s droPse3.chr3 1344228 10 - 19787792 GCACAGTGGT s droPer1.super_34 533082 10 - 916997 GCACAGTGGT s droMir2.chr3 1385320 10 - 20862834 GCACAGTGGT a score=15817.000000 s dm6.chr2R 24344954 8 + 25286936 CGGGAT--AG s droSim1.chr2R 18691756 8 + 19596830 CGGGAT--AG s droSec1.super_23 111511 8 + 989336 CGGTAT--AG s droYak3.chr2R 20200520 8 + 21139217 CGGGAT--GG s droEre2.scaffold_4845 21598477 8 + 22589142 CGGGAT--AG s droBia2.KB462602 790145 8 + 3129309 GGGGAT--AG s droSuz1.KI419649 12035277 8 - 14502029 GAGGAT--AG s droBip2.KB464407 1955028 8 + 2915140 TGaaat--tc s droEug2.KB465067 595667 1 + 1515531 ---------G s droEle2.KB458573 515685 8 - 5320397 GAGGAT--AG s droKik2.KB459527 270797 10 - 1234237 CAGTTTTAAA s droTak2.KB461535 135303 8 - 669855 GAGGAT--GG s droPse3.chr3 1344238 8 - 19787792 CGGAAT--GG s droPer1.super_34 533092 8 - 916997 CGGAAT--GG s droMir2.chr3 1385330 8 - 20862834 CGGAAT--GG a score=8997.000000 s dm6.chr2R 24344962 20 + 25286936 CTGGCGCACAATAGGAGAAC s droSim1.chr2R 18691764 20 + 19596830 CTGGCACCCAATAAGAATAC s droSec1.super_23 111519 20 + 989336 CTGGCACCCAATAAGAATAC s droYak3.chr2R 20200528 20 + 21139217 CTGGCACACAGGAGAAGCAC s droEre2.scaffold_4845 21598485 20 + 22589142 CTGGCACACAATAGGAGTAC s droBia2.KB462602 790153 20 + 3129309 CGGGGGTTCCCTAGGAATAC s droSuz1.KI419649 12035285 20 - 14502029 CGGGGATTCCACAGGAATAC s droBip2.KB464407 1955036 20 + 2915140 ttaatttattttaaaaatat s droEug2.KB465067 595668 18 + 1515531 CAG--TCCTAAAGGGAAGAC s droEle2.KB458573 515693 11 - 5320397 ---------GATAGGAAAAT s droKik2.KB459527 270807 20 - 1234237 GAGGGTTCCAATAGGAAAAA s droTak2.KB461535 135311 20 - 669855 CGGGGAAATTCTAGGGAGGA s droRho2.KB449310 28920 19 - 65043 -GAAGATTGGAGGGGAAAAA s droFic2.KB457177 75826 20 + 995874 AGGGATTAGGGAAGGTGAAC a score=2261.000000 s dm6.chr2R 24344982 8 + 25286936 CATCTCGG s droSim1.chr2R 18691784 8 + 19596830 CATCTGAA s droSec1.super_23 111539 8 + 989336 CATCTCAA s droYak3.chr2R 20200548 8 + 21139217 TATCTTGG s droEre2.scaffold_4845 21598505 8 + 22589142 TATCTGGG s droSuz1.KI419649 12035305 6 - 14502029 --TGGGGA s droBip2.KB464407 1955056 5 + 2915140 ---tttaa s droKik2.KB459527 270827 8 - 1234237 CATGGGGA a score=-96457.000000 s dm6.chr2R 24344990 17 + 25286936 AATATCA----------AGTA-----CCCAA-----T s droSim1.chr2R 18691792 1 + 19596830 A------------------------------------ s droSec1.super_23 111547 1 + 989336 A------------------------------------ s droYak3.chr2R 20200556 16 + 21139217 AATATCA-----CTTCAAGTA---------------- s droEre2.scaffold_4845 21598513 22 + 22589142 AATATCA-----CTTCCAGTA-----CCCAA-----T s droSuz1.KI419649 12035311 25 - 14502029 AAAAGAA---TCCTTAAGGAA-----TCCAA----TT s droBip2.KB464407 1955061 36 + 2915140 agcttaaa-agtctgataggaaaaaccctaaaaaaat s droEle2.KB458573 515704 18 - 5320397 ---------CCCCTTCAAGTA-----GCCAAT----- s droKik2.KB459527 270835 16 - 1234237 AGTATAGG-TATTTTTT-------------------- s droTak2.KB461535 135336 17 - 669855 -----------CCTCCAATTA-----GCCAAAT---- s droRho2.KB449310 28939 18 - 65043 ---------GACTTCAAAGTA-----CCCAAT----- s droFic2.KB457177 75846 10 + 995874 -----------AATTTGGGTA---------------- s droWil2.CH963894 1302033 17 + 2843958 -------AAGAACTAATAGCA-----AAC-------- a score=-53168.000000 s dm6.chr2R 24345007 20 + 25286936 GGAT-------------------------ATATCCAACAGTTAGA---------- s droYak3.chr2R 20200572 13 + 21139217 --------------------------------GCCTCTGATTGGA---------- s droEre2.scaffold_4845 21598535 20 + 22589142 AGAT-------------------------ATCACCACTGATTACA---------- s droSuz1.KI419649 12035336 20 - 14502029 AGAT-------------------------TTCCTTATCGAAACGA---------- s droBip2.KB464407 1955097 21 + 2915140 gaatc------------------------atttccaaaaaagaaa---------- s droEug2.KB465067 595687 24 + 1515531 ----CCTAT-----------------tagattttcttaaaaaagg---------- s droKik2.KB459527 270851 43 - 1234237 --ATCTTATCTTTTTGTTGTAAGTAGTTGACTTTTTATAGGAAAA---------- s droTak2.KB461535 135353 7 - 669855 --------------------------------------GGACTTA---------- s droRho2.KB449310 28957 17 - 65043 ----------------------------TAGATTCCGAAATTGGA---------- s droFic2.KB457177 75856 10 + 995874 -----------------------------------ACCACGTAGA---------- s droWil2.CH963894 1302050 22 + 2843958 ---------------------------------TCAGAAATTCAAATTCGTTtga a score=-363103.000000 s dm6.chr2R 24345027 137 + 25286936 CCATTTG--------------------------------TGTAC---------ATT-------ACTCGT-----CAGTTCAAATATTCAAA------TCTTTCTCTTGTGT-------------------------CCATTACCAATTATT----------------AGTTC--------CACTTGGAAGT-----ATGTTTATTGGACC---AATACA-----AATTCTGCTTGG------AA---ATTGCTTAT-AGGCCACCT-TA s droSim1.chr2R 18691793 109 + 19596830 ---------------------------------------------------------------ACTCT-------AATTCAAATATTCAA--------CTTTCTTTTGTGA-------------------------CCACTACCAAGAATT----------------GCTTC--------CACTTGGAAGC-----ATGCTTATTGGTCC---AATACA-----AATTCTACTTGG------AA---ATTGTTTAT-AG---------- s droSec1.super_23 111548 120 + 989336 ---------------------------------------------------------------ACTCTT-----CAATTCAAATATTCAA--------CTTTCATTTGTGA-------------------------CCACTACCAAGTATT----------------GCTTC--------CACTTGGAGGC-----ATGCTTATTGGACC---AATACA-----AATTCTACTTGG------AA---ATTGTTTAT-AGGCCACCT-TA s droYak3.chr2R 20200585 72 + 21139217 ACTTTGGAG----------------CGAGCGAAGAT-AATGGAC----------------------------------TTACTTATTCTA--------TTTCCATTCAAG--------------------------------------------------------------------------------------------------------TTACA-----AGTTCTACTTGG------AA---AT-------------------- s droEre2.scaffold_4845 21598555 144 + 22589142 CCACTTGGG----------------CAACCAAAGAT-AATGAACAAGCGCCGAGTT-------TCTTCT-----CAATTCAAATATCCAA--------CTTTCATTTGCGA-------------------------CCACT----------------------------------------ACTTCGAAGC-----AAACCTATTGGACC---ATTACA-----AAGTCTACTTGG------AA---ATTACTTAC-AGGCTAGCTGTA s droSuz1.KI419649 12035356 164 - 14502029 CCTTGCAGG----------------GAACGTTATATCAATACA--------------------------------AActcaaaactttaaaacagTTTCTTAAAATGATAA-------------------------CAGATGGCAATGAATTATAACA---------AATTC--------TACCATGATATCTCCAACATTTGCGGGACA---AATAGG-----AATTTCAGCTTA------ACTTTATTGGTTATCATGTCACTT-TA s droBip2.KB464407 1955118 84 + 2915140 ctaactgaa----------------gaaacttatctaaaaGGGA-------------------------------ACTTTAATGATTca---------ctttcttttgtt---------------------------------------------------------ttata--------agTTGAGAAGA-----GAGGTTCTTAGTTC----------------------------------------------------------- s droEug2.KB465067 595711 150 + 1515531 CAAGCTGAAACTGAAGGTTCTTCCTTATTGGTATAAGAATGGTTCTGGGACATTTT--CTTACAGTTCT-----AGACTGAGAGTTACGAG-------CCTTAATCTGTA---------------------------------------------------------GTTTCATTTACCTCTTTTTGAGGC-----ATTAAAGTAGCACC-----TATA-----AATAGTAACAAA--------------------------------- s droKik2.KB459527 270894 134 - 1234237 TTACTAAGT----------------TAAACAGAGGTGAC------------------------AAACTT-----Cgtttcatatatgtat--------tttgtctctttta-------------------------ataataatgacaGAATTTTAAA---------CCTTCAAATCGGACAATAAAAACC-----TTATTATTCAGTTT---AGTACA--CTCAAGATTA-------------------------------------- s droTak2.KB461535 135360 154 - 669855 ATTTTCGAA----------------TAA-----------------------------------GTTTTT-----CACTTATTTTATTCAG--------TTTTCtattagaaaacatttttccatAAAACCTATCTTCAAATCTCAAAAAATGTTAGGAAGTAG---tggttt--------gatttaaaaaa-----atatcgactAAAAT---TACATATGTTTAATagcaacttt------a-------------------------- s droFic2.KB457177 75866 136 + 995874 -------------------------------------------------TTATTTTAGATTATACTCCTAGACAAAGTTAAAGTCTAAAAGGGGTAAACTTTTATCACAGA-------------------------TTCTTAACAATCACA----------------ATTTA--------GACAGAATGAT-----GGGTTTGTAAGAATTaaagctta-----aatattattaaagcaGACAA------------------------- s droWil2.CH963894 1302072 123 + 2843958 -------------------------------------------------atatatatgaatatattgaT-----CAGTATAAAGGCTCAA--------TATTCATTTTGCA-------------------------TATTCATTGGTTGGCTAGCCCTTGTAAAGTCTTTTG--------TATATCTAATG-----ATATCGATTTGCCT---ATTGAT-----ATCATTA-------------------------------------- a score=1351.000000 s dm6.chr2R 24345164 12 + 25286936 TGTTGGGATCCC--- s droSim1.chr2R 18691902 11 + 19596830 -GATGTGATCCC--- s droSec1.super_23 111668 12 + 989336 TGGTGGGATCCC--- s droYak3.chr2R 20200657 12 + 21139217 GGTTGGAATCCC--- s droEre2.scaffold_4845 21598699 12 + 22589142 GGTTGGAACCCC--- s droEug2.KB465067 595861 12 + 1515531 TATTGAGTTCTT--- s droKik2.KB459527 271028 11 - 1234237 -TAAGGGATTTT--- s droFic2.KB457177 76002 7 + 995874 -----AGATCTt--- s droWil2.CH963894 1302195 9 + 2843958 ------GGTCATCAT a score=7445.000000 s dm6.chr2R 24345176 13 + 25286936 AAACCTAATGCTA s droSim1.chr2R 18691913 13 + 19596830 AAACCTAATGCTA s droSec1.super_23 111680 13 + 989336 AAACCTTATGCCA s droYak3.chr2R 20200669 13 + 21139217 AAACCAAATCCTA s droEre2.scaffold_4845 21598711 13 + 22589142 AAACCAAATCCTA s droSuz1.KI419649 12035861 13 - 14502029 AGATCATatctca s droKik2.KB459527 271040 11 - 1234237 --agtaaatatca s droTak2.KB461535 135514 13 - 669855 aaatttaaagcca s droFic2.KB457177 76014 10 + 995874 -aaacatattt-- s droWil2.CH963894 1302204 6 + 2843958 -------ATGCAA a score=3260.000000 s dm6.chr2R 24345189 5 + 25286936 AACAA s droSim1.chr2R 18691926 5 + 19596830 AACAA s droSec1.super_23 111693 5 + 989336 AACGA s droYak3.chr2R 20200682 5 + 21139217 AATGA s droEre2.scaffold_4845 21598724 5 + 22589142 AACGA s droSuz1.KI419649 12035874 5 - 14502029 aatat s droEle2.KB458573 516162 5 - 5320397 AAGAA s droKik2.KB459527 271051 5 - 1234237 aataa s droTak2.KB461535 135527 4 - 669855 aGTT- s droFic2.KB457177 76024 5 + 995874 tacaa s droWil2.CH963894 1302210 5 + 2843958 TACAA a score=-16995.000000 s dm6.chr2R 24345194 12 + 25286936 TTTGATTT---------------------------AAGA s droSim1.chr2R 18691931 12 + 19596830 TTTGATTC---------------------------AAGA s droSec1.super_23 111698 12 + 989336 TTTGATTC---------------------------AAGA s droYak3.chr2R 20200687 39 + 21139217 TTTGATTTGGAACTCCCTAAGTTCTATATTGTTCAAAGA s droEre2.scaffold_4845 21598729 39 + 22589142 TTTGATTTAAAACTCCTTTAGGTCTGCATTGTTCAAAGA s droBia2.KB462602 790775 12 + 3129309 TTTAATTC---------------------------TAAA s droSuz1.KI419649 12035884 12 - 14502029 tttaattc---------------------------taaa s droEug2.KB465067 595873 7 + 1515531 -----TTC---------------------------AAGA s droEle2.KB458573 516167 12 - 5320397 TCTTTTCT---------------------------GAAA s droKik2.KB459527 271056 8 - 1234237 ----atat---------------------------aata s droTak2.KB461535 135531 12 - 669855 TCGGattc---------------------------aaag s droFic2.KB457177 76037 7 + 995874 tttaatt-------------------------------- s droWil2.CH963894 1302215 1 + 2843958 -----T--------------------------------- a score=-9543.000000 s dm6.chr2R 24345206 7 + 25286936 CTCAAAA- s droSim1.chr2R 18691943 7 + 19596830 CTCAAAA- s droSec1.super_23 111710 7 + 989336 CTTAAAA- s droYak3.chr2R 20200726 7 + 21139217 CTCCAGA- s droEre2.scaffold_4845 21598768 7 + 22589142 CTCCAGA- s droBia2.KB462602 790787 5 + 3129309 CTG--AA- s droSuz1.KI419649 12035896 5 - 14502029 ttc--ga- s droAna3.scaffold_13266 5706453 7 - 19884421 CTGAAGC- s droBip2.KB464407 1955202 7 + 2915140 CTTAAAT- s droEle2.KB458573 516179 7 - 5320397 CTTATAG- s droKik2.KB459527 271064 1 - 1234237 ------t- s droTak2.KB461535 135543 7 - 669855 tttaaaa- s droFic2.KB457177 76044 6 + 995874 -tataaa- s droWil2.CH963894 1302216 4 + 2843958 ----AAAT a score=-6311.000000 s dm6.chr2R 24345213 1 + 25286936 -A s droSim1.chr2R 18691950 1 + 19596830 -A s droSec1.super_23 111717 1 + 989336 -A s droYak3.chr2R 20200733 1 + 21139217 -A s droEre2.scaffold_4845 21598775 1 + 22589142 -A s droBia2.KB462602 790792 1 + 3129309 -C s droSuz1.KI419649 12035901 1 - 14502029 -a s droAna3.scaffold_13266 5706460 1 - 19884421 -C s droBip2.KB464407 1955209 1 + 2915140 -C s droEle2.KB458573 516186 1 - 5320397 -A s droKik2.KB459527 271065 1 - 1234237 -c s droTak2.KB461535 135550 1 - 669855 -a s droFic2.KB457177 76050 1 + 995874 -a s droPse3.chr3 1344290 1 - 19787792 -A s droPer1.super_34 533144 1 - 916997 -A s droWil2.CH963894 1302220 1 + 2843958 T- a score=-18307.000000 s dm6.chr2R 24345214 4 + 25286936 --CCCG s droSim1.chr2R 18691951 4 + 19596830 --CCCG s droSec1.super_23 111718 4 + 989336 --CCCG s droYak3.chr2R 20200734 4 + 21139217 --CCCC s droEre2.scaffold_4845 21598776 4 + 22589142 --CCCT s droBia2.KB462602 790793 4 + 3129309 --CCTC s droSuz1.KI419649 12035902 4 - 14502029 --ctaC s droAna3.scaffold_13266 5706461 4 - 19884421 --CTCT s droBip2.KB464407 1955210 4 + 2915140 --CCTA s droEug2.KB465067 595880 4 + 1515531 --ATCA s droEle2.KB458573 516187 3 - 5320397 --CCC- s droKik2.KB459527 271066 4 - 1234237 --caAG s droFic2.KB457177 76066 3 + 995874 --CTT- s droPse3.chr3 1344292 3 - 19787792 --CTC- s droPer1.super_34 533146 3 - 916997 --CTC- s droWil2.CH963894 1302221 4 + 2843958 CTCC-- a score=10920.000000 s dm6.chr2R 24345218 1 + 25286936 A s droSim1.chr2R 18691955 1 + 19596830 A s droSec1.super_23 111722 1 + 989336 A s droYak3.chr2R 20200738 1 + 21139217 A s droEre2.scaffold_4845 21598780 1 + 22589142 A s droBia2.KB462602 790797 1 + 3129309 A s droSuz1.KI419649 12035906 1 - 14502029 A s droAna3.scaffold_13266 5706465 1 - 19884421 A s droBip2.KB464407 1955214 1 + 2915140 A s droEug2.KB465067 595884 1 + 1515531 A s droEle2.KB458573 516190 1 - 5320397 A s droKik2.KB459527 271070 1 - 1234237 A s droTak2.KB461535 135780 1 - 669855 A s droRho2.KB449310 29606 1 - 65043 A s droFic2.KB457177 76069 1 + 995874 A s droWil2.CH963894 1302225 1 + 2843958 A a score=169139.000000 s dm6.chr2R 24345219 37 + 25286936 ACCACTGTGC-CCG--CGAAGTACCTCT-GCTCATCTCTAG s droSim1.chr2R 18691956 37 + 19596830 ACCACTGTGC-CCG--CGAAGTTCCTCT-GCTCATCTCTAG s droSec1.super_23 111723 37 + 989336 ACCACTGTGC-CCG--CGAAGTTCCTCT-GCTCATCTCTAG s droYak3.chr2R 20200739 23 + 21139217 ACCACTGTG-----------------TT-GCTCATCTCCAG s droEre2.scaffold_4845 21598781 37 + 22589142 ACCACTGTGC-CCG--CGAAGTTCCCTT-GCTCATCTCCAG s droBia2.KB462602 790798 37 + 3129309 ACCACTGTGC-CCG--CGCAGTTCTCTC-GCCAGTCTCCTG s droSuz1.KI419649 12035907 37 - 14502029 ACCACTGTGC-CCG--CGAAGTTCTCTC-GCTTGTCTCTAG s droAna3.scaffold_13266 5706466 26 - 19884421 ACCACTGTAC-TTGGCTGCAG--------------CTCCAG s droBip2.KB464407 1955215 26 + 2915140 CCCACTGTAC-TTGGATGGAG--------------CTCCAG s droEug2.KB465067 595885 37 + 1515531 ACCACTGTGC-CCG--GCAAGTTGCCTG-GCTCATCTCTAG s droEle2.KB458573 516191 37 - 5320397 ACCACTGTGC-CAG--CGAACTTTCCTC-GCTCCGCTCTAG s droKik2.KB459527 271071 37 - 1234237 ACCACTGTCC-CTG--TGAAGTTCCCTC-GCTCAGTTTTAG s droTak2.KB461535 135781 37 - 669855 ACCACTGTGC-CCG--CGAAGTTCCCTC-GCTCGCCTCTAG s droRho2.KB449310 29607 37 - 65043 ACCACTGTGC-CTG--TGAACTTACCTC-GCTCCGCTCTAG s droFic2.KB457177 76070 36 + 995874 ACCACTGTGT-ACG--CGAACTTCCCTT-GCTC-TTAAAAG s droPse3.chr3 1344296 38 - 19787792 ACCACTGTGC-CAT--CGTGCCCCGCTCAGATCAGCTCTAG s droPer1.super_34 533150 38 - 916997 ACCACTGTGC-CAT--CGTGCTCCGCTCAGATCAGCTCTAG s droMir2.chr3 1385388 38 - 20862834 ACCACTGTGC-CAT--CGTGCTCCGCTCAGATCAGCTCTAG s droWil2.CH963894 1302226 36 + 2843958 GTCACTGTGCATCG--CGCATTCATTTT---CCAATTTGAA a score=198729.000000 s dm6.chr2R 24345256 37 + 25286936 AAC--AGTAG--------C---CG--CAGA-----TCCTCT-GCTTTT-GGC-CAGATCG s droSim1.chr2R 18691993 37 + 19596830 AAC--AGTAG--------C---CG--CAGA-----TCCTCT-GCTTTT-GGC-CAGATCG s droSec1.super_23 111760 37 + 989336 AAC--AGTAG--------C---CG--CAGA-----TCCTCT-GCTTTT-GGC-CAGATCG s droYak3.chr2R 20200762 39 + 21139217 AAC--GGTAGCCT-----C---CT--CTGA-----T-ctct-gctttt-ggc-cagaacG s droEre2.scaffold_4845 21598818 45 + 22589142 AAC--AGTAGCCCAGTAGC---CG--CGGA-----TCCTCT-GCTTTT-GGC-CAGATCG s droBia2.KB462602 790835 38 + 3129309 AAC--AGTAG--------C---CC--CAGA-----TCCTCT-GGTTTTCGGC-CAGATCG s droSuz1.KI419649 12035944 38 - 14502029 AAC--AGTAG--------C---CG--CAGA-----TCCTCT-GCTTTTTGGC-CAGATCG s droAna3.scaffold_13266 5706492 30 - 19884421 AAC--AGTAG--------CTGGCGAACAGA-----TCCTCT--------GGC-C------ s droBip2.KB464407 1955241 27 + 2915140 AAC--AGTAG--------C---CCAAAAGA-----TCCTCG--------CAA-C------ s droEug2.KB465067 595922 38 + 1515531 AAC--AGTAG--------C---CG--AAga-----tcttcttgttttt-ggc-cagatCG s droEle2.KB458573 516228 38 - 5320397 AAC--AGTAA--------C---CA--CAGA-----TCCTCT-GGTTTTTAGC-CAGATCG s droKik2.KB459527 271108 43 - 1234237 AAC--AGTAG--------C---CA--CCAAGATCCTCCTCT-GCTTTTCGCC-CGAATCG s droTak2.KB461535 135818 38 - 669855 AAC--AGTAG--------C---AG--CAGA-----TCCTCT-GCTTTTTGGC-CAGATCG s droRho2.KB449310 29644 38 - 65043 AAC--AGTAG--------C---TG--CAGA-----TCCTGT-GGTTTCTGGC-CAGATCG s droFic2.KB457177 76106 37 + 995874 AAC--AGTAG--------C---CG--GAGA-----TCCTCT-TGTTTT-GGC-CAGATCG s droPse3.chr3 1344334 37 - 19787792 AAC--AGTAG--------C---CA--GAGA-----TCCTCT-GTTCTT-GGT-CCCCCCA s droPer1.super_34 533188 37 - 916997 AAC--AGTAG--------C---CA--GAGA-----TCCTCT-GTTCTT-GGT-CCCCCCA s droMir2.chr3 1385426 38 - 20862834 AAC--AGTAG--------C---CA--GAGA-----TCCTCT-GTTCTT-GGTcccccccA s droWil2.CH963894 1302262 35 + 2843958 AACCAAGTAG--------T---TG-----------GTCCCT-GTCTTT-GTG-TCTGTCG s droGri2.scaffold_15245 893839 37 + 18325388 AAC--TGTTG--------C---CG--TTTT-----GCTTCA-GCTTCA-GTT-GCAGTTG a score=75517.000000 s dm6.chr2R 24345293 9 + 25286936 CGTCTGTTT s droSim1.chr2R 18692030 9 + 19596830 CGTCTGTTT s droSec1.super_23 111797 9 + 989336 CGTCTGTTT s droYak3.chr2R 20200801 9 + 21139217 CGTCTGTTT s droEre2.scaffold_4845 21598863 9 + 22589142 CGTCTGTTT s droBia2.KB462602 790873 9 + 3129309 CGTCTGTCC s droSuz1.KI419649 12035982 9 - 14502029 CGTCTGTTC s droBip2.KB464407 1955268 1 + 2915140 --------T s droEug2.KB465067 595960 9 + 1515531 CGTCTGTTT s droEle2.KB458573 516266 9 - 5320397 CGTCTGTTT s droKik2.KB459527 271151 5 - 1234237 CGTCT---- s droTak2.KB461535 135856 9 - 669855 CGTCTGTTC s droRho2.KB449310 29682 9 - 65043 CGTCTGTTT s droFic2.KB457177 76143 9 + 995874 CGTCTGTTT s droPse3.chr3 1344373 9 - 19787792 CTTCAGTTC s droPer1.super_34 533227 9 - 916997 CTTCAGTTC s droMir2.chr3 1385466 9 - 20862834 CTTCAGTTC s droWil2.CH963894 1302297 6 + 2843958 ---CCGTTT s droVir3.scaffold_12875 7345935 8 + 20611582 CGTCTGTT- s droGri2.scaffold_15245 893879 9 + 18325388 CTTCTGTTT a score=-1670.000000 s dm6.chr2R 24345302 1 + 25286936 G s droSim1.chr2R 18692039 1 + 19596830 G s droSec1.super_23 111806 1 + 989336 G s droYak3.chr2R 20200810 1 + 21139217 G s droEre2.scaffold_4845 21598872 1 + 22589142 G s droBia2.KB462602 790882 1 + 3129309 G s droSuz1.KI419649 12035991 1 - 14502029 A s droBip2.KB464407 1955269 1 + 2915140 G s droEug2.KB465067 595969 1 + 1515531 A s droEle2.KB458573 516275 1 - 5320397 A s droTak2.KB461535 135865 1 - 669855 A s droRho2.KB449310 29691 1 - 65043 A s droFic2.KB457177 76152 1 + 995874 G s droPse3.chr3 1344382 1 - 19787792 C s droPer1.super_34 533236 1 - 916997 C s droMir2.chr3 1385475 1 - 20862834 C s droWil2.CH963894 1302303 1 + 2843958 G a score=1976396.000000 s dm6.chr2R 24345303 114 + 25286936 GCCAACTG-----TT---GG------CCGCTTTGGCGGCGT--------------TGTGTAAGCGCGGTAGCCCACG------------------------ATTCCGCGTTG-CCTTTGTTTTCG---GCTTCATAAAATGTTAATTTGCCG---CCGCAATTGCATTCAAAG s droSim1.chr2R 18692040 114 + 19596830 GCCAACTG-----TT---GG------CCGCTTTGGCGGCGT--------------TGTGTAAGCGGGGTAGCCCACG------------------------ATTCCGCGTTG-CCTTTGTTTTCG---GCTTCATAAAATGTTAATTTGCCG---CCGCAATTGCATTCAAAG s droSec1.super_23 111807 114 + 989336 GCCAACTG-----TT---GG------CCGCTTTGGCGGCGT--------------TGTGTAAGCGCGGTAGCCCACG------------------------ATTCCGCGTTG-CCTTTGTTTTCG---GCTTCATAAAATGTTAATTTGCCG---CCGCAATTGCATTCAAAG s droYak3.chr2R 20200811 115 + 21139217 GCCAACTGT----TT---GG------CCGCTTTGGCGGCGT--------------TGTGTAAGCGCGGTAGCCCACG------------------------ATTCCGCGTTG-CCTTTGTTTTCG---GCTtcataaaatgttaatttgcCG---CCGCAATTGCATTCAAAG s droEre2.scaffold_4845 21598873 115 + 22589142 GCCAACTGT----TT---GG------CCGCTTTGGCGGCGT--------------TGTGTAAGCGCGGTAGCCCACG------------------------ATTCCGCGTTG-CCTTTGTTTTCG---GCTTCATAAAATGTTAATTTGCCG---CCGCAATTGCATTCAAAG s droBia2.KB462602 790884 112 + 3129309 GCCAAC--------T---GG------TGGCTTTGGCGGCGT--------------GGTGTAAGCGCGGTAGCCCACG------------------------ATTCCGCGTTTCCCTTTGTTTTCG---GCttcataaaatgttaatttgcCG---CCGCAATTGCATTCAAAG s droSuz1.KI419649 12035993 116 - 14502029 GCCAACTGT----TT---GG------TGGCTTTGGCGGCGT--------------TGTGTAAGCGCGGTAGCCCACG------------------------ATTCCGCGTTTCCCTTTGTTTTCG---GcttcataaaatgttaatttgcCG---CCGCAATTGCATTCAAAG s droAna3.scaffold_13266 5706522 105 - 19884421 ------------------GA------CTCCTTTGGCGGCGT--------------TGGGTAAGCGCGGTAGCCCACG------------------------ATTCCGCATTTCCCTTTGTTTTCG---GCTTCATAAAATGTTAATTTGCCG---CCGCAATTGCATTCAAAA s droBip2.KB464407 1955270 106 + 2915140 --------------T---GA------CTCCTTTGGCGGCGT--------------TGGGTAACCGCGGTAGCCCACG------------------------ATTCCGCATTTCCCTTTGTTTTCG---GCTtcataaaatgttaatttgCCG---CCGCAATTGCATTCAAAA s droEug2.KB465067 595971 116 + 1515531 GCCAACTGT----TT---GG------CCGCTTTGGCGGCGT--------------TGTGTAAGCGCGGTAGCCCACG------------------------ATTCCGCGTTTCCCTTTGTTTTCG---GCttcataaaatgttaatttgcCG---CCGCAATTGCATTCAAAG s droEle2.KB458573 516277 116 - 5320397 GCCAACTGT----TT---GA------ACGCTTTGGCGGCGT--------------TGTGTAAGCGCGGTAGCCCACG------------------------ATTCCGCGTTTCCCTTTGTTTTCG---GCttcataaaatgttaatttgccG---CCGCAATTGCATTCAAAG s droKik2.KB459527 271156 122 - 1234237 GCCGGCTGTTGGCTT---TG------GCTCTTTGGCGGCGTTG------------TGTGTAAGCACGGTAGCCCACG------------------------ATTCCGCATTTCCCTTTGTTTTCG---GCttcataaaatgttaatttgcCG---CCGCAATTGCATTCAAAG s droTak2.KB461535 135867 122 - 669855 GCCAACTGT----TT---GGTGGCTTTCGCTTTGGCGGCGT--------------TGTGTAAGCGCGGTAGCCCACG------------------------ATTCCGCGTTTCCCTTTGTTTTCG---GCTtcataaaatgttaatttgcCG---CCGCAATTGCATTCAAAG s droRho2.KB449310 29693 116 - 65043 GCCAACTGT----TT---GG------CCTCTTTGGCGGCGT--------------TGTGTAAGCGCGGTAGCCCACG------------------------ATTCCGCGTTTCCCTTTGTTTTCG---GCttcataaaatgttaatttgccG---CCGCAATTGCATTCAAAG s droFic2.KB457177 76154 116 + 995874 GCCGACTGT----TC---GG------TCGCTTTGGCGGCGT--------------TGTGTAAGCGCGGTAGCCCACG------------------------ATTCCGCGTTTCCCTTTGTTTTCG---GCttcataaaatgttaatttgccG---CCGCAATTGCATTCAAAG s droPse3.chr3 1344383 114 - 19787792 CCCAACTGT----T-----G------CCGCTTTGGCGGCGT--------------TGTGTAAGCGCGGTAGCCCACG------------------------ATTCCGCATTTCCCTTTGTTTTCG---GCTTcataaaatgttaatttgcCG---CCGCAATTGCATTCAAAG s droPer1.super_34 533237 114 - 916997 CCCAACTGT----T-----G------CCGCTTTGGCGGCGT--------------TGTGTAAGCGCGGTAGCCCACG------------------------ATTCCGCATTTCCCTTTGTTTTCG---GCTTCATAAAATGTTAATTTGCCG---CCGCAATTGCATTCAAAG s droMir2.chr3 1385476 114 - 20862834 CCCAACTGT----T-----G------CCGCTTTGGCGGCGT--------------TGTGTAAGCGCGGTAGCCCACG------------------------ATTCCGCATTTCCCTTTGTTTTCG---GCTtcataaaatgttaatttgcCG---CCGCAATTGCATTCAAAG s droWil2.CH963894 1302304 114 + 2843958 --CCGTTG-----TT---GG------CCTCTTTGGCGGC-T--------------TGTGTAAGCGCGGTAG-CCACG------------------------ATTCTGCATTTCCCTTTGTTTTCGGCTGCTTcataaaatgttaatttgccG---CCACAATTGCATTCAaaa s droVir3.scaffold_12875 7345944 139 + 20611582 GCCAACTGT----TGCCTGT------TTGCTTTGGCGGCGGCGGCGC--------TGTGTAAGCGCGGTAG-CCACG------------ATTCCGATTCCGATTCCGAATTTCCCTTTGTTTTCG---GCTTCATAAAATGTTAATTTGCCGGCCGCGCAATTGCATTCAAAG s droMoj3.scaffold_6496 26140977 151 + 26866924 ACCAACTGT----TGCCCGC------TTGTTTTGGCGGCGACGGCGC--------TGTGTAAGCGAGGTAG-CCACGattccaattccaattccaattccgattcccaattTCCCTTTGTTTTCG---GTTTCATAAAATGTTAATTTGCCGAACGCGCGATTGCATTCAAAG s droAlb1.JH854640 304641 151 + 406291 GACAACTGT----TGC--AT------TTACTTTGGCGGCGACGGCGCTGTCGCTGTGTGTAAGCGTGGTAG-CCACG------ATTCTGATTCCGATTTCGATTCCGAATTTCCCTTTGTTTTCG---GCttcataaaatgttaatttgccGGCCCCGCAATTGCATTCAAAG s droGri2.scaffold_15245 893889 134 + 18325388 ---TGCTTC----TGC--TT------TTGCTTTGGCGGCGGCGGCGC--------TGTGTAAGCGCGGTAG-CCACG------------ATTCCGATTCCGATTCCGAATTTCCCTTTGTTTTCG---GCTTCATAAAATGTTAATTTGCCGGCCCCGCAATTGCATTCAAAG a score=-339639.000000 s dm6.chr2R 24345417 25 + 25286936 G-------------AGG--CT------------------------CCTGCCC-------ACG--------------------------GAGCACT--------C-C s droSim1.chr2R 18692154 25 + 19596830 G-------------AGG--CT------------------------CCTGCCC-------ACG--------------------------GAGCACT--------C-C s droSec1.super_23 111921 25 + 989336 G-------------ATG--CT------------------------CCTGCCC-------ACG--------------------------GAGCACT--------C-C s droYak3.chr2R 20200926 27 + 21139217 G-------------AGGCTCT------------------------CCTGCCC-------ACG--------------------------GAGCACT--------C-C s droEre2.scaffold_4845 21598988 25 + 22589142 G-------------AGG--CT------------------------CCTGCCC-------ACG--------------------------GAGCACT--------C-C s droBia2.KB462602 790996 56 + 3129309 A------GGCTGGTGGG--CT---GCCCACCAGTTG---------CCGGCCC-------ACAATCCG--------------CATCCACAGCCACT--------C-C s droSuz1.KI419649 12036109 61 - 14502029 G-------------AGG--CT---GCCCACCAGTTG---------CCAGCCC-------ACaatccgca--tccacatccacatccacagccACT--------C-C s droAna3.scaffold_13266 5706627 25 - 19884421 G-------------GAGA-GT------------------------CCTAA---------GCA--------------------------GCCCAGT--------CTC s droBip2.KB464407 1955376 33 + 2915140 G-------------GAG--GC------------------------CCTAACCCACCGGCCCA--------------------------GCTAAGC--------CTC s droEug2.KB465067 596087 50 + 1515531 G-------------AGG--CT---GGCCACCAGTTGGCC----CAGCTACCC-------ACA--------------------------ATCCACTGGCTTCCAC-T s droEle2.KB458573 516393 61 - 5320397 G-------------AGG--CTGCTGCCCACCAGTT----------GCTACCC-------ACAATCCACAGGCCCACCACTACAC----TACCACT--------C-C s droKik2.KB459527 271278 64 - 1234237 G-------------AGG--CC------TACCAGTTAGTTGCTAccccggccc-------cccatttccagttcccaatcccaa-----tcccaat--------c-c s droTak2.KB461535 135989 56 - 669855 G-------------AGG--CTGCTGCCCACCAGTTG---------CCAGCCC-------ACAATCCACAACCACTTGC----------ATCCGCT--------C-C s droRho2.KB449310 29809 46 - 65043 G-------------AGC--CT---GCCCACCAGTT----------ACTGCCC-------ACAATCCATTGCC----------------CGCCACT--------C-C s droFic2.KB457177 76270 39 + 995874 G-------------AGG--CT---GCCCACCAGTT----------GCTGCCC-------ACAGTC-----------------------CTCTGCT--------C-C s droPse3.chr3 1344497 54 - 19787792 G-------------AGG--CT---ACCCACAAGTTG---------CAAGTCC-------ACCTTCATCCGTTGCTgccc---------catcctc--------c-a s droPer1.super_34 533351 54 - 916997 G-------------AGG--CT---ACCCACAAGTTG---------CAAGTCC-------ACCTTCATCTGTTGCTGCCC---------CATCCTC--------C-A s droMir2.chr3 1385590 54 - 20862834 G-------------AGG--CT---ACCCACAAGTTG---------CAAGTCC-------ACCTTCATCTGTTGCTgccc---------catcctc--------c-a s droWil2.CH963894 1302418 43 + 2843958 ggagaaggagagagagg--tT-----TAACCAACTA---------CTTACCC-------ACA--------------------------G-----T--------C-C s droMoj3.scaffold_6496 26141128 21 + 26866924 ----------------------AGAGCTGCCCAATG---------CCAGCAC------------------------------------------------------ s droAlb1.JH854640 304792 20 + 406291 -----------------------AGTATCCCCAATA---------CCAATCC------------------------------------------------------ s droGri2.scaffold_15245 894449 11 + 18325388 --------------------------------ACTG---------CCACTGT------------------------------------------------------ a score=27851.000000 s dm6.chr2R 24345442 15 + 25286936 TCCCCCG-----A---AACAATT s droSim1.chr2R 18692179 15 + 19596830 TCCCCCG-----A---AACAATT s droSec1.super_23 111946 15 + 989336 TCCCCCG-----A---AACAATT s droYak3.chr2R 20200953 20 + 21139217 TCCCCCGCCAGTG---CACAATT s droEre2.scaffold_4845 21599013 15 + 22589142 TCCCCCG-----A---AACAATT s droBia2.KB462602 791052 16 + 3129309 TCCCCCG-----A--CAACAATT s droSuz1.KI419649 12036170 16 - 14502029 TCCCCCA-----A--AAACAATT s droAna3.scaffold_13266 5706652 16 - 19884421 TCCCCCA-----A--CAACTGCG s droBip2.KB464407 1955409 16 + 2915140 ACCCCCA-----A--CCAAAGTG s droEug2.KB465067 596137 15 + 1515531 CCGCCCC-----A---AACAATT s droEle2.KB458573 516454 16 - 5320397 TCCCCCA-----A--AAACAATT s droKik2.KB459527 271342 16 - 1234237 ctccccG-----C--CAGCAATT s droTak2.KB461535 136045 16 - 669855 TCCCCCA-----A--AAACAATT s droRho2.KB449310 29855 18 - 65043 TCctcta-----aaaaaacaatt s droFic2.KB457177 76309 15 + 995874 TCCCCCA-----A---AACAATT s droPse3.chr3 1344551 15 - 19787792 tcctcca-----t---cccaGTT s droPer1.super_34 533405 15 - 916997 TCCTCCA-----T---CCCAGTT s droMir2.chr3 1385644 15 - 20862834 tcctcca-----t---cccaGTT s droWil2.CH963894 1302461 8 + 2843958 TCCTACA-----A---------- s droAlb1.JH854640 304824 5 + 406291 ------------------CAATC s droGri2.scaffold_15245 894474 1 + 18325388 ----------------------T a score=-75187.000000 s dm6.chr2R 24345457 51 + 25286936 GATGCG--------TGC---TCCT----TG--T--------------GGATGGT------------GGCCCA-------CAAG-----TCGCTGCAAC------TGGCAA---------------------CG s droSim1.chr2R 18692194 51 + 19596830 GATGCG--------TGC---TCCT----TG--T--------------GGATGGT------------GGCCCA-------CAAG-----TCGCTGCAAC------TGGCCA---------------------CG s droSec1.super_23 111961 51 + 989336 GATGCG--------TGC---GCCT----TG--T--------------GGATGGT------------GGCCCA-------CAAG-----TCGCTGCAAC------TGGCCA---------------------CG s droYak3.chr2R 20200973 73 + 21139217 GATGCG--------TGC---TCCT----TG--T--------------GGATTCC------------GGCCCA-------CAAG---TCTCGTTGCAAC------TGGCTGGC-CACGTTGCCCCTTTGCGCCG s droEre2.scaffold_4845 21599028 51 + 22589142 GATGCG--------TGC---TCCT----TG--T--------------GGATTCC------------GGCCCA-------CAAG-----TCGTTGCAAC------TGGCCA---------------------CG s droBia2.KB462602 791068 47 + 3129309 GATGCG--------TGC---TCCT----GG--C--------------GGATTCT------------GGCCCA-------C--------TCGCTGCAATG-----TGGC-----------------------CG s droSuz1.KI419649 12036186 47 - 14502029 GATGCG--------TGC---TCCT----TG--C--------------GGATTCT------------GGCCCA-------C--------TCGCTGCAATG-----TGGC-----------------------CA s droAna3.scaffold_13266 5706668 55 - 19884421 TGATGG--------GGCAGTGGCA----GG--A--------------GGCAGTAGGCAGTAGTATAGCCCCA-------T--------TCCTTG----------TGGT------------------------- s droBip2.KB464407 1955425 46 + 2915140 GGTGCG--------TGCAGGGGCT----GG--A--------------GGATTCA---------ATACCCTCA-------T--------TCGATG----------TGGT------------------------- s droEug2.KB465067 596152 47 + 1515531 GATGCG--------TGC---TCCT----TG--C--------------GGATTCT------------GGCCCA-------G--------TCGTTGCAATG-----TGGC-----------------------CA s droEle2.KB458573 516470 47 - 5320397 GATGCG--------TGC---TCCT----TG--C--------------GGATTCT------------GCCCCA-------C--------TCGTTGCAATG-----TGGC-----------------------CA s droKik2.KB459527 271358 43 - 1234237 GATGCG--------TGC---CGT-------------------------GCTCCT------------GGCTC-----------------TCGCTGCAATG-----CGGCCGC--------------------CA s droTak2.KB461535 136061 47 - 669855 GATGCG--------TGC---TCCT----TG--C--------------GGATTCT------------GGCCCA-------C--------TCGCTGCAATG-----TGGC-----------------------CA s droRho2.KB449310 29873 47 - 65043 gatgCG--------TGC---TCCT----TG--C--------------GGATTCT------------GCCCCA-------C--------TCGTTGCAATG-----TGGC-----------------------CA s droFic2.KB457177 76324 47 + 995874 GATGCG--------TGC---TCCT----CG--C--------------GGATTCC------------GGCCCA-------C--------TCCTTGCAGCG-----TGGC-----------------------CA s droPse3.chr3 1344566 54 - 19787792 GATGCG--------TGC---TCCTTCTGTG--T--------------GTATTCT------------ACCCCA-------C--------TCATTGTCATG--CACGGGC-----------------------CG s droPer1.super_34 533420 54 - 916997 GATGCG--------TGC---TCCTTCTGTG--T--------------GTATTCT------------ACCCCA-------C--------TCATTGTCATG--CACGGGC-----------------------CG s droMir2.chr3 1385659 54 - 20862834 GATGCG--------TGC---TCCTTCTGTG--T--------------GTATTCT------------ACCCCA-------C--------TCATTGTCATG--CACGGGC-----------------------CG s droWil2.CH963894 1302469 80 + 2843958 -TTGCG--------TGC---TCTT--------T--------------GGTTTTG------------GTCCCG-------CCAAGCATCCCATTTCCATTCTCTCCAGCTCCTGCGCCTCCACCCACTCCTTCG s droMoj3.scaffold_6496 26141318 28 + 26866924 GCTGC-----------C---TGCT----TGGCC--------------AATTCCT------------GCGGCT------------------------------------------------------------- s droAlb1.JH854640 304844 52 + 406291 GTTGCG--------TGC---TGCT----TGGTCTCATTGTCATGCGAAGATGCA------------GCCACTGCCTTTG------------------------------------------------------ s droGri2.scaffold_15245 894489 38 + 18325388 gctgctgttactgctgc---tgct----TGGCC--------------AACT-CG------------GCGTTG------------------------------------------------------------- a score=2628911.000000 s dm6.chr2R 24345508 260 + 25286936 TT--GCCTTGGCATT---------------------------------------------------------------------------------TTCAAATGACCAATTTTCACACGCAAACTTACATAATG-------------------------------CCACTGCA-----------------TTAGCTCCTGC-------------------T-GCTTTCCATCGATCTGG-GGGCC---------------------------------GTATATGAAATTTTTCACATTTCTGAAATAGA-C-TTCCCT-------GGCCACT------------------------A------------------------------------G--------------CTGAACCA--AG--CCCCGATCAAAATCAGAC--------AAAAAGCATCAACATCGCGGCGCTAAATCACGATCTCAGCACGATCTTTGC-------------------------------------------------CCA------AGACAC-------------------------A-----------AAATCTTATGAAATATTT--GACC-CAAGCA------------GA s droSim1.chr2R 18692245 260 + 19596830 TT--GCCTTGGCATT---------------------------------------------------------------------------------TTCAAATGACCAATTTTCACACGCAAACTTACATAATG-------------------------------CCACTGCA-----------------TTAGCTCCTGC-------------------T-GCTTTCCATCGATCTGG-GGGCC---------------------------------GCATATGAAATTTTTCACATTTCTGAAATAGA-C-TTCCCT-------GGCCACT------------------------A------------------------------------G--------------TTGAACCA--AG--CCCCGATCAAAATCAGAC--------AAAAAGCATCAACATCGCGGCGCTAAATCACGATCTCAGCACGATCTTTGC-------------------------------------------------CCA------AGACAC-------------------------A-----------AAATCTTATGAAATATTT--GACC-CAAGCA------------GG s droSec1.super_23 112012 260 + 989336 TT--GCCTTGGCATT---------------------------------------------------------------------------------TTCAAATGACCAATTTTCACACGCAAACTTACATAATG-------------------------------CCACTGCA-----------------TTAGCTCCTGC-------------------T-GCTTTCCATCGATCTGG-GGGCC---------------------------------GCATATGAAATTTTTCACATTTCTGAAATAGA-C-TTCCCT-------GGCCACT------------------------A------------------------------------G--------------CTGAACCA--AG--CCCCGATCAAAATCAGAC--------AAAAAGCATCAAAATCGCGGCGCTAAATCACGATCTCAGCACGATCTTTGC-------------------------------------------------CCA------AGACAC-------------------------A-----------AAATCTTATGAAATATTT--GACC-CAAGCA------------GG s droYak3.chr2R 20201046 274 + 21139217 CT--GCCTTGGCATT---------------------------------------------------------------------------------TTCAAATGACCAATTTTCACACGCAAACTTACATAATG-------------------------------GCACTGCA-----------------TTAGCTCCTGC-------------------C-GCTTTCCATCGATCTGG-GGGCC---------------------------------GCATATGaaatttttcacatttctcaAATAGA-C-TTCCCT-------GGCCACT------------------------T------------------------------------GCAACCAcacttggccaaaacca--ag--CCCCGATCAAAATCAGAC--------AAAAAGCATCAACATCGCGGCGCTAAATCACGATCTCAGCACGATCTTTGC-------------------------------------------------CCA------AGACAC-------------------------A-----------AAATCTTATGAATTATTT--GACC-CAAGCG------------GA s droEre2.scaffold_4845 21599079 260 + 22589142 CT--GCCTTGGCATT---------------------------------------------------------------------------------TTCAAATGACCAATTTTCACACGCAAACTTACATAATG-------------------------------CCACTGCA-----------------TTAGCTCCTGC-------------------T-GCTTTCCATCGATCTGG-GGGCC---------------------------------GCATATGAAATTTTTCACATTTCTGAAATAGA-C-TTCCCT-------GGCCACT------------------------A------------------------------------G--------------CTAAACCA--AG--CCCCGATCAAAATCACAC--------AAAAAGCATCAACATCTCGGCGCTAAATCACGATCTCAGCACGATCTTTGC-------------------------------------------------CCA------AGACAC-------------------------A-----------AAATCTTATGAAATATTT--GACC-CAAGCG------------GG s droBia2.KB462602 791115 258 + 3129309 GT--GCCTTGGCATT---------------------------------------------------------------------------------TTCaaatgaccaattttcacACGCAAACTTACATAAGG-------------------------------CCACCGca------------------ctgctcctgc-------------------t-gctttcCATCGATCTGC-GGGCC---------------------------------GCATATgaaatttttcacatttttgaaataga-C-TTCCCT-------GGCCACT------------------------A------------------------------------G--------------CTAAACCA--AG-CCCCCGATCAAAATCAGAC--------AAAAAGCATCAACATCGCGGCGCTAAATCACGATCTCAGCACGATCTTTGC-------------------------------------------------CCA------A-ACAC-------------------------A-----------AAATCTTATGAAATACTT--GACC-CAA-CG------------GG s droSuz1.KI419649 12036233 263 - 14502029 GT--GCCTTGGCATT---------------------------------------------------------------------------------TTCAAATGACCAATTTTCACACGCAAACTTACATAATG-------------------------------CCACTGCA-----------------TTTGCTCCTGC-------------------T-GCTTTCCATCGATCTGCGGGGCC---------------------------------GCATATGaaatttttcacatttttgaaataGA-C-TTCCCT-------GGCCACT------------------------A------------------------------------G--------------CTAAACCA--AG-CCCCCGATCAAAATCAGAC------A-AAAAAGCATCAACATCGCGGCGCTAAATCACGATCTCAGCACGATCTTTGC-------------------------------------------------CCA------AGACAC-------------------------A-----------AAatcttatgaaatattt--gacC-CAAGCA------------GG s droAna3.scaffold_13266 5706723 211 - 19884421 -----CTCTGGCATT---------------------------------------------------------------------------------TTCAAATGACCAATTTTCACACGCAAACT-------------------------------------------------------------------------------------------------------------CCTGC-TC-CT---------------------------------GCATATGAAATTTTTCACATTTTCTAAATAGA-C-TTCTCC---------------------------------------------------------------------------G--------------CCAAGCCG--AACCTCCCGATCGAAATCAGAA------ACAAAAAGCATCAACATCGCGGCGCTAAATCACGATCCCAGCACGATCTCTGC-------------------------------------------------CAG------AGTCAC-------------------------A-----------AAATCTTATGAAATACTT--GACC-CAACCA------------GG s droBip2.KB464407 1955471 250 + 2915140 -----CTTTGGCATT---------------------------------------------------------------------------------TTCAAATGACCAATTTTCACACGCAAACTTACATAATG-------------------------------CAGGAGCA------------------------------------------------------------ACCTCC-TAGTT---------------------------------GCATATgaaatttttcacattttttaaataga-c-tTCTCTTGGACATGGTTTCC------------------------AG---------------------------AGA-----G--------------CCAAACCACCAAACACCCGATCGAAATCAGAG------A-AAAAAGCATCAACACCGCGGCGCTAAATCACGATCTCAGCACGATCTTTGC-------------------------------------------------CAG------AGTCAC-------------------------A-----------AAATCTTATGAAATATTT--GACC-CAagca------------gg s droEug2.KB465067 596199 260 + 1515531 AT--GGCTTGGCATT---------------------------------------------------------------------------------TTCAAATGACCAATTTTCACACGCAAACTTACATAATG-------------------------------CCACTGCA-----------------TTTGCTCCTGC-------------------T-GCTTTCCATCGATCTGG-GGGCC---------------------------------GCATATgaaatttttcacatttttcaaataGA-C-TTCCCT-------GGCCACT------------------------A------------------------------------G--------------CT-AACCA--AG-CCCCCGATCAAAATCAGAC--------AAAAAGCATCAACATCGCGGCGCTAAATCACGATCTCAGCACGATCTTTGG-------------------------------------------------CCA------AGACAC-------------------------A-----------AAATCTTATGAAATATTT--GACC-CAACca------------gg s droEle2.KB458573 516517 263 - 5320397 GT--GCCTTGGCATT---------------------------------------------------------------------------------TTCAAATGACCAATTTTCACACGCAAACTTACATAATG-------------------------------CCACTGGATTTGC------------TTTGCTCCTGC-------------------T-GCTTTCCATCGATCTGG-CGGCT---------------------------------GCATATGaaatttttcacatttctGAAATAGA-C-TTCTAT-------GGCC----------------------------------------------------------------G--------------CTAGACCA--AA-CCCCCGATCAAAATCAGAC------A-AAAAAGCATCAACATCGCGGCGCTAAATCACGATCTCAGCACGATCTTTGC-------------------------------------------------CCA------AGACAC-------------------------A-----------AAATCTTATGAAATATTT--GACC-CAGGca------------gg s droKik2.KB459527 271401 281 - 1234237 GT--GCCTTGGTATT---------------------------------------------------------------------------------TTCAAATGACCAATTTTCACACGCAAACTTACATAATG-------------------------------CCACCACATTTGCtgctctcctgctcctgctcctgc-------------------t-gctttcCATCGATCTGG-CGGCT---------------------------------GCATATgaaatttttcacattttttaaatagacc-TTTTCT-------GGTCGCA------------------------A------------------------------------C--------------AGAAACCA--AG-CCCGCGATCAAAATCAGAC------ACAAAAAGCATCAACATCGCGGCGCTAAATCACGATCTCAGCACGATCTTTGG-------------------------------------------------CCA------AGACAC-------------------------A-----------AAATCTTATGAAATATTT--GACC-CAAGCA------------AG s droTak2.KB461535 136108 264 - 669855 TT--GGCTTGGCATT---------------------------------------------------------------------------------TTCAAATGACCAATTTTCACACGCAAACTTACATAATG-------------------------------CCCCTGCA-----------------TTTGCTCCTGC-------------------T-GCTTTCCATCGATCTGCGGGGcc---------------------------------gcatatgaaatttttcacatttttcgaATAGA-C-TTCCCT-------GGCCACT------------------------A------------------------------------G-------------CCTAAACCA--AG-CCCCCGATCAAAATCAGAC------A-AAAAAGCATCAACATCGCGGCGCTAAATCACGATCTCAGCACGATCTTTGC-------------------------------------------------CCA------AGACAC-------------------------A-----------AAATCTTATGAAATATTT--GACC-CAAGCA------------GG s droRho2.KB449310 29920 258 - 65043 AT--GCCTTGGCATT---------------------------------------------------------------------------------TTCAAATGACCAATTTTCACACGCAAACTTACATAATG-------------------------------CCCCTGCA-----------------TTTGCTCCTGC-------------------T-GCTTTCCATCGATCTGG-GGGCC---------------------------------GCATATGAAATTTTTCACATATTTGAAATAGA-C-TTCTAT-------GGCC----------------------------------------------------------------G--------------CCAAGCCA--AA-CCCCCGATCAAAATCAGAC------A-AAAAAGCATCAACATCGCGGCGCTAAATCACGATCTCAGCACGATCTTTGC-------------------------------------------------CCA------AGACAC-------------------------A-----------AAAtcttatgaaatattt--gacC-CAAGCA------------Gg s droFic2.KB457177 76371 255 + 995874 AT--GCCTTGGCATT---------------------------------------------------------------------------------TTCAAATGACCAATTTTCACACGCAAACTTACATAATG-------------------------------CCGCTGCA----------------ttttgctcctgc-------------------t-gctttCCATCGATCTGG-GGGCC---------------------------------gcatatgaaatttttcacattttttaaataga-c--tCTTT-------GGCC----------------------------------------------------------------G--------------CTTGGCCG--AA-CCCccgatcaaaatcggac--------aaaaaGCTTCAACATCGCGGCGCTAAATCACGATCTCAGCACGATCTTTG--------------------------------------------------CCA------AGACAC-------------------------A-----------AAATCTTATGAAATATTT--GACC-CAGGC-------------Ga s droPse3.chr3 1344620 357 - 19787792 TG--GCATTGGCATT---------------------------------------------------------------------------------TTCAAATGACCAATTTTCACACGCAAACTTATATAATGGTGGTTCCTACAACTGCTCCTCCCACTCTTTCCactcca-----------------tctgctgctgcttatgctgcttctgtgctgt-gctttcTATCCATCTGG-CGGGT---------------------------------GCATATGaaatttttcacatttttcaaatAGA-C-TTCTTT-------GGCCTCA------------------------AA----CCGAGCctcgatccgatccgaaccgaaccgta--------------cCGAACCG--AA-CACCCGATCAAAATCAGAC------ACAAAAACCATCAACATTGCGGCGCTAAATCACGATCCCAGCACGATCTTTGC-------------------------------------------------CAA------AGACAC-------------------------A-----------AAATCTTATGAAATATTT--GACC-CAAGTCgggggggggaaaaa s droPer1.super_34 533474 378 - 916997 TG--GCATTGGCATT---------------------------------------------------------------------------------TTCAAATGACCAATTTTCACACGCAAACTTATATAATGGTGGTTCCTACAACTGCTCCTCCTACTCCTCCTACTCCC-----------------TCTGCTGCTGCTTATGCTGCTTCTATGCTGT-GCTTTCTATCCATCTGG-CGGGT---------------------------------GCATATGAAATTTTTCACATTTTTCAAATAGA-C-TTCTTT-------Ggcctcaaaccgagcctcgaaccgagcctcgaa----ccgagcctcgatccgatccgaaccgaaccgta--------------ccgaaccg--aa-cACCCGATCAAAATCAGAC------ACAAAAACCATCAACATTGCGGCGCTAAATCACGATCCCAGCACGATCTTTGC-------------------------------------------------CAA------AGACAC-------------------------A-----------AAATCTTATGAAATATTT--GACC-CAAGTC---GGGGGGAAAAA s droMir2.chr3 1385713 351 - 20862834 TG--GCATTGGCATT---------------------------------------------------------------------------------TTCAAATGACCAATTTTCACACGCAAACTTATATAATGGTGGTTCCTACAACTGCTCCTCCCACTCTTTCCactccc-----------------tctgctgctgcttatgctgcttctgtgctgt-gctttctATCCATCTGG-CGGGT---------------------------------GCATATgaaatttttcacatttttcaaataGA-C-TTCTTT-------GGCCTCA------------------------AA----CCGAGcctcgatccgatccgaaccga-----a--------------ccgaaccg--aa-caccCGATCAAAATCAGAC------ACAAAAACCATCAACATTGCGGCGCTAAATCACGATCCCAGCACGATCTTTGC-------------------------------------------------CAA------AGACAC-------------------------A-----------AAAtcttatgaaatattt--gacC-CAAGTC-gggggggggaaaa s droWil2.CH963894 1302549 267 + 2843958 TTTGGCTTTGGCATT---------------------------------------------------------------------------------TTCAAATGAACAGTTTTCACacgcaaaaaaaga-aaca-------------------------------ccgaaaaa-----------------ataac---------------------------------------------aactt---------------------------------GCATATGAAATCCTTAGCATTTTTCACATACA-TAGACTCT-------GATCACT------------------------G------------------------------------G--------------ACGATCAC--AA--TGCCGATCAAAATCCC----------AAAAATCGTTGTCGCCGCTGTCTTAAATCACGATCTCAGCACGATCTTTGG-------------------------------------------------CAACCCCGCAAacacacaccaaaaaaaaaaaaaacaaaaaa-----------aaatcttatgAAATATTT--GACC-CAAGCA------------AA s droVir3.scaffold_12875 7346335 241 + 20611582 TT--GCCTT----CT---------------------------------------------------------------------------------TTCAACTGACCAATTTTCACACGCAAACTTACATAATG----------------------------------------------------------------TGC-------------------C-GCTT--------------GGCTC---------------------------------GCATATGAAATGCTTAACA-TTTTTAAATAGA-C-TTC-TT-------GGCCTCA------------------------AAGTCGCTACG--------------------------A--------------TCAAAATA--CA-ACAAAAAAAAAACAGGGAA--------AAAAATGGAAAAATCGCCAGCGCTAAATCACGATCTCAGCACGATCTTAAC-------------------------------------------------TAC------A---AC-------------------------A-ACAACAGCAAAAATCTTATGAAATATTTTGGTTT-CAAA---------------- s droMoj3.scaffold_6496 26141346 299 + 26866924 TT--TGTTG----CT---------------------------------------------------------------------------------TTCAAATGACCAATTTTCACACGCAAACTTACATAATG----------------------------------------------------------------CGC-------------------C-GCTT--------------AGCTC---------------------------------GCATATGAAATGCTTAACA-TTTTTAAATAGA-C-TCC-TT-------GGCCTCA------------------------AAGTCGCTGCG--------------------------A--------------TCAAAACA--CA-ACAACAACAACACTGAAAAAGACTAGCAAAAATGGGAAACTCGCCAGAGTTAAATCACGATCTCAGCACGATCTTAACACAGGCACAGCTAGCCAAATCTTATGAAATATTTTCGTTTCAAACGAGACAC------A---AT-------------------------GTAAAAAGGAAAAAATCTTGTAAGTTCTCTTCGGCT-CGGT---------------- s droAlb1.JH854640 304899 347 + 406291 TT--GCctc----ctctctgctctgctctgctctctctcctcCTTTACCTGGAACAGTTCAGTGCTTACAAATAGTAAGACTCTTGGATTTTCTTCTTCAAATGACCAATTTTCACACGCAAGCTTACATAATG----------------------------------------------------------------GCC-------------------C-GTTC--------------GGGTCTTGggctcagtctcagtctcagttcgGGCCGCGACATATGAAatgcttaacatttttttaaaaga-c-TTCTTT-------GGCCTCA------------------------AAGTTGCTGCG--------------------------A--------------TCAccgca--aa-aaaccaaaaaaaaataaag------tcaaaaatCGCCAGCT--TCAGCGCTAAATCACGATCTCGCCACGATCCGAGC-------------------------------------------------TAC------A---AC-------------------------A-----------Aaagtttatgaaatattttccaca-aaaa---------------- s droGri2.scaffold_15245 894527 238 + 18325388 TT--GCTTT----TT---------------------------------------------------------------------------TTTTATTTCAAATGACCAATTTTCACACGCAAACTTACATAATG----------------------------------------------------------------CGC-------------------CTGCTT--------------GGCTC---------------------------------GCATATGAAATGCTTAACA-TTTTTAAATAGA-C-TTC-TT-------GGCCTCA------------------------AAGTCGCTACG--------------------------A--------------TCAAAAAA--TA-ACACAACAACAACACAAAC--------AACAAACAGAAAATCGCCAGCGCCAAATCACGATCTCAGCACGATCTTAAC----------------------------------------------------------A---GC-------------------------G---------AAAAATCTTATGAAATATTTTTGCTTAAAAA---------------- a score=21813.000000 s dm6.chr2R 24345768 4 + 25286936 CCAA- s droSim1.chr2R 18692505 4 + 19596830 CCAA- s droSec1.super_23 112272 4 + 989336 CCAA- s droYak3.chr2R 20201320 4 + 21139217 CCAA- s droEre2.scaffold_4845 21599339 4 + 22589142 CCAA- s droBia2.KB462602 791373 4 + 3129309 CCaa- s droSuz1.KI419649 12036496 4 - 14502029 CCAA- s droAna3.scaffold_13266 5706934 4 - 19884421 CCAA- s droBip2.KB464407 1955721 4 + 2915140 ccaa- s droEug2.KB465067 596459 4 + 1515531 ccaa- s droEle2.KB458573 516780 4 - 5320397 ccaa- s droKik2.KB459527 271682 4 - 1234237 CCAA- s droTak2.KB461535 136372 4 - 669855 CCAA- s droRho2.KB449310 30178 4 - 65043 ccaa- s droFic2.KB457177 76626 4 + 995874 ccaa- s droPse3.chr3 1344977 4 - 19787792 caaa- s droPer1.super_34 533852 4 - 916997 CAAA- s droMir2.chr3 1386064 4 - 20862834 caaa- s droVir3.scaffold_12875 7346576 4 + 20611582 -CGAG s droMoj3.scaffold_6496 26141645 4 + 26866924 -TAAT s droAlb1.JH854640 305246 4 + 406291 -ggaa s droGri2.scaffold_15245 894765 4 + 18325388 -CGAG a score=-28082.000000 s dm6.chr2R 24345772 6 + 25286936 AAACAA--------------------- s droSim1.chr2R 18692509 6 + 19596830 AAACAA--------------------- s droSec1.super_23 112276 6 + 989336 AAACAA--------------------- s droYak3.chr2R 20201324 6 + 21139217 AAACTA--------------------- s droEre2.scaffold_4845 21599343 6 + 22589142 AAACAA--------------------- s droBia2.KB462602 791379 6 + 3129309 aaacaa--------------------- s droSuz1.KI419649 12036502 6 - 14502029 AAACAA--------------------- s droBip2.KB464407 1955725 6 + 2915140 aaaaaa--------------------- s droEug2.KB465067 596464 5 + 1515531 aaaca---------------------- s droEle2.KB458573 516790 6 - 5320397 aaacaa--------------------- s droKik2.KB459527 271687 6 - 1234237 AAACCA--------------------- s droTak2.KB461535 136378 6 - 669855 AAACAA--------------------- s droRho2.KB449310 30184 6 - 65043 aaacaa--------------------- s droFic2.KB457177 76632 6 + 995874 aaacaa--------------------- s droPse3.chr3 1344981 6 - 19787792 aaacag--------------------- s droPer1.super_34 533856 6 - 916997 AAACAG--------------------- s droMir2.chr3 1386068 6 - 20862834 aaacag--------------------- s droVir3.scaffold_12875 7346580 3 + 20611582 -----AC-------------------A s droMoj3.scaffold_6496 26141649 22 + 26866924 -----ACCCTCGCCAAAGGCAATGTGG s droAlb1.JH854640 305250 19 + 406291 -----aa---acttcAAGTTGGCCTCG s droGri2.scaffold_15245 894769 4 + 18325388 -----AC------------------AA a score=22875.000000 s dm6.chr2R 24345778 41 + 25286936 AGACGTTGGAGCACTTAAATTTAAAA-----------GGGGAG-ATTT----------GGGAA---------------- s droSim1.chr2R 18692515 41 + 19596830 AGACGTTGGAGCTCTTAAATTTAAAA-----------GGGGAG-ATTT----------GGGAA---------------- s droSec1.super_23 112282 41 + 989336 AGACGTTGGAGCTCTTAAATTTAAAA-----------GGGGAG-ATTT----------GGGAA---------------- s droYak3.chr2R 20201330 41 + 21139217 AGACGTTGCAGCGCTTATATTTTAAA-----------Ggggat-attt----------aagaa---------------- s droEre2.scaffold_4845 21599349 41 + 22589142 AGTCGTTGCAGCTCTTAAATTTAGGA-----------GGGGAT-ATTT----------GAGAA---------------- s droBia2.KB462602 791385 38 + 3129309 aaacg---aaGCTCTAAAATGTAAAG-----------ggggaa-tttt----------aaaaa---------------- s droSuz1.KI419649 12036508 41 - 14502029 AAACGTACGAGCTCTTAAAATCAAAA-----------ggggaa-tata----------aaaaa---------------- s droEug2.KB465067 596469 42 + 1515531 aaacgtaggagctcgaaaatttaaaa-----------agggaatattt----------aaaca---------------- s droEle2.KB458573 516796 41 - 5320397 aatcgtaGGAGCTCTAAAAATCAAGA-----------GGTGAA-TGTT----------TTGCA---------------- s droKik2.KB459527 271696 41 - 1234237 CGTTGTaggagctttaaaaaaaaatg-----------tacaaa-atat----------ttaag---------------- s droTak2.KB461535 136384 41 - 669855 AAACGTACGAgctctaaaatttaaaa-----------ggagaa-tatt----------tggaa---------------- s droRho2.KB449310 30190 42 - 65043 aaacgtAGGAGCTCTACAATTGAAAA-----------GTTGAATGTTT----------TGCAA---------------- s droFic2.KB457177 76638 41 + 995874 aaacgtAGGAGCTCTAAAACCACAAA-----------GGTGAA-TATA----------TTGTC---------------- s droPse3.chr3 1344991 41 - 19787792 cgctgctgcagctccaaaaatgaaag-----------gcaaaa-aCAT----------TGGGG---------------- s droPer1.super_34 533866 41 - 916997 CGCTGCTGCAGCTCCAAAAATGAAAG-----------GCAAAA-ACAT----------TGGGG---------------- s droMir2.chr3 1386078 41 - 20862834 cgctgctgcagctccaaaaatgaaag-----------gcaaaa-acaT----------TGGGG---------------- s droVir3.scaffold_12875 7346583 30 + 20611582 ----------------AAATGTGAAA-----------AGGAAA-AACT----------CTAAAGTTGG----------- s droMoj3.scaffold_6496 26141671 51 + 26866924 ----------------GGGCGTGGAA-----------GCAAAT-AAATGATCTGGCGACTAGAATTGGGAATGTTATCA s droAlb1.JH854640 305269 52 + 406291 ----------------AAGTGTGTTGTTTTTTAGCTTGgttga-aatt----------tttatattgagtACGTGGGTG s droGri2.scaffold_15245 894773 25 + 18325388 ----------------AAATTTAAAA-----------AGGAAA-AACT----------CGAAA---------------- a score=-437113.000000 s dm6.chr2R 24345819 55 + 25286936 AA------------------CGT--TTAGCTTGT-TGTACGCT-------AG-------------------AA------TGGC--AATAA--AA-------------------------------------------------------------------------------------TGTCAAGTA--------------------------TAAACTAAA s droSim1.chr2R 18692556 55 + 19596830 AA------------------CGT--TTAGCTTGT-TGCACTCT-------AG-------------------AA------TGGC--AACAA--AA-------------------------------------------------------------------------------------TGTCAAGTA--------------------------TAAACTCTA s droSec1.super_23 112323 55 + 989336 AA------------------CGT--TTAGCTTGT-TGCACTCT-------AG-------------------AA------TGGC--AACAA--AA-------------------------------------------------------------------------------------TGTCAAGTA--------------------------TATAGTCAA s droYak3.chr2R 20201371 55 + 21139217 aa------------------tgc--TAAGCTTGA-TATACTCT-------AG-------------------AA------TGGC--ACTTA--AA-------------------------------------------------------------------------------------TGTGAAGCT--------------------------TGCAATCAA s droEre2.scaffold_4845 21599390 55 + 22589142 AA------------------TGT--TAAGCTTGA-TATACTCT-------AG-------------------AA------TGGC--AATCC--AA-------------------------------------------------------------------------------------TGTGTAGCC--------------------------TAAAATCAA s droBia2.KB462602 791423 111 + 3129309 ag---------------agctTT--GACGTTACA-AGTGCTCT------AAG-------------------AA------CAGG--ACTAG--AAGTAATGGTAT------------------------------------------------------AACC-AAAAATTACCTT----TGTTAGTTTCacaaattgttttatgttCCGCAAAATGAATTAAG s droSuz1.KI419649 12036549 165 - 14502029 agttta-----------aacttt--aaagctTTA-AGTACACT------CAG-------------------AA------TAGG--ATTAG--aagtaataatatatatatcaagaacatatttttttgctttataGATACTTTTAGATTTTGTAAAACAACCAAAAGATGCCCTTAAAGTGGTAGATACCTTCTTAGTTTCCATT---------Cgtagtaaa s droEug2.KB465067 596511 62 + 1515531 aa------------------agc--ttaaactta-aatactttgGGAAAATG-------------------AA------TAGC--AAAAT--CG-------------------------------------------------------------------------------------AGTAAAACA--------------------------TAAATTGAA s droEle2.KB458573 516837 76 - 5320397 AA------------------AAC--GAAGTTTTC-AATACCCT-------AgatgaataaatattgtaGATAA------TTGC--AGATA--AA-------------------------------------------------------------------------------------CAGAAGACaga------------------------taaaaagaa s droKik2.KB459527 271737 57 - 1234237 aa------------------atc--gAATTAGGA-AATACTCT-------TG-------------------AA------AAGT--ATTAGTTAA-------------------------------------------------------------------------------------AATAggctt--------------------------taaagtatt s droTak2.KB461535 136425 53 - 669855 aa-------------------aa--aaaatgtca-agtACTTT--------A-------------------CT------Tggc--aatag--aa-------------------------------------------------------------------------------------aatgtagca--------------------------gaaaataaa s droRho2.KB449310 30232 56 - 65043 AA------------------AAC--GAAGTTTTA-AATACCCT-----CGAT-------------------AA------TGAT--A-TAG--AT-------------------------------------------------------------------------------------AATTggata--------------------------taaaacaaa s droFic2.KB457177 76679 44 + 995874 AG------------------TCC--GAAGTTTAA-AGTactct----------------------------aa------ttaa--a------aa-------------------------------------------------------------------------------------tacagaaaa--------------------------tagA----- s droPse3.chr3 1345032 34 - 19787792 GC------------------AAC--GAATTTTGG-AATACCCT------TTG-------------------TA------TACC--GAA--------------------------------------------------------------------------------------------------------------------------------------- s droPer1.super_34 533907 34 - 916997 GC------------------ATC--GAATTTTGG-AATACCCT------TTG-------------------TA------TACC--GAA--------------------------------------------------------------------------------------------------------------------------------------- s droMir2.chr3 1386119 34 - 20862834 GC------------------AAC--GAATTTTGG-AATACCCT------TTG-------------------TA------TACC--GAA--------------------------------------------------------------------------------------------------------------------------------------- s droVir3.scaffold_12875 7346632 59 + 20611582 --CTTGCCTAACTGGGTGTGTGTGGGTGTCTCATCAGAGAGCT--------A-------------------AGCACAGCTGAT--ACG-A--A---------------------------------------------------------------------------------------------------------------------------------- s droMoj3.scaffold_6496 26141746 61 + 26866924 --AAGAATTTATTGGGTCAATTT--TTATTTCTTCAATTAATT-------AA-------------------AATATATGTGATTAACGTA--A---------------------------------------------------------------------------------------------------------------------------------- s droAlb1.JH854640 305345 48 + 406291 --AATATTAGATTGCTTGA------CTATTACAT-AATAACTT-------GA-------------------AA------TGAT--AAGCG--A---------------------------------------------------------------------------------------------------------------------------------- a score=-9772.000000 s dm6.chr2R 24345874 2 + 25286936 TG s droSim1.chr2R 18692611 2 + 19596830 TG s droSec1.super_23 112378 2 + 989336 TG s droYak3.chr2R 20201426 2 + 21139217 GA s droEre2.scaffold_4845 21599445 2 + 22589142 GG s droBia2.KB462602 791534 2 + 3129309 AA s droSuz1.KI419649 12036714 2 - 14502029 aa s droEug2.KB465067 596573 2 + 1515531 TC s droEle2.KB458573 516913 2 - 5320397 ta s droKik2.KB459527 271794 2 - 1234237 tt s droRho2.KB449310 30289 2 - 65043 tg s droFic2.KB457177 76724 1 + 995874 T- s droPse3.chr3 1345066 1 - 19787792 -G s droPer1.super_34 533941 1 - 916997 -G s droMir2.chr3 1386153 1 - 20862834 -G s droVir3.scaffold_12875 7346691 2 + 20611582 TA s droMoj3.scaffold_6496 26141807 2 + 26866924 TG s droAlb1.JH854640 305393 2 + 406291 Cg a score=-805893.000000 s dm6.chr2R 24345876 89 + 25286936 T-----------TTAATAAGTTTA--------ATTTATTTACTG--AAGTT--------------TATTTAC-TTTCATT------A-TTAAGTCGCAAAG-TAAC-----TTATGATT---------CTTG-------------------AATTAG------------AGGAAGTGA s droSim1.chr2R 18692613 100 + 19596830 T-----------TTAATAACTCCA--------ATTTATTTACTG--AATTTACTCCCTCAGAAACTAGATTC-TTTTATC------A-TTAGGTCGCAAAG-TAACCTA--TTATGATT---------CTTG-------------------GATTAG------------AGG------ s droSec1.super_23 112380 86 + 989336 -------------------CTTTA--------ATTTATATACTA--AAGATACTCTTTCAGAAAGTAGATTC-TTTCATT-------------------AG-TAACTTA--TTATGATT---------CTTG-------------------AATTAG------------AGGAAGTGT s droYak3.chr2R 20201428 73 + 21139217 C-----------TAAAACACATCA--------ATT------------------------------TAGATTC-CTGCA------------AAGCCGCAAAG-TAATTAA--GTATGATT---------GCGT-------------------AGTTTA------------AAATGGCTT s droEre2.scaffold_4845 21599447 68 + 22589142 G-----------AAAAATACATAA--------ATT------------------------------TACATTC-TTACA------------AAGCCACAAAG-TAATTAG--GTATGGTT---------CCGT-------------------AATTCA------------AAAC----- s droBia2.KB462602 791536 135 + 3129309 TGTGTGTTTAGAGTATAATGAGCC--------gtt-ttttaatagtaaaagtaaaaaaatacattttaatgcattttgtt----------AATTCACAAATACAATGTG--TTATCATTTGCGGATGCTTT----------------------TTAGAGTAATAGTAGTAGACAGTCT s droSuz1.KI419649 12036716 109 - 14502029 tatatatacatattaagAAGCTca--------attaatttgcta--aatagtTTATTACTATTTGCAGATGC-TTTCATT----------A---tgcaaagaaaatgtt--ttatcatt---------ttt----------------------taag------------agGCAAATT s droEug2.KB465067 596575 56 + 1515531 G--------------------TTA--------GTTTGGTCTTTA--AATA------------------ATGG-TTACAGC------T-GTAGGatactaaataaatatc--tta---------------------------------------------------------------- s droEle2.KB458573 516915 97 - 5320397 aataaaacaaggtGCAGCATAtga--------actttgttttaa-----------------------aattc-tttaact------a-AAGAAAAGTTGAGTTGATTGAGTTTATGagt-----------tt-------------------aataga------------aaaaaatgt s droKik2.KB459527 271796 80 - 1234237 t------------------tttta--------gttttaataatg--------------cttatttgggattt-ttccata------t-tttgtaTCCTTAG-AAAT--A--GTGTCACA---------ACAT-------------------AACCAG------------AAGT----- s droTak2.KB461535 136748 96 - 669855 ---TGTctcaaaaatgtaatatta--------attatgGTTTCT---------------------TAGATTT-CATTATG------A-TTATTAGATTATGGTGATTTC--TTAGACTG---------TGTA-------------------AAAATA------------AGACTAAAT s droRho2.KB449310 30569 109 - 65043 ------------tttaaaaggccG--------AAtagacttttt---------------------taaaaac-tttgaaactaaaca-aaaacttaCACAG-TTATATG--TTA-Gatt---------ctttacatttttaaagacttaaaaaataa------------acataagc- s droFic2.KB457177 76725 101 + 995874 ------------TCAAAGaagtga--------attttaattatt-------gattttgcatTCTGTCGATAT-TTTTAGA------ACCTCTTTAGTTAAG-TAAAAGT--ATGTGAGT--TGGGTGCTATT-------------------AACCAA------------AC------- s droPse3.chr3 1345068 66 - 19787792 ---------------CGTATCCTA--------ACTGACATTCCC--------TTTTCGTCTGTACCAAAATA-TTTGACC------C-CTGGGACACATCA-GATC------------------------------------------------------------------------ s droPer1.super_34 533943 66 - 916997 ---------------CGTATCCTA--------ACTGACATTCCC--------TTTTTGTCTATACCAAAATA-TTTGACC------C-CTGGGACACATCA-GATC------------------------------------------------------------------------ s droMir2.chr3 1386155 66 - 20862834 ---------------CGTATCCTA--------ACTGACATTCCC--------TTTTCGTCtataccaaaata-tttgaCC------C-CTGGGACACATCA-GATC------------------------------------------------------------------------ s droVir3.scaffold_12875 7346693 78 + 20611582 ---TTACCTAAGC--AGGATTTCA-------------------------AGGAAATGTCTT----GAAATTT-CATTATA-ATGTAA-TTTAGTCTTTAAG--ATTGGA--TAAAGTTA----------------------------------------------------------- s droMoj3.scaffold_6496 26141809 108 + 26866924 ---TTACTCGATCCAAGAATTCTAATCCCGGCACTTACTGTATG--AGTAACAAATACCTCCTGAGCAATTA-GATCAAATATTTAC-CTTGAACACAATA--GCTAAG--GAATGTTG----------------------------------------------------------- s droAlb1.JH854640 305395 101 + 406291 ---tgaaaaaaactaaagcttTCT---CGTAAACTGATTAATTG--ATCAGCTACTAATC-----GCAGTAA-GAACAATGAtcgca-tttgtatttattg-tatttga--aagtataa----------------------------------------------------------- a score=-25658.000000 s dm6.chr2R 24345965 12 + 25286936 G--------------CAACCCAAACC----------------- s droSec1.super_23 112466 12 + 989336 T--------------TATCCCAAACT----------------- s droYak3.chr2R 20201501 12 + 21139217 T--------------GAGTTAATGCA----------------- s droEre2.scaffold_4845 21599515 8 + 22589142 ------------------TTAAAACT----------------- s droBia2.KB462602 791671 13 + 3129309 T-------------AGATTCTGTATT----------------- s droSuz1.KI419649 12036825 13 - 14502029 T-------------AGATTCTGTAGT----------------- s droEle2.KB458573 517012 26 - 5320397 ttgtttaattttatatattcaagagt----------------- s droTak2.KB461535 136844 1 - 669855 T------------------------------------------ s droMoj3.scaffold_6496 26141917 22 + 26866924 ---------------------GCATCTCTTTGGGTTAATCAAC a score=-315117.000000 s dm6.chr2R 24345977 70 + 25286936 TGT------------------------TAAACTGTTCCTC-----TT----------------TAC--------------------------------CCAATCTCAG-TTGATCCCGAAA-----------TGGTGTTTCCTTATC------GGTGAGGGTATC s droSim1.chr2R 18692713 66 + 19596830 ----------------------------AAACTGTTCCTC-----TT----------------TAT--------------------------------CCAATCTCAT-TTGATCCCGAAA-----------TGGTGTTTCCTTATC------GATGAGGGTATC s droSec1.super_23 112478 70 + 989336 GGT------------------------TAAACTGTTCCTC-----TT----------------TAC--------------------------------CAAATATCGT-TTGATCCCGAAA-----------TGGTGTTTCCTTATC------GATGAGGGTATC s droYak3.chr2R 20201513 91 + 21139217 TCCA-----------------------CGACTTGATTCCC-----TTATGAA--AGCGCTCAGTAC--------------------------CCGTAGCCGATCTCAT-TTGGTCCCGAAT-----------TGGTGCTGGCTCATC------GGTGAGGGTATC s droEre2.scaffold_4845 21599523 84 + 22589142 TCC------------------------TGAATTGTTTCGC-----CTATGAA--AGCGCCCAGTAC--------------------------------CCAATCTCAT-TTGATCCCGAAA-----------TGGTGTTTCCTTATC------GGTTAGGGTATC s droBia2.KB462602 791684 112 + 3129309 TCCACCACAAAGTAAGACATTGGGTGATCGATTTCtcctt-----ttttaaa--gcaatttagcAC--------------------------TTAGT-CAAAGGTTAT-TGGGTGCCAAAA-----------TGGCATTGCTTCATC------GG-TAGGGTATC s droSuz1.KI419649 12036838 103 - 14502029 TGCACCGCAACTTTACACATAAGGTGCTAGATTTATTC-----------------CACTTCAGCAC--------------------------TTATT-CAAAGGTTAT-TTGATACCAAAA-----------AGGCATTGCTTCATC------GGTTAGGGTATC s droBip2.KB464407 1955731 61 + 2915140 -----------------tgttagctGGTAGCTTGTACCCT-----------------------TAC--------------------------------CATgtatcct-t------------------------gtttttttttatt------tttttggtaat- s droEug2.KB465067 596631 55 + 1515531 --------------------------------------------------------------------------------------------CTTTTGCAAAAGTCAT-TTGATCCGAAAG-----------TGGTATTACTCCGTC------GGTTAGGGTATC s droEle2.KB458573 517050 83 - 5320397 -------------------------tgtaaact----------------aaa--gGAACTTAGTTA--------------------------------TTATACtcct-taaatttataaaaatgagtCTTTAGGCCTTACTTTAAT------GTTTAGGGCATC s droKik2.KB459527 271876 68 - 1234237 ------------------------TCGTACCCTATTCTTTCAT-TTTACAAA--GTAAGCCAGCTC--------------------------------CCTACATCCC-CCATTACCAAAA-------------------------------------GGGTATC s droTak2.KB461535 136845 102 - 669855 -------------TATTCGTCAGGTTTTAGATTCTGTATT-----TTTCTAGTTTCTCTttatcat--------------------------ttttt-caaaggTTAT-TTGATACCAAAA-----------TGGCATTACTTCGTC------GGTTAGAGTATC s droRho2.KB449310 30678 83 - 65043 --------------------------tTACACAGAtcctttgtatttattaa--aatcgccA------------------------------------GAAGAGGTAT-TTGATCTGAAAG-----------AGGTATTACTTTATC------GGTTAGGGcatc s droFic2.KB457177 76826 64 + 995874 --------------------------------------------------------ACTTTGACAC--------------------------TTTTT-CAAGGGTTAT-TTGATCCCAAGG-----------AGATATTACCTCGTC------AGTTAGGGTATC s droPse3.chr3 1345134 39 - 19787792 --------------------------------------------------------------------------------------------TCTTGacc-----------ggtc-----------------tggtctggtctggtc------acTCATGTCGTT s droPer1.super_34 534009 49 - 916997 --------------------------------------------------------------------------------------------TCTTGACCggtctcgt-ctggtc-----------------tggtctggtctggtc------ACTCATGTCGTT s droMir2.chr3 1386221 49 - 20862834 --------------------------------------------------------------------------------------------TCTTGaccggtctggt-ctggtc-----------------tggtctggtctggtc------acTCATGTCGTT s droMoj3.scaffold_6496 26141939 90 + 26866924 ---------------------------------------------------------------TGTTAAACGAAATTCATATAATAAGACAAATATT-TAGCATCTGCATCTATCCGAAAG-----------AAGAGCTTACGAATATGATTCGGTGCGAGCGCA s droAlb1.JH854640 305496 38 + 406291 --------------------------------------------------------------------------------------------atact-tgaaatatGT-TTGACCCCAAA---------------------------------GTTGTGAGTTTC a score=76882.000000 s dm6.chr2R 24346047 25 + 25286936 CAAAACATTTGACCCCTGGGACG------------------TG-------------------------- s droSim1.chr2R 18692779 25 + 19596830 CAAAACATTTGACCCCTGGGACG------------------TG-------------------------- s droSec1.super_23 112548 25 + 989336 CCAAACATTTGACCCCTGGGACG------------------TG-------------------------- s droYak3.chr2R 20201604 41 + 21139217 CAAAACATTTGACCCCTGGGACGTGGATTCTCGA--GTTCTCG-------------------------- s droEre2.scaffold_4845 21599607 25 + 22589142 CAAAACATTTGACCCCTGGGACG------------------CG-------------------------- s droBia2.KB462602 791796 25 + 3129309 CAAAACATTTAACCCCTGGGACG------------------TG-------------------------- s droSuz1.KI419649 12036941 25 - 14502029 CAAAACATTTGACCCCTGGGACG------------------TG-------------------------- s droAna3.scaffold_13266 5707016 25 - 19884421 CATAATATTTGACCCCTGGGAGG------------------CA-------------------------- s droBip2.KB464407 1955792 22 + 2915140 ---aatATCTGACCCCTGGGATG------------------TA-------------------------- s droEug2.KB465067 596686 25 + 1515531 CCAAACATTTGACCCCTGGGACG------------------TG-------------------------- s droEle2.KB458573 517133 25 - 5320397 CAAAACATTTGACCCCTGGGACG------------------TG-------------------------- s droKik2.KB459527 271944 28 - 1234237 CATAATATTTGACCCCTGGGACG---------------ACAAA-------------------------- s droTak2.KB461535 136947 25 - 669855 CAAAACATTTGACCCCTGGGACG------------------TG-------------------------- s droRho2.KB449310 30761 25 - 65043 caaaatatttgacCCCTGGGACG------------------TG-------------------------- s droFic2.KB457177 76890 25 + 995874 CGCAATACTTGACCCCTGGGACG------------------TG-------------------------- s droPse3.chr3 1345173 5 - 19787792 --------------------------------------CTTTG-------------------------- s droPer1.super_34 534058 5 - 916997 --------------------------------------CTTTG-------------------------- s droMir2.chr3 1386270 5 - 20862834 --------------------------------------CTTTG-------------------------- s droMoj3.scaffold_6496 26142033 69 + 26866924 TAAAATATTTGACCCGAGAGATACGAGTTTGCTGCTGACTTTGTGGCGACTCCTCCTCATGTTGCAGTG s droAlb1.JH854640 305538 32 + 406291 CAGGATTGCTGACT----------------------Gcttctgcagca---------------gcaatt a score=26903.000000 s dm6.chr2R 24346072 3 + 25286936 GA---T s droSim1.chr2R 18692804 3 + 19596830 GG---T s droSec1.super_23 112573 3 + 989336 GG---T s droYak3.chr2R 20201645 3 + 21139217 GG---T s droEre2.scaffold_4845 21599632 3 + 22589142 GG---T s droBia2.KB462602 791821 3 + 3129309 GG---C s droSuz1.KI419649 12036966 3 - 14502029 GG---T s droAna3.scaffold_13266 5707041 3 - 19884421 GG---C s droBip2.KB464407 1955814 6 + 2915140 GGCTTC s droEug2.KB465067 596711 3 + 1515531 GG---T s droEle2.KB458573 517158 3 - 5320397 GG---C s droKik2.KB459527 271972 3 - 1234237 GG---T s droTak2.KB461535 136972 3 - 669855 GG---T s droRho2.KB449310 30786 3 - 65043 GG---C s droFic2.KB457177 76915 3 + 995874 GG---C s droPse3.chr3 1345178 3 - 19787792 GG---T s droPer1.super_34 534063 3 - 916997 GG---T s droMir2.chr3 1386275 3 - 20862834 GG---T s droMoj3.scaffold_6496 26142102 3 + 26866924 GT---T s droAlb1.JH854640 305570 3 + 406291 gt---t s droGri2.scaffold_15245 895301 3 + 18325388 GA---C a score=-71619.000000 s dm6.chr2R 24346075 13 + 25286936 TCTC-----------------------GGGG-CCG-AG s droSim1.chr2R 18692807 13 + 19596830 TCTC-----------------------GGGG-CCG-AG s droSec1.super_23 112576 13 + 989336 TCTC-----------------------GGGG-CCG-AG s droYak3.chr2R 20201648 14 + 21139217 TCTC----------------------GGGGG-CCG-AG s droEre2.scaffold_4845 21599635 14 + 22589142 TCTC----------------------GGGGG-CCG-AG s droBia2.KB462602 791824 36 + 3129309 TCCCCC-ACCCGAGATTGAGGTTCTCGGATG-CCGAAA s droSuz1.KI419649 12036969 36 - 14502029 TCCCCC-ACCCGAGATTGTGGTTCTCGGGGG-CCGAAA s droAna3.scaffold_13266 5707044 28 - 19884421 TCCA---------GATTTCTGCTCTCGAAGA-CCCAAA s droBip2.KB464407 1955820 14 + 2915140 TCCT---------GATTTCTG---------------GA s droEug2.KB465067 596714 35 + 1515531 TAGCCC-GCTCGGGATTGTGGTTCTCGGGGG-CCA-AA s droEle2.KB458573 517161 36 - 5320397 TCGCCCAACTCGAAATTGTGGTTCTCGGGGG-CCA-AA s droKik2.KB459527 271975 30 - 1234237 TCTC------CTCCTTGCTTGTTCTCGGGGG-CCA-AA s droTak2.KB461535 136975 35 - 669855 TCCC--CGTTCGCAATTGTGGTTCTCGGGGG-CCGAAA s droRho2.KB449310 30789 36 - 65043 TCCCCCGACTGTGGATTGTGGTTCTCGGGGG-CCA-AA s droFic2.KB457177 76918 36 + 995874 TCTGCCAGCTTGAGATTGTGGTTCTCGGGGG-CCG-AA s droPse3.chr3 1345181 18 - 19787792 CCCT------------------TCCTGGGGG-CCG-GA s droPer1.super_34 534066 18 - 916997 CCCT------------------TCCTGGGGG-CCG-GA s droMir2.chr3 1386278 18 - 20862834 CCCT------------------TCCTGGGGG-CCG-GA s droVir3.scaffold_12875 7347155 13 + 20611582 -----------------------TTTGGGGGCCCT-A- s droMoj3.scaffold_6496 26142118 12 + 26866924 -----------------------TTTGGGGG-CCT-A- s droAlb1.JH854640 305586 12 + 406291 -----------------------tttGGGGC-CCT-A- s droGri2.scaffold_15245 895304 13 + 18325388 -----------------------TTTGGGGGCCCT-A- a score=1773453.000000 s dm6.chr2R 24346088 151 + 25286936 CTTATGACAGGCGCACG-CCC-------GG--GACAAAAGGCCGCT-------TC----CATA------ATATGCGTTCC-------AAAAAA-------------------ATA---------------------TCGTTTTGGTGACTTTGATG-C--GGTCCCTCATCG-------A---------TGTCCAGCC-------------G-G---CGGACAGTTGACAGGC----AGACAATGGGATTTT-GA---CTTGGCGCTA---C s droSim1.chr2R 18692820 151 + 19596830 CTTATGACAGGCGCACG-CCC-------GG--GACAAAAGGCCGCT-------TC----CATA------ATATGCGTTCC-------AAAAAA-------------------ATA---------------------TCGTTTTGGTGACTTTGATG-C--GGTCCCTCATCG-------A---------TGTCCAGCC-------------G-G---CGGACAGTTGACAGGC----AGACAATGGGATTTT-GA---CTTGGCGCTA---C s droSec1.super_23 112589 151 + 989336 CTTATGACAGGCGCACG-CCC-------GG--GACAAAAGGCCGCT-------TC----CATA------ATATGCGTTCC-------AAAAAA-------------------ATA---------------------TCGTTTTGGTGACTTTGATG-C--GGTCCCTCATCG-------A---------TGTCCAGCC-------------G-G---CGGACAGTTGACAGGC----AGACAATGGGATTTT-GA---CTTGGCGCTA---C s droYak3.chr2R 20201662 158 + 21139217 CTTATGACAGGCGCACG-CCC-------GG--GACAAAAGGCCGCT-------TC----CATA------ATGTGCGTTccaagtacaaaaaaa-------------------ata---------------------tcgttTTGGTGACTTTGATG-C--GGTCCCTCATCG-------A---------TGTCCAGCC-------------G-G---CGGACAGTTGACAGGC----AGACAATGGGATTTT-GG---CTTGGCGCTA---C s droEre2.scaffold_4845 21599649 151 + 22589142 CTTATGACAGGCGCACG-CCC-------GG--GACAAAAGGCCGCT-------TC----CATA------ATATGCGTTCC-------AAAAAA-------------------ATA---------------------TCGTTTTGGTGACTTTGATG-C--GGTCCCTCATCG-------A---------TGTCCAGCC-------------G-G---CGGACAGTTGACAGGC----AGACAATGGGATTTT-GA---CTTGGCGCTA---C s droBia2.KB462602 791860 147 + 3129309 CTTATGACAGGCGCACG-CCC-------GG--GACAAAAGGCCGCC-------TC----TATA---------TGcgttcc--------aaaaa-------------------ata---------------------tcattttggTGACTTTGATG-C--GGTCCCTCATCG-------A---------TGTCCAGCC-------------G-G---CGGACAGTTGACAGGC----AGACAATGGGACCTC-GG---CTTGGCGCTA---C s droSuz1.KI419649 12037005 149 - 14502029 CTTATGACAGGCGCACG-CCC-------GG--GACAAAAGGCCGCC-------TC----TATA---------TGcgctcc------aaaaaaa-------------------ata---------------------tcattttggTGACTTTGATG-C--GGTCCCTCATCG-------A---------TGTCCAGCC-------------G-G---CGGACAGTTGACAGGC----AGACAATGGGATTTC-GA---CTTGGCGCTA---C s droAna3.scaffold_13266 5707072 150 - 19884421 CTTATGACAGGCGCACA-CCC-------GA--GAC-------TGC--------------TGTT------TTTTGCCTTTC------AGGAATA-------------------ATA---------------------TCGATTTGGTGACTTTGATGTC--CATCCCTCATCGCTGTCCCA---------TGTCCAGAC-------------A-C---TGGACACTTGACGGGC----AGACAATGGCCAGGC-GA---GTTGGCGCTT---C s droBip2.KB464407 1955834 158 + 2915140 CTTATGACAGGCGCACG-CCC-------GA--GACA------TGcc-------tcgatttttt------ttttgtatttc------tggAATA-------------------ATA---------------------TCGATTTGGTGACTTTGATG-C--GGTCCCTCATCGCTGTCCAA---------TGTCCAGAG-------------ATC---CAGACACTTGACAGGC----AGACAATGGGATTGC-AA---GTTGGCGCTT---C s droEug2.KB465067 596749 148 + 1515531 CTTATGACAGGCGCACG-CCC-------GG--GACAAAAGGCTGCC-------TC----TATA---------TGCGTTCC-------aaaaaa-------------------aTA---------------------TCGTTTTGGTGACTTTGATG-C--GGTCCCTCATCG-------A---------TGTCCAGCC-------------G-G---CGGACAGTTGACAGGC----AGACAATGGGATATC-GA---CTTGGCGCTA---C s droEle2.KB458573 517197 154 - 5320397 CTTATGACAGGCGCACG-CCC-------GG--GACAAAAGAGCGCT-------GCGC--TGCT------ATATGCGttcc-------aaaaaa-------------------ata---------------------tcgttttgGTGACTTTGATG-C--GGTCCCTCATCG-------A---------TGTCCAGCC-------------G-G---CGGACAGTTGACAGGC----AGACAATGGGATTTTGGA---CTTGGCGCTA---C s droKik2.KB459527 272005 174 - 1234237 CTTATGACAGGCGCACGCCCC-------GA--GACAAAATCGcgat-------tc----tatata---tatatgtctctc-------aaaaaaatacaaaccaaaaaaatatata---------------------tcgttTTGGTGACTTTGATG-C--GGTCCCTCATCG-------A---------TGTCCAGCC-------------G-G---CGGACAGTTGACAGGC----AGACAATGGGATTGC-GA---CTTGGCGCTA---C s droTak2.KB461535 137010 149 - 669855 CTTATGACAGGCGCACG-CCC-------GG--GACAAAAGACCGCT-------TC----TATA---------Tgcgttcc------aaaaaaa-------------------ata---------------------tcattttggtgACTTTGATG-C--GGTCCCTCATCG-------A---------TGTCCAGCC-------------G-G---CGGACAGTTGACAGGC----AGACAATGGGATTTC-GA---CTTGGCGCTA---C s droRho2.KB449310 30825 149 - 65043 CTTATGACAGGCGCACG-CCC-------GG--GACGAAAGACCGCT-------GC----TATA---------TGCGttcc-------aaaaaa-------------------ata---------------------tcgttttgGTGACTTTGATG-C--GGTCCCTCATCG-------A---------TGTCCAGCC-------------G-G---CGGACAGTTGACAGGC----AGACAATGGGATTTGGGA---CTTGGCGCTA---C s droFic2.KB457177 76954 148 + 995874 CTTATGACAGGCGCACG-CCC-------GG--GACAAGGGACCGCT-------TC----TAAA---------TGCGTCCC--------AAAAA-------------------ATA---------------------TCGATTTGGTGACTTTGATG-C--GGTCCCTCATCG-------A---------TGTCCAGCC-------------G-G---CGGACAGTTGACAGGC----AGACAATGGGATTCGGGA---CTTGGCGCTA---C s droPse3.chr3 1345199 182 - 19787792 CTTATGACAGGCGCACG-CCC-------GA--GGCCACAAACCCTT-------GC----CGTACA--CCATACGCCATCTGAAtgcagaaaaa-------------------ata----------tatataatatttcgATTTGGTGACTTTGATG-T--GGTCCCTCATCG-------A---------TGTCCAGGC-------------G-ATGTCGGACAGTTGACAGGC----AGACAATGGGATTTT-GACTTCTTGGCGCTAcggc s droPer1.super_34 534084 189 - 916997 TTTATGACAGGCGCACG-CCC-------GA--GACCACAAACCCTTGCCGTACGC----CGTACG--CCATACGCCATCTGAATGCAGAAAAA-------------------ATA----------TATATAATATTTCGATTTGGTGACTTTGATG-T--GGTCCCTCATCG-------A---------TGTCCAGGC-------------G-ATGTCGGACAGTTGACAGGC----AGACAATGGGATTTT-GACTTCTTGGCGCTACGGC s droMir2.chr3 1386296 182 - 20862834 CTTATGACAGGCGCACG-CCC-------GA--GACCACAAACCCTT-------GC----CGTACG--CCATACGCCATCTGAAtgcagaaaaa-------------------ata----------tatataatatttcgATTTGGTGACTTTGATG-T--GGTCCCTCATCG-------A---------TGTCCAGGC-------------G-ATGTCGGACAGTTGACAGGC----AGACAATGGGATTTT-GACTTCTTGGCGCTACGGC s droWil2.CH963894 1304129 204 + 2843958 CTTATGACAGGCGCACG-CCT-------TGCAGACAGCGGgccaaa-------ga----caaaaaaaaaatcagcaaaac------aGGAgac-------------------aaacttttgttttttttttttgtttttttttgttgactttGATG-TGGGGGCCCTCAACG-------ATATATTCCCTGTCCAGCTATAGTCAGTTTCGG-G---CCAACAGTTGACAGTTGGCAAGACAATGGG------CA---GTCGTTCCTA---C s droVir3.scaffold_12875 7347168 132 + 20611582 CTTATGACAGGCGCGCG-CCTCTTGACAGG--GACAAAA-----CT-------TT----TGTT-------------------------------------------------ATA---------------------TATTTTTAGTGACTTTGATG-T--GG-CCCTCATCG-------A---------TGTCCACGC-------------C-G---TGGACAGTTGACAGGC----AGACAATGGA---TG-CG---CTTGGCGCTa---c s droMoj3.scaffold_6496 26142130 129 + 26866924 CTTATGACAGGCGCGCG-CCTCTTGACAGG--GACAGAA-----GT-------TT----TGTT-------------------------------------------------ATA---------------------TATTTTTAGTGACTTTGATG-T--GG-CCCTCATCG-------A---------TGTCCACGC-------------C-G---CGGACAGTTGACAAGC----AGACAATGGG-------G---CTTGGCGCTA---T s droAlb1.JH854640 305598 132 + 406291 CTTATGACAGGCGCGCG-TCTCTTGACAGG--GACAAAA-----Ct-------ct----tgtt-------------------------------------------------ata---------------------tatttttagtgacTTTGATG-T--GG-CCCTCATCG-------A---------TGTCCGCAG-------------C-C---TGGACAGTTGACAGGC----ATACAATGGA---TT-CG---CTTGGCgcta---c s droGri2.scaffold_15245 895317 132 + 18325388 CTTATGACAGGCGCGCG-CCTGTTGACAGG--GACAAAA-----CT-------TT----TGTT-------------------------------------------------ATA---------------------TATTTTTAGTGACTTTGATG-T--GG-CCCTCATCG-------A---------TGTCCACGC-------------C-G---CGGACAGTTGACAGGC----ACACAATGGA---TA-CG---CTTGGCGCTa---c a score=-426364.000000 s dm6.chr2R 24346239 77 + 25286936 C-AGC-------------GGTAGC---------------------AG----CAA-----AAAGCGCA-----------------------GAGGcaatctgcaatccg------c--------------c-------atcccaatcccaa------ttcgaatccc---TAGCAGC--------CA----AC s droSim1.chr2R 18692971 82 + 19596830 C-AGC-------------GGTAGC---------------------AG----CAA-----AAAGCGCA-----------------------G-GGCAATCTGCAATCCG------C--------------C-------ATCCCAATCCCAATCCCAATTCGAATCCC---TAGCAGC--------CA----AC s droSec1.super_23 112740 83 + 989336 C-AGC-------------GGTAGC---------------------AG----CAA-----AAAGCGCA-----------------------GAGGCAATCTGCAATCCG------C--------------C-------ATCCCAATCCCAATCCCAGTTCGAATCCC---TAGCAGC--------CA----AC s droYak3.chr2R 20201820 91 + 21139217 C-AGC-------------GGTAGC---------------------AG----CAA-----AAAGCG-------------------------GTAGCGATCTGCAATCGGCCATCcc--------------c-------atcccaatcccaattccaATCGCAATCCC---TACCAGC--------CAGGCGAC s droEre2.scaffold_4845 21599800 82 + 22589142 C-AGC-------------GGCAGC---------------------AG----CAA-----AAAGCGCAGA-------------GCCGATCTGAGGCAATCTGCAATCGG--------------------------------------CCAATCCCTATCCCAATCCC---TACCAGC--------CA----AC s droBia2.KB462602 792007 74 + 3129309 C-AGC-------------GGTGGC---------------------AG----CAA-----AAAGCGCAAA-------------GCCGGGCAAAGGCAATCTGCAATCCG------C--------------C-------ATCCA----CCAA-------------CCC---TACCGGC--------CA------ s droSuz1.KI419649 12037154 88 - 14502029 C-AGC-------------GGTGGC---------------------AG----CAA-----AAAGCGCAGA-------------GCAAGGCAAAGGCAATCTGCAATCCG------CCATACGCCATACGAC-------ATCCA----CCAA-------------CCC---TACCGGC--------CA------ s droAna3.scaffold_13266 5707222 65 - 19884421 C-ACCGGGCGCAGTTtcagaaatc---------------------agaaatcag-----aaatcgga----------------------------aatcTGCAATCCG------C---------------------------------------------AATCCC---TA--------------T----AC s droBip2.KB464407 1955992 60 + 2915140 C-AGC--------TACCAGGTACC---------------------AGGTTCCATCTTCCAGATCTGA----------------------------AATCTGCAATCCG------A---------------------------------------------AATCCC-------------------T----AC s droEug2.KB465067 596897 94 + 1515531 C-ATC-------------GCTGCC---------------------AG----CAA-----AAAGCgcaaaagcaaaggcagaGGCAAAAGCGGGGCAATCTGCAATCGG------C--------------C-------ATCCACCATCCAC----------CATCCC---TACCGAC--------CA------ s droEle2.KB458573 517351 71 - 5320397 C-AGC-------------GGTCGC---------------------AG----CAA----AAAAGcgca-----------------aaagcaaaggcaatCTGCAATTCG------C--------------A-------ATTCGC-----------------AATCCC---TAGCAAC--------CA------ s droKik2.KB459527 272179 84 - 1234237 C-AGC-------------AGCGGCTGG------------------AG----CAA-----AAAGCGAA-----------------------AAGGCAATCTGCAATCCG------C--------------C-------ATCCGCCATGCGC----------AATCCC---TAGCAGCAGCCGTAGCA----GC s droTak2.KB461535 137159 65 - 669855 C-AGC-------------GGTGGC---------------------AG----CAA-----AAAGCGCA----------------AAAAGCAAAGCCAATCTGCAATCCG------C---------------------------------------------CATCCC---TACCGGC--------CA-----G s droRho2.KB449310 30974 82 - 65043 C-AGC-------------GGTCgc---------------------ag----caa-----aaagtgga-----aaagcaaaatcaaaagcaaaggcaatctgcaatccg------c--------------a-------atccgc-----------------aatcCC---TACCAAC--------CA------ s droFic2.KB457177 77102 69 + 995874 CGGGC-------------AATCGC---------------------AG----CAA-----AAAGCGCT-------------------GAGGAGGGCGATCTGCGATCCG------A--------------A-------ATACGC-----------------CATCCC---TACCAAG--------CG------ s droPse3.chr3 1345381 76 - 19787792 c-aca-------------ggccacaggccacagccagagccccaaAG----CCA-----GCGGCAAA-----------------------T-AAGAAACAGCAGCCAG------C--------------G-------AG---------------------GATCCC---TAG------------CA------ s droPer1.super_34 534273 55 - 916997 C-ACA-------------GGCCAC---------------------AG----CCA-----GCGGCAAA-----------------------T-AAGAAACAGCAGCCAG------C--------------G-------AG---------------------GATCCC---TAG------------CA------ s droMir2.chr3 1386478 77 - 20862834 C-ACA-------------GGCCAcgggccacagccacagccccacag----cca-----gcggcaaa-----------------------taaaaaaacagcagccag------c--------------G-------AG---------------------GATCCC---TAG------------CA------ s droWil2.CH963894 1304333 47 + 2843958 C-CCC-------------TCCGTC---------------------TT----CTC------------------------------------------CCCGGTAGTTCC------T--------------T-------TTT--------------------GATTTC---GGCTTGG--------CG------ s droVir3.scaffold_12875 7347300 47 + 20611582 -----------------------------------------------------a-----cacacaca-----------------------cacacacacaggcatacg------c--------------a----------cacacgcaca----------cGTCCT---GG--------------------- s droMoj3.scaffold_6496 26142259 57 + 26866924 -----------------------------------------------------A-----TAAACACA-----------------------CAGACGCACAGACGCATA------C--------------AGATAGAGATGCACACACATG----------CATCCT---GG--------------------- s droAlb1.JH854640 305730 45 + 406291 -----------------------------------------------------g-----cacacaca-----------------------cacatacacacaagcaCG------T--------------G----------CACAC---------------TGTCCTACAGG--------------------- a score=1695118.000000 s dm6.chr2R 24346316 225 + 25286936 CAACAAATTGCGGCCAATGAACTTGGCC----------CA--------------------------------------------GAGA----G--TTGTC-------------------------GCGC-----CAACCTGCTGGCATGC-----TTT-CCACTGG------------------------CCAATTTTGGTCA--TTTCGA-------TCTGGCCGA-GA----G----CCGGG------------------------------GCTCT--TTTGGCGTG---------GGTGG----------------CGGT-----GGTCAA---AA-GG------------CCAAAAAAGGCGACGAGAGTGAAAAGTGAGCTAAT----GTC-----CA-GAAGTGATCTCATTT-G------CTGGCC-A---GCCTAATTGCGTGGGCC------G--------------CA--TCA---------------------------------- s droSim1.chr2R 18693053 225 + 19596830 CAACAAATTGCGGCCAATGAACTTGGCC----------CA--------------------------------------------GAGA----G--TTGTC-------------------------GCGC-----CAACCTGCTGGCATGC-----TTT-CCACTGG------------------------CCAATTTTGGTCA--TTTCGA-------TCTGGCCGA-GA----G----CCGGG------------------------------GCTCT--TTTGGCGTG---------GGTGG----------------CGGT-----GGTCAG---AA-GG------------CCAAAAAAGGCGACGAGAGTGAAAAGTGAGCTAAT----GTC-----CA-CAAGTGATCTCATTT-G------CTGGCC-A---GCCTAATTGCGTGGGCC------G--------------CA--TCA---------------------------------- s droSec1.super_23 112823 225 + 989336 CAACAAATTGCGGCCAATGAACTTGGCC----------CA--------------------------------------------GAGA----G--TTGTC-------------------------GCGC-----CAACCTGCTGGCATGC-----TTT-CCACTGG------------------------CCCATTTTGGTCA--TTTCGA-------TCTGGCCGA-GA----G----CCGGT------------------------------GCTCT--TTTGGCGTG---------GGTGG----------------CGGT-----GGTCAA---AA-GG------------CCAAAAAAGGCGACGAGAGTGAAAAGTGAGCTAAT----GTC-----CA-AAAGTGATCTCATTT-G------CTGGCC-A---GCCTAATTGCGTGGGCC------G--------------CA--TCA---------------------------------- s droYak3.chr2R 20201911 231 + 21139217 CAACAAATTGCGGCCAATGAACTTGGCC----------CA--------------------------------------------GAGA----G--CTGTC-------------------------GCGC-----CAACCTGCTGGCATGC-----TTT-CCACTGA------------------------CCAATTTTGGTCA--TTTCGA-------TCTGGCCGA-GA----G----TCGGG------------------------------GCTTGGATTTGGCGTG---------GGTGG----------------CGGT-----GGTCAG---AA-GG------------CCAAAAAAGGCGACGAGAGTGAAAAGTGAGCTAATGTCCGTC-----CA-GAAGTGATCTCATTT-G------CTGGCC-A---GCCTAATTGCGTGGGCC------G--------------CA--TCA---------------------------------- s droEre2.scaffold_4845 21599882 234 + 22589142 CAACAAATTGCGGCCAATGAACTTGGCC----------CA--------------------------------------------GAGA----G--TTGTC-------------------------GCGC-----CAACCTGCTGGCATGC-----TTT-CCACAGG------------------------CCAATTTTGGTCA--TTTCGA-------TCTGGCCGA-GA----G----TCGGG------------------------------GCTCT--TTTGGCGTGGGTGGCGCTGGTGG----------------CGGT-----GGTCAG---AA-GG------------CCAAAAAAGGCCACGAGAGTGAAAAGTGAGCTAAT----GTC-----CA-GAAGTGATCTCATTT-G------CTGGCC-A---GCCTAATTGCGTGGGCC------G--------------CA--CCA---------------------------------- s droBia2.KB462602 792081 231 + 3129309 --ACAAATTGCGGCCAATGAACTTGGCC----------CA--------------------------------------------GAGAGTCGG--TTGTC-------------------------GCGC-----CAACCTGTTGGCATGC-----TTT-CCACTGG------------------------CCAATTTTGGTCA--TTTCGA-------TCTGGCCAA-GACGATC----TGGGG------------------------------ACGCTT-TTTCGCGTG---------GGTGG----------------CAGT-----GGT-AC---GG-GG------------CCAAAAAAGGCCACAAGAGTGAAAAGTGAGCTAAT----GTC-----CA-GAAGTGATCTCATTT-G------CTGGCC-A---GCCTAATTGCGTGGGCC------G--------------CA--TTA---------------------------------- s droSuz1.KI419649 12037242 222 - 14502029 --ACAAATTGCGGCCAATGAACTTGGCC----------CA--------------------------------------------GAGA----G--TGGTC-------------------------GCGC-----CAACCTGTTGGCATGC-----TTT-CCACTGG------------------------CCAATTTTGGTCA--TTTCGA-------TCTGGCCAA-GACGATC----TGGGG------------------------------ACGCTT-TTTCGCGTG---------GGTGG----------------CAGT--------------GG-GG------------CCAAAAAAGGCCACAAGAGTGAAAAGTGAGCTAAT----GTC-----CA-GAAGTGATCTCATTT-G------CTGGCC-A---GCCTAATTGCGTGGGCC------G--------------CA--TTA---------------------------------- s droAna3.scaffold_13266 5707287 236 - 19884421 CAACAAATTGCGGCCAATGAACTTGGCC----------CA--------------------------------------------CAGA----C--GGGCG-------------------------GCGA-----CAACCTGTTCGCGTGC-----TTT-CCACTGG------------------------CCAATTTTGGTCA--TTTCGA-------TCTGGCCAGCGG----A----TC--T------------------------------GTGTG--GCAAGCGTG---------GGTGGGCGGG-----------CGGTCGGTTGGTCGGCCAGA-GT------------CCAAAAAAGGTCACAAAAGTGAAAAGTGAGCTAAT----GTC-----CA-GAAGTGATCTCATTT-G------CTGGC-------CCAGAGTGCGTGGGTT------G--------------GTGGCTA---------------------------------- s droBip2.KB464407 1956052 239 + 2915140 CAACAAATTGCGGCCATTGAACTTGGCC----------CA--------------------------------------------CAGA----CG-GGGCA-------------------------GCGA-----CAACCTGTTCGCGTGC-----TTT-CCACTGG------------------------CCAATTTTGGTCA--TTTCGA-------TCTGGCCAATGG----A----TCGGT------------------------------GTGTG--GAGTGCGTG---------GGTGGGCGGGTG-------GACAgtcggtcggtcggttggA-GT------------CCAAAAAAGGTcacaaaagtgaaaagtgaGCTAAT----GTC-----CA-GAAGTGATCTCATTT-G------CTGGCC-----GCCAAACTGCGTGGGC--------------------------CCA---------------------------------- s droEug2.KB465067 596991 223 + 1515531 --ACAAATTGCGGCCAATGAACTTGGCC----------CA--------------------------------------------GAGA----G--TTGTC-------------------------GCGC-----CAACCTGTTGGCATGC-----TTT-CCACTGG------------------------CCAATTTTGGTCA--TTTCGC-------TCTGGCCGA-TA----G----CTGCG------------------------------AATC---TTTGGCGTG---------GGTGGT---------------CGGA-----GGTAGT---GA-GG------------CCAAAAAAGGCcacaaaagtgaaaagtgagcTAAT----GTC-----CA-GAAGTGATCTCATTT-G------CTGGCC-A---GCCTAATTGCGTGGGCC------G--------------CA--TTA---------------------------------- s droEle2.KB458573 517422 259 - 5320397 --ACAAATTGCGGCCAATGAACTTGGCC----------CA--------------------------------------------AAGA----G--TTGTC-------------------------GCGTTGCGGCAACCTGTTGGCATGC-----TTT-CCACTGG------------------------CCAATTTTGGTCA--TTTCGA-------TCTGGCCGCCGA----G----CTGGA------------------------------GATC---TTtggcgtg---------ggtgggcggtggtggtggtggttgt-----ggtggt---ga-gg------------ccaaaaaaggcaacaaaagtgaaaagtgagcTAAT----GTC-----CA-GAAGTGATCTCATTTGG------CTGGTC-A---GCCTAATTGCGTGGGCT------ATTGTGGCTGTTGGCCG--TTA---------------------------------- s droKik2.KB459527 272263 249 - 1234237 CAACAAATTGCGGCCAATGAACTTGGCC----------CA--------------------------------------------GAGA----G--TGGTCACA----------------------ACGA-----CAACCTGTTGGCATGC-----TTTCCCGCTGG------------------------CCAATTTTGGTCA--TTTCGA-------TCC-GTTGC-GA----G----CACAG------------------------------ATCTT--TTTGGCGTG---------GGCGGGCGGCGGCGGTAGTG-TGGT-----AGTAAG---GGTGG------------CCAAAAAAGGCcacaaaagtgaaaagtgagCTAAT----GTCCAGATCA-GAAGTGATCTCATTT-G------TTGGCC-A---GCCTAATTGCGTGGGCT------C--------------AG--GCG---------------------------------- s droTak2.KB461535 137224 220 - 669855 CAACAAATTACGGCCAATGAACTTGGCC----------CA--------------------------------------------GAGA----G--TTGTCGCC----------------------GCGG-----CAACCTGTTGGCATGC-----TTT-CCTCTGG------------------------CCAATTTTGGTCA--TTTCGA-------TCTGGCCAA-GA----G----CTGG---------------------------------CCA--AGACGTGTG---------GGTGG----------------CGGC--------------GA-GG------------CCAAAAAAGGCCACGAGAGTGAAAAGTGAGCTAAT----GTCC----CA-GAAGTGATCTCATTT-G------CTGGCC-A---GCCTAATTGCGTGGGCC------G--------------CA--TTA---------------------------------- s droRho2.KB449310 31056 240 - 65043 --ACAAATTGCGGCCAATGAACTTGGCC----------CA--------------------------------------------GAGA----G--TTGTC-------------------------GCGC-----CAACCTGTTGGCATGC-----TTT-CCACTGG------------------------CCAATTTTGGTCA--TTTCGA-------TCTGGCCGGCGA----A----CTGGG------------------------------GATC---TGTGGCGTG---------ggtgggcggtgg---------tggt-----ggtagt---GA-GG------------CCAAAAAAGGCcacaaaagtgaaaagtgaGCTAAT----GTC-----CA-GAAGTGATCTCATTTGG------CTGGCC-AGCCGCCTAATTGCGTGGGCCCGATGTG--------------TG--TTA---------------------------------- s droFic2.KB457177 77171 225 + 995874 -AACAAATTGCGGCCAATGAACTTGGCC----------CA--------------------------------------------GAGA----G--TTGTC-------------------------GCGG-----CAACCTGTTGGCATGC-----TTT-CCTCTGG------------------------CCAATTTTGGTCA--TTTCGA-------TCTGGCCAA-GA----G----CCGA-------------------------------GCTC---CGAGGCGTG---------GGTGGG---------------CGGT-----GGTAGT---GA-GG------------CCAAAAAAGGCcacaaaagtgaaaagtgagCTAAT----GTC-----CA-GAAGTGATCTCATTT-G----GCCGGGTG-A---GCCCAATTGCGTGGGCC------G--------------CA--TTA---------------------------------- s droPse3.chr3 1345457 261 - 19787792 --ACAAATTGCGGCCAATGAACTTGGCC----------Ca--tgaagagagacagaaagagtgAAACTG--GGAGACGGGCGACGGGG----A--CGGAG-------------------------ATGG-----CAACCTGTTGGCATGC-----TTT-CCACTGG------------------------CCAATTTTGGGCA--TTTTG---------CAGGC--A-GA----G----------------------------------------------CGTGGCGTG---------GGCGG----------------CGCA-----GAGCGG---AG-CGACACGGCCAGTCCCAAAAATGGCcacaaaagtgaaaagtgagcTAAT----GTC-----CA-GAAGTGATCTCATTT-G------TTGGTC-A---ACCTAATTGCGTGGGCC------G--------------AT--CGA---------------------------------- s droPer1.super_34 534328 261 - 916997 --ACAAATTGCGGCCAATGAACTTGGCC----------CA--TGAAGAGAGACAGAAAGAGTGAAACCG--GGAGACGGGAGACGGGG----A--CGGAG-------------------------ATGG-----CAACCTGTTGGCATGC-----TTT-CCACTGG------------------------CCAATTTTGGGCA--TTTTG---------CAGGC--A-GA----G----------------------------------------------CGTGGCGTG---------GGCGG----------------CGCA-----GAGCGG---AG-CGACACGGCCAGTCCCAAAAATGGCCACAAAAGTGAAAAGTGAGCTAAT----GTC-----CA-GAAGTGATCTCATTT-G------TTGGTC-A---ACCTAATTGCGTGGGCC------G--------------AT--CGA---------------------------------- s droMir2.chr3 1386555 254 - 20862834 --ACAAATTGCGGCCAATGAACTTGGCC----------Ca--tgaagagagacagaaagagtgAAACCG--gga-------gacgggg----a--cggag-------------------------aTGG-----CAACCTGTTGGCATGC-----TTT-CCACTGG------------------------CCAATTTTGGGCA--TTTTG---------CAGGC--A-GA----G----------------------------------------------CGTGGCGTG---------GGCGG----------------CGCA-----GAGCGG---AG-CGACACGGCCAGTCCCAAAAATGGccacaaaagtgaaaagtgagcTAAT----GTC-----CA-GAAGTGATCTCATTT-G------TTGGTC-A---ACCTAATTGCGTGGGCC------G--------------AT--CGA---------------------------------- s droWil2.CH963894 1304380 190 + 2843958 CTACAAATTGCGGCCAATGAACTTGATC--------------------------------------------------------Agac----g--ccatc-------------------------atca-----tcatcaatgg---------------cCAATGG------------------------CCAATTTTGGTCATTTTTTGG-------GCTAGCTAG-AA----A-------------------------------------------------GGCGTG---------GGCGG-------------------------G--------AT-CG------------CTGAAAAACgcagaaaaagtgaaaagcgAA---------GCT-----AC-TAAGTGATCTCATTTTG------TTGACTTA---ACCTAATTGCGTAGGTC------G---------------A--TGA---------------------------------- s droVir3.scaffold_12875 7347347 292 + 20611582 CTACAAATTGCGGTTATTGAACCTGATCAGCTCAGCT-CAGCTGGATTGGCACAG----------------GCAGACGC-----CACA----G--TGCCG-------------------------AAAG-----CAACCTG--------------TGT-CCAATAC-------------------------CAATTTTGGTCA--TTTAGCAAAAGCTACTAACAGA-AA----G----CAAAACAAAAAAAAAAGAT----------------GTGAT--CTTCGCGTG---------GGCGC----------------------------------TT-GG------------CCCAAAAAGGC--CAAAAGTGAAAAGTGAGCTAAT----GTC-----AACGCAATGATCTCATTT-G------TAGGCCTG---GCCTAATTGCGTGGGCT------G--------------AG--TTGTTGCTGCTTCTTCAAAAAGTCTGCATAAAATGCA s droMoj3.scaffold_6496 26142316 288 + 26866924 CAACAAATTGCGGTCATTGAACCCGCTCAATTCTGGTGCTGCTGCTGCTGCTCGCTGCTACTGGCA--GAGGTTGACGC-----CACT----G--CTGCG-------------------------AAAG-----CAACCTG--------------CGG-CCAATAC-------------------------CAATTTTAGACA--TTTAGCGAGAGCTACTAGCAGA-AA----GAAGACGAGACGGAAAACAGTGATCGAAACC---------GAGCT--CTGGTCGTG---------GGCGTGC--------------------------CAA---GT-GG------------CCGAAAAAGGC--CAAAAGTGAAAAGTGAGCTAAT----GCC-----AACGC-ATGATCTCATTT-G------TAGGCCTG---GCCTAATTGCGTAGGCT------G--------------AG------------------------------------GCA s droAlb1.JH854640 305775 360 + 406291 GTACAAATTGCGGTTATTGAACCTGATCAAGTTGTGG-CAGATGCCGAtgtcgat----atcgatatcgagGCAGACGC-----CACG----C--Acgcactcaaacacacacacacacacacatgaaa-----caACCTG--------------TGG-ACATCATCGGTGCTTTCCACTGT--------ACAATTTTGGGCA--TTtagc-aaagcaactaaaatt-cA----G----CTCGCCGCTGTCCACTGTTTga-------------tgggc--gtgggcgtg---------ggcgaTCGTA-----------CGCTTGGC-GAGTGA---GT-GG------------CCAAAAAAGgc--caaaagtgaaaagtaaGCTAAT----GTC-----AACGCAATGATCTCATTT-GTACGAATAGGCATG---GCCCAATTGCGTAGGTT------G--------------TC----------GCTTCttctctttgtctgtct-----gca s droGri2.scaffold_15245 895502 323 + 18325388 CAACAAATTGCGGTTATTGAACTTGATCAGTTAGTTT-TGTTTG---------------------------GCAGACGC-----CACA----GATTTCCA-------------------------AAGG-----CAACCTGTGCGTTTGCTTTCTTGC-CCAGTGCGTTCTTCTTTCACCGTCTCCATAACCAATTTTGGTCA--TTTGGCAAAAGCTACTAACAAA-AA----T----CAatatatatataaatatataaatatatataGCTGTCTGT--TTTGGTGTG---------GGCGTGCTCG-----------CATC--------------TT-GG------------CCGAAAAAGGC--CAAAAGTGAAAAGTGAGCTAAT----GTC-----AACGCAATGATCTCATTT-G------TAGGCCTG---GCCTAATTGCGTAGGCT------G--------------CA---AGGCGTTGCTTCT----------------------- a score=-115538.000000 s dm6.chr2R 24346541 12 + 25286936 TC--------GATGGATTCG------------- s droSim1.chr2R 18693278 12 + 19596830 TC--------GATCGATTCG------------- s droSec1.super_23 113048 12 + 989336 TC--------GATGAATTCG------------- s droYak3.chr2R 20202142 12 + 21139217 TC--------GATGGATTCG------------- s droEre2.scaffold_4845 21600116 12 + 22589142 TC--------GATGGATTCG------------- s droBia2.KB462602 792312 11 + 3129309 TC---------ACCGGTCCG------------- s droSuz1.KI419649 12037464 11 - 14502029 TC---------ATCGATCCG------------- s droAna3.scaffold_13266 5707523 16 - 19884421 TCTGA----GGAGCAGTTGG------------- s droBip2.KB464407 1956291 13 + 2915140 TC-------GATCCAGCTGG------------- s droEug2.KB465067 597214 8 + 1515531 TC------------GATCCG------------- s droEle2.KB458573 517681 8 - 5320397 TC------------GATTTG------------- s droKik2.KB459527 272512 10 - 1234237 ----------GATCGATTCG------------- s droTak2.KB461535 137444 11 - 669855 TC---------ATCGATCGA------------- s droRho2.KB449310 31296 8 - 65043 TC------------GATTCG------------- s droFic2.KB457177 77396 13 + 995874 TC-------GGATCGATTTG------------- s droPse3.chr3 1345718 20 - 19787792 TGGGAGCCGCGATTGAGCCA------------- s droPer1.super_34 534589 20 - 916997 TGGGAGCCGCGATTGAGCCA------------- s droMir2.chr3 1386809 20 - 20862834 TGGGAGCCGCGATTGAGCCA------------- s droWil2.CH963894 1304570 20 + 2843958 CGGTGAATGtggttgatgtt------------- s droVir3.scaffold_12875 7347720 12 + 20611582 -----------Gtgtctgcc----------tgg s droMoj3.scaffold_6496 26142733 12 + 26866924 -----------tcggctgct----------cgg s droAlb1.JH854640 306138 8 + 406291 ---------------ATGCA----------AGA s droGri2.scaffold_15245 895832 22 + 18325388 -----------ATGTCTGCAACAAATGCAGAAG a score=-98872.000000 s dm6.chr2R 24346553 15 + 25286936 CAGCTTTCGCTT-----------------------CTG s droSim1.chr2R 18693290 15 + 19596830 CAGCTTTCGCTT-----------------------CTG s droSec1.super_23 113060 15 + 989336 CAGCTTTCGCTT-----------------------CTG s droYak3.chr2R 20202154 29 + 21139217 CAGCTTTCGCTTGTGACTTCTGGCTT---------CTG s droEre2.scaffold_4845 21600128 36 + 22589142 CAGCTTTCgcttctgacttctggcttctggcta--ctg s droBia2.KB462602 792323 15 + 3129309 GGGCTTTCGCTT-----------------------CTG s droSuz1.KI419649 12037475 15 - 14502029 AGGCTTTCGCTT-----------------------CTG s droAna3.scaffold_13266 5707539 12 - 19884421 AAGCGAAAGCGC-------------------------- s droBip2.KB464407 1956304 12 + 2915140 AAGCGAAAGCGC-------------------------- s droEug2.KB465067 597222 21 + 1515531 -GGCTTTCGCTT-------CTGGCTT---------CTG s droEle2.KB458573 517689 11 - 5320397 -AGCTTTCGCTT-------------------------- s droTak2.KB461535 137459 15 - 669855 AAGCTTTCGCTA-----------------------CTT s droRho2.KB449310 31304 7 - 65043 -AGCTTTC------------------------------ s droFic2.KB457177 77409 14 + 995874 -AGCTTTCGCTT-----------------------CTG s droPse3.chr3 1345765 10 - 19787792 cagcgaaaGC---------------------------- s droPer1.super_34 534630 10 - 916997 CAGCGAAAGC---------------------------- s droMir2.chr3 1386856 10 - 20862834 cagcgaaagC---------------------------- s droWil2.CH963894 1304602 7 + 2843958 cttctta------------------------------- s droVir3.scaffold_12875 7347732 31 + 20611582 ccgcctgtctgc-------cagcctggctgcctgactg s droMoj3.scaffold_6496 26142745 15 + 26866924 ctgctcgcctgc-----------------------ctg s droAlb1.JH854640 306146 31 + 406291 TCgcatgtggca-------cacacacactcacacactt s droGri2.scaffold_15245 895854 15 + 18325388 CAGCTtgtgtgt-----------------------ctg a score=96565.000000 s dm6.chr2R 24346568 18 + 25286936 GCTTCTGCATAA-TGCAC-------G s droSim1.chr2R 18693305 18 + 19596830 GCTTCTGCATAA-TGCAC-------G s droSec1.super_23 113075 18 + 989336 GCTTCTGCATAA-TGCAC-------G s droYak3.chr2R 20202183 18 + 21139217 GCTTCTGCATAA-TGCAC-------G s droEre2.scaffold_4845 21600164 18 + 22589142 gcttctgCATAA-TGCAC-------A s droBia2.KB462602 792338 18 + 3129309 GCTTCTGCATAA-TGCAC-------A s droSuz1.KI419649 12037490 18 - 14502029 GCTTCTGCATAA-TGCAC-------A s droAna3.scaffold_13266 5707551 16 - 19884421 --TTCTGCATAA-TGCAA-------T s droBip2.KB464407 1956316 15 + 2915140 ---TCTGCATAT-TGTAA-------T s droEug2.KB465067 597243 18 + 1515531 GCTTCTGCATAA-TGCAC-------A s droEle2.KB458573 517700 14 - 5320397 ----CTGCATAA-TGCAC-------G s droKik2.KB459527 272547 18 - 1234237 GCTCCTGCATAA-TGCAC-------A s droTak2.KB461535 137475 25 - 669855 GCTTCTGCATAA-TGCACACAGCGAA s droRho2.KB449310 31311 17 - 65043 GCTTCTGCATGA--ATGC-------A s droFic2.KB457177 77423 11 + 995874 -------CATAA-TGCAC-------G s droPse3.chr3 1345775 18 - 19787792 GCTTCTGCATAA-TGCAC-------A s droPer1.super_34 534640 18 - 916997 GCTTCTGCATAA-TGCAC-------A s droMir2.chr3 1386866 18 - 20862834 GCTTCTGCATAA-TGCAC-------A s droWil2.CH963894 1304617 18 + 2843958 ACTTTTGCATAA-TGCAG-------A s droVir3.scaffold_12875 7347763 12 + 20611582 ---gctgactggctg----------- s droMoj3.scaffold_6496 26142760 12 + 26866924 ---gctgcctggctg----------- s droAlb1.JH854640 306177 12 + 406291 ---actGAATGTCTG----------- s droGri2.scaffold_15245 895869 12 + 18325388 ---tctctgtgtgtg----------- a score=-188372.000000 s dm6.chr2R 24346586 15 + 25286936 ----------GCCATCGAACAAG------------------------AA s droSim1.chr2R 18693323 15 + 19596830 ----------GCCATCGAACAAG------------------------AA s droSec1.super_23 113093 15 + 989336 ----------GCCATCGAACAAG------------------------AA s droYak3.chr2R 20202201 12 + 21139217 ----------GCCATCGAAC---------------------------AA s droEre2.scaffold_4845 21600182 12 + 22589142 ----------GCCATCGAAC---------------------------AA s droBia2.KB462602 792356 12 + 3129309 ----------GCCATCGAAC---------------------------AA s droSuz1.KI419649 12037508 12 - 14502029 ----------GCCATCGAAC---------------------------AA s droAna3.scaffold_13266 5707567 31 - 19884421 ----------GTC------TGGGTTTGGG--TCTGGGTCTAAGAGCCTG s droBip2.KB464407 1956331 37 + 2915140 ----------GCAATGCAGAAGGGGCGAG--GCCGGGGGCGGGTGGAAG s droEug2.KB465067 597261 8 + 1515531 ----------GC----GAAC---------------------------AA s droEle2.KB458573 517714 10 - 5320397 ----------GCCATCGACG----------------------------- s droKik2.KB459527 272565 5 - 1234237 ----------ACA----------------------------------AG s droTak2.KB461535 137500 12 - 669855 ----------GCCATCGAAC---------------------------AA s droRho2.KB449310 31328 12 - 65043 ----------GACGGCGAAC---------------------------AA s droFic2.KB457177 77434 8 + 995874 ----------GC----GAAC---------------------------AA s droPse3.chr3 1345793 26 - 19787792 ----------ATGTCCACACACATGTAGGTTGCT-------------AC s droPer1.super_34 534658 26 - 916997 ----------ATGTCCACACACATGTAGGTTGCT-------------AC s droMir2.chr3 1386884 26 - 20862834 ----------ATGTCCACACACATGTAGGTTGCT-------------AC s droWil2.CH963894 1304635 12 + 2843958 ----------AAA---GAACGAA------------------------AA s droVir3.scaffold_12875 7347777 9 + 20611582 --------CTGTCGTTT-------------------------------- s droMoj3.scaffold_6496 26142774 9 + 26866924 --------CTGTCGTTT-------------------------------- s droAlb1.JH854640 306200 17 + 406291 TTCTCCGTCTGTCGTTT-------------------------------- a score=1124518.000000 s dm6.chr2R 24346601 91 + 25286936 GCCAT-CGA-CAAGTTC----CC-------------------------AACAATTG----GCCATGGCTAAAA------------------GGGCA----------------------GCCGGGCGCAAAATGCCGCCAAAAGGTGTTAAATTGAAATCACGAGGC------------------------------------------------------------------------------ s droSim1.chr2R 18693338 91 + 19596830 GCCAT-CGA-CAAGTTC----CC-------------------------AACAATTG----GCCATGGCTAAAA------------------GGGCA----------------------GTCGGGCGCAAAATGCCGCCAAAAGGTGTTAAATTGAAATCACGAGGC------------------------------------------------------------------------------ s droSec1.super_23 113108 91 + 989336 GCCAT-CGA-CAAGTTC----CC-------------------------AACAATTG----GCCATGGCTAAAA------------------GGGCA----------------------GTCGGGCGCAAAATGCCGCCAAAAGGTGTTAAATTGAAATCACGAGGC------------------------------------------------------------------------------ s droYak3.chr2R 20202213 91 + 21139217 GCCAT-CGA-CAAGTTC----CC-------------------------AACAATTG----GCCATGGCTAAAA------------------GGGCA----------------------GCCGGGCGCAAAATGCCGCCAAAAGGTGTTAAATTGAAATCACGAGGc------------------------------------------------------------------------------ s droEre2.scaffold_4845 21600194 90 + 22589142 GCCAT-CGA-CAAGTTC----CC-------------------------AACAATTG----GCCATGGCTAAAA------------------GGGCA-----------------------CCGGGCGCAAAATGCCGCCAAAAGGTGTTAAATTGAAATCACGAGGC------------------------------------------------------------------------------ s droBia2.KB462602 792368 91 + 3129309 GCCAT-CGA-CAAGTTC----CC-------------------------AACAATTG----GCCGTGGCTAAAA------------------GGGCA----------------------CACGGGCGCAAAATGCCGCCAAAAGGTGTTAAATTGAAATCACGAGGC------------------------------------------------------------------------------ s droSuz1.KI419649 12037520 91 - 14502029 GCCAT-CGA-CAAGTTC----CC-------------------------AACAATTG----GCCATGGTTAAAA------------------GGGCA----------------------CACGGGCGCAAAATGCCGCCAAAAGGTGTTAAATTGAAATCACGAGGC------------------------------------------------------------------------------ s droAna3.scaffold_13266 5707598 94 - 19884421 GTTCC-CAGCCCAGTTA----CC-------------------------GACAATCG----GTTTTGGCCAAAA------------------GGGCAAA--------------------CACAGGCGCAAAATGCCGCCAAAAGGTGTTAAATTGAAATCACGAGGC------------------------------------------------------------------------------ s droBip2.KB464407 1956368 93 + 2915140 GTTCC-CAG-CCAGTTA----CC-------------------------AACAATTG----GCGATGGCCAAAA------------------GGGCAAA--------------------CACAGGCGCAAAATGCCGCCAAAAGGTGTTAAATTGAAATCACGAGGC------------------------------------------------------------------------------ s droEug2.KB465067 597269 91 + 1515531 GCCAT-CGA-CAAGTTC----CC-------------------------AACAattg----gccatggccaaaa------------------gGGCA----------------------CAGGGGCGCAAAATGCCGCCAAAAGGTGTTAAATTGAAATCACGAGGC------------------------------------------------------------------------------ s droEle2.KB458573 517724 85 - 5320397 -------GA-CAAGTTC----GC-------------------------AACAattg----gccatggccaaaa------------------gGGCA----------------------CACAGGCGCAAAATGCCGCCAAAAGgtgttaaattgaaatcacgaggc------------------------------------------------------------------------------ s droKik2.KB459527 272570 113 - 1234237 CCCAT-CGA-CAAGTTC----CC-------------------------AACAATTG----GCCATGGCCAAAA------------------GGGCGCAAGCATGAACGCAGCCACAGGCACAGGCGCAAAATGCCGCCAAAAGGTGTTAAATTGAAATCACGAGGC------------------------------------------------------------------------------ s droTak2.KB461535 137512 91 - 669855 GCCAT-CGA-CAAGTTC----CC-------------------------AACAATTG----GCCATGGTTAAAA------------------GGGCA----------------------CACGGGCGCAAAATGCCGCCAAAAGGTGTTAAATTGAAATCACGAGGc------------------------------------------------------------------------------ s droRho2.KB449310 31340 93 - 65043 GCCAT-CGA-CAAGTTC----CC-------------------------AACAATTG----GCCATGGCCAAAA------------------GGGCACA--------------------CACAGGCGCAAAATGCCGCCAAAAGGTGTTAAATTGAAATCACGAGGC------------------------------------------------------------------------------ s droFic2.KB457177 77442 95 + 995874 GCCGT-CGA-CAAGTTCCCAGCC-------------------------AACAATTG----gcaatggccaaaa------------------gggcA----------------------CACAGGCGCAAAATGCCGCCAAAAGGTGTTAAATTGAAATCACgaggc------------------------------------------------------------------------------ s droPse3.chr3 1345819 115 - 19787792 TCCAC-AGA-CCCGATC----CCCACGCCATGCGTCTCCCCTAACCCAAACCATTA----AACATGGCCAAAA------------------GGGCA----------------------CA-AGGCGCAAAATGCCGCCAAAAGGTGTTAAATTGAAATCACGAGGC------------------------------------------------------------------------------ s droPer1.super_34 534684 115 - 916997 TCCAC-AGA-CCCGATC----CCCACGCCATGCGTCTCCCCTAACCCAAACCATTA----AACATGGCCAAAA------------------GGGCA----------------------CA-AGGCGCAAAATGCCGCCAAAAGGTGTTAAATTGAAATCACGAGGC------------------------------------------------------------------------------ s droMir2.chr3 1386910 115 - 20862834 TCCAC-AGA-CCCGATC----CCCACGCCATGCGTCTCCCCTAACCCAAACCAtta----aacatggccaaaa------------------gggCA----------------------CA-AGGCGCAAAATGCCGCCAAAAGGTGTTAAATTGAAATCACGAGGC------------------------------------------------------------------------------ s droWil2.CH963894 1304647 94 + 2843958 TCGAA-CGA-AATGTCC----GC----------------------GCACACACATGTAAAACAATGGCCAAAA---------------CCTGGCCA----------------------AA-------AAGGTGCCGCCAAAAGGTGTTAAATTGAAATCACGAGGC------------------------------------------------------------------------------ s droVir3.scaffold_12875 7347786 94 + 20611582 GCCATGTAA-AACGCTT----GC-------------------------AACAATGG----GGCACCGCCAGAG----------------------------------------------GCAGGCGCAAAATGCCGCCAAAAGGTGTTAAATTGAAATCACGAGGC-------------GC--------------------------------------------------------GCAGA-C s droMoj3.scaffold_6496 26142783 110 + 26866924 GCCATGTAA-AACGTTT----GC-------------------------AACAATGG----GACACCGACAGAG----------------------------------------------GCAAGCGCAAAATGCCGCCAAAAGGTGTTAAATTGAAATCACGAGGC-------------GCGC-------------------------------------TCTGCGCGCAAGCT---GCGAG-C s droAlb1.JH854640 306217 102 + 406291 GCCATGTAA-AACGGCC-----C-------------------------AACAATGG----GGCACCGCCACAGGCC-ACAGGC-----TTCAGGCC-----------------------GCAGGCGCAAAATGCCGCCAAAAGgtgttaaattgaaatcacGAGG------------------------------------------------------------------------------C s droGri2.scaffold_15245 896381 192 + 18325388 GCCATGTAA-AACGTTT----GC-------------------------AACAATGG----GGCACCGCCACAAGCCggcaggcaagcaggcaggcagtga------------------ggcaggcGCAAAATGCCGCCAAAAGGTGTTAAATTGAAATCACGAGGCTACGCGAGACACAGCGAAAGAGAGAGAGAGAGAGATTGAgtatgtgtgtgtgtgtgtgtgtgtgAGATGGGGCGAGTG a score=-202662.000000 s dm6.chr2R 24346692 32 + 25286936 CTgggattgggatt------ggggat-tggggat--------------------tgggC-------------------------------- s droSim1.chr2R 18693429 25 + 19596830 CTGGGATT-------------GGGAT-TGGGGAT--------------------TGGGC-------------------------------- s droSec1.super_23 113199 19 + 989336 C------T-------------GGGAT-TGGGGAT--------------------TGGGC-------------------------------- s droYak3.chr2R 20202304 45 + 21139217 ctgggatt-------------gggat-tcgggattcgggattggggattgggcctgggc-------------------------------- s droEre2.scaffold_4845 21600284 25 + 22589142 CTGGGATT-------------GGGAT-TGGGGAT--------------------TGGGC-------------------------------- s droBia2.KB462602 792459 18 + 3129309 TTGGGATT---------------------GGGCT--------------------GGAGC-------------------------------- s droSuz1.KI419649 12037611 18 - 14502029 TTGGGATT---------------------GGGCT--------------------GGAGC-------------------------------- s droBip2.KB464407 1956477 34 + 2915140 CTGGGAATTGTTTtc----agggggg-ggggggg--------------------ggagc-------------------------------- s droEug2.KB465067 597360 6 + 1515531 -----------------------------------------------------ATGGGC-------------------------------- s droEle2.KB458573 517809 18 - 5320397 tttggctt---------------------tggct--------------------ttggc-------------------------------- s droKik2.KB459527 272689 18 - 1234237 cttggctt---------------------tggct--------------------ttggc-------------------------------- s droTak2.KB461535 137603 24 - 669855 tggggatt-------------gggat-t-gggct--------------------tgggc-------------------------------- s droRho2.KB449310 31433 7 - 65043 --------------------------------TT--------------------TTGGC-------------------------------- s droFic2.KB457177 77537 12 + 995874 ---------------------------tttggct--------------------ttggc-------------------------------- s droPse3.chr3 1345938 19 - 19787792 -------------------CTCAGGC-TCAGGCT--------------------TGAGC-------------------------------- s droPer1.super_34 534803 19 - 916997 -------------------CTCAGGC-TCAggct--------------------tgagc-------------------------------- s droMir2.chr3 1387029 19 - 20862834 -------------------CTCAGGC-TCAGGCT--------------------TGAGC-------------------------------- s droWil2.CH963894 1304741 16 + 2843958 ----------------------TCTT-TTGAGCT--------------------TGGga-------------------------------- s droVir3.scaffold_12875 7347880 36 + 20611582 --------------CTGAGGCCAAGC-TGGGGGC--------------------CAAGC--------------------ATTGGCTTTGGC s droMoj3.scaffold_6496 26142893 31 + 26866924 --------------CTGAGGCCAAGC-TGGGGGC--------------------CAAGC-------------------------TTTTAGC s droAlb1.JH854640 306319 56 + 406291 --------------CTGAGGCCAAGC-TGGGGGC--------------------CAAGCGCTTGTCTcggctttgctttgcttggcttggc s droGri2.scaffold_15245 896573 41 + 18325388 --------------CTGAGGGCAAACTTGGGGGC--------------------CAAGC----------------GCATTTTGGCTTTGGC a score=3159918.000000 s dm6.chr2R 24346724 533 + 25286936 TTGGGAATTGTTTGTT--TC------GGGGC-CAGC-------TTGCA------------------GCACGGA------------------AGC-TTA--------------------------------------------------------------------------GGCCGCAGC--------CTCGT-----------------------CGGCAGATTGTGCCCAGATAAGA-------------------------------------------------CC---CAG---AAAGCCG-------------------GGCCA-AGAGGCT----------------------------------------CCACGTCGGC---------TCGCCTTTTG----GCCACATGCAA-C------------A-----GGC--T----GTG--------------G---CCTC----------------------TGCCACATA-------CGGGGA------------------------------AAAC----AGG------------------------------------------------CAACAATCGGCTTCTAACAAATGACTCTC-------------------C--ATCTGG----------------ACGGA-------------------GC-----GG-T-----CGC-------GGTCTCTGGG---GC--TGCC--------TTCTTGTCCTGTCAAC-------GCGC------------------------TCGTACC--------------------CCAAT-CCTC--G-C------------CCGAAT-----------C--------CGA--------GTCGTGTCCTTTTGTCTT--TGTTCGAAATTCAAATTGACATGAATTGTTGG---------------------C-------CTG-CTCG-----------------------------CGG---TGCCCAAGT-----AG-------CC--------------------------------TTCCTTCCTAGC----CGC------------------ACAATCGACACCTACtcagaa------------ccagcatctgaatcagaatccgaatgcgatt-------------tcgaatcggaatcagaacgagaat--aatcggaatc--c-gattcagattcCG------------CTTTCGG-----ACCGTGTCAATTGTTTGCATTTACACATGT-----TACACATAAAATTGGCAGCCA s droSim1.chr2R 18693454 550 + 19596830 TTGGGAATTGTTTGTT--TC------GGGGC-CAGC-------TTGCA------------------GCACGGA------------------AGC-TTA--------------------------------------------------------------------------GGCCGCAGC--------CTCGT-----------------------CGGCAGATTGTGCCCAGATAAGC-------------------------------------------------CC---CAG---AAAGCCG-------------------GGCCA-AGAGGCT----------------------------------------CCACGTCGGC---------TCGCCTTTTG----GCCACATGCAA-C------------A-----GGC--T----GTG--------------G---CCTC----------------------TGCCACATA-------CGGGGG------------------------------AAAC----AGG------------------------------------------------CAACAATCGGCTTCTAACAAATGACTCTC-------------------C--ATCTGG----------------ACGAAgcggtcgcggtcg-cggtcgc-----gg-t-----cgc-------ggtcTCTGGG---GC--TGCC--------TTCTTGTCCTGTCAAC-------GCGC------------------------TTGTACC--------------------CCAAT-CCTC--G-C------------CCGAAT-----------C--------CGA--------GTCGTGTCCTTTTGTCTT--TGTTCGAAATTCAAATTGACATGAATTGTTGG---------------------C-------CT--CTCG-----------------------------CGG---TGCCCAAGT-----AG-------CC--------------------------------TTCCTTCCTAGC----CAC------------------ACAATCGACACCTACTCAGAA------------GCAGCATCAGAATCAGAATCCGAATCCGATT-------------TCGAATCGGAATCAGAACGAGAAT--AATCGGAATC--C-GATTCAGATTCCG------------CTTTCGG-----ACCGTGTCAATTGTTTGCATTTACACATGT-----TACACATAAAATTGGCAGCCA s droSec1.super_23 113218 532 + 989336 TTGGGAATTGTTTGTT--TC------GGGGC-CAGC-------TTGCA------------------GCACGGA------------------AGC-TTA--------------------------------------------------------------------------GGCCGCAGC--------CTCGT-----------------------CGGCAGATTGTGCCCAGATAAGC-------------------------------------------------CC---CAG---AAAGCCG-------------------GGCCA-AGAGGCT----------------------------------------CCACGTCGGC---------TCGCCTTTTG----GCCACATGCAA-C------------A-----GGC--T----GTG--------------G---AGTC----------------------TGCCACATA-------CGGGGG------------------------------AAAC----AGG------------------------------------------------CAACAATCGGCTTCTAACAAATGACTCTC-------------------C--ATCTGG----------------ACGGA-------------------GC-----GG-T-----CGC-------GGTCTCTGGG---GC--TGCC--------TTCTTGTCCTGTCAAC-------GCGC------------------------TTGTACC--------------------CCAAT-CCTC--G-C------------CCGAAT-----------C--------CGA--------GTCGTGTCCTTTTGTCTT--TGTTCGAAATTCAAATTGACATGAATTGTTGG---------------------C-------CT--CTCG-----------------------------CGG---TGCCCAAGT-----AG-------CC--------------------------------TTCCTTTCTAGC----CAC------------------ACAATCGACACCTACTCAGAA------------GCAGCATCAGCATCAGAATCCGAATCCGATT-------------TCGAATCGGAATCAGAACGAGAAT--AATCGGAATC--C-GATTCAGATTCCG------------CTTTCGG-----ACCGTGTCAATTGTTTGCATTTACACATGT-----TACACATAAAATTGGCAGCCA s droYak3.chr2R 20202349 569 + 21139217 ttgggaattgtttgtt--tc------ggggC-CAGC-------TTGCA------------------GCACGGA------------------AGC-TTA--------------------------------------------------------------------------GGCCGCTGC--------CTCGT-----------------------CGGCAGATTGTGCCCAGATAAGC-------------------------------------------------CG---CAG---AAAGCCG-------------------GGCCA-AGAGGCT----------------------------------------CCACGTCGGC---------TCGCCTTTTG----GCCACATGCAA-C------------A-----GCC--T----GTTGC------------G---CCTT----------------------TGCCACATA-------CGGGGGC-A--------------TCGGGCATCGGGCAAGG-----GG------------------------------------------------CAACAATCGGCTTCTAACAAATGACTCTC-------------------C--ATCTGG----------------ACGAA-------------------GC-----GG-T-----CGC-------GGTCTCTGGG---GC--TGCC--------TTCTTGTCCTGTCAAC-------GCGC------------------------TCGTACC--------------------CCAAT-CCTC--G-CCCGaatccgattccgaat-----------c--------cga--------GTCGTGTCCTTTTGTCTT--TGTTCGAAATTCAAATTGACATGAATTGTTGG---------------------C-------CTG-CTCG-----------------------------CGG---TGCCCAAGT-----AG-------CC--------------------------------CTC----CTAGC----CAC------------------ACAATCGACACCTActcagaaccagaaccagaaccagaagcagcatcagaatcagaatccgATT-------------TCGAATCGGAATCAGAACGAGAAT--AATCGGAATA--C-GATTCAGATTCCG------------CTTTCGG-----ACCGTGTCAATTGTTTGCATTTACACATGT-----TACACATAAAATTGGCAGCCA s droEre2.scaffold_4845 21600309 540 + 22589142 TTGGGAATTGTTTGTT--TC------GGGGC-TAGC-------TTGCA------------------GCACGGA------------------AGC-TTA--------------------------------------------------------------------------GGCCGCAGC--------CTCGT-----------------------CGGCAGATTGTGCCCAGATAAGC-------------------------------------------------CG---CAG---AAAGCCG-------------------GGCCA-AGAGGCT----------------------------------------CCACGTCGGC---------TCGCCTTTTG----GCCACATGCAA-C------------A-----GGC--T----GTG--------------G---CCTC----------------------AGCCACATA-------CGAGGG------------------------------AAAC-----GG------------------------------------------------CAACAATCGGCTTCTAACAAATGACTCTC-------------------C--ATCTGG----------------ACGGA-------------------GC-----AG-T-----CGC-------GGTCTCTGGG---GC--TGCC--------TTCTTGTCCTGTCAAC-------GCGC------------------------TGGTACC--------------------CCAAT-CCTC--G-C------------CCGAAT-----------C--------CGA--------GTCGTGTCCTTTTGTCTT--TGTTCGAAATTCAAATTGACATGAATTGTTGG---------------------C-------CTG-CTCG-----------------------------CGG---TGCCCAAGT-----AG-------TC--------------------------------TTC----CTAGC----CAC------------------ACAATCGACACCTACTCAGAACCAGACGCAGACGCAGACTCAGACTCAGAATCAGAATCCGATT-------------TTGAATCGGAATCAGAACGAGAAT--AATCGGAATC--C-GATTCAGATTCCG------------CATTCGG-----ACCGTGTCAATTGTTTGCATTTACACATGT-----TACACATAAAATTGGCAGCCA s droBia2.KB462602 792477 560 + 3129309 TTGGGAATTGTTTGCT--TT----GGGGGAC-CAGC-------TTGCAGCTCGCCTTCAGCTTCCAGCACGGA------------------AGC-TTA--------------------------------------------------------------------------AGCCGCGGC--------CGCGT-----------------------CGGCAGATTGTGCCCAGATAAGC-------------------------------------------------CG---CGG---AAAGCCG-------------------GGCCA-AGAGGCT----------------------------------------CCGAGTCGGC---------TCGCCTTTTG----GCCACATGCAA-C------------A-----GGC--CAGCAGTT--------------G---CCTT----------------------AACAACACA-------GGGGGCA-ACACATATGCA----GGGGGCAACGA--AAAC----AGG------------------------------------------------CAACAATCGGCTTCTAACAAATGACTCTC-------------------C--ATCTGG----------------ACGGC-------------------AC-----GGCC-----CGC-------GGTCTCTGGG---GC--CGCC--------TTCTTGTCCTGTCAAC-------GCTT------------------------TCGGACC--------------------CCAAT-CCTC--G-C------------CCCAAT----------GC--------CGA--------GTCGTGTCCTTTTGTCTT--TgttcgaaattcaaattgaCATGAATTGTTGG---------------------C-------CTG-CTCG-----------------------------CGG-C-TACGCGGGC-----AG--------C--------------------------------TAC----CTAGG----CAC------------------ACAATCGACACCTACTCAGAC------------------------TCAGAATGTGCATC-------------------GGCATCGGAATCAGAACGAGAAT--AATCGAAATC--C-GATTCGGATTCCG------------CTTTCGG-----ACCGTGTcaattgtttgcatttacACATGT-----TACACATAAAATTGGCAGCCA s droSuz1.KI419649 12037629 560 - 14502029 TTGggaattgtttgtt--tt--tggggggAC-CAGC-------TTCCA----GCCTTCAGCTTCCAGCACGGA------------------AGC-TTA--------------------------------------------------------------------------AGCCCCAGC--------CGCGT-----------------------CGGCAGATTGTGCCCAGATAAGC-------------------------------------------------CC---CAG---AAAGCCG-------------------GGCCA-AGAGGCT----------------------------------------CCAAGTCGGC---------TCGCCTTTTG----GCCACATGCAA-C------------A-----GGC--T-GTTGTT--------------G---CCTC----------------------TACAACACA-------AGGGGCA-ACACATATGTAAgg-gggggCAACGA--AAAC----AGG------------------------------------------------CAACAATCGGCTTCTAACAAATGACTCTC-------------------C--ATCTGG----------------ACGGA-------------------AC-----AGCC-----CGC-------GGTCTCTGGG---GC--TGCC--------TTCTTGTCCTGTCAAC-------GCTT------------------------TCGTACC--------------------CCAAT-CCTC--G-C------------CCCAAT----------CC--------CGA--------GTCGTGTCCTTTTGTCTT--TGttcgaaattcaaattgaCATGAATTGTTGG---------------------C-------CTG-TTCG-----------------------------CGG-A-TACGCGGGC-----AG--------C--------------------------------TAC----CTAGG----CAC------------------ACAATCGACACCTACTCAGAA------------------------TCAGATTCAGAATG-------------------TGAATCGGAATCAGAACGAGAAT--AATCGAAATC--C-GATTCAGATTCCG------------CTTTCGG-----ACCGTGTCAATTGTTTGCATTTACACATGT-----TACACATAAAATTGGCAGCCA s droAna3.scaffold_13266 5707709 556 - 19884421 CTGGGAATTGTTTGTG--GC----AAGGAGC-TCGA-------AGGCA------------------GCACGGA------------------AGC-GTA-----------------------------------------------------------------------------TTGATA--------CTCG------------------------CGGCAGATTGTGGCCAGATAAGT---------------------------------------------CGG-CC---CCG---AAAGCCA-------------------GGCCA-AGAGGCTCCGGCGCggctggctggctggctggctggctTGGCCTTCGCCGCGTCGGC---------TTGCCTTTTGGCTTGCCACATGCAA-C------------A-----GAA--C----AGA--------------A---------------------------------------------------------------------------------GAAC----AGG------------------------------------------------CAACAATCGGCTTCTAACAAATGACTCTC-------------------C--ATCTGG----------------CCT-------------------------------C-------C-------GGTCTCTGGG---GC--TACC---------TCTTGTCCTGTCATC-------GCTT------------------------TCG----GGGCTATATCCTCTCCAGAGCCTATGCCTA--TGC------------CTCCTT-----------C--------TGCCGCGT---GTCGTGTCCTTTTGTCTT--TGTTCGAAATTCAAATTGACATGAATTGTTGG------------C--------C-------CTG-TTGG-----------------------------CGG-T-GGATCGCGG-----AG------------------------------------------------CTAGG----CTTGGCCCAAAAGGCCCAGCCACAATCGACACCTACTCAGAT------------------------TCCGATTCCGATTCAGAAT-------------CTGAATC-----------------------GAAATG--G-AATTCAGATTCCG------------CTTTCGGACCAGACCGTGTCAATTGTTTGCCTTTACACATGT-----TACACATAAAATTGGCAGCCA s droBip2.KB464407 1956511 534 + 2915140 -aggagcaggaccagg--ac----caggagc-aCCATACAACCATACA-------------ACCAGGCACGGA------------------AGC-GTA-----------------------------------------------------------------------------TTGATA--------CTCG------------------------CGGCAGATTGTGCCCAGATAAGT----------------------------------------------------------------CCA-------------------GGCCA-AGAGGCTCCGCCATGGCTGGC--------------------------CTTCGTCGGC---------TTGCCTTTTG----GCCACATGCAACC------------C-----CAG--T----CGA--------------G---------------------------------------------------------------------------------AAAC----AGG------------------------------------------------CAACAATCGGCTTCTAACAAATGACTCTC-------------------C--ATCTGG----------------CCTTT--------------------C-----GG-T-------C-------GGTCTCTGGG---GC--TACCTTGCCTGCTTCTTGTCCTGTCAAC-------GCTT------------------------ACGTACTGGGGTCCAGCCCAAGCCAAGCCAAT-CCTC--T-C------------CAGCCT-----------C--------TGCCGCGTGTCGTCGTGTCCTTTTGTCTT--TGTTCGAAATTCAAATTGACATGAATTGTTGG---------------------C-------CTG-TT-------------------------------TTG-T-GGATCGCAG-----AG-------------------------------------------C----CTAGG----CTT-------ATGGTCCAGGGACAATCGACACCTACTCAGAT------------------------TCCGATTCAGAAaccgatt-------------ctgattc----------------------tgaaATG--G-AATTCAGATTCCG------------CATTCGG---AGACCGTGTCAATTGTTTGCATTTACACATGT-----TACACATAAAATTGGCAGCCA s droEug2.KB465067 597366 536 + 1515531 TTGGGAATTGTTT-----TC----GGGGGAT-CAGC-------TTCCG------------------TGCTGGA------------------AGG-TAA--------------------------------------------------------------------------AGCCCCAGC--------CTCGT-----------------------CGGCAGATTGTGCCCAGATAAGC-------------------------------------------------CC---CAGAAAAAAGCCG-------------------GGCCA-AGAGGCT----------------------------------------CCACGTCGGC---------TCGCCTTTTG----GCCACATGCAA-C------------A-----GGC--C----GTA--------------G---CCCC----------------------AGCAACATACAACACTCGGGGC------------ACCA-AGGGGAAACTGGCAAAC----AGG------------------------------------------------CAACAATCGGCTTCTAACAAATGACTCTC-------------------C--ATCTGG----------------AGGGA-------------------GC-----AG-CCAGCGCGC-------GGTCTCTGGG---GC--TGCC--------TTCTTGTCCTGTCAAC-------GATT------------------------TCGTACC--------------------CCAAT-CCTC--G-C------------CCGAAT-----------C--------CGA--------GTCGTGTCCTTTTGTCTT--TGTTCGAAATTCAAATTGACATGAATTGTTGG---------------------C-------CTG-TTCG-----------------------------CGG-T-TGCCCGGGC-----AG--------C--------------------------------TAC----CTAGG----CAT------------------ACAATCGACACCTACTCAGAA------------------------Ccagaatc-------------------------ggaatcggaatcacAACGAGAAT--AATCGAAATC--C-GATTCAGATTCCG------------CTTTCGG-----ACCGTGtcaattgtttgcatttacaCATGT-----TACACATAAAATTGGCAGCCA s droEle2.KB458573 517827 535 - 5320397 ttgggAATTGTTT-----TC----GGgggcc-cagc--------agca------------------gcacgga------------------AGC-TAA--------A-----------------------------------------------------------------GGCTGCAGC--------CTCGT-----------------------CGGCAGATTGTGCCCAGATAAGC-----------------------------------------------C-CC---CAG---AAAGCCG----------------------------GGCT----------------------------------------CCACGTCGGC---------TCGCCTTTTG----GCCACATGCAA-C------------A-----GGC--T----gta--------------agaacaac----------------------aacaacata-------aggAGG-----------------AAGGGGCCGGG--AAAC----AGG------------------------------------------------CAACAATCGGCTTCTAACAAATGACTCTC-------------------C--ATCTGG------------------------------------------------G-C-----CGC-------GGTCTCTGGGGCTGC--TGCC--------TTCTTGTCCTGTCAAC-------GCTT------------------------TCGTACC--------------------CCAAT-CCTC--G-C------------CAGTG------------C--------AGT--------GTCGTGTCCTTTTGTCTT--TGTTCGAAATTCAAATTGACATGAATTGTTGG---------------------C-------CTGTTTTG-----------------------------CGGAT-TACCCGGGT-----AT-------CCGCAATATCCAATACCAAACACCCAATACCCGGTAC----CTAGG----CAT------------------ACAATCGACACCTACTCAGAa------------------------gcaga-------------------------------atcagaatcagaacaAGAAT--AATCGaaatt--cagattcagattccg------------CTTTCGG-----ACCGTGTCAATTGTTTGCATTTACACATGT-----TACATATAAAATTGGCAGCCA s droKik2.KB459527 272712 516 - 1234237 ttgggaATTGTTT-----TC----GGgggcc-ccag-------cagca------------------gcacgga------------------AGC-TTC--------------------------------------------------------------------------------ACC--------ATCGG-----------------------CGGCAGATTGTGCCCAGATAAGC-------------------------------------------------CC---CT----AAAGCCG-------------------GGCCAGAGAGGCTCCTCCATGGCTGGG--------------------------CCGTGGCGGC---------TCGCCTTTTG----GCCACATGCAA-C------------A----------C----ATG--------------C---ATgc----------------------agccaggca-------ggcagcctACA-------------------------AAAC----AGG------------------------------------------------CAACAATCGGTTTCTAACAAATGACTCTC-------------------C--ATCTGG----------------TCGGA-------------------GC-----AG-C-----AAC-------AGTCTCTGGG---GCTGTGCC--------TTCTTGTCCTGTCAAC-------GCTT------GCCCTCAC----------CCTTACC---------------CTTAACCAAT-CCTC--G-C-----------------------------C--------AGT--------GTCGTGTCCTTTTGTCTT--TGTTCGAAATTCAAATTGACATGAATTGTTGG---------------------C-------TTG-CTCGGGTC-----------------------CCTGG-C-TGTTCGG--------------------------------------------------GAC----CTAGGCTCACAT------------------ACAATCGACACCTACTCAGAA------------------------TCGGa----------------------------ggaatcgaaatcga-----------aatccgattc--a-gattcagattccg------------CATTCGG-----ACCGTGTCAATTGTTTGCATTTACACATGT-----TACACATAAAATTGGCAGCCA s droTak2.KB461535 137627 556 - 669855 ttgggaattgtttgct--tttttggggggaG-CAAC-------TTTCA-----------GCTTCCAGCACGGA------------------AGC-TTA--------------------------------------------------------------------------AGCCCCAGC--------CTCGT-----------------------CGGCAGATTGTGCCCAGATAAGC-------------------------------------------------CC---CAG---AAAGCCG-------------------GGCCA-AGAGGCT----------------------------------------CCAAGTCGGC---------TCGCCTTTTG----GCCACATGCAA-C------------A-----GGC--T----GTGTTGTTGccttaacaa---caac----------------------aacaacaca-------ggGGGC------------AGCACAAGGGGTATGA--AAAC----AGG------------------------------------------------CAACAATCGGCTTCTAACAAATGACTCTC-------------------C--ATCTGG----------------ACGGA-------------------GCACACAGG-C-----CGC-------GGTCTCTGGG---GC--TGCC--------TTCTTGTCCTGTCAAC-------GCTT------------------------TCGTACC--------------CTCGTACCAAT-CCTC--G-C------------CCCAAT----------CC--------CGA--------GTCGTGTCCTTTTGTCTT--TgttcgaaattcaaattgaCATGAATTGTTGG---------------------C-------CTG-TTCG-----------------------------CGG-A-TACGCGGCT-----ACGCGGCTACC--------------------------------TAC----CTAGG----CAT------------------ACAATCGACACCTActcagaa------------------------tcaga-------------------------------atcggaATCAG------TAT--AATCGAAATC--C-GATTCAGATTCCG------------CTTTCGG-----ACCGTGTCAATTGTTTGCATTTACACATGT-----TACACATAAAATTGGCAGCCA s droRho2.KB449310 31440 493 - 65043 TTGGGAATTGTTT-----TC----GGgggcc-cagc--------agca------------------gcacggA------------------AGC-TTG-AGGTTTAA-----------------------------------------------------------------GGCTGTAGCCTTAGCCACTCGT-----------------------CGGCAGATTGTGCCCAGATAAGC-------------------------------------------------CC--GCAG---AAAGCCG-------------------GGCCA-AGAGGCT----------------------------------------CCACGTCGGC---------TCGCCTTTTG----GCCACATGCAA-C------------A-----GGCCAT----GTG--------------G---CA---------------------------CACAAA-------AGGGGA-----------------AGAGGCAGGGGAAAAAC----AGG------------------------------------------------CAACAATCGGCTTCTAACAAATGACTCTC-------------------C--ATCTG-----------------------------------------GC--------C-----CGC-------GGTCTCTGGG---GC--TGCC--------TTCTTGTCCTGTCAAC-------GCTT------------------------TCGTacc--------------------ccaat-ccca--a-t-----------------------------c--------cca--------atcgtGTCCTTTTGtctt--tgttcgaaattcaaATTGACATGAATTGTTGG---------------------C-------CCGTTTCG-----------------------------CGG---------------------------T--------------------------------TAC----CTAGC----CAC------------------ACAATCGACACCTACTCAGAA------------------------TCCGA-------------------------------------ATCACAACAAGAAT--AATCGAAATC--C-GATTCAGATTCCG------------CTTTCGG-----ACCGTGTCAATTGTTTGCATTTACACATGT-----TACACATAAAATTGGCAGCCA s droFic2.KB457177 77549 542 + 995874 ttggGAATTGTTT-----TC----GGTGGCC-CAGA-----------A------------------GCACGGAAGCCCCGGCTTCAGTCGCAGC-TTC--------------------------------------------------------------------------AGCCTCAGC--------CTCGT-----------------------CGGCAGATTGTGGCCAGATAAGC-------------------------------------------------CG---CAG---AAAGCCG-------------------GGCCA-AGAGGCT----------------------------------------CCGCGGCGGC---------TCGCCTTTTG----GCCACATGCAA-C------------A-----GGC--T----GAA--------------C------------------------------ACAACACA-------CGGGGC----ACAGGCGAACACTCGGGGCA------AAAC----AGG------------------------------------------------CAACAATCGGCTTCTAACAAATGACTCTC-------------------C--ATCTG------------------------------------------------GA-C-----CGC-------GGTCTCTGGG---GC--TGCC--------TTCTTGTCCTGTCAAC-------GCTT---------------------------------------------------------CCGA--G-C-----------------------------C--------CCA--------ATCGTGTCCTTTTGTCTT--TGttcgaaattcaaattgaCATGAATTGTTGG---------------------C-------CTG-TTTGGGTCCAGGGTTCCTCGGCTCTTCAGCTCCTGG-G-TTCCTGGGTTCCTGAG-----------------------------------------CAC----CTAGG----CAC------------------ACAATCGACACCTACTCGGAA------------------------TCAGAAAC-------------------------AGAATCGGAGTGAGAATAAGAATCGAAATCGAATC--C-GATTCAGATTCCG------------CTTTCGG-----ACCGTGtcaattgtttgcatttacaCATGT-----TACACATAAAATTGGCAGCCA s droPse3.chr3 1345983 614 - 19787792 TTGGGAATTGTTT-----TC----gggggctgctgc-------ttcca------------------GCACGGA------------------AGC-GTATTGATGCAC-----------------------------------------------------------------AGAAGCGGC--------AGCGTCAGCACCAGGGGCAGCACCAGTGCGGCAGATTGTCCACAGATAAGC----------------------------------------------GG-CC---CCC---AAGACC--------------------------AGAGGCT----------------------------------------CCTCGATGgctggtcggctttgccttttg----gccacatgcaa-c------------accaacaga--a----aca--------------g---caac----------------------agcaacaga-------------------------------------------aaac----aac------------------------------------------------caacaaTCGCCTTCTAACAAATGACTcttgccgctctctctctccctgc--gcctggtgcctgttgcctgctgcctgg--------------tgcctgc-----tg-c-----c-c-------ggtctctggg---gc--tgcc-----------ttgtcctgTCAAC------AGATT------------------------TCTTACC--------------------CCAAT-CCTCCAA-T------------CCAAGCCTTCTGCTGCCT--------CGT--------GTCGTGTCCTTTTGTCTT--TGTTCGAAATTCAAATTGACATGAATTGTTGGTGTTGgatctggc--------c-------ctg-gccc-----------------------------ctg---gACCTAGGG-----CA-------CC--------------------------------ATC----CTCGG------T------------------ACAATCGACACCTACtcagaa------------------------cgagaacgagaat--------------------cGAATGAGAATCGG-----------ATccggattc--a-gattcagattcagttgctgctcctcctttcgG-ACCGACCGTGtcaattgtttgcatttacACATGT-----TACACATAAAATTGGCAGCCA s droPer1.super_34 534848 608 - 916997 ttggGAATTGTTT-----TC----GGGGGCTGCTGC-------TTCCA------------------GCACGGA------------------AGC-GTATTGATGCAC-----------------------------------------------------------------AGAAGCGGC--------AGCGTCAGCACCAGGGGCAGCACCAGTGCGGCAGATTGTCCACAGATAAGC----------------------------------------------GG-CC---CCC---AAGACC--------------------------AGAGGCT----------------------------------------CCTCGATGGCTGGTCGGCTTTGCCTTTTG----GCCACATGCAA-C------------ACC--------A----ACA--------------G---CAAC----------------------AGCTACAGA-------------------------------------------AAAC----AAC------------------------------------------------CAACAATCGCCTTCTAACAAATGACTCTTGCCGCTCTCTCTCTCCCTGC--GCCTGGTGCCTGTTGCCTGCTGCCTGG--------------TGCCTGC-----TG-C-----C-C-------GGTCTCTGGG---GC--TGCC-----------TTGTCCTGTCAAC------AGATT------------------------TCTTACC--------------------CCAAT-CCTCCAA-T------------CCAAACCTTCTGCTGCCT--------CGT--------GTCGTGTCCTTTTGTCTT--TGTTCGAAATTCAAATTGACATGAATTGTTGGTGTTGGATCTGGC--------C-------CTG-GCCC-----------------------------CTG---GACCTAGGG-----CA-------CC--------------------------------ATC----CTCGG------T------------------ACAATCGACACCTACTCAGAA------------------------CGAGAACGAGAAT--------------------CGAATGAGAATCGG-----------ATCCGGATTC--A-GATTCAGATTCAGTTACTGCTCCTCCTTTCGG-ACCGACCGTGTCAATTGTTTGCATTTACACATGT-----TACACATAAAATTGGCAGCCA s droMir2.chr3 1387074 614 - 20862834 TTGGGAATTGTTT-----TC----GGGGGCTGTTGC-------TTCCA------------------GCACGGA------------------AGC-GTATTGATGCAC-----------------------------------------------------------------AGAAGCGGC--------AGCGT------------CAGCACCAGTGCGGCAGATTGTCCACAGATAAGC----------------------------------------------GG-CC---CCC---AAGACC--------------------------AGAGGCT----------------------------------------CCTCGATGgctggtcggctttgccttttg----gccacatgcaa-c------------accaacacc--a----aca--------------g---caac----------------------agcaacaga-------------------------------------------aaac----aac------------------------------------------------caacaaTCGCCTTCTAACAAATGACTcttgccg--ctctctctccctgc--gcctggtgcctgttgcccggtgcctgttgcccggtgccttctgcctgc-----tg-c-----c-c-------ggtCTCTGGG---GC--TGCC-----------TTGTCCTGTCAAC------AGATT------------------------TCTTACC--------------------CCAAT-CCTCCAA-T------------CCAAGCCTTCTGCTGCCT--------CGT--------GTCGTGTCCTTTTGTCTT--TGttcgaaattcaaattgacatgaattgttggtgttggatctggc--------c-------ctg-gccc-----------------------------ctg---gACCTAGGG-----CA-------CC--------------------------------ATC----CTCGG------T------------------ACAATCGACACCTACtcagaa------------------------cgagaacgagaat--------------------cGATTGAGAGTCGG-----------ATccggattc--a-gattcagattcagttgctgctcctcctttcgG-ACCGACCGTGtcaattgtttgcatttacaCATGT-----TACACATAAAATTGGCAGCCA s droWil2.CH963894 1304776 522 + 2843958 ttgttttttttttttt--tt-------tttt-ttgt-------tagta------------------gCACGGA------------------AGCAACA--------------------------------------------------------------------------GGCAGCGGC--------AGCCC----------------------GCGGCAGATTGTGAACAGATAAGC-------------------------------------------------CGAGACTT---GGGGCTA-------------------TACGC-CGCGGCT----------------------------------------CCTTCTTGGC---------TGGCATT-------GCC-CACGTCG-T------------C-----GGC--T----TTA--------------G---CTTTTGCTTGCTTCTTCTGAGTCTCATGCAACACA-------TGCAAC-----------------aagaataa-----aaacaacaagc------------------------------------------------cAACAATCGCCTTCTAACAAATGACTCTC---------------------------------------------------------------------------AG-G-----------------TCTCTGGG---GC--TGCC-----------TTGTCCTGTCACCTACCACCAATT------------------------CCATCCC------------------CTCCTTC-CCTT--C-C------------TCGAATGTT--------G--------CTT--------GTCGTGTCCTTTTGTCTT--TGTTCGAAATTCAAATTGACATGAATTGTTGGGTTCAGGCtaggcaacaacaac-------gtg-cCTG-----------------------------CCA------ATAGGC-----TA-------CC--------------------------------AGT----TTGCC----CGC------------------CCCCTCGACACCTACTCATCC----------------------------------------------------------------------------------AGCTAGTTTT--G-GGATCATCCTCAC------------TATCCAA----TATAGCGTCAATTGTTTGCATTTACACATGTTACGATACACATAAAATTGGCAGGCA s droVir3.scaffold_12875 7347916 512 + 20611582 TTGGGAATTGTTTGCG--TC------------TTGT-------GGCCA-----------------AGCACGGA------------------AGC-GTATTGATACCC------------------------------------------------------------------------GT--------AGCAG-----------------------CGGCAGATTGTGCACAGATAAGCC--------------------------------------AACCGGGCA-CA---GCC---GGCACAG-------------------GGCCG-ACAGTTT------------GG--------------------------CTGCGTCGGC---------TCGCCTTTTG----GCCACATGcaa-catgcagcagcaac-----agc--a----aca--------------g---aaac----------------------agcagcagc--------------------------------------------agc----agcagaagcagcagccgatgcaacagcggcggcagcagcagcaacatcagccaacaATCGCCTTCTAACAAATGACTCTG-------------------C--CGCT-------------------------------------------------CG-C-----TGC-------GGTCTCTGGG---GC-----------------TTGTCCTGTCAAC-------AA-----------------------------------------------------CCTGC-CCCC--G-C------------CCAGCCCTAG-------C--------TGC--------TTCGTGTCCTTTTGTCTTTGTGTTCGAAATTCAAATTGACATGAATTGTTGG---------------------C-------CCG-CTGA-----------------------------CTG-C-TGCTCGGCC-----CG-------GCCTA-----------------------------GTC----CCAGA----CCC------------------C-----------AGTCCACGG------------------------TCCCG-----------------------------------------GTTGCAGA----CAC---------C-TACTCAG---CGG------------C--CCGG-----GCCGTGTCAATTGTTTGCATTTACACATGT-----TACACATAAAATTGGCAGCCA s droMoj3.scaffold_6496 26142924 574 + 26866924 TTGGGAATTGTTCACT--------------------------------------------------GCACGGA------------------AGC-ATATTGAGACCCCTGgcagcagagccaacctcagcctcagccttagcagcaacagcagcagcagctaaagcagcagcagcagctaa--------agcag-----------------------cggcaGATTGTGCACAGATAAGC-------------------------------------------------GA---GCA---GGCACAG-------------------GGCCG-ACAGTTT------------GG--------------------------CTGCGTCGGC---------TCGCCTTTTG----GGCACATgcaa-c-tgcaactgcaac-----agc--a----gca--------------g---gaac----------------------agcaacagc--------------------------------------------aac----ag-------------------------------------------------caacaATCGCCTTCTAACAAATGACTCTG-------------------C--CTCT-------------------------------------------------CG-C-----TGC-------GGTCTCTGGG---GC-----------------TTGTCCTGTCAGC-------AAGC---------AGCAC----------GCACAGC--------------------CCCTC-TCCC--G-G------------GCTGCTCTAG-------C--------TAC--------ATCATGTCC-TTTGTCTTTGTGTTCGAAATTCAAATTGACATGAATTGTTGG---------------------C-------CCG-CTCG-----------------------------CTG-C-TGCCGAGCCT----CA-------CCCCA-----------------------------GTC----CCTGT----CCC------------------C------------GTCCCCAG------------------------TCTCAATCCCAATCCCAATCCGAATCCTCTGTCCTCATCTGCCTCCATCGCAGA----CACCTAC-TCAGC-TACTCAG---CGG------------C--CCGG-----ACCGTGTCAATTGTTTGCATTTACACATGT-----TACACATAAAATTGGCAGCCC s droAlb1.JH854640 306375 511 + 406291 ttgggaATTGTCTGCG--TC------------TTGT-------GGCCA------------------GCACGGA------------------AGC-GTATTGATACCC-------------------------------------------------------------------------G--------AACAG-----------------------CGGCAGATGGTGCACAgataaga---------------------------------------------gcagca---gca---gctgcagc------------------agccg-aCAGTTT------------GG--------------------------CTGCCTTG-----------TCGCCTTTTG----GCCACATGCAA-G-----------AC-----ACT--A----GCA--------------G-----------------------------AGGAGCAGC------------------------------------------------------------------------------------------------------CAACAATCGCCTTCTAACAAATGACTCTG-------------------CCTCGCT-------------------------------------------------CG-C-----TAC-------GGTCTCTGGG---GC-----------------TTGTCCTGTCAAC-------GTTTTCGTATCTGGCCACTGACTCAGCAGCACAGC--------------------TCCTC-TCCT--G-C------------TCCGCCCCTT-------CTTTCGCAGTGT--------GTCGTGTCCTTTTGTCTTTGTgttcgaaattcaaattgacaTGAATTGTTGG---------------------A-------TCG-CTGA-----------------------------CTG-CATGCTGCTTG-----TT-------GCCTG-----------------------------TTC----CCTGT----TGC------------------CTGTTGGATG-CCGCCTGCAG------------------------TCTAG---------------------------TTGCAGCAGCTCCCTGGGAAGA----GAACAACGTCACC-TACTCAG---TGG------------C--CCGG-----GCCGTGtcaattgtttgcatttacaCATGT-----TACACATAAAATTggcagcca s droGri2.scaffold_15245 896614 525 + 18325388 TTGGGAATTGTTTGCGCGTC------------TTGT-------GGCCA-----------------AGCACGGA------------------AGC-GTATTGATACCA-----------------------------------------------------------------------AGT--------AGCAG-----------------------CGGCAGATTGCGCGCAGATAAGACACAAgcaggagctggagctgaagctgaagctggagctgaagctggaA-CT---GCA---GCTATAGCAGAAGTGGCTAACAGTTTGGCCG-ACAGTTT------------GG--------------------------CTGCGTCGGC---------TCGCCTTTTG----GCCACATGCAA-C------------A-----GCC--A----ACA--------------G------------------------------GCAACAGC-------C-----------------------------------AAAC----AGCAAGGAA------------------------------------------CAACAATCGCCTTCTAACAAATGACTCGG-------------------C--CGCTCT----------------------------------------CG-----CG-C-----TGCTTGGCTTGGTCTCTGGG---GC-----------------TTGTCCTGTCAAT-------AGCC------------------------TCATAGC--------------------CCTGt-gtat--a-t------------gtatgtgtat-------gtgta----tgt--------gtCGTGTCCTTTTGTCTTTGTGTTCGAAATTCAAATTGACATGAATTGTTGG---------------------CAGCCTAGCCG-CCAG-----------------------------TTG-C---------------AA-------TCGTA-----------------------------TTC----CCAGC----CAC------------------A---------------------------------------------------------------------------------------------GCAGA----CACCTAC-----T-CACTGAG--TTGG------------C--CCGG-----GCCGTGTCAATTGTTTGCATTTACACATGT-----TACACATAAAATTGGCAGCCA a score=-509671.000000 s dm6.chr2R 24347257 115 + 25286936 ATCGATGT--CT-----GGCA-------GGGATGG------G-GTAG---------------CC--c--------aatccaatcc-----g-----------atcctatccgatacgata-cgatgcggtg-----cgatgcgatCCCCGGTATCCAATA-------------CCCAATACCCAATCC-----------------CCAT--CGC-A s droSim1.chr2R 18694004 110 + 19596830 ATCGATGT--CT-----GGCA-------GGGACGG------G-GTAG---------------Cc--c--------aatccaatcc-----g-----------atcctatc-----cgata-cgatgcggtg-----cgatgcgatccccggtatccaata-------------cccaatacccaatcc-----------------acat--cgc-a s droSec1.super_23 113750 103 + 989336 ATCGATGT--CT-----GGCA-------GGGACGG------G-GTAG---------------Cc--c--------aatccaatcc-----g-----------atcctatc-----cgata-cgatgcggtg-----cgatgcgatccccggtat--------------------ccaatacccaatcc-----------------acat--cgc-a s droYak3.chr2R 20202918 116 + 21139217 ATCGATGT--CT-----GCCAGGCTTTGGGGTTGG------G-GTAg---------------cc--c--------aatccaatcc-----a-----------atccaatg-----cGATC-CTATCCGATG-----CGATGCGATCCGCGGTATCCACTA--------------CCAATACCCAATTC-----------------GCAT--CGC-A s droEre2.scaffold_4845 21600849 123 + 22589142 ATCGATGT--CT-----GGCA-------GGGTGGG------G-GTAG---------------Cc--c--------aatccaatcc-----g-----------atccgatc-----cgatc-ctatccgatG-----CGAAGCGATCCCCGGCATCCAATAGCGATACCCAATACCCAATACCCAATCC-----------------CCAT--CGC-A s droBia2.KB462602 793037 90 + 3129309 ATCGAT----------------------GGAGTGG------G-TTAG---------------CC--------------CCCACCC-----C-----------ATCCAGTC-----CGATG-CGATACGATC-----CTATGCGATCCCCAGcac--------------------ccaat-cccaatcc-----------------ccat--CGC-A s droSuz1.KI419649 12038189 103 - 14502029 ATCGAT----------------------GGAGTGG------GTTTAA---------------CC--------------CCCATCC-----CATTCccatccaatccaatc-----cgatC-CGATACGATC-----CTATGCGATCCCCAATAC--------------------TCAATACCCAATCC-----------------CCAT--CGC-A s droAna3.scaffold_13266 5708265 106 - 19884421 ATCGATGT--AT-----TGGT-------TGGATGG------A-GGAGGAGATGCCCCCAACTCC--A--------CAGCTCTTCAGG---T-----------CTCCACTT-----GGAAAGCAATCCGATCTGAATCGATGCGATC----------------------------CCAAT-CCAG-------------------------------A s droBip2.KB464407 1957045 98 + 2915140 ATCGATGTCGATGT--ATGCT-------TGGATGG------G-GG-----------------CC--A--------TACCTCTTCA-----C-----------CTCTACCC-----CAAAACCAATCCGATC-----CGATGcgatc----------------------------ccaat-cccaatcc-----------------ccaA--TCC-A s droEug2.KB465067 597902 105 + 1515531 ATCGATGT--CG-----GGTG-------GAGTGGG------G-CTAA---------------CC--C--------AATCCGATCC-----C-----------ATCCAATC-----------CGATCTGTTC-----CGATGCGATCCCCAATACCCAATG-------------CCCAATGCTCAATGC-----------------CCAT--CGC-A s droEle2.KB458573 518362 112 - 5320397 ATCGATGT--CTGT---GTAT-------GGAGTGG------G-GCat---------------ccccc--------catcccatcc-----g----------aaaccaatc-----caatc-caatccgatc-----cgatgcgatccccaat-cccaatc--------------gcaat-cgcaatcc-----------------ccaa--tcc-a s droKik2.KB459527 273228 103 - 1234237 ATCGATGT--GT-----CTTG-------GAGTGGG------G-GAAA---------------CC--CCCAACCCAAACCCATTCC-----A-----------gaccaatc-----caatc-caatccgatc-----cgaggcgatc----------------------------ccaat-ccgaatcc-----------------caat--cccga s droTak2.KB461535 138183 73 - 669855 ATCGATG---------------------GGGTCGG------G-GTAA---------------CC--C-----------------C-----A-----------TCCCAATC-----CAATC-GAATCCGATC-----CTATGCGATC----------------------------------CCCAATCC-----------------CCAT--CGC-C s droRho2.KB449310 31933 91 - 65043 ATCGATGT--CTGTGTATGGT-------AGTTGGG------G-gtaa---------------tc--c-----------------------a-----------atccaatc-----------caatccgatg-----cgatgcgatccccaatc---------------------ccaat-cgcaatac-----------------ccaa--tcc-a s droFic2.KB457177 78091 97 + 995874 ATCGATGT--GT-----TAAG-------GGGTCGG------G-GTAA---------------CC--C--------AATCCAAACC-----A-----------ATCCAATC-----CAGTA-CGATCGGATG-----CGATGCGATCC---------------------------CCAAT-CGCAATCC-----------------CCACAGCCC-A s droPse3.chr3 1346597 53 - 19787792 ATCggtgt---------agca-------gc-----------a-gcag---------------ca--g-----------------------a-----------agccgatC--------------------------C-------------------------------------CGAAT-CACAGATC-----------------CCAG--ATC-C s droPer1.super_34 535456 53 - 916997 ATCGGTGT---------AGCA-------GC-----------A-GCAG---------------CA--G-----------------------A-----------AGCCGATC--------------------------C-------------------------------------CGAAT-CACAGATC-----------------CCAG--ATC-C s droMir2.chr3 1387688 64 - 20862834 ATCggtgt---------agca-------gcagcagcagaaga-gcag---------------ca--g-----------------------a-----------agccgatc--------------------------c-------------------------------------cgaat-cacagatc-----------------ccag--atc-c s droWil2.CH963894 1305298 72 + 2843958 ATCGATGT--AG-----ACCA-------ACACCAA------C-ATCG---------------CA--C---------------TCC-----G-----------TCGCACTA-----CATAA-TGCTCCGTTG-----C-------------------------------------TTCGT-CGC----T-----------------CCAT----C-G s droVir3.scaffold_12875 7348428 36 + 20611582 ------------------------------------------------------------------------------------------C-----------TGGCAACA-----------AGAGGCAGCA-----AGA-----------------------------------CCAGT-CTCACT-------------------GCC-------- s droMoj3.scaffold_6496 26143498 25 + 26866924 ------------------------------------------------------------------------------------------C-----------TGCCAGAG-----------ATTGGCAACC-----AGA------------------------------------------------------------------GCA-------- s droAlb1.JH854640 306886 74 + 406291 -------------------------------------------------------------------------------------agcagc-----------agccaaca-----------acgtgcaacg-----tgcactGAGTGCCAGTC---------------------CCAGT-CCCATTCCCAGtctcattctcattcgca-------- a score=1731625.000000 s dm6.chr2R 24347372 219 + 25286936 ATTCAG-------C-------------------CAACAA--TGTGTACAACAATTTCATTAATAT---TAATAAATGTT-CTCGAA-------------GCGTT-------------------TGC------TTCTCGGT--CGGTCGGCC---------A---------------------------------------G---TTATTTATGCGCT--GTGTTTTT--------CG------ACTCACG------GCAGCAAAAGTGG--------CGG------------------AAAGCAG-----------CAGAAACTGTTT----------------CCAGCC--------------A----GACTGAC--------TCGACTTTATCGCTTTTATAGTAATTACGAGCTGTTGATAGG-CAGCTTAGGCTACCG-------TC s droSim1.chr2R 18694114 220 + 19596830 atccaG-------C-------------------CAACAA--TGTGTACAACAATTTCATTAATAT---TAATAAATGTT-CTCGGA-------------GCGTT-------------------TGC------TTCTCGCT--CGGTCGGCC---------A---------------------------------------G---TTATTTATGCGCT--GTGTTTTT--------CG------ACTCACG------GCAGCAAAAGTGG--------CGG-----------------AAAAGCAG-----------CAGAAACTGTTT----------------CCAGCC--------------A----GACTGAC--------TCGACTTTATCGCTTTTATAGTAATTACGAGCTGTTGATAGG-CAGCTTAGGCTACCG-------TC s droSec1.super_23 113853 220 + 989336 atccaG-------C-------------------CAACAA--TGTGTACAACAATTTCATTAATAT---TAATAAATGTT-CTCGGA-------------GCGTT-------------------TGC------TTCTCGCT--CGGTCGGCC---------A---------------------------------------G---TTATTTATGCGCT--GTGTTTTT--------CG------ACTCACG------GCAGCAAAAGTGG--------CGG-----------------AAAAGCAG-----------CAGAAACTGTTT----------------CCAGCC--------------A----GACTGAC--------TCGACTTTATCGCTTTTATAGTAATTACGAGCTGTTGATAGG-CAGCTTAGGCTACCG-------TC s droYak3.chr2R 20203034 233 + 21139217 ATCCAG-------G-------------------CAACAA--TGTGTACAacaatttcattaatat---taataaatgtt-cTCGCA-------------GCGTT-------------------TGC------TTC----T--CGGTCGGCC---------A---------------------------------------G---TTATTTATGCGCT--GTGTTTTT--------CGACTCACACTCACG------GCAGCAAAAGTGG--------CGG-----------------AAAAGTGGCAGAAAAGCAGCCGAAACTGTTT----------------CCAGCC--------------A----GACCGAC--------TCGACTTTATCGCTTTTATAGTAATTACGAGCTGTTGATAGG-CAGCTTAGGCTACCG-------TC s droEre2.scaffold_4845 21600972 215 + 22589142 ATCCAG-------G-------------------CAACAA--TGTGTACAACAATTTCATTAATAT---TAATAAATGTT-CTCGGA-------------GCGTT-------------------TGC------TTC----T--CGGTCGGCC---------A---------------------------------------G---TTATTTATGCGCT--GTGTTTTT--------CG------ACTCACG------GCAGCAAAAGTGG--------CGG-----------------AAAAGCAG------------CGAAACTGTTT----------------CCAGCC--------------A----GACCGAC--------TCGACTTTATCGCTTTTATAGTAATTACGAGCTGTTGATAGG-CAGCTTAGGCTACCG-------TC s droBia2.KB462602 793127 245 + 3129309 ATCCGG-------CAATCCGGCAAT-----CCGCAACAA--TGtgtaaaacaatttcattaatat---taataaatgtt-ccCGAA-------------GCGAT-------------------TGC-CTGGCTTC----T--TGGTCCGCC---------A---------------------------------------G---TTATTTATGCGCT--GTGCTCTT--------CG------ACTCACG------GCAGCAAAAGTGG--------CGG-----------------AAAAGTAG-----------CAAAAACTGTTTT--------------GCCCGCC--------------A----GACCGAC-------AGCGACTTTATCGCTTTTATAGTAATTACGAGCTGTTGATAGG-CAGCTTAGGCTACCGTCTACCATC s droSuz1.KI419649 12038292 232 - 14502029 ATCCGA-------C-------------------CAACAA--TGTGTACAAcaatttcattaatat---taataaatgtt-cCCGAA-------------GCGTT-------------------TGCTTTTGCTTC----T--TGGTCCGCC---------A---------------------------------------G---TTATTTATGCGCT--GTGTTTTT--------CG------ACTCACG------GCAGCAAAAGTGG--------CGG-----------------AAAAGTAG-----------CAAAAACTGTTTT--------------GCCCGCC--------------A----GACCGAC-------AGCGACTTTATCGCTTTTATAGTAATTACGAGCTGTTGATAGG-CAGCTTAGGCTACCGTCTACCATC s droAna3.scaffold_13266 5708371 211 - 19884421 GACTCG-------C-------------------CAACAA--TGTGTACAACAATTTCATTAATAT---TAAT-ATTATA-----------------------------------------------------TTC----T--TGGTCCGCC---------ACT-------------TGGTAGCCCGGAGTAGCTGGAGCAG---TTATTTATGCGCT--GTGTTCTT-------GTG------CCTCC--------------------------------------------------AGAGCAG-----------CAGCAGCCGACA---------------GCCAGAC--------------A----GCCAGAC-------AGCGACTTTATCGCTTTTATAGTAATTACGAGCTGTTGATAGG-CAGCTTAGGCTACCG-------TC s droBip2.KB464407 1957143 231 + 2915140 GACTCGTACACATC-------------------CAACAA--TGTGTACAacaatttcattaatat---taataaatgtt-----------------------------------------------------tCC----C--TGgtccacc---------actaccaccaccaccaccaccaccgggGGCAGTAGCAGTGG---TTATTTATGCGCT--GTGTTCTT-------TTG------ACTCC--------------------------------------------------AAAGTAG-----------CAGCCAATGTTG---------------GCC-GAC--------------A----GCCAGAC-------AGCGACTTTATCGCTTTTATAGTAATTACGAGCTGTTGATAGG-CAGCTTAGGCTACCG-------TC s droEug2.KB465067 598007 214 + 1515531 ATGC---------C-------------------CAACAA--TGTGTACAAcaatttcattaatat---taataaatggt-CCTGGA-------------GCGTT-------------------TGC------TTC----T--CGGTCCGCC---------A---------------------------------------G---TTATTTATGCGCT--GTGTTTTT--------CG------ACTCACG------GCAGCCAAAGTGG--------CGG------------------AAAGCGG-----------CAGAAACTGTTG----------------CCAGCC--------------A----GACCGAC-------AGCGACTTTATCGCTTTTATAGTAATTACGAGCTGTTGATAGG-CAGCTTAGGCTACCG-------TC s droEle2.KB458573 518474 237 - 5320397 GACTCG-------C-------------------CAACAA--TGTGTACAacaatttcattaatat---taataaatgtt-tccGAA-------------GCGTT-------------------TGC------TTC----T--TGGTTCGCC---------A---------------------------------------G---TTATTTATGCGCT--GTGTT-----------CG------ACTctcgccagcagcagcagtagtag--------TGGCACAGTGGCGTAGTggaaaaagtgg-----------caaaaactGTTG----------------CCCGCC--------------A----GACCGAC-------AGCGACTTTATCGCTTTTATAGTAATTACGAGCTGTTGATAGG-CAGCTTAGGCTACCG-------TC s droKik2.KB459527 273331 206 - 1234237 GGCTCG-------C-------------------CAACAA--TGTGTACAACaatttcattaatat---taataaatgtt-cCCGAA-------------GCGTT-------------------CGC------TTC----T--TG-----CC---------A---------------------------------------G---TTATTTATGCGCT--CTGCTC----------CG------CTCCACG------------------G--------CGG--------------------AGTAG-----------CAAAAACTGTTGTTGCCcgcca-----gccagtc--------------a----gccagaC-------AGCGACTTTACCGCTTTTATAGTAATTACGAGCTGTTGATAGG-CAGCTTAGGCTACCG-------TC s droTak2.KB461535 138256 236 - 669855 ATTCGG-------C-------------------CAACAA--TGTGTACAACaatttcattaatat---taataaatgtt-cCCGAA-------------GCGTT-------------------TGC------TTC----T--TGGTCCGCC---------A---------------------------------------G---TTATTTATGCGCT--GTGTTTTTCGCTC-CTCG------ACTcacg---gcagcagcaaaagtGG--------CGG-----------------AAAAGTAG-----------CAAAAACTGTTT---------T-----GCCCGCC--------------A----GACCGAC-------AGCGACTTTATCGCTTTTATAGTAATTACGAGCTGTTGATAGG-CAGCTTAGGCTACCGTCTACCATC s droRho2.KB449310 32024 202 - 65043 GACCGG-------G-------------------CAACAA--TGTGTacaacaatttcattaatat---taataaatgtt-ccCGAA-------------GCGTT-------------------TGC------TTC----T--TGGTCCGCC---------A---------------------------------------G---TTATTTATGCGCT--GTGTTT----------CG------ACTCTTT---------------------------TGC-----------------AGTAGTAG-----------CAAGAACTGTTG----------------CCCGCC--------------A----GACCGTC-------AGCGACTTTATCGCTTTTATAGTAATTACGAGCTGTTGATAGG-CAGCTTAGGCTACCG-------TC s droFic2.KB457177 78188 223 + 995874 GGCTCG-------C-------------------CAACAA--TGTGTACaacaatttcattaatat---taataaatgtt-cCCGGA-------------GCGTT-------------------TGC------TTC----T--TGGTCCGCC---------A---------------------------------------G---TTATTTATGCGCA--GTGCTTTC--------CG------ACTCGCC------GCGGCAGAAGAGG--------CGG-------------CGGGAAAAGCAG-----------CAAAAACTGTTT---------T-----GCCCGCC--------------A----GACCGAC-------AGCGACTTTATCGCTTTTAAAGTAATTACGAGCTGTTGATAGG-CAGCTTAGGCTACCG-------TC s droPse3.chr3 1346650 237 - 19787792 GAAGGA-------G-------------------CAACAA--TGTGTacaacaatttcattaatat---taataaatgttCCCCGAA-------------GCGTtgggctggc--------tgctgc------ttc----t--tgccGCGCC---------A---------------------------------------G---TTATTTATGCGCT--GTGTCTGCCACTCGCTCG------CTGCACG------GCAGGcagacagc--------ccg------------------acagcca-----------gacagtcagaca---------------gccagac--------------a----acccgac-------agcAACTTTATCGCCTTTATAGTAATTACGAGCTGTTGATAGC-CAGCTTAGGCTACCG-------TC s droPer1.super_34 535509 237 - 916997 GAAGGA-------G-------------------CAACAA--TGTGTACAACAATTTCATTAATAT---TAATAAATGTTCCCCGAA-------------GCGTTGGGCTGGC--------TGCTGC------TTC----T--TGCCGCGCC---------A---------------------------------------G---TTATTTATGCGCT--GTGTCTGCCACTCGCTTG------CTGCACG------Gcaggcagacagc--------ccg------------------acagcca-----------gacagtcagaca---------------gccagac--------------a----acccgac-------agcAACTTTATCGCCTTTATAGTAATTACGAGCTGTTGATAGC-CAGCTTAGGCTACTG-------TC s droMir2.chr3 1387752 245 - 20862834 gaagca-------g-------------------caacaa--tgtgtacaacaatttcattaatat---taataaatgttCCCCGAA-------------GCGttgggctggc--------tgctgc------ttc----t--tgccgCGCC---------A---------------------------------------G---TTATTTATGCGCT--GTGTCTGCCACTCGCTCG------CTGCAcg------gcaggcagacagccagacagtcag------------------acagcca-----------gacagtcggaca---------------gccagac--------------a----acccgac-------agcAACTTTATCGCCTTTATAGTAATTACGAGCTGTTGATAGC-CAGCTTAGGCTACCG-------TC s droWil2.CH963894 1305370 175 + 2843958 GTCC---------C-------------------AATCGA--TTCGAGCAacaatttcattaatat---taataaatgct-tct--a-------------gttgt-------------------tgt------ttt----t--tgctgcCTCTTGCTTAAAA---------------------------------------G---TTATTTATGC-------GTTTCT--------CC------ACCAAGA---------------------------CAG-----------------CAAAGCAA---------------------------------------------------------------------------------AACTTTATCGC-TTTACAGTAATTACGAGCTGTTGATAGCTTGGCTAAGACTACCG-------TC s droVir3.scaffold_12875 7348465 239 + 20611582 ------------------CGTCAACAGCGACAACAACAA--TGTGCACAACAATTTCATTAATAT---TAATAAATGCT-ATGAGT---------GCGCGCGTTTTGCGCGCGTTTCTTGCGCGAT------TCC----C--TCGCTAGCG---------A---------------------------------------G---TTATTTATGCGCTCAAAGCCATT--------GG------ctctgct---------------------------cggct-------------------ctct-----------gctcagctctct---------------gcccggc--------------ATCGCAGCAGAC-------AGCAACTTTATCGC-CTTAGAGTAATTACGAGCTGTTGATAGG-CAGCTTAAGCTACCG-------TC s droMoj3.scaffold_6496 26143524 197 + 26866924 ------------------CGTCCACGG------CAACAA--TGTGCACAACAATTTCATTAATAT---TAATAAATGCT-ATG-------------------------------CTCTCGCGCGAC------TTC----C--TCGCTTGAG---------A---------------------------------------G---TTATTTATGCGTT--GAGCCGCT--------GG----------------------------------------------------------------CTCT-----------GCTGAGAACTCT---------------GCACGGC--------------ATTGCGCCGCAC-------AGCAGTTTTATCGC-CTTGAAGTAATTACGAGCTGTTGATAGC-TAGCTTAAGCTACCG-------TC s droAlb1.JH854640 306961 254 + 406291 ------------------TCTGAGTGCCAGTCACAACAA--TGTgtacaacaatttcattaatattaataataaatgct-gtGTGC------AAAGCGCGCGATTTGTGCGCGTTATGTGCGCGAT------TTT----CGTTTACCTTTG---------C---------------------------------------G---CGATTTGTTCAGCCAATGCT-TC--------GG------CTGCTCC---------------------------CAACT---------------TCCATTCT-----------CCTT--CTTCCC---------------ACCCGCC--------AATCCAATCACCTCTTGC-------AGCAACTTTATCGC-TTTAGAGTAATTACGAGCTGTTGATAGG-CAGCTTTGGCTACCG-------AC s droGri2.scaffold_15245 897206 286 + 18325388 ------------------AGTCTGC--------CAACAATGTGTGTACAACAATTTCATTAATAT---TAATAAATGCT-ATGCAATCGAGGGGCGCGCGCGTTTTGTGCGCGTTTCTCGCGCG-T------TTC----C--TCGCCACGC---------C---------------------------------------GTGTTTATTTATGCGCT--GAGCCGCC--------Gg------ctctgct---------------------------cagctcagc-----------tcaactca-----------gctcaactctgctGTGCTATGCTCTGCGCATGGCTCACTACCACTACCACTACCACTAACACAGAAGAGCAACTTTATCGC-TTTGGAGTAATTACGAGCTGTTGATAGG-CAGCTTAAGCTACCG-------TC a score=18459.000000 s dm6.chr2R 24347591 1 + 25286936 T s droSim1.chr2R 18694334 1 + 19596830 T s droSec1.super_23 114073 1 + 989336 T s droYak3.chr2R 20203267 1 + 21139217 T s droEre2.scaffold_4845 21601187 1 + 22589142 T s droBia2.KB462602 793372 1 + 3129309 T s droSuz1.KI419649 12038524 1 - 14502029 T s droAna3.scaffold_13266 5708582 1 - 19884421 T s droBip2.KB464407 1957374 1 + 2915140 T s droEug2.KB465067 598221 1 + 1515531 T s droEle2.KB458573 518711 1 - 5320397 T s droKik2.KB459527 273537 1 - 1234237 T s droTak2.KB461535 138492 1 - 669855 T s droRho2.KB449310 32226 1 - 65043 C s droFic2.KB457177 78411 1 + 995874 T s droPse3.chr3 1346887 1 - 19787792 T s droPer1.super_34 535746 1 - 916997 T s droMir2.chr3 1387997 1 - 20862834 T s droWil2.CH963894 1305545 1 + 2843958 T s droVir3.scaffold_12875 7348704 1 + 20611582 T s droMoj3.scaffold_6496 26143721 1 + 26866924 T s droGri2.scaffold_15245 897492 1 + 18325388 T a score=259949.000000 s dm6.chr2R 24347592 113 + 25286936 AATGTGCAGTAACACGGTCTGTGGCCC---------------------GGGGAACTATCC--------ACGTCCAC-----CATGGA--------GCT----------CC-ATCGCGATGCTTGCGTGACTTTCGGGTCTTTTGCGTGGGCGTCCTGT-GA----GAAA---------AA s droSim1.chr2R 18694335 113 + 19596830 AATGTGCAGAAACACGGTCTGTGGCCC---------------------GGGGAGCAATCC--------ACATCCAC-----CACGGA--------GCT----------CC-ATCGCGATGCTTGCGTGACTTTTGGGTCTTTTGCGTGGGCGTGCTGT-GA----GAAA---------AA s droSec1.super_23 114074 113 + 989336 AATGTGCAGAAACACGGTCTGTGGCCC---------------------GGGGAGCAATCC--------ACATCCAC-----CACGGA--------GCT----------CC-ATCGCGATGCTTGCGTGACTTTCGGGTCTTTTGCGTGGGCGTGCTGT-GA----GAAA---------AA s droYak3.chr2R 20203268 123 + 21139217 AATGTGCAGCAACACGGTCCATGGCCC---------------------GGGG-gctatcc--------acatccac---agcaTGGAGCTCCATCGCT----------CC-ATCGCGATGCTTGCGTGACTTTCGGGTCTTTTGCGTGGGCGTGCTGGTGG----AAAA---------AG s droEre2.scaffold_4845 21601188 112 + 22589142 AATGTGCAG-AACACGGTCTGTGGCCC---------------------GGGGTGCTATCC--------ACATCCAC-----CATGGA--------GCT----------CC-ATCGCGATGCTTGCGTGACTTTCGGGTCTTTTGCGTGGGCGTGCTGG-GA----GAAA---------AG s droBia2.KB462602 793373 102 + 3129309 AATGTGCAGGAACACGGTCC----------------------------GGGAGGTGATAC------------CGAC-----CATGGG--------GCT----------CC-ATGGCGATGCTTGCGTGACTTTCGGGTCTTTTGCGTGGGCGTCCTGA-GA----AGCA---------CG s droSuz1.KI419649 12038525 109 - 14502029 AATGTACAGAAACTTGGTCCG---------------------------GGGAGGTGATGC------GAGTATCGAC-----CATGGA--------GCT----------CC-ATCGCGATGCTTGCGTGACTTTCGGGTCTTTTGCGTGGGCGTCCTGA-GA----AACA---------TG s droAna3.scaffold_13266 5708583 112 - 19884421 AATGTGGAGAAGCCGAAACTA-GGCAC---------------------GAGGAGGTGTTA------------TCACGGGAGCAGGCA--------GCCAGGCAACCCGCC-ATCGCGATGCTTGCGTGACTTCTGGCCCAGTTGCGTGGGTGTGC------------------------- s droBip2.KB464407 1957375 131 + 2915140 AATGTGGAGAAACCGAAACTG-AGCACTCGCTTCATGGCACGAGGAAGGAGGTGGTGTTG------------TTAT-----CATGAA--------GCTGGG-AGCACACC-ATCGCGATGCTTGCGTGACTTCTGGGCCAATTGCGTGGGTGTGATGG-T-------------------- s droEug2.KB465067 598222 104 + 1515531 AATGTGCAGAGCCAGAAGCAGTCG------------------------GGGAGGTGATAT--------CGGCTCCA-----TGAGGA--------ACT----------CC-ATCGCGATGCTCGCGTGACTTTCGGGTCTTTTGCGTGGGCGTGATGG-GA------------------- s droEle2.KB458573 518712 110 - 5320397 AATGTACAGCAACACGGTCTGTGGCCC---------------------GGGGAGGTGTTA-----------TCCAG-----CGTGCA--------GCT----------CC-ATCGCGATGCTTGCGTGACTTTCGGGTCTCTTGCGTGGGCGTGCTGA-GC----ggaa---------ag s droKik2.KB459527 273538 98 - 1234237 aatgtgcagcagcag---cactgggTC---------------------TAGGTGTTATCC--------------AG-----CACGGAGA------GCA----------CC-ATCGCGATGGTTGCGTGACTTCTGGGCCATTTGCGTGGGTGGAGTGT---------------------- s droTak2.KB461535 138493 99 - 669855 AATGTACAT---------------------------------------G-------------------ATATCGAC-----CATGGA--------ACT----CGAACTCC-ATCGAGATGCTTGCGTGACTTTCGGGTCTTTTGCGTGGGCGTgctca-ga----aaaaaagtttaataa s droRho2.KB449310 32227 123 - 65043 AATGTGCAGGCACATGCTCTGTGGCCC---------------------GGGGAGGTGTTGAGTGTCGAGCGTGGAG-----CATGGA--------GCT----------CC-ATCGCGATGCTTGCGTGACTTTCGGCGCTTTTGCGTGGgcgttttta-gatttttaga----------- s droFic2.KB457177 78412 106 + 995874 AATGTGCAGAAACACGGCTTGCGGCCC---------------------GGGGAGGTGTTA-----------TCGAG-----CACGGA--------GCC----------CCAATCGCGATGGTTGCGTGACTTCGGG---TCTTGCGTGGGCGTTTCGA-GA----GGAA----------- s droPse3.chr3 1346888 110 - 19787792 AATGTACGG--ACCGACTCCACAGC-----------------------GAGGCGGGTCTA-----------TTGAC-----TATGGA--------ACT----ATGCATCT-ATCGAGATGGTTGCGTGACTCCTATGGCTTTTGCGTGGGAGAGCAGG-GA----ACCC----------- s droPer1.super_34 535747 110 - 916997 AATGTACGG--ACCGACTCCACAGC-----------------------GAGGCGGGTCTA-----------TTGAC-----TATGGA--------ACT----ATGCATCT-ATCGAGATGGTTGCGTGACTCCTATGGCTTTTGCGTGGGAGAGCAGG-GA----ACCC----------- s droMir2.chr3 1387998 110 - 20862834 AATGTACGG--ACCGACTCCACAGC-----------------------GAGGCGGGTCTA-----------TTGAC-----TATGGA--------ACT----ATGCATCT-ATCGAGATGGTTGCGTGACTCCAATGGCTTTTGCGTGGGAGAGCAGG-GA----ACCC----------- s droWil2.CH963894 1305546 89 + 2843958 AACGCCTTT-----ATGTCTATGCCCT---------------------GGAGCGGCTCGC---------------------TATAGA---------CA----------CC-ATCGAGATGGTTGCGTGATTTACCA--TAATTGCGTGggag-------aa----acat----------- s droVir3.scaffold_12875 7348705 86 + 20611582 -------------------CGCGGCCT---------------------GGAGCAGGCCGC----------TTTCAA-----TATCTG---------------------CA-TTAGAGATGAGCGCGTGA-TTTAGCCCACGAAATGTGGGTGCTGGCA-GA----AGGA----------- s droMoj3.scaffold_6496 26143722 86 + 26866924 -------------------ACCGGCCT---------------------GGAGCAGTGTGC----------TTTGAA-----TATCTA---------------------CA-TTAGAGATGAGCGCGTGA-TTTCGCTCACGTAGCGTGAGAGCTGAGG-AA----GCGA----------- a score=-16209.000000 s dm6.chr2R 24347705 12 + 25286936 CAGGGGAAAGAA s droSim1.chr2R 18694448 12 + 19596830 CAGGGGAATGAA s droSec1.super_23 114187 12 + 989336 CAGGGGAAAGAA s droYak3.chr2R 20203391 11 + 21139217 TA-GGGAAAGAA s droEre2.scaffold_4845 21601300 11 + 22589142 TA-GGGAAATAA s droBia2.KB462602 793475 12 + 3129309 AAAGGGAACGAA s droSuz1.KI419649 12038634 12 - 14502029 AAAGGGAATGAA s droBip2.KB464407 1957506 9 + 2915140 ---GCTGGCGAT s droEug2.KB465067 598326 9 + 1515531 ---GAAAAGGAA s droEle2.KB458573 518822 12 - 5320397 caaaaagaaaaa s droKik2.KB459527 273636 1 - 1234237 -----------A s droTak2.KB461535 138592 12 - 669855 aagGGAAAAGAA s droRho2.KB449310 32350 9 - 65043 ---ggaAAGGAA s droPse3.chr3 1346998 4 - 19787792 --------CAAT s droPer1.super_34 535857 4 - 916997 --------CAAT s droMir2.chr3 1388108 4 - 20862834 --------CAAT s droWil2.CH963894 1305635 9 + 2843958 ---tttgtttaa s droVir3.scaffold_12875 7348791 12 + 20611582 AAGATTAGACAA a score=36372.000000 s dm6.chr2R 24347717 35 + 25286936 GGG-CCTGACTTGGCGATTTCTCTGGC-ATAGAGGTT s droSim1.chr2R 18694460 35 + 19596830 GGG-CCTGACTTGGCGATTTCTCTGGC-ATGAAGGTT s droSec1.super_23 114199 35 + 989336 GGG-CCTGACTTGGCGATTTCTCTAGC-ACGGAGGTT s droYak3.chr2R 20203402 35 + 21139217 GGG-CCTGACTTGGCGATTTCTCTGGC-ATAGTAGTT s droEre2.scaffold_4845 21601311 35 + 22589142 GGG-CCTGACTTGTCGATTTCTCTGGC-ATGGAAGTT s droBia2.KB462602 793487 36 + 3129309 GGGTCCGGACCCACTGACTTCTCTGGC-GCAGACGTA s droSuz1.KI419649 12038646 36 - 14502029 GGGTCCGGACCTACTGACTTCTCTGGC-ATAGACATA s droAna3.scaffold_13266 5708695 24 - 19884421 --T-GCTGACTTGCCGATTTCTCCAAC---------- s droBip2.KB464407 1957515 35 + 2915140 GGT-GCTGACTTCTTGATTTCTCCAAG-ACTATGGTT s droEug2.KB465067 598335 35 + 1515531 GGG-TTTGACTTAGTGATTTCTCCGGC-ATAGACTTA s droEle2.KB458573 518834 35 - 5320397 ggg-tCCGACTTACTGATTTCTCTGGC-ACACAACAT s droKik2.KB459527 273637 27 - 1234237 GGG-TTCGACTTGCAGACTTTGCACAC-A-------- s droTak2.KB461535 138604 35 - 669855 GGG-TCCGACTTACCGATTTCTCTGGC-GTAGACATA s droRho2.KB449310 32359 35 - 65043 GGG-TCCGACTTACTGATTTCTCTGGC-ATCAACATA s droFic2.KB457177 78518 32 + 995874 -GG----GACTCACTGATTTGCCTGGCGACGGCCACT s droPse3.chr3 1347002 8 - 19787792 GAG-CATAA---------------------------- s droPer1.super_34 535861 8 - 916997 GAG-CATAA---------------------------- s droMir2.chr3 1388112 8 - 20862834 GAG-CAGAA---------------------------- s droWil2.CH963894 1305644 32 + 2843958 ggA-CATTACTTAGGGAATGCACAATA-AGGGAA--- a score=149433.000000 s dm6.chr2R 24347752 49 + 25286936 CGAAATAGG-TT-GGCCGTGATC--------------------ATTGAGGATTAAAGATGTTTTACAAAAC----------- s droSim1.chr2R 18694495 49 + 19596830 CGAAATGGG-TT-GGCCGTGATC--------------------ATTGGGGATTAAAGATGTTTTACAAAAC----------- s droSec1.super_23 114234 49 + 989336 CGAAATGGG-TT-GGCCGTGATC--------------------ATTGGGGATTAAAGATGTTTTACAAAAC----------- s droYak3.chr2R 20203437 60 + 21139217 CGAAATGGG-TT-GGCTGCGATC-------TGTC--TGGTTTTATTGAAGATTAAAGATGTTTTACAAAAC----------- s droEre2.scaffold_4845 21601346 60 + 22589142 CGAAATGGG-CT-GGCCGTGATC-------TGCT--TGGTGTTATTGAAGATTAAAGATGTTTTACAAAAC----------- s droBia2.KB462602 793523 60 + 3129309 CGTCATGGG-CT-TGCCGTGATC-------TAGT--CGGTTTTACTACAGATTAGGGATGTTTTACAAAGC----------- s droSuz1.KI419649 12038682 60 - 14502029 CGAAATGGG-CT-TGCCGTGATC-------TACT--TGGGTTTATTACAGATTAGGGATGTTTTACAAAAC----------- s droAna3.scaffold_13266 5708719 35 - 19884421 ---------------CCGAGATC-------TGGTTATGGTTTTATT------------TTCTTTACAAA------------- s droEug2.KB465067 598370 59 + 1515531 CGAAATGGG-GT-TGCCTTGATC-------TAC---TTATTTTATTGGAGATTAAAGATGTTTTACAAAAC----------- s droEle2.KB458573 518870 60 - 5320397 CGAAATGTC-TT-TGCCGTGATC-------TACT--TGGTTTTATTGCAGATTAAGcttgttttataaaac----------- s droKik2.KB459527 273664 61 - 1234237 CGAAATGGGCCC-TGGCGTGATC-------CAGT--TGCCTTTATGGGAGATTAAGCTTGTTTTACAAAAC----------- s droTak2.KB461535 138639 60 - 669855 CGAAATGGG-TT-TGCCATGATC-------TACT--TGGATTCATTACAGATTAGGGATGTTTTACAAAAC----------- s droRho2.KB449310 32394 60 - 65043 CGAAATGGG-TT-TGCCGTGATC-------CACT--TGGTTTTATTGCAGATTAAGGTTGTTTTACAAAAC----------- s droFic2.KB457177 78550 67 + 995874 CGGAATGGG-TT-TGCCCAGATCTTGGGTTTGCT--TGGGCTTATAGAAGATTAAGGTTTCTTTACAAAAA----------- s droPse3.chr3 1347010 40 - 19787792 -GAAATGGG-TTAGGTTGTAAGC-------CTTT---------------------AAATGTTTC-CAGATC----------- s droPer1.super_34 535869 40 - 916997 -GAAATGGG-TTAGGTTGTAAGC-------CTTT---------------------AAATGTTTC-CAGATC----------- s droMir2.chr3 1388120 40 - 20862834 -GAAATGGG-TTAGGTTGTAAGC-------CTTT---------------------AAATGTTTC-CAGATC----------- s droWil2.CH963894 1305676 35 + 2843958 -----------------------------------------------AGAACTATAGTTTTGTCAGAAAGCAGATTTATAAT a score=-100501.000000 s dm6.chr2R 24347801 48 + 25286936 GTAAACGATTG--------------------------CTTGGGTGACACCATACAGTGATATGGGTACCTAGGC----- s droSim1.chr2R 18694544 47 + 19596830 GTACACGATTG--------------------------CTTATG-GACACCATACAGTGATATAGGTAACTAGTC----- s droSec1.super_23 114283 48 + 989336 GTACACGATTG--------------------------CTTAGGTGACACAATACAGTGATATAGGTAACTAGGC----- s droYak3.chr2R 20203497 48 + 21139217 GCACACGATTG--------------------------CTTATGCGACACCATGCAGTTATATGGGTAACTGTGT----- s droEre2.scaffold_4845 21601406 48 + 22589142 GTTCATGATGG--------------------------CTTATGTGACACCATACAGTAATAGGGGTAACTAGGT----- s droBia2.KB462602 793583 29 + 3129309 AAATACGAC---------------------------------------------AGTGATGTAGGTTAATAAGC----- s droSuz1.KI419649 12038742 48 - 14502029 ATATACGATTG--------------------------TGTAGGGGGCTAATAAAAGTGATATGGGTTAATAAGT----- s droAna3.scaffold_13266 5708754 20 - 19884421 ---CACGAT--------------------------------------ATTACAAAGTGAGA------------------ s droEug2.KB465067 598429 71 + 1515531 ATGTACGATTGTGGGAAGGAGTCCCCTTAGTGGGTTCCCTTAGTGGGtccataaattaata---ataaatattt----- s droKik2.KB459527 273725 32 - 1234237 ATATATATCAA--------------------------TTGTTGTGACGCCACAAAAGC--------------------- s droTak2.KB461535 138699 48 - 669855 ATAAACGATTA--------------------------GGTAAGGGGATAGTAAAAGTTATGTGGGTTATTAAGT----- s droRho2.KB449310 32454 37 - 65043 -------------------------------------AATATAGGGCAGCTAAATCTGATATGGGTTAGTAAGC----- s droFic2.KB457177 78617 37 + 995874 ---CACAGCTA---------------------------------GACACCTCA-ATTGATACGGGCTGATAAGC----- s droPse3.chr3 1347053 45 - 19787792 TTAAGCACTTC--------------------------TTTCTTTAACATACTGTGGTTCCAGTGCTTGGAA-------- s droPer1.super_34 535912 45 - 916997 TTAAGCACTTC--------------------------TTTCTTTAACATACTGTGGTTCCAGTGCTTGGAA-------- s droMir2.chr3 1388163 45 - 20862834 TTAAGCACTTC--------------------------ATTCTTTAACATACTGTGGTTCCAGTGCTTCGAA-------- s droWil2.CH963894 1305711 46 + 2843958 ---------------------------------GAAACCGATTTATAACCAGAATAAGCCATAGGTAAATGTTTTGCAC a score=-336063.000000 s dm6.chr2R 24347849 49 + 25286936 AGTT-------AAGTAGTGCAATAG---------------------------------------ATAAACACTCAGAT----------------TT-TAAT---------------------AATAAAGAT--TA s droSim1.chr2R 18694591 44 + 19596830 AGTT-------ATGTAGTGCAACAG---------------------------------------ATAAATCTTCAGAT----------------TT-TAAT---------------------AATAAA------- s droSec1.super_23 114331 49 + 989336 AGTT-------AAGTAGTGCAACAA---------------------------------------ATAAATCTTCAGAT----------------TT-TAAA---------------------AATAAAGAT--CG s droYak3.chr2R 20203545 33 + 21139217 TGTT-------AAGTAGTGCAACAT-----------------TATAG--------------------------------------------------TTAT---------------------GGTAAT------- s droEre2.scaffold_4845 21601454 70 + 22589142 AGTT-------GAGC-GTGCAACATATTGTTTTAAGTACAAATACAG-----------------ATAACACCTAGGAT----------------GT-TTGT---------------------GATAATGAT--TG s droBia2.KB462602 793855 37 + 3129309 agtt-------aaatactttaaaaa---------------------------------------gtaaa----------------------------taat---------------------aataataa---ca s droSuz1.KI419649 12038790 37 - 14502029 CATT-------AAGAGC-TTAAAgc---------------------------------------gtaaa----------------------------aaaa---------------------aacaagaag--cg s droAna3.scaffold_13266 5708774 17 - 19884421 ------------------------------------------------------------------AAACGATTAGCT----------------TT-TAA----------------------------------- s droEug2.KB465067 598501 67 + 1515531 catt-------aaaaagaggaaaaa---------------------------------------cttaaaatcgaAGTACTCTTTCCATTGATATT-GAAT---------------------AGTCAAGATACGA s droKik2.KB459527 273757 72 - 1234237 TGAA-------AAGTAGggcaataatattttattttgatggcTGAAA-------T---------AGAAACAAGAAAGT----------------CT-CGAT---------------------CACAAAACT--TA s droTak2.KB461535 138747 52 - 669855 TGTA-------aaaaagacaaataa---------------------------------------aaaGAGAATTGTAT----------------TTCGAAT---------------------AACTAAATAAGCA s droRho2.KB449310 32491 48 - 65043 -ATTCA----GAAGTAGAGCATCAA---------------------------------------GAgtggtttaaaat----------------aa-taaa---------------------gacaaaca----- s droFic2.KB457177 78654 74 + 995874 -----AATTAAAAGTAGGCCAAAAA---------------------------------------GGAGTGTTTCGAAG----------------TT-TGATTTCGTGTTAACTATTacttgcaataaaaaaagta s droPse3.chr3 1347098 45 - 19787792 ------------------------------------------------------TATTCGTTTTCTGAACTCTTTGATCTCCCTGAAGGAGGGTTT-CCA----------------------------------- s droPer1.super_34 535957 45 - 916997 ------------------------------------------------------TATTCGTTTTCTGAACTCTTTGATCTTCCTGAAGGAGGGTTT-CCA----------------------------------- s droMir2.chr3 1388208 45 - 20862834 ------------------------------------------------------TATTCGTTTTCTGAACTCTTTGATCTTCCTGAAGGGGGGTTT-CCA----------------------------------- s droWil2.CH963894 1305757 59 + 2843958 AACT-------AATTAATTCAAAGA-------------GAGTTTTAAGCAAACGGATTCCTCTTAAAAACGTTTTGAT----------------A---------------------------------------- a score=-37678.000000 s dm6.chr2R 24347898 5 + 25286936 -TTAC----------------A s droSec1.super_23 114380 5 + 989336 -TTAG----------------A s droYak3.chr2R 20203578 1 + 21139217 ---------------------A s droEre2.scaffold_4845 21601524 19 + 22589142 -CTAGCAAATGGGCCTAAC--A s droBia2.KB462602 793892 8 + 3129309 -gcaaTGA-------------A s droSuz1.KI419649 12038827 8 - 14502029 -ttactga-------------a s droEug2.KB465067 598568 21 + 1515531 -GTAGTACTTCTGGGTAACAGA s droKik2.KB459527 273829 8 - 1234237 -TTCAGGC-------------T s droTak2.KB461535 138799 2 - 669855 -CT------------------- s droFic2.KB457177 78728 3 + 995874 -tta------------------ s droGri2.scaffold_15245 897948 5 + 18325388 TTTCC----------------- a score=-3904.000000 s dm6.chr2R 24347903 4 + 25286936 AATT s droSim1.chr2R 18694635 1 + 19596830 ---G s droSec1.super_23 114385 4 + 989336 AATG s droYak3.chr2R 20203579 4 + 21139217 TATG s droEre2.scaffold_4845 21601543 4 + 22589142 AGTG s droBia2.KB462602 793900 4 + 3129309 TAGA s droSuz1.KI419649 12038835 4 - 14502029 aaga s droEug2.KB465067 598589 4 + 1515531 TATA s droKik2.KB459527 273837 4 - 1234237 AATA s droTak2.KB461535 139056 4 - 669855 AGTT s droRho2.KB449310 32539 4 - 65043 tatt s droFic2.KB457177 78731 4 + 995874 gatg s droPse3.chr3 1347143 4 - 19787792 CATC s droPer1.super_34 536002 4 - 916997 CATC s droMir2.chr3 1388253 4 - 20862834 CATC s droWil2.CH963894 1305816 3 + 2843958 -ACT s droGri2.scaffold_15245 897953 4 + 18325388 AACT a score=-13263.000000 s dm6.chr2R 24347907 5 + 25286936 AAACT s droSim1.chr2R 18694636 5 + 19596830 AAGCT s droSec1.super_23 114389 5 + 989336 AAACT s droYak3.chr2R 20203583 5 + 21139217 CCACT s droEre2.scaffold_4845 21601547 5 + 22589142 TCATT s droBia2.KB462602 793904 5 + 3129309 AACCA s droSuz1.KI419649 12038839 5 - 14502029 aaaaa s droEug2.KB465067 598593 5 + 1515531 AGACA s droKik2.KB459527 273841 5 - 1234237 TGTCG s droTak2.KB461535 139060 5 - 669855 AAAGA s droRho2.KB449310 32543 5 - 65043 aagct s droFic2.KB457177 78735 5 + 995874 gattt s droPse3.chr3 1347147 5 - 19787792 ATCGT s droPer1.super_34 536006 5 - 916997 ATCGT s droMir2.chr3 1388257 5 - 20862834 ATCGA s droGri2.scaffold_15245 897957 5 + 18325388 AGACT a score=-38852.000000 s dm6.chr2R 24347912 13 + 25286936 TACC-------TCGGGCTTA s droSim1.chr2R 18694641 13 + 19596830 CACC-------TTGGACTTA s droSec1.super_23 114394 13 + 989336 TACC-------CCGGACTTA s droYak3.chr2R 20203588 13 + 21139217 TTCA-------TCCGTCTTA s droEre2.scaffold_4845 21601552 13 + 22589142 TTCA-------TTGGCCGTA s droBia2.KB462602 793909 13 + 3129309 AACA-------TCGAATATA s droSuz1.KI419649 12038844 20 - 14502029 aacagaagtctttaaaaata s droEug2.KB465067 598598 13 + 1515531 TCTC-------TCAAGTCTT s droKik2.KB459527 273846 13 - 1234237 TTGC-------CTAGGTCTG s droTak2.KB461535 139065 13 - 669855 TATC-------GCATATACA s droRho2.KB449310 32917 13 - 65043 TATT-------GTGGGCTTA s droFic2.KB457177 78750 13 + 995874 taag-------atgggtatt s droPse3.chr3 1347152 9 - 19787792 TCCC-------CCATG---- s droPer1.super_34 536011 9 - 916997 TCCC-------CCATG---- s droMir2.chr3 1388262 9 - 20862834 TCCC-------CCATG---- s droGri2.scaffold_15245 897962 14 + 18325388 ------AAGTTTTTGGCATA a score=7253.000000 s dm6.chr2R 24347925 8 + 25286936 CTTCTAGC s droSim1.chr2R 18694654 8 + 19596830 CTTTTAGC s droSec1.super_23 114407 8 + 989336 GTTTTAGC s droYak3.chr2R 20203601 8 + 21139217 CTTTTAGT s droEre2.scaffold_4845 21601565 8 + 22589142 TTTTTGGT s droBia2.KB462602 793922 8 + 3129309 TTGATGGA s droEug2.KB465067 598612 6 + 1515531 --TTTCGT s droKik2.KB459527 273868 8 - 1234237 ATTTCAGC s droTak2.KB461535 139078 1 - 669855 -------C s droRho2.KB449310 32930 6 - 65043 --CTTGAa s droFic2.KB457177 78771 8 + 995874 tttttaat s droPse3.chr3 1347161 8 - 19787792 ATTTGAAT s droPer1.super_34 536020 8 - 916997 ATTTGAAT s droMir2.chr3 1388271 8 - 20862834 ATTTGAAT s droGri2.scaffold_15245 897976 7 + 18325388 -CTTTGGC a score=-37103.000000 s dm6.chr2R 24347933 5 + 25286936 --CAGAA s droSim1.chr2R 18694662 5 + 19596830 --TAGAA s droSec1.super_23 114415 5 + 989336 --TAGAA s droYak3.chr2R 20203609 5 + 21139217 --CAGAA s droEre2.scaffold_4845 21601573 5 + 22589142 --CAGAA s droBia2.KB462602 793930 5 + 3129309 --TATTA s droAna3.scaffold_13266 5708791 1 - 19884421 ------G s droBip2.KB464407 1957562 5 + 2915140 --CAAAA s droEug2.KB465067 598620 4 + 1515531 --CCGA- s droKik2.KB459527 273876 4 - 1234237 ---TGAA s droTak2.KB461535 139079 1 - 669855 ------A s droRho2.KB449310 32938 2 - 65043 -----aa s droFic2.KB457177 78790 4 + 995874 --TGGA- s droPse3.chr3 1347169 5 - 19787792 --CTGAT s droPer1.super_34 536028 5 - 916997 --CTGAT s droMir2.chr3 1388279 5 - 20862834 --CTGAT s droGri2.scaffold_15245 897983 5 + 18325388 AACAA-- a score=-96115.000000 s dm6.chr2R 24347938 18 + 25286936 TTTCT-------------------------------------AAATACTATAGT-------------------T----- s droSim1.chr2R 18694667 18 + 19596830 GTTTG-------------------------------------GAATACTATAGT-------------------T----- s droSec1.super_23 114420 18 + 989336 GTTTT-------------------------------------GAATACTATAGT-------------------T----- s droYak3.chr2R 20203614 33 + 21139217 GTGAA----------------------ACAGCTTTAAGTACGGAATACTATAGT-------------------C----- s droEre2.scaffold_4845 21601578 55 + 22589142 GTGAGACCTTTCGATTGCCTAATAGTCACATATTGTGGTACGGAATACCAAAGT-------------------T----- s droBia2.KB462602 793935 13 + 3129309 -TACT-------------------------------------TAAGACCA-----------------------T----- s droSuz1.KI419649 12039100 18 - 14502029 tcTTT-------------------------------------GAATATTATAGT-------------------T----- s droAna3.scaffold_13266 5708792 18 - 19884421 CTTCT-------------------------------------AAACATTATTGt-------------------t----- s droBip2.KB464407 1957567 37 + 2915140 GTctt-------------------------------------aaatataattgtttttacaacttagtttacgt----- s droEug2.KB465067 598624 8 + 1515531 -----------------------------------------------CTATAGT-------------------T----- s droKik2.KB459527 273881 18 - 1234237 -------------------------------------CACCTGAATACTTAATT-------------------T----- s droTak2.KB461535 139080 18 - 669855 TTTca-------------------------------------gaatattatatt-------------------t----- s droRho2.KB449310 32944 17 - 65043 tttaa-------------------------------------aaagcttttaga------------------------- s droFic2.KB457177 78799 11 + 995874 CCTTT-------------------------------------AAAGAT------------------------------- s droPse3.chr3 1347174 9 - 19787792 ----------------------------------------------ATTCTTGA-------------------T----- s droPer1.super_34 536033 9 - 916997 ----------------------------------------------ATTCTTGA-------------------T----- s droMir2.chr3 1388284 9 - 20862834 ----------------------------------------------ATTCTTGA-------------------T----- s droGri2.scaffold_15245 897992 23 + 18325388 TTTTT-------------------------------------AAGTCTTATCAT-------------------GGAATT a score=-83152.000000 s dm6.chr2R 24347956 6 + 25286936 C-------------------GGTTT---- s droSim1.chr2R 18694685 6 + 19596830 C-------------------AGTTT---- s droSec1.super_23 114438 6 + 989336 C-------------------GGCTT---- s droYak3.chr2R 20203647 6 + 21139217 C-------------------AACCT---- s droEre2.scaffold_4845 21601633 5 + 22589142 C--------------------GCTT---- s droBia2.KB462602 793948 19 + 3129309 TAAAATTAGGTT------TTGGTTT---- s droSuz1.KI419649 12039118 19 - 14502029 TGCAGTTAGGTT------TGAGCTT---- s droAna3.scaffold_13266 5708810 6 - 19884421 t-------------------atatt---- s droBip2.KB464407 1957604 6 + 2915140 t-------------------ttatt---- s droEug2.KB465067 598632 6 + 1515531 A-------------------GGTTT---- s droKik2.KB459527 274136 6 - 1234237 -------------------CAATCT---- s droTak2.KB461535 139098 15 - 669855 -----ttagatga-----TTAGCTC---- s droRho2.KB449310 32961 13 - 65043 ------------ATAACCAAAACTT---- s droFic2.KB457177 78810 11 + 995874 --------------CTGTATTGATT---- s droPse3.chr3 1347183 11 - 19787792 --------------CGACTGGTTTC---- s droPer1.super_34 536042 11 - 916997 --------------CGACTGGTTTC---- s droGri2.scaffold_15245 898015 6 + 18325388 -----------------------TTGTAT a score=-32221.000000 s dm6.chr2R 24347962 10 + 25286936 CAAGTTTAGG- s droSim1.chr2R 18694691 10 + 19596830 CAAGTTTAGC- s droSec1.super_23 114444 10 + 989336 CAAGTTTAGC- s droYak3.chr2R 20203653 10 + 21139217 CTAGTTTAAG- s droEre2.scaffold_4845 21601638 10 + 22589142 TTAGTTTAAG- s droBia2.KB462602 793967 10 + 3129309 TAGGATTACT- s droSuz1.KI419649 12039137 10 - 14502029 ATGGGTTACT- s droAna3.scaffold_13266 5708816 10 - 19884421 tagtttttta- s droBip2.KB464407 1957610 10 + 2915140 tagtttttat- s droEug2.KB465067 598638 10 + 1515531 TAGCTAACAA- s droKik2.KB459527 274142 9 - 1234237 CTCGTTGAG-- s droTak2.KB461535 139113 10 - 669855 TAGGATTACT- s droRho2.KB449310 32974 10 - 65043 ATAGCCCATT- s droFic2.KB457177 78821 10 + 995874 Gctatttaac- s droPse3.chr3 1347194 10 - 19787792 CACTGTTGAA- s droPer1.super_34 536053 10 - 916997 CACTGTTCAA- s droWil2.CH963894 1306441 9 + 2843958 caaatttaa-- s droGri2.scaffold_15245 898021 10 + 18325388 -AAGTTTTACA a score=-55166.000000 s dm6.chr2R 24347972 10 + 25286936 TG------ACTAACTC----- s droSim1.chr2R 18694701 10 + 19596830 TG------GCTAACTC----- s droSec1.super_23 114454 10 + 989336 TG------GCTAACTC----- s droYak3.chr2R 20203663 10 + 21139217 TG------GCCAACTT----- s droEre2.scaffold_4845 21601648 10 + 22589142 TG------GCTAACTT----- s droBia2.KB462602 793977 4 + 3129309 TA------------CC----- s droSuz1.KI419649 12039147 14 - 14502029 TG--GTATATCAACCC----- s droAna3.scaffold_13266 5708826 10 - 19884421 tt------aaaaaaat----- s droBip2.KB464407 1957620 10 + 2915140 tt------aagaaatc----- s droEug2.KB465067 598648 10 + 1515531 AT------ACTTAGTA----- s droTak2.KB461535 139123 16 - 669855 TGATATATATTAACTA----- s droRho2.KB449310 32984 1 - 65043 T-------------------- s droFic2.KB457177 78831 2 + 995874 ta------------------- s droPse3.chr3 1347204 2 - 19787792 TG------------------- s droPer1.super_34 536063 2 - 916997 TG------------------- s droWil2.CH963894 1306450 9 + 2843958 -g------acCACCTC----- s droAlb1.JH854640 307295 15 + 406291 TG------ACTAACACCCATT s droGri2.scaffold_15245 898036 7 + 18325388 TG------GCCAA-------- a score=4397.000000 s dm6.chr2R 24347982 4 + 25286936 AAGC s droSim1.chr2R 18694711 4 + 19596830 AAGC s droSec1.super_23 114464 4 + 989336 AAGC s droYak3.chr2R 20203673 4 + 21139217 AGTC s droEre2.scaffold_4845 21601658 4 + 22589142 AATC s droBia2.KB462602 793981 4 + 3129309 AAAC s droSuz1.KI419649 12039161 4 - 14502029 AAAC s droAna3.scaffold_13266 5708836 3 - 19884421 aaa- s droEug2.KB465067 598658 4 + 1515531 CAAC s droEle2.KB458573 519353 4 - 5320397 AAAC s droTak2.KB461535 139139 4 - 669855 AAAC s droRho2.KB449310 32985 4 - 65043 AAAC s droFic2.KB457177 78833 4 + 995874 aaat s droPse3.chr3 1347206 1 - 19787792 ---C s droPer1.super_34 536065 1 - 916997 ---C s droWil2.CH963894 1306459 4 + 2843958 TATT s droAlb1.JH854640 307310 4 + 406291 ACAC s droGri2.scaffold_15245 898043 2 + 18325388 --AT a score=-84779.000000 s dm6.chr2R 24347986 7 + 25286936 ----TTCCC------AA s droSim1.chr2R 18694715 7 + 19596830 ----TACGC------AA s droSec1.super_23 114468 7 + 989336 ----TACCC------AA s droYak3.chr2R 20203677 7 + 21139217 ----CGCCC------AA s droEre2.scaffold_4845 21601662 7 + 22589142 ----TTTAC------AA s droBia2.KB462602 793985 6 + 3129309 ----CCCCC-------G s droSuz1.KI419649 12039165 7 - 14502029 ----TTCCC------AG s droAna3.scaffold_13266 5708839 3 - 19884421 --------G------AA s droBip2.KB464407 1957630 3 + 2915140 --------g------AA s droEug2.KB465067 598662 7 + 1515531 ----TTACT------AA s droEle2.KB458573 519357 7 - 5320397 ----TCTTT------AA s droTak2.KB461535 139143 7 - 669855 ----TTACC------TA s droRho2.KB449310 32989 7 - 65043 ----TCTCT------AA s droFic2.KB457177 78837 13 + 995874 ----atCCCTATTTGAA s droPse3.chr3 1347211 5 - 19787792 ----TCTCC-------- s droPer1.super_34 536070 5 - 916997 ----TCTCC-------- s droMir2.chr3 1388321 5 - 20862834 ----TCTCC-------- s droWil2.CH963894 1306463 7 + 2843958 ----------ACCATAT s droAlb1.JH854640 307314 7 + 406291 TCACTAT---------- s droGri2.scaffold_15245 898045 7 + 18325388 TTGCTTT---------- a score=154955.000000 s dm6.chr2R 24347993 62 + 25286936 CTCACGCTGCCATC------------------TCTGGTAATTT-----------AAA----GTCCG---GCACAT-----TCGG---G-ATCC-CGCTTAA----CGC-------------ACCT s droSim1.chr2R 18694722 62 + 19596830 GTCACGCTGCCATC------------------TCTGCTAATTT-----------AAA----GTCCG---GCACAT-----TCGG---G-ATCC-CGCTTAA----CGC-------------GCCT s droSec1.super_23 114475 62 + 989336 GTCACGCTGCCATC------------------TCTGCTAATTT-----------AAA----GTCCG---GCACAT-----TCGG---G-ATCC-CGCTTAA----CGC-------------GCCT s droYak3.chr2R 20203684 62 + 21139217 CTCACGCCGCCATC------------------TCTGGTAATTT-----------AAA----GTCCG---GCACAT-----TCGG---G-ATCC-CGCTTAA----CGC-------------GCCT s droEre2.scaffold_4845 21601669 62 + 22589142 CTCACGCTGCCATC------------------TCTGGTAATTT-----------AAA----GTCCG---GCACAT-----TCGG---G-ATCC-CGCTTAA----CGC-------------GCCT s droBia2.KB462602 793991 62 + 3129309 ATCACGCTGCCATC------------------TCTGGTAATTT-----------AAA----GTCCG---GCACAT-----TCGG---G-GTCC-CGCTTAA----CGC-------------TTCT s droSuz1.KI419649 12039172 62 - 14502029 ATCACGCTGCCATC------------------TCTGGTAATTT-----------AAA----GTCCG---GCACAT-----TCGA---G-GTCC-CGCTTAA----CGC-------------TTCT s droAna3.scaffold_13266 5708842 71 - 19884421 ATCACGCTGCCATC------------------TCTGGTAATTTTTAAAG-----AAA----AAGAG---GCACAGTGCCGCCGT---T-GCCT-CGC--CG----GCC-------------ATCT s droBip2.KB464407 1957633 58 + 2915140 ATCACGCTGCCATC------------------TCtggtaatttttaaaa-----gaggCACACGAG---GCACAG------------------------AG----GCC-------------ATCT s droEug2.KB465067 598669 62 + 1515531 ATCACGCTGGCATC------------------TCTGGTAATTT-----------AAA----GTCCG---GCACAT-----TCGA---G-GTCC-CGCTTAA----CGC-------------TTCT s droEle2.KB458573 519364 63 - 5320397 ATCACGTGGCCATC------------------TCTGGTAATTT-----------AAA----GTCCG---CCAGAT-----TCGA---G-GTCCACGCTTAA----CGC-------------TTCT s droKik2.KB459527 274151 59 - 1234237 -TCACGCTCCCATC------------------TCTGGTAATTT-----------AAA----ATCC---------------AAGC---G-GTCCACGCTTAGACTCCTC-------------TCCT s droTak2.KB461535 139150 62 - 669855 GTCACGCGGACATC------------------TCTGGTAATTT-----------AAA----GTCCG---GCACAT-----TCGG---G-GTCC-CGCTTAA----CGC-------------TCCT s droRho2.KB449310 32996 64 - 65043 ATCACGTTGCCATC------------------TCTGGTAATTT-----------AAA----GTCCG---GCACAT-----TCGA---G-GTCCCCGCTTAA----CGC------------GTTCT s droFic2.KB457177 78850 48 + 995874 ATCACGTTGCCATC------------------TCTGGTAACCT------------AA----GTCCG---CCGCGT-----------------------TAG----CGC-------------TTCT s droPse3.chr3 1347216 68 - 19787792 -TCACGCTCCCATC------------------TCTAATCGTTT-----------TAA----GGCC---------------TCGT---C-CTCTCTGCCAAA----CTTTTGTTGCTACTCGTTCT s droPer1.super_34 536075 68 - 916997 -TCACGCTCCCATC------------------TCTAATCGTTT-----------TAA----GGCC---------------TCGT---C-CTCTCTGCCAAA----CTTTTGTTGCTACTCGTTCT s droMir2.chr3 1388326 68 - 20862834 -TCACGCTCCCATC------------------TCTAATCGTTT-----------TAA----GGCC---------------TCGT---C-CTCTCTGCCAAA----CTTTTGTTGCCACTCGTTCT s droWil2.CH963894 1306470 81 + 2843958 ATCACGTTCCCATcgccaaaaatgtttttttttttggtgtttt-taaag-----aaa----atctg---CAACGT-----TTAT---T------TGCCTGC----CTC-------------GTGT s droVir3.scaffold_12875 7349517 54 + 20611582 CTCACGCGGCCAGC------------------TCCAAGAATTT-----------GGT----AGCTGCAGCAGCAT-----TTGGCCTG-ATCT-------------------------------- s droAlb1.JH854640 307321 55 + 406291 CTCACGCGGTCCTC------------------TCTGGCAATTT-----------GAT----AGCCA-GGCAAAATC----TCAGCCTGCCTTT-------------------------------- s droGri2.scaffold_15245 898055 64 + 18325388 CTCACGCGGCCATC------------------TCAAACAGTTTTCATAGTTTTCGCT----GGTTGCAGCCGCAT-----TTGG-CTA-ATCT-------------------------------- a score=547535.000000 s dm6.chr2R 24348055 132 + 25286936 TATCGCTGCAACATAATCGCATAGTTTGGTGGGG-----AAATTTATGTGCCGCT---------CGGGCAACAGAGGCACACACGCTTCTCCAG-----TC-----------------------------------------------------------------------------------------------CGC------AGA----TA-GGCGATACA-G--------------A--------CT-CAGATAG-CAT------CGAGTACTTACCACGA-----------T-----CC s droSim1.chr2R 18694784 132 + 19596830 TATCGCTGCAACATAATCGCATAGTTTGGTGGGG-----AAATTTATGTGCCGCT---------CGGGCAACAGAGGCACACACCCTTCCCCAA-----TC-----------------------------------------------------------------------------------------------CCC------AGA----TA-GGCGATACA-G--------------A--------CT-CAGATAA-CAT------CGAGTACTTACCACGA-----------T-----CC s droSec1.super_23 114537 132 + 989336 TATCGCTGCAACATAATCGCATAGTTTGGTGGGG-----AAATTTATGTGCCGCT---------CGGGCAACAGAGGCACACACGCTTCTCCAG-----TC-----------------------------------------------------------------------------------------------CGC------AGA----TA-GCCGATACA-G--------------A--------CT-CAGATAA-CAT------CGAGTACTTACCACGA-----------T-----CC s droYak3.chr2R 20203746 136 + 21139217 TATCGCTGCAACATAATCGCATAGTTTGGTGGGG-----AAATTTATGTGCCGCT---------CGGGCAAC--AGGCACACACGCTTCTCCAGTCCAATC-----------------------------------------------------------------------------------------------CGC------AGA----TA-CGCGATACGCG--------------A--------TC-GAGATAG-CAT------CGAGTACTTACCACGA-----------T-----CC s droEre2.scaffold_4845 21601731 130 + 22589142 TATCGCTGCAACATAATCGCATAGTTTGGTGGGG-----AAATTTATGTGCCGCT---------CGGGCAAC--AGGCACACACGCTTCTCCAG-----TC-----------------------------------------------------------------------------------------------CGC------AGA----TA-CGCGATACA-G--------------A--------CT-CAGATAG-CAT------CGAGTACTTACCACGA-----------T-----CC s droBia2.KB462602 794053 152 + 3129309 TATCGCTGCAACATAATCGCATAGTTGGTGTGGT-----AAATTTATGTGCCGCA---------C-GGCAAC--------ACACGCTTCGGCAG-----CC--------TGCC----------------------------TCGC--CAG---------TCGG--CT-----------------------------GGC------AAG----TA-GCCGATacc-gattccgattccc--a--------tT-CCGATAG-CAT------CGAGTACTTAACACGA-----------T-----CC s droSuz1.KI419649 12039234 153 - 14502029 TATCGCTGCAACATAATCGCATAGTTGGTGGGGT-----AAATTTATGTGCCGCT---------CGGGCAAC--------ACACGCCTCGCCAG-----TC--------TGCC----------------------------TGGC--CAG---------TTGG--CT-----------------------------CGC------AAG----TA-CCCGATACC-GATTCCGATTCCT--A--------TT-CCGATAG-CAT------CGAGTACTTAACACGA-----------T-----CC s droAna3.scaffold_13266 5708913 146 - 19884421 TATCGCTGCAACATAATCGCATAGTTCGGTGGGG-----AAATTTATGTGCCGCT---------TGGGC--T------ACACACGCCTCGACAG-----TT---------TCC----------------------------TGGC--CG----------GCAA--CTACCCCTCCT--------------------TCC------AAA----T--CCCGATATC-C--------------C--------AA-CCGATA-------------AGTACTTAACACGG-----------TAACTAAC s droBip2.KB464407 1957691 179 + 2915140 TATCGCTGCAACATAATCGCATAGTTTGGTGGGG-----AAATTTATGTGCCGCT---------TGGGCAAC------ACACACGCCTCGACAG-----TT---------TCC----------------------------TGGC--CGGC--------GCAA--CTAGTTCTCCCCCTTCCCCTGCAACTAAATATCC------AAA----TGCCCCGATATC-C--------------A-------GAA-CCGATAC-CAT------CGAGTACTTAACACGG-----------TAACTAAC s droEug2.KB465067 598731 147 + 1515531 TATCGCTGCAACATAATCGCATAGTTTGGTGGGT-----AAATTTATGTGCCGCT---------CGGGCAAC--------ACACGCTTCGCCAG-----TC----------------------------------------TGGT--CCGC-----CAGTTGG--CT-----------------------------CGC------AGA----TA-CCCGATACC-GATACCG--------A--------TT-CCGATAG-CAT------CGAGTACTTAACACGA-----------T-----CC s droEle2.KB458573 519427 148 - 5320397 TATCGCTGCAACATAATCGCATACTTTGGTGGGT-----AAATTTATGTGCCGCT---------CGGCCAAC--------ACACGCTTCGCCAG-----TC----------------------------------------TGGC--CAGT-----CTTCCGA--GTCTTCCCA----------------------GTC------TGA----TA-CCCGATACC-G--------------A--------TT-CCGATAC-CAT------CGAGTACTTAACACGA-----------T-----CC s droKik2.KB459527 274210 141 - 1234237 TATCGCCGCAACATAATCGCATAGTTTGGTGGGG-----AAATTTATGTGCCGCT---------TGGCCAAC--------ACACGCGTCGACAG-----TT----------------------------------------------------------TCCG--CG-----------------------------GCC------AGA----TA-CCCAATCCT-GATACCGATACC---G--------AA-CCGATAC-CAT------CGAGTACTTAACACGA-----------T-----CC s droTak2.KB461535 139212 151 - 669855 TATCGCTGCAACATAATCGCATAGTTGGTGGGGT-----AAATTTATGTGCCGCT---------GGGGCAAC--------ACACGCTTCGCCAG-----TC--------AGCT----------------------------TCGT--CTGCCTCGGCAGTTGG--CT-----------------------------AGC------AGA----TA-CCCGATACC-G--------------A--------TTCCCGATAG-CAT------CGAGTACTTAACACGA-----------T-----CC s droRho2.KB449310 33060 142 - 65043 TATCGCTGCAACATAATCGCATAGTTTGGTGGGT-----AAATTTATGTGCCGCT---------GGGGCAAC--------ACACGCTTCGCCTG-----GC----------------------------------------CAGT--CAG---------CCAG--AT-----------------------------ACC------CGA----TA-CCCGATACC-GATTCC---------G--------AT-CCGATAC-CAT------CGAGTACTTAACACGA-----------T-----CC s droFic2.KB457177 78898 117 + 995874 TATCGCTGCAACATAATCGCATAGTTTGGTGGGG-----AAATTTATGTGCCGCT---------CGGGCAAC--------ACACGCTTCGCCAG-----AC----------------------------------------------------------------------------------------------------------------A-ACCGATACC-G--------------A--------AT-TCGATAC-CAT------CGAGTACTTAACACGA-----------T-----CC s droPse3.chr3 1347284 186 - 19787792 TATCGCTGCCACATAATCGCATAGTTTGCttggg-----aaatttatgtgcCGCT---------GTGGCAAC--------ACACGCTTCGACAG-----TT--------Accc---cagcttcagc-------------ttcagcttcagcctcagtCCCCAA--TC-----------------------------CCC------ATG----CC-CGCGATAGC-A--GGCGATACTTGAA--------GA-CCGATAT-CATCGAATACGAGTACTTAACACACG-------TTTC-----CC s droPer1.super_34 536143 174 - 916997 TATCGCTGCCACATAATCGCATAGTTTGCTTGGG-----AAATTTATGTGCCGCT---------GTGGCAAC--------ACACGCTTCGACAG-----TT--------ACCC----------------------------CAGCTTCAGCCTCAGTCCCCAA--TC-----------------------------CCC------ATG----CC-CGCGATAGC-A--GGCGATACTTGAA--------GA-CCGATAT-CATCGAATACGAGTACTTAACACACG-------TTTC-----CC s droMir2.chr3 1388394 180 - 20862834 TATCGCTGCCACATAATCGCATAGTTTGCttggg-----aaatttatgtgcCGCT---------GTGGCAAC--------ACACGCTTCGACAG-----TT--------accc---------cagc-------------ttcagcttcagcctcagtcCCCAA--TC-----------------------------CCC------ATG----CC-CGCGATAGC-A--GGCGATACTTGAA--------GA-CCGATAT-CATCGAATACGAGTACTTAACACACG-------TTTC-----CC s droWil2.CH963894 1306551 205 + 2843958 TATCGCAGCAACATAATCGCATAGTTTACTCGAGGGGTAAAATTTATGTGCCGTT---------TGGGCAAC----------ACGCTTCGACAG-----CTTCAGTTTTAGCCTTTTAGCTTCTTCCTCCAATATACTTTTTGATATCAAAGATTGCAAACGAATCT-----------------------------ACt------taa----ca-caaaacaca-c--------------a--------ca-cacacacacac------agaccaTTTACCTCTCTAACGTTCTCTt-----ct s droVir3.scaffold_12875 7349573 101 + 20611582 TATCGCTGCAACATAATCGCATAGTTTAACTGA------AAATTTATGTGCCGCTTTTAGCTAAGGGGCA-----------------------G-----AC-----------------------------------------------------------------------------------------------TAC------GTG----TA-GTAAACATA-A--------------T---------T-TTAACCA-CAC------T--------------------------T-----CC s droMoj3.scaffold_6496 26144661 117 + 26866924 TAACGATGCCACGTAATCGCATAGTTTGACTGT------AAATTTATGTGCCGCCTGCGGCT--GGGGCAGC--------A---GC-------G-----AG-----------------------------------------------------------------------------------------------TAC------GTGGGGCTA-GCGAACCTA-A--------------TCTAATCAGCT-CTAATCA-CAC------C--------------------------T-----CC s droAlb1.JH854640 307378 107 + 406291 TATCGTTGCAAGTTAATCGCAtagtttatttgc------aaatttatgttcCACTTTTCGAT--GAAGTAGC--------GATCGC-------G-----TC-----------------------------------------------------------------------------------------------TAC------GAA----TA-GTTCACACA-T--------------C---------T-TTAACCG-AAA------C--------------------------T-----tc s droGri2.scaffold_15245 898121 108 + 18325388 TATCGCTGCAACATAATCGCATAGTTTAACTTA------AAATTTATGTGCCGCTTTCGGCAAAAGCGCA-----------------------G-----AC-----------------------------------------------------------------------------------------------TGCTCTGCGTTG----TA-GTTAACACA-A--------------C--------TT-TTAACCA-CAC------T--------------------------T-----CC a score=2871.000000 s dm6.chr2R 24348187 5 + 25286936 TCTG---------C- s droSim1.chr2R 18694916 4 + 19596830 TCTG----------- s droSec1.super_23 114669 4 + 989336 TCTG----------- s droYak3.chr2R 20203882 4 + 21139217 TCTG----------- s droEre2.scaffold_4845 21601861 4 + 22589142 TCTG----------- s droBia2.KB462602 794205 4 + 3129309 TCTG----------- s droSuz1.KI419649 12039387 4 - 14502029 TCTG----------- s droAna3.scaffold_13266 5709059 7 - 19884421 TCCA-------CAC- s droBip2.KB464407 1957870 4 + 2915140 TCTA----------- s droEug2.KB465067 598878 4 + 1515531 TCTG----------- s droEle2.KB458573 519575 4 - 5320397 TCTG----------- s droKik2.KB459527 274351 14 - 1234237 TCTCTGACTCACTT- s droTak2.KB461535 139363 4 - 669855 TCTG----------- s droRho2.KB449310 33202 4 - 65043 TCTG----------- s droFic2.KB457177 79015 4 + 995874 TCTG----------- s droPse3.chr3 1347470 4 - 19787792 TTTG----------- s droPer1.super_34 536317 4 - 916997 TTTG----------- s droMir2.chr3 1388574 4 - 20862834 TTTG----------- s droWil2.CH963894 1306756 4 + 2843958 tctg----------- s droVir3.scaffold_12875 7349674 4 + 20611582 TCTt----------- s droMoj3.scaffold_6496 26144778 4 + 26866924 TTGC----------- s droAlb1.JH854640 307485 4 + 406291 aaca----------- s droGri2.scaffold_15245 898229 4 + 18325388 TCCA----------- s anoGam1.chr3L 3978280 5 + 41284009 TTTG----------T a score=87172.000000 s dm6.chr2R 24348192 7 + 25286936 TCTCTCC s droSim1.chr2R 18694920 6 + 19596830 -CTCTCC s droSec1.super_23 114673 6 + 989336 -CTCTCC s droYak3.chr2R 20203886 6 + 21139217 -CTCTCC s droEre2.scaffold_4845 21601865 6 + 22589142 -CTCTCC s droBia2.KB462602 794209 6 + 3129309 -CTCTCC s droSuz1.KI419649 12039391 6 - 14502029 -CTCTCC s droAna3.scaffold_13266 5709066 7 - 19884421 TCTCTCT s droBip2.KB464407 1957874 6 + 2915140 -CTCTCC s droEug2.KB465067 598882 6 + 1515531 -CTCTCT s droEle2.KB458573 519579 6 - 5320397 -CTCTCT s droKik2.KB459527 274365 7 - 1234237 CCTCTCT s droTak2.KB461535 139367 6 - 669855 -Ctcttt s droRho2.KB449310 33206 6 - 65043 -CTCACT s droFic2.KB457177 79019 6 + 995874 -CTCTCC s droPse3.chr3 1347474 6 - 19787792 -CTCCTT s droPer1.super_34 536321 6 - 916997 -CTCCTT s droMir2.chr3 1388578 6 - 20862834 -CTCCTT s droWil2.CH963894 1306760 6 + 2843958 -ttctgt s droVir3.scaffold_12875 7349678 6 + 20611582 -ctctct s droMoj3.scaffold_6496 26144782 6 + 26866924 -CGTTCC s droAlb1.JH854640 307489 6 + 406291 -ctctct s droGri2.scaffold_15245 898233 6 + 18325388 -CTCTTT s musDom2.KB857237 19823 5 - 101287 --tcttt s anoGam1.chr3L 3978285 6 + 41284009 -TTGTTC a score=-170324.000000 s dm6.chr2R 24348199 6 + 25286936 CTC-----------CAC s droSim1.chr2R 18694926 6 + 19596830 CTC-----------CAC s droSec1.super_23 114679 6 + 989336 CTC-----------CAC s droYak3.chr2R 20203892 6 + 21139217 CTC-----------CAC s droEre2.scaffold_4845 21601871 6 + 22589142 CTC-----------CAC s droBia2.KB462602 794215 8 + 3129309 CTC---------TTTGC s droSuz1.KI419649 12039397 8 - 14502029 CTC---------TTTGC s droAna3.scaffold_13266 5709073 10 - 19884421 CTCTG-------TCCAC s droBip2.KB464407 1957880 10 + 2915140 CTCCG-------TCCAC s droEug2.KB465067 598888 7 + 1515531 CTT----------CCTC s droEle2.KB458573 519585 11 - 5320397 CTCCA------CTTCAC s droKik2.KB459527 274372 8 - 1234237 CTT---------GTTTC s droTak2.KB461535 139373 7 - 669855 cct----------ccac s droRho2.KB449310 33212 17 - 65043 CCTCTCCTCTCCTCCAC s droFic2.KB457177 79025 3 + 995874 TCC-------------- s droPse3.chr3 1347480 8 - 19787792 TCC---------ACTCG s droPer1.super_34 536327 8 - 916997 TCC---------ACTCG s droMir2.chr3 1388584 8 - 20862834 TCC---------ACTCG s droWil2.CH963894 1306766 9 + 2843958 tct--------gttcgc s droVir3.scaffold_12875 7349684 16 + 20611582 ctccctctc-tctctct s droMoj3.scaffold_6496 26144788 2 + 26866924 TT--------------- s droAlb1.JH854640 307495 17 + 406291 ctctctttcttctcttt s droGri2.scaffold_15245 898239 6 + 18325388 GC--------TCTC--- s musDom2.KB857237 19828 8 - 101287 tct---------tttat s anoGam1.chr3L 3978291 6 + 41284009 TTT-----------TCA s apiMel4.Group11 6690459 6 - 14726556 -----------CTCTGA a score=11938960.000000 s dm6.chr2R 24348205 490 + 25286936 T--------TT-CAGGCCTACGAGCTGTCCACGCTGACCGGGACGCAGGTGATGCTGCTGGTGGCCAGCGAGACGGGCCACGTGTACACATTTGCCACGCGCAAGCTGCAGCCGATGATCACCTCGGAGGCGGGAAAGCAGCTCATCCAGACCTGCCTCAACTCGCCGGATCCGCC--CA-GTGTGGG---CGG-CGGCGACCAACGGATGTCGGCCACCGGGTTCGAGGAGACGGAGCTCAGCTACAACATCGCCGACGAGGACTCGAAAGTAAGACAATTGATAT------ACGGT------CAC---CACGGGCACGCTCAT--CTAGGTCACCCGCCGGCGCCGCCCTCGCACTACAGCCTCGAGCAGAGCCTGAT-G----CAGTCGGGCTACAGCGGC----------------GGCCAGGCCTCGCCGCTTTCCCACGCCCAG------------TACG---GCGGACACGGGCACCACGCCCACGTGCCGCACGTGCCGCCGCCGCATTCGACGCACTCGCACATG-TCCCACACGCATGCGCAG---CGCTAGG s droSim1.chr2R 18694932 490 + 19596830 T--------TT-CAGGCCTACGAGCTGTCCACGCTGACCGGGACGCAGGTGATGCTGCTGGTGGCCAGCGAGACGGGCCACGTGTACACATTTGCCACGCGCAAGCTGCAGCCGATGATCACCTCGGAGGCGGGCAAGCAGCTCATCCAGACCTGCCTCAACTCGCCGGATCCGCC--CA-GTGTGGG---CGG-CGGCGACCAACGGATGTCGGCCACCGGGTTCGAGGAGACGGAGCTCAGCTACAACATCGCCGACGAGGACTCGAAAGTAAGACAATTGATAT------ACGGT------CAC---CACGGGCACGCTCAT--CTGGGTCACCCGCCGGCGCCGCCCTCGCACTACAGCCTCGAGCAGAGCCTGAT-G----CAGTCGGGCTACAGCGGC----------------GGCCAGGCCTCGCCGCTTTCCCACGCCCAG------------TACG---GCGGACACGGGCACCACGCCCACGTGCCGCACGTGCCGCCGCCGCATTCGACGCACTCGCACATG-TCCCACACGCATGCGCAG---CGCTAGG s droSec1.super_23 114685 490 + 989336 T--------TT-CAGGCCTACGAGCTGTCCACGCTGACCGGGACGCAGGTGATGCTGCTGGTGGCCAGCGAGACGGGCCACGTGTACACATTTGCCACGCGCAAGCTGCAGCCGATGATCACCTCGGAGGCGGGCAAGCAGCTCATCCAGACCTGCCTCAACTCGCCGGATCCGCC--CA-GTGTGGG---CGG-CGGCGACCAACGGATGTCGGCCACCGGGTTCGAGGAGACAGAGCTCAGCTACAACATCGCCGACGAGGACTCGAAAGTAAGACAATTGATAT------ACGGT------CAC---CACGGGCACGCTCAT--CTGGGTCACCCGCCGGCGCCGCCCTCGCACTACAGCCTCGAGCAGAGCCTGAT-G----CAGTCGGGCTACAGCGGC----------------GGCCAGGCCTCGCCGCTTTCCCACGCCCAG------------TACG---GCGGACACGGGCACCACGCCCACGTGCCGCACGTGCCGCCGCCGCATTCGACGCACTCGCACATG-TCCCACACGCATGCGCAG---CGCTAGG s droYak3.chr2R 20203898 490 + 21139217 T--------TT-CAGGCCTACGAGCTGTCCACGCTGACCGGGACGCAGGTGATGCTGCTAGTGGCCAGCGAGACGGGCCACGTGTACACATTTGCCACGCGCAAGCTGCAGCCGATGATCACCTCGGAGGCGGGCAAGCAGCTCATCCAGACCTGCCTCAACTCGCCGGATCCGCC--CA-GCGTGGG---CGG-CGGCGACCAGCGGATGTCGGCCACCGGGTTCGAGGAGACGGAGCTCAGCTACAACATCGCCGACGAGGACTCGAAAGTAAGACAATTGATAT------ACGGT------CAC---CACGGGCACGCTCAT--CTGGGTCACCCGCCGGCGCCGCCCTCTCACTACAGCCTCGAGCAAAGCCTGAT-G----CAGTCGGGCTACAGCGGC----------------GGCCAGGCCTCGCCGCTTTCCCACGCCCAG------------TACG---GCGGACACGGGCACCACGCCCACGTGCCGCACGTGCCGCCGCCGCACTCGACGCACTCGCACATG-TCCCACACGCATGCGCAG---CGCTAGG s droEre2.scaffold_4845 21601877 490 + 22589142 T--------TT-CAGGCCTACGAGCTGTCCACGCTGACCGGGACGCAGGTGATGCTGCTGGTGGCCAGCGAGACGGGCCACGTGTACACATTTGCCACGCGCAAGCTGCAGCCGATGATCACCTCGGAGGCGGGCAAGCAGCTCATCCAGACCTGCCTCAACTCGCCGGATCCGCC--CA-GCGTGGG---CGG-CGGCGACCAGCGGATGTCGGCCACCGGGTTCGAGGAGACGGAGCTCAGCTACAACATCGCCGACGAGGACTCGAAAGTAAGACAATTGATAT------ACGGT------CAC---CACGGGCACGCTCAT--CTAGGTCACCCGCCGGCGCCGCCCTCGCACTACAGCCTCGAGCAGAGCCTGAT-G----CAGTCGGGCTACAGCGGC----------------GGCCAGGCCTCGCCGCTTTCCCACGCCCAG------------TACG---GCGGACACGGGCACCACGCCCACGTGCCGCACGTGCCGCCGCCGCACTCGACGCACTCGCACATG-TCCCACACGCATGCGCAG---CGCTAGG s droBia2.KB462602 794223 490 + 3129309 T--------TG-CAGGCCTACGAGCTGTCCACGCTGACCGGGACGCAGGtgatgctgctggtggccaGCGAGACGGGCCACGTGTACACATTTGCCACGCGCAAGCTGCAGCCGATGATCACCTCGGAGGCGGGCAAGCAGCTCATCCAGACCTGCCTCAACTCGCCGGATCCGCC--CA-gcgtcgg---cgg-cggcgacCAGCGGATGTCGGCCACCGGGTTCGAGGAGACGGAGCTCAGCTACAACATCGCCGACGAGGACTCGAAAGTAAGACAATTGATAT------ACGGC------CAC---CACGGGCACGCTCAT--CTGGGTCACCCGCCGGCGCCGCCCTCGCACTACAGCCTCGAGCAGAGCCTGAT-G----CAGTCGGGCTACAGCGGC----------------GGCCAGGCGTCGCCCCTTTCCCACGCCCAA------------TACG---GCGGACACGGGCACCACGCCCACGTGCCGCACGTGCCGCCGCCGCATTCGACGCACTCGCACATG-TCGCACACGCATGCGCAG---CGCTAGG s droSuz1.KI419649 12039405 490 - 14502029 T--------TG-CAGGCCTACGAGCTGTCCACGCTGACCGGGACGCAGGTGATGCTGCTGGTGGCCAGCGAAACGGGCCACGTGTACACATTTGCCACGCGCAAGCTGCAGCCGATGATCACCTCGGAGGCGGGCAAGCAGCTCATCCAGACCTGCCTCAACTCGCCGGATCCGCC--CA-GCGTCGG---TGG-CGGCGACCAGCGGATGTCGGCCACCGGATTCGAGGAGACGGAGCTCAGCTACAACATCGCCGACGAGGACTCGAAAGTAAGACAATTGATAT------ACGGC------CAT---CACGGGCACGCTCAT--CTGGGTCACCCGCCGGCGCCGCCCTCGCACTACAGCCTCGAGCAGAGCCTGAT-G----CAGTCGGGCTACAGCGGT----------------GGCCAGGCCTCGCCCCTTTCCCACGCCCAA------------TACG---GCGGACATGGGCACCACGCCCACGTGCCGCACGTGCCGCCGCCGCATTCGACGCACTCGCACATG-TCGCACACGCATGCGCAG---CGCTAGG s droAna3.scaffold_13266 5709083 494 - 19884421 T--------TTGCAGGCCTACGAGCTGTCCACTCTGACCGGAACGCAGGTGATGCTACTGGTGGCCAGCGAAACGGGCCACGTCTACACATTTGCCACGCGGAAGCTCCAGCCGATGATCACCTCGGAGGCGGGCAAGCAGCTCATCCAGACCTGCCTCAATTCGCCGGATCCGCC--GA-GCGTCGG---TGG-CGGCGACCAACGGATGTCGGCCACGGGCTTCGAGGAGACGGAGCTCAGCTACAACATCGCCGACGAGGACTCCAAAGTAAGACAATTGATTT------ACGGC------CAC---CACGGGCACGCTCAT--TTGGCACACCCGCCGGCACCGCCCTCGCACTACAGCCTCGAGCAGAGCCTGAT-G----CAGTCCGGCTACAGTGGC----------------GGCCAGGCGTCGCCCCTGTCCCACGCCCAGGCG---------TACG---GCGGGCATGCCCACCATGCGCACGTGCCCCATGTGCCGCCGCCGCACTCGACGCACTCGCATATG-TCGCACACACATGCGCAG---CGCTAGG s droBip2.KB464407 1957890 494 + 2915140 T--------TTCTAGGCCTACGAGCTGTCAACACTGACCGGAACGCAGGTGATGCTCCTGGTGGCCAGCGAGACCGGCCACGTCTACACATTTGCCACGCGCAAGCTCCAGCCGATGATCACCTCGGAGGCGGGCAAGCAGCTCATCCAGACCTGCCTCAATTCGCCGGATCCGCC--GA-GCGTCGG---TGG-TGGGGATCAACGGATGTCGGCCACGGGCTTCGAGGAGACGGAGCTCAGCTACAATATCGCCGACGAGGACTCCAAAGTAAGACAATTGATTT------ACGGT------CAC---CATGGGCACGCTCAT--TTGGCACACCCGCCGGCACCGCCCTCGCACTACAGCCTCGAACAGAGCCTGAT-G----CAGTCCGGCTACAGTGGC----------------GGCCAGGCGTCGCCTCTGTCCCATGCCCAGGCC---------TACG---GCGGACATGCGCACCATGCGCACGTGCCCCACGTGCCGCCGCCGCACTCGACGCACTCGCATATG-TCGCACACGCATGCGCAG---CGCTAGG s droEug2.KB465067 598895 490 + 1515531 T--------TT-CAGGCCTACGAGCTGTCCACGCTGACCGGGACGCAAGTGATGCTGCTGGTGGCCAGCGAGACGGGCCACGTGTACACATTTGCCACGCGCAAGCTGCAGCCGATGATCACCTCGGAGGCGGGCAAGCAGCTCATCCAGACCTGCCTCAACTCGCCGGATCCGCC--CA-GCGTTGG---CGG-CGGCGACCAGCGGATGTCGGCCACCGGGTTCGAGGAGACGGAGCTCAGCTACAACATCGCCGACGAGGACTCGAAAGTAAGACAATTGATAT------ACGGT------CAC---CACGGGCACGCTCAT--CTGGGTCACCCGCCGGCACCGCCCTCGCACTATAGCCTCGAGCAGAGCCTGAT-G----CAGTCGGGCTATAGTGGC----------------GGCCAGGCCTCGCCGCTTTCCCACGCCCAA------------TACG---GCGGCCACGGGCACCATGCCCACGTGCCGCACGTGCCGCCGCCGCATTCGACGCACTCGCACATG-TCCCACACGCATGCGCAG---CGCTAGG s droEle2.KB458573 519596 490 - 5320397 T--------TG-CAGGCCTACGAGCTGTCTACGCTGACCGGGACACAGGtgatgctgctggtggccaGCGAGACGGGCCACGTGTACACATTTGCAACGCGCAAGCTGCAGCCGATGATCACCTCGGAGGCGGGCAAGCAGCTCATCCAGACCTGCCTCAATTCGCCGGATCCGCC--CA-GCGTCGG---CGG-CGGCGACCAGCGGATGTCGGCCACCGGGTTCGAGGAGACGGAGCTCAGCTACAACATCGCCGACGAGGACTCGAAAGTAAGACAATTGATAT------ACGGC------CAC---CACGGGCACGCTCAT--CTGGGCCATCCGCCGGCGCCGCCCTCGCACTACAGCCTCGAGCAGAGTCTGAT-G----CAGTCGGGCTACAGCGGT----------------GGCCAGGCCTCGCCGCTTTCCCACGCCCAG------------TACG---GCGGACACGGGCACCACGCCCACGTCCCGCACGTGCCGCCGCCGCACTCGACGCACTCGCACATG-TCGCACACGCATGCGCAG---CGCTAGG s droKik2.KB459527 274380 493 - 1234237 C--------TG-CAGGCCTACGAGCTGTCCACGCTGACCGGAACGCAAGtgatgctgctggtggccagcGAAACAGGCCACGTGTACACATTTGCCACGCGCAAGCTGCAGCCGATGATCACCTCGGAGGCGGGCAAACAGCTCATCCAGACCTGCCTTAACTCGCCGGATCCGCC--CA-GCGTTGG---TGG-CGGCGATCAACGGATGTCGGCCACCGGCTTCGAGGAGACGGAGCTCAGCTATAACATCGCCGATGAGGACTCCAAAGTAAGACAATTGATTT------ACGGT------CAC---CATGGGCACGCTCAT--CTGGCGCACCCGCCGGCACCGCCCTCGCACTACAGCCTCGAGCAGAGTCTGAT-G----CAGTCCGGCTATAGTGGA----------------GGCCAGGCGTCGCCCCTGTCCCACGCCCAGGCC---------TACG---GCGGACATGCGCACCATGCGCATGTACCGCACGTGCCGCCGCCGCATTCGACGCACTCGCACATG-TCCCACACGCATGCGCAG---CGCTAAA s droTak2.KB461535 139380 490 - 669855 t--------tg-caggCCTACGAGCTGTCCACGCTGACCGGGACGCAGGTGATGCTGCTGGTGGCCAGCGAGACGGGCCACGTGTACACATTTGCCACGCGCAAGCTGCAGCCGATGATCACCTCGGAGGCGGGCAAGCAGCTCATCCAGACCTGCCTCAACTCGCCGGATCCGCC--CA-GCGTGGG---CGG-CGGCGACCAGCGGATGTCGGCCACCGGATTCGAGGAGACGGAGCTCAGCTACAACATCGCCGACGAGGACTCGAAAGTAAGACAATTGATAT------ACGGC------CAC---CACGGGCACGCTCAT--CTGGGTCACCCGCCGGCGCCGCCCTCGCACTACAGCCTCGAGCAGAGCCTGAT-G----CAGTCGGGCTACAGCGGC----------------GGCCAGGCCTCGCCCCTTTCCCACGCCCAA------------TACG---GCGGACACGGGCACCACGCCCACGTGCCGCACGTGCCGCCGCCGCATTCGACGCACTCGCACATG-TCCCACACGCATGCGCAG---CGCTAGG s droRho2.KB449310 33229 490 - 65043 T--------TG-CAGGCCTACGAACTATCCACGCTGACCGGGACGCAGGTGATGCTGCTGGTGGCCAGCGAGACGGGCCACGTGTACACATTTGCCACGCGCAAGCTGCAACCGATGATCACCTCGGAGGCGGGCAAGCAGCTCATCCAGACCTGCCTCAACTCGCCGGATCCGCC--GA-GCGTCGG---TGG-CGGCGATCAGCGGATGTCGGCCACCGGATTCGAGGAGACGGAACTCAGCTACAACATCGCCGACGAGGACTCGAAAGTAAGACAATTGATAT------ACGGC------CAC---CACGGGCACGCTCAT--CTGGGCCATCCGCCGGCGCCGCCCTCGCACTACAGCCTCGAGCAGAGTCTGAT-G----CAGTCGGGCTACAGCGGC----------------GGCCAGGCCTCGCCGCTTTCCCACGCCCAG------------TACG---GCGGACACGGGCACCACGCCCACGTGCCGCACGTGCCGCCGCCGCACTCGACGCACTCGCACATG-TCCCACACGCATGCGCAG---Cgctagg s droFic2.KB457177 79028 490 + 995874 T--------TG-CAGGCATACGAGCTGTCGACGCTGACCGGAACGCAGGtgatgctgctggtggccAGCGAAACGGGCCACGTGTACACATTTGCCACGCGCAAGCTCCAGCCGATGATCACCTCGGAGGCGGGAAAGCAGCTCATCCAGACCTGCCTCAACTCGCCGGACCCGCC--GA-gcgtcgg---cgg-cggcgaccAGCGGATGTCGGCCACCGGGTTCGAGGAGACGGAGCTCAGCTACAACATCGCCGACGAGGACTCGAAAGTAAGACAATTGATAT------ACGGC------CAC---CACGGGCACGCTCAC--CTCGGTCACCCGCCGGCGCCGCCCTCGCACTACAGCCTCGAGCAGAGTCTGAT-G----CAGTCGGGCTACAGCGGC----------------GGCCAGGCCTCGCCGCTCTCGCACGCCCAG------------TACG---GCGGCCACGGGCACCACGCCCACGTGCCGCACGTGCCGCCGCCGCACTCGACGCACTCGCACATG-ACCCACACGCATGCGCAG---CGCTAGG s droPse3.chr3 1347488 493 - 19787792 T--------TG-CAGGCCTACGAGCTGTCGACGCTGACTGGGACACAGGTAATGCTGCTGGTTGCCAGCGAGACGGGTCACGTCTACACATTTGCCACGCGCAAGCTGCAGCCGATGATCACCTCGGAGGCGGGCAAACAGCTCATACAGACCTGCCTCAACTCGCCGGATCCGCC--CA-GCGTGGG---CGG-CGGGGACCAGCGCATGTCGGCCACGGGCTTCGAGGAGACGGAGCTCAGCTACAACATCGCGGACGAGGACTCCAAAGTAAGACAATTGATTT------ATGGT------CAC---CACGGGCACGCTCAT--CTCGCCCATCCGCCGGCGCCACCCTCGCACTACAGCCTCGAGCAGAGTCTGAT-G----CAGTCCGGGTACAGCGGT----------------GGCCAGGCCTCGCCCCTGTCCCATGCCCAGGCC---------TACG---GCGGACATGCGCACCATGCGCATGTGGCCCacgtgccgccgccgcattcGACGCACTCGCACATG-TCGCATACGCATGCGCAG---CGCTAGG s droPer1.super_34 536335 493 - 916997 T--------TG-CAGGCCTACGAGCTGTCGACGCTGACTGGGACACAGGTAATGCTGCTGGTTGCCAGCGAGACGGGTCACGTCTACACATTTGCCACGCGCAAGCTGCAGCCGATGATCACCTCGGAGGCGGGCAAACAGCTCATACAGACCTGCCTCAACTCGCCGGATCCGCC--CA-GCGTGGG---CGG-CGGGGACCAGCGCATGTCGGCCACGGGCTTCGAGGAGACGGAGCTCAGCTACAACATCGCGGACGAGGACTCCAAAGTAAGACAATTGATTT------ATGGT------CAC---CACGGGCACGCTCAT--CTCGCCCATCCGCCGGCGCCACCCTCGCACTACAGCCTCGAGCAGAGTCTGAT-G----CAGTCCGGGTACAGCGGT----------------GGCCAGGCCTCGCCCCTGTCCCATGCCCAGGCC---------TACG---GCGGACATGCGCACCATGCGCATGTGGCCCACGTGCCGCCGCCGCATTCGACGCACTCGCACATG-TCGCATACGCATGCGCAG---CGCTAGG s droMir2.chr3 1388592 493 - 20862834 T--------TG-CAGGCCTACGAGCTGTCGACGCTGACTGGGACACAGGTAATGCTGCTGGTTGCCAGCGAGACGGGTCACGTCTACACTTTTGCCACGCGCAAGCTGCAGCCGATGATCACCTCGGAGGCGGGCAAACAGCTCATCCAGACCTGCCTCAACTCGCCGGATCCGCC--CA-GCGTGGG---CGG-CGGGGACCAGCGCATGTCGGCCACGGGCTTCGAGGAGACGGAGCTCAGCTACAACATCGCGGACGAGGACTCCAAAGTAAGACAATTGATTT------ATGGT------CAC---CACGGGCACGCTCAT--CTCGCCCATCCGCCGGCGCCACCCTCGCACTACAGCCTCGAGCAGAGTCTGAT-G----CAGTCCGGGTACAGCGGT----------------GGCCAGGCCTCGCCCCTGTCCCATGCCCAGGCC---------TACG---GCGGACATGCGCACCATGCGCATGTGGCCCacgtgccgccgccgcattcGACGCACTCGCACATG-TCGCATACGCATGCGCAG---CGCTAGG s droWil2.CH963894 1306775 487 + 2843958 T--------TG-CAGGCCTACGAGCTGTCAACATTGACTGGAACGCAGGTAATGCTGCTGGTTGCCAGCGAAACGGGTCACGTCTACACATTTGCCACGCGCAAACTGCAACCGATGATCACCTCGGAGGCGGGCAAACAGCTCATACAGACCTGCCTCAATTCACCAGATCCGCC--CA-GTGTGGG---CGG-CGGCGATCAACGGATGTCGGCCACAGGCTTTGAGGAGACCGAGCTCAGCTACAACATTGCCGATGAGGACTCCAAAGTAAGACAATTGATTT------ATGGT------CAT---CATGGGCACGCTCAT--TTAGCCCATCCGCCAGCGCCACCCTCCCACTATAGCCTCGAACAGAGTCTTAT-G----CAATCGGGCTATAGTGGA----------------GGTCAGGCATCACCATTATCCCATGCCCAGGCC---------TATG---GGGGTCAT------CATGCGCATGTGCCACACGTGCCACCGCCCCATTCAACGCATTCCCATATG-TCGCATACGCATGCGCAG---CGTTAGA s droVir3.scaffold_12875 7349700 501 + 20611582 cCACGCCCGTG-CAGGCCTACGAGCTGTCGACGCTGACTGGTACCCAGGTGATGCTGCTGGTGGCCAGCGAGACGGGTCACGTCTACACATTTGCCACGCGCAAGCTGCAGCCGATGATAACGTCGGAGGCGGGCAAACAGCTGATACAGACGTGCCTCAATTCGCCGGATCCGCC--AA-GCGTTGG---CGG-CGGAGATCAGCGCATGTCCGCGACGGGCTTCGAGGAGACGGAGCTGAGCTACAACATCGCCGACGAGGACTCCAAAGTAAGACAATTGATTT------ACGGC------CAT---CACGGGCACGCTCAT--CTCGCACACCCCCAGGCGCCGCCCTCGCACTACAGCCTGGAGCAGAGCCTTAT-G----CAGTCCGGCTACAGCGGC----------------GGCCAGGCCTCGCCCCTGTCGCATGCCCAGGCC---------TACG---GCGGACATGCGCACCATGCGCATGTGCCGCATGTGCCGCCGCCGCACTCTACACATTCACACATG-TCCCATACGCATGCCCAG---CGCTAGG s droMoj3.scaffold_6496 26144790 492 + 26866924 ---------TG-CAGGCCTACGAGCTATCAACGCTGACTGGGACCCAGGTGATGCTGCTGGTGGCCAGTGAAACGGGTCACGTGTACACATTCGCCACGCGCAAACTGCAGCCGATGATAACGTCGGAGGCGGGCAAGCAGCTGATACAGACGTGCCTGAACTCGCCGGATCCGCC--GA-GCGTGGG---CGG-CGGCGATCAGCGCATGTCCGCGACGGGCTTCGAGGAGACGGAGCTCAGCTACAACATCGCCGACGAGGACACCAAAGTAAGACAATTGATTT------ACGGC------CAT---CACGGGCACGCTCAT--CTCGCACACCCCCAGGCGCCACCCTCGCACTACAGCCTCGAGCAGAGCCTCAT-G----CAGTCCGGCTACACCGGT----------------GGCCAGGCCTCGCCCCTGTCGCACGCCCAGGCC---------TACG---GCGGACATGCGCACCACGCGCACGTGCCACACGTGCCGCCGCCGCACTCCACGCACTCGCACATG-TCGCATACGCATGCGCAG---CGCTAGG s droAlb1.JH854640 307512 491 + 406291 t--------tg-caGGCCTACGAGCTGTCGACGCTGACTGGCACCCAGGTGATGTTGCTGGTGGCCAGCGAGACGGGTCATGTGTACACATTTGCCACGCGCAAGCTGCAGCCGATGATCACCTCGGAGGCGGGTAAGCAGCTCATACAGACGTGCCTCAACTCGCCGGATCCGCC--CA-GCGTCGG---TGG-CGGCGATCAGCGCATGTCCGCCACGGGCTTCGAGGAGACGGAGCTCAGCTACAACATCGCCGACGAGGACTCCAAAGTAAGACAATTGATTT------ACGGC------CAT---CATGGGCACGCTCAT--CTTGCACACCCGCAGGCGCCGCCCTCGCATTACAGCCTCGAACAGAGCCTCAT-G----CAGTCCGGCTACAGCGGT----------------GGCCAGGCGTCGCCCCTCTCCCATGCACAGGCC---------TACG---GCGGCCACGCCCACCACGCGCACGTGCCACACGTTCCACCGCCCCACTCGACACATTCGCACATG-TCGCACACGCATGCGCAG---CGTTG-- s droGri2.scaffold_15245 898245 492 + 18325388 ---------TG-CAGGCCTACGAGCTGTCGACGCTGACTGGTACTCAGGTGATGCTGCTGGTTGCCAGCGAGACGGGACACGTTTACACATTTGCGACGCGCAAGCTGCAGCCGATGATAACGTCGGAGGCGGGCAAACAACTGATACAGACATGCCTCAATTCACCGGATCCGCC--AA-GTGTTGG---CGG-TGGCGATCAGCGCATGTCTGCCACCGGATTCGAGGAGACGGAGCTCAGCTATAACATCGCCGACGAGGACTCCAAAGTAAGACAATTGATTT------ACGGC------CAT---CACGGGCACGCTCAT--CTCGCCCACCCCCAGGCGCCGCCCACCCACTACAGTCTCGAGCAGAGTCTCAT-G----CAGTCCGGCTACAGTGGC----------------GGCCAGGCATCGCCCCTATCACACGCCCAGGCC---------TACG---GCGGGCATGCGCATCATGCGCATGTGCCGCACGTGCCACCGCCGCACTCCACACACTCGCACATG-TCGCACACGCATGCGCAA---CGCTAGG s musDom2.KB857237 19836 490 - 101287 t--------tc-tagGCTTACGAATTGTCCACGTTAACTGGTACACAAGTTATGCTTTTAGTTGCTTCAGAGACTGGTCATGTGTATACATTTGCAACCCGCAAGTTACAACCAATGATAACATCAGAAGCAGGGAAACAGCTTATTCAGACGTGTCTAAACTCTCCAGATCCGCC--TA-GTGTTGG---TGG-CGGGGATCAACGTATGTCAGCGACAGGCTTCGAAGAAACCGAACTCAGTTACAACATAGCAGATGAGGACTCAAAAGTAAGACAATTAATTT------ATGGT------CAT---CATGGTCACGCTCAT--CTAGGGCATCCTCAGGCTCCCGCGTCTCATTACGGTCTCGACCAAAGTTTAAT-G----CAATCCCCATATAGTGGA----------------GGCCAACCTTCCCCATTATCCCATTCGCAAGCA---------TATGCGCATGGACATGCTCATCATTCGCACGTTTCACACGT------GCCTCATTCAACACATTCCCATATG-TCCCACACGCATCCCCAG---CGGTAGG s anoGam1.chr3L 3978297 487 + 41284009 T--------TA-CAGGCATATGAACTGTCAACACTTACCGGCACGCAAGTTATGTTGCTGGTGGCCTCCGAAACCGGTCACGTGTACACGTTTGCGACCCGCAAGCTGCAACCGATGATCACGTCGGAGGCGGGCAAGGCGCTCATCCAGACCTGCCTAAATTCGCCCGATCCACC--GACGGGTTCA---TCG--GGCGACCAGCGCATGTCCGCGACCGGCTTCGAGGAGACCGAGCTCAGCTACAACATCGGCGACGAAGACTCCAAAGTAAGGCAATTAGTGTACGGCCACGGC------CAC---CACGGGCATGCTCAT--TTAGGTCACCCGCAG--ACCGGC----CACTACGGGCTCGACCAGGGCTTGAT-G----CAGCAGCCGTACCCCGGA----------------GGCCAGGGCTCCCCACTTTCCCATGCCCAATCCTATCCGCCGCACT---CCGGCCACACCCATCATTCCCACATCCCCCAT------------CACTCC---CACACGCATATG-ACTCATGCGCACGCGCAA---CGGTAGT s apiMel4.Group11 6690465 452 - 14726556 T--------TG-CAGGCGTACGAGCTGTCGACATTGACAGGTACACAAGTGATGCTGCTCGTGGCAAGCGAGACCGGCCACGTGTACACATTCGCGACACGGAAACTGCAGCCGATGATAACGAGCGAAGCCGGGAAAGCGTTGATCCAGACCTGCCTGAACAGCCCGGACCCGCC--CG-CCTCCGGTTCCTC-CGGCGACCAGAGGATGTCCGCGACCGGGTTCGAGGAGACAGAATTGACCTACAACATAGCCGACGACGAGCAGAAAGTAAGGCAACTGGTGT------ATGGC----------------------------------TCGCCGCACGGTGGCTCGCT-GCACGGCGG--------ATATCCTGGTGG----CGGGCCGACCGGAG-------------------------GTCCTCCTGGCCATCCGCCAcccc-------------cgcc---gccgccgccgccgccgggttc----gcagcacgcgccaccctcgcacgcgcagcacgcgcacctgattgcgcatgcacacgcgGGCTCGCCGAG s triCas2.ChLG1X 6851302 493 + 8109244 T--------TC-CAGGCCTACGAGCTGTCGACCCTCACCGGGACGCAGGTGATGCTCCTGGTGGCGTCGGAGACGGGGCACGTGTACACCTTCGCAACCCGCAAACTCCAACCCATGATAACCAGCGAGGCTGGCAAAGCCCTGATCCAGACCTGCTTGAACTCCCCGGATCCTCCGGCG-GGTTCGG---CGTCCGGTGACCAGCGAATGTCGGCCACCGGCTTCGAGGAAACGGAACTCACCTACAACATCAGCGACGAGGACTCCAAAGTAAGACAAATGGTGT------ACGGTTCGCCGCATACACACACGCACGCGCATTCTTTGAGCGGCCAGGGGCACTA--TTCGCAC------CTAGAGCAAAGTCACCT-GGGCCTAGGCGGCTCCCCGCAGCATGGGGGCTATTCGCAGGCCTGTCCTAGTCCGCTGCCGCCGCCC--------------CATC---AGGGCTACGGACACC------------------CGCAACACCCGCATTCG---CACTCGCACATG-ACGCACTCCCATCCCCAG---CGGTAGG a score=-102862.000000 s dm6.chr2R 24348695 6 + 25286936 C----------------TTC------TG---- s droSim1.chr2R 18695422 6 + 19596830 C----------------TTC------TG---- s droSec1.super_23 115175 6 + 989336 C----------------TTC------TG---- s droYak3.chr2R 20204388 8 + 21139217 T--------------GATTC------TG---- s droEre2.scaffold_4845 21602367 6 + 22589142 C----------------TTC------TG---- s droBia2.KB462602 794713 6 + 3129309 C----------------TTC------TG---- s droSuz1.KI419649 12039895 6 - 14502029 C----------------TTC------TG---- s droAna3.scaffold_13266 5709577 18 - 19884421 A----CATTTAGAGATATCC------TT---- s droBip2.KB464407 1958384 22 + 2915140 ATGACCCTCGAGAGCTATCC------TT---- s droEug2.KB465067 599385 6 + 1515531 T----------------TTC------TG---- s droEle2.KB458573 520086 6 - 5320397 T----------------TTC------TG---- s droKik2.KB459527 274873 4 - 1234237 T------------------C------CG---- s droTak2.KB461535 139870 12 - 669855 C----------------TTCTCCTTTTA---- s droRho2.KB449310 33719 6 - 65043 t----------------ttc------tg---- s droFic2.KB457177 79518 7 + 995874 A---------------GCTC------TG---- s droPse3.chr3 1347981 11 - 19787792 C-----------AAATCCTT------CC---- s droPer1.super_34 536828 11 - 916997 C-----------AAATCCTT------CC---- s droMir2.chr3 1389085 11 - 20862834 C-----------AAATCCTT------CC---- s droWil2.CH963894 1307262 6 + 2843958 A----------------TTA------GA---- s droAlb1.JH854640 308003 6 + 406291 ----------------ACTC------CA---- s musDom2.KB857237 20326 7 - 101287 ---------------AGTTT------TG---- s anoGam1.chr3L 3978786 6 + 41284009 ----------------CTTC------TG---- s apiMel4.Group11 6690917 5 - 14726556 -----------------CTC------GC---- s triCas2.ChLG1X 6851795 6 + 8109244 --------------------------TGGATG a score=3833.000000 s dm6.chr2R 24348701 4 + 25286936 ---GCTA s droSim1.chr2R 18695428 4 + 19596830 ---GCTA s droSec1.super_23 115181 4 + 989336 ---GCTA s droYak3.chr2R 20204396 4 + 21139217 ---GCTA s droEre2.scaffold_4845 21602373 4 + 22589142 ---GCTA s droBia2.KB462602 794719 4 + 3129309 ---GCCA s droSuz1.KI419649 12039901 4 - 14502029 ---GCCA s droAna3.scaffold_13266 5709595 4 - 19884421 ---GAGA s droBip2.KB464407 1958406 4 + 2915140 ---GAGA s droEug2.KB465067 599391 4 + 1515531 ---GCTA s droEle2.KB458573 520092 4 - 5320397 ---GCTA s droKik2.KB459527 274877 4 - 1234237 ---GATG s droTak2.KB461535 139882 4 - 669855 ---GCTA s droRho2.KB449310 33725 4 - 65043 ---gcta s droFic2.KB457177 79525 4 + 995874 ---GTCG s droPse3.chr3 1347992 4 - 19787792 ---GCTC s droPer1.super_34 536839 4 - 916997 ---GCTC s droMir2.chr3 1389096 4 - 20862834 ---GCTC s droWil2.CH963894 1307268 4 + 2843958 ---TTTG s droVir3.scaffold_12875 7350201 4 + 20611582 ---GCCA s droAlb1.JH854640 308009 4 + 406291 ---GCCA s musDom2.KB857237 20333 3 - 101287 ---GTA- s apiMel4.Group11 6690923 4 - 14726556 ---CCTG s triCas2.ChLG1X 6851801 4 + 8109244 GGGG--- a score=26239.000000 s dm6.chr2R 24348705 6 + 25286936 -GGATTC s droSim1.chr2R 18695432 6 + 19596830 -GGATTC s droSec1.super_23 115185 6 + 989336 -GGATTC s droYak3.chr2R 20204400 6 + 21139217 -GGATTC s droEre2.scaffold_4845 21602377 6 + 22589142 -GGATTC s droBia2.KB462602 794723 6 + 3129309 -GGATTC s droSuz1.KI419649 12039905 6 - 14502029 -GGATTC s droAna3.scaffold_13266 5709599 5 - 19884421 -T-CCTT s droBip2.KB464407 1958410 6 + 2915140 -GATCCT s droEug2.KB465067 599395 6 + 1515531 -GGATTC s droEle2.KB458573 520096 6 - 5320397 -GGATTC s droKik2.KB459527 274881 6 - 1234237 -AGATCC s droTak2.KB461535 139886 6 - 669855 -GGATGC s droRho2.KB449310 33729 6 - 65043 -ggattc s droFic2.KB457177 79529 6 + 995874 -GGATTC s droPse3.chr3 1347996 6 - 19787792 -AGATTC s droPer1.super_34 536843 6 - 916997 -AGATTC s droMir2.chr3 1389100 6 - 20862834 -AGATTC s droWil2.CH963894 1307272 6 + 2843958 -AGGCAG s droVir3.scaffold_12875 7350205 6 + 20611582 -TGCCCC s droAlb1.JH854640 308013 6 + 406291 -GATCCT s apiMel4.Group11 6690927 6 - 14726556 -GTACCC s triCas2.ChLG1X 6851805 6 + 8109244 AGGGCC- a score=114352.000000 s dm6.chr2R 24348711 11 + 25286936 CTAG--G-----CAA-TAT--- s droSim1.chr2R 18695438 11 + 19596830 CTAG--G-----CAA-TAT--- s droSec1.super_23 115191 11 + 989336 CTAG--G-----CAA-TAT--- s droYak3.chr2R 20204406 11 + 21139217 CTAG--G-----CAA-TAT--- s droEre2.scaffold_4845 21602383 11 + 22589142 CTAG--G-----CAA-TAT--- s droBia2.KB462602 794730 11 + 3129309 CTAG--G-----CAA-TTT--- s droSuz1.KI419649 12039912 11 - 14502029 CTAG--G-----CAA-TAT--- s droAna3.scaffold_13266 5709604 11 - 19884421 TTAG--G-----CAA-TAT--- s droBip2.KB464407 1958416 11 + 2915140 TTAG--G-----CAA-TAT--- s droEug2.KB465067 599402 11 + 1515531 CTAG--G-----CAA-TAT--- s droEle2.KB458573 520105 11 - 5320397 CTAG--G-----CAA-TAT--- s droKik2.KB459527 274904 11 - 1234237 CTAG--G-----CAA-TAT--- s droTak2.KB461535 139893 13 - 669855 CTAGATG-----CAA-TAT--- s droRho2.KB449310 33754 11 - 65043 CTAG--G-----CAA-TAT--- s droFic2.KB457177 79536 11 + 995874 CTAG--G-----CAA-TGT--- s droPse3.chr3 1348003 11 - 19787792 CTAG--g-----caa-tat--- s droPer1.super_34 536850 11 - 916997 CTAG--G-----CAA-TAT--- s droMir2.chr3 1389107 11 - 20862834 CTAG--g-----caa-tat--- s droWil2.CH963894 1307278 11 + 2843958 ATAA--A-----CCA-TAG--- s droVir3.scaffold_12875 7350218 12 + 20611582 CTAG--A-----TAGCTAT--- s droAlb1.JH854640 308026 14 + 406291 GCAA--AAG---TAGCTAT--- s triCas2.ChLG1X 6851811 19 + 8109244 CCAA--AGGGGCCGA-TTTTAG a score=64056.000000 s dm6.chr2R 24348722 8 + 25286936 CCGGGACT s droSim1.chr2R 18695449 8 + 19596830 CCGGGACT s droSec1.super_23 115202 8 + 989336 CCGGAACT s droYak3.chr2R 20204417 8 + 21139217 CCGGGACT s droEre2.scaffold_4845 21602394 8 + 22589142 CTGGGGCT s droBia2.KB462602 794741 8 + 3129309 CCGGGACT s droSuz1.KI419649 12039923 8 - 14502029 CCGGGACT s droAna3.scaffold_13266 5709615 8 - 19884421 CTGGAGAA s droBip2.KB464407 1958427 8 + 2915140 CTGGAGAT s droEug2.KB465067 599413 8 + 1515531 CTGGGACT s droEle2.KB458573 520116 8 - 5320397 CTGGGACT s droKik2.KB459527 274915 8 - 1234237 CTGGGACT s droTak2.KB461535 139906 8 - 669855 CTGGGACT s droRho2.KB449310 33765 8 - 65043 CTGGGACT s droFic2.KB457177 79547 8 + 995874 CTGGCACT s droWil2.CH963894 1307295 8 + 2843958 CTAGaaaa s droVir3.scaffold_12875 7350232 8 + 20611582 TTGGGCCT s droAlb1.JH854640 308041 6 + 406291 --GGGATT s triCas2.ChLG1X 6851830 8 + 8109244 TCATGATT a score=2096.000000 s dm6.chr2R 24348730 8 + 25286936 -TGG-TTTGT-- s droSim1.chr2R 18695457 5 + 19596830 -TGG-T---T-- s droSec1.super_23 115210 5 + 989336 -TGG-T---T-- s droYak3.chr2R 20204425 6 + 21139217 -TGGTT---T-- s droEre2.scaffold_4845 21602402 5 + 22589142 -TGG-T---T-- s droBia2.KB462602 794749 5 + 3129309 -TGG-T---T-- s droSuz1.KI419649 12039931 5 - 14502029 -TGG-T---T-- s droAna3.scaffold_13266 5709623 5 - 19884421 -TGG-T---T-- s droBip2.KB464407 1958435 5 + 2915140 -TGG-T---T-- s droEug2.KB465067 599421 5 + 1515531 -TGG-A---T-- s droEle2.KB458573 520124 5 - 5320397 -TGG-T---T-- s droKik2.KB459527 274923 5 - 1234237 -TGG-T---T-- s droTak2.KB461535 139914 5 - 669855 -TGG-T---T-- s droRho2.KB449310 33773 5 - 65043 -TGG-T---T-- s droFic2.KB457177 79555 5 + 995874 -TGG-T---T-- s droWil2.CH963894 1307303 2 + 2843958 -aa--------- s droAlb1.JH854640 308051 4 + 406291 -TAG-T------ s triCas2.ChLG1X 6851838 8 + 8109244 TAGG-T---TAT a score=-42262.000000 s dm6.chr2R 24348738 26 + 25286936 ---TGTGCGGT-GAG------AGCGGAAGGGGTG--TG s droSim1.chr2R 18695462 25 + 19596830 ---TGTGCGGT-GAG------AGCGGAAGGGGTG---G s droSec1.super_23 115215 25 + 989336 ---TGTGCGGT-GAG------AGCGGAAGGGGTG---G s droYak3.chr2R 20204431 16 + 21139217 ---TGTGCGGT-GAG------AGCGG------------ s droEre2.scaffold_4845 21602407 22 + 22589142 ---TGTGCGCT-GCG------AGCGGAGGGG------G s droBia2.KB462602 794754 21 + 3129309 ---GGTGCGGA-GAG------AGCG-GGGGG------C s droSuz1.KI419649 12039936 22 - 14502029 ---GGTGCGGG-GAG------AGCGAAGGGG------G s droEug2.KB465067 599426 19 + 1515531 ---GGTGCGGA-GAG------AGCGTCG---------T s droEle2.KB458573 520129 27 - 5320397 ---GCTGCGGA-CAG------CGTCGGAGGCTTG-GGG s droKik2.KB459527 274929 24 - 1234237 -------CGGTGGAC------AGCCTGTTAAGTG-GTT s droTak2.KB461535 139919 23 - 669855 ---GGTGCGGA-GAG------ATCGGAGGGGG-----A s droRho2.KB449310 33778 28 - 65043 ---GGTGCGGA-CAG------CGTCGGAGTGACGAGGG s droFic2.KB457177 79560 24 + 995874 ---GCCGCGGA-GAG------AGCGTCGGAGGTG---- s droWil2.CH963894 1307305 28 + 2843958 ---aGTGAGGT-CTA------AGGGTCATGGTTATCGG s droAlb1.JH854640 308060 26 + 406291 ---Gacttagt-gtg------tgtgtgtgtggtg--tg s triCas2.ChLG1X 6851846 29 + 8109244 TTTAGCGCGTT-TGGGCCCGAAACGGGGGG-------- a score=11672.000000 s dm6.chr2R 24348764 16 + 25286936 GGGTGATCCT-------GTTCAG s droSim1.chr2R 18695487 16 + 19596830 GGGTGATCCT-------CTTCAG s droSec1.super_23 115240 16 + 989336 GGGTGATCCT-------CTTCAG s droYak3.chr2R 20204447 2 + 21139217 ---------------------AG s droEre2.scaffold_4845 21602429 16 + 22589142 AGGTGATCCT-------CTCCAG s droBia2.KB462602 794775 16 + 3129309 AGGTGATTCC-------CTCCAG s droSuz1.KI419649 12039958 16 - 14502029 AGGTGATCCC-------CTTCAG s droAna3.scaffold_13266 5709628 6 - 19884421 -GGTG----------------TG s droEug2.KB465067 599445 16 + 1515531 AGGTGATCCT-------CTCCAG s droEle2.KB458573 520156 16 - 5320397 TGGTGAGCCC-------CTCCAG s droKik2.KB459527 274953 16 - 1234237 CTTTAATCCT-------AATTAG s droTak2.KB461535 139942 7 - 669855 AGGTGAT---------------- s droRho2.KB449310 33806 16 - 65043 TGGCGATCCC-------CTCCAG s droWil2.CH963894 1307333 23 + 2843958 TTGTGATTTTGCATTAACTTTAT s droAlb1.JH854640 308086 16 + 406291 tggtgtgtgt-------gtgcag a score=20774.000000 s dm6.chr2R 24348780 9 + 25286936 GCT--AAAGCT s droSim1.chr2R 18695503 9 + 19596830 GCT--ACAGCT s droSec1.super_23 115256 9 + 989336 GCT--ACAGCT s droYak3.chr2R 20204449 9 + 21139217 GCT--ACAGCT s droEre2.scaffold_4845 21602445 9 + 22589142 GCC--ACAGCT s droBia2.KB462602 794791 9 + 3129309 GCT--ATAGCT s droSuz1.KI419649 12039974 9 - 14502029 GCT--ATAGCT s droAna3.scaffold_13266 5709634 9 - 19884421 GCT--GAAGTA s droEug2.KB465067 599461 9 + 1515531 ACT--TTAGCT s droEle2.KB458573 520172 9 - 5320397 CAC--ATAGCT s droKik2.KB459527 274969 11 - 1234237 ACTCGACAACA s droTak2.KB461535 139949 6 - 669855 -----CTAGCT s droRho2.KB449310 33822 9 - 65043 CAC--ATAGCT s droFic2.KB457177 79584 6 + 995874 -----GAAGTA s droWil2.CH963894 1307356 9 + 2843958 ACT--AAAGat a score=76792.000000 s dm6.chr2R 24348789 31 + 25286936 --TTCTTTATCAGTTCCT----TTAAGATAGGCTTTT s droSim1.chr2R 18695512 31 + 19596830 --TTCTTTATCAGTTCCT----TTAAGATAGGCTTTT s droSec1.super_23 115265 33 + 989336 AAAGAATTATCAGTTCCT----TTAAGATAGGCTTTT s droYak3.chr2R 20204458 31 + 21139217 --TTCTTCATAAGTTCCT----CTAAGATAGGCTTCT s droEre2.scaffold_4845 21602454 31 + 22589142 --TTCTTTATCAGTTCCT----CTAAGATTGGCTTCT s droBia2.KB462602 794800 35 + 3129309 --TTCAGTGTCAGTTCCTGAACTTTCGATAGGCTCCT s droSuz1.KI419649 12039983 35 - 14502029 --TTCAGTGTCAGTTCCTGAACTTACCATAGGCTCAT s droAna3.scaffold_13266 5709643 23 - 19884421 --TTTCAT--------CT----TTTTGTTGATTATTT s droEug2.KB465067 599470 35 + 1515531 --TTCAGTATCAGTTCCTGAACTTAAGATAGGCTTAT s droEle2.KB458573 520181 35 - 5320397 --TTCAATATCAGTTCCTGAACCTAAGCTAGGCAGTC s droKik2.KB459527 274980 26 - 1234237 --TTC-----CAGATCat----tttaagtataatttt s droTak2.KB461535 139955 35 - 669855 --TTCAGTGTCAGTTCCTGAACTTACGATAGGCATAT s droRho2.KB449310 33831 35 - 65043 --TTCAATATCAGTTCCTGAACTTAAGCTAGGCACAC s droFic2.KB457177 79590 35 + 995874 --CTCGTTGCCAGTTCCTTGGCTCTTACTGGGCTCAC a score=20878.000000 s dm6.chr2R 24348820 18 + 25286936 AGGATGCTATGATCCACT s droSim1.chr2R 18695543 18 + 19596830 AGGATGCTATGGTCCACG s droSec1.super_23 115298 18 + 989336 AGGACGCTATGGTCCACT s droYak3.chr2R 20204489 18 + 21139217 AGGATGCTATGGTCCACC s droEre2.scaffold_4845 21602485 18 + 22589142 GGGATGCTGTGGTCCACT s droBia2.KB462602 794835 17 + 3129309 AGGACTCCATAGTGTGC- s droSuz1.KI419649 12040018 18 - 14502029 AGGACTCCATAATGTGCT s droAna3.scaffold_13266 5709666 18 - 19884421 GAAAAATTATTATCTTTT s droEug2.KB465067 599505 18 + 1515531 AGGATGGTAATCTCGGTT s droEle2.KB458573 520216 18 - 5320397 AAGGTCTTAAAATTGGGT s droTak2.KB461535 139993 18 - 669855 AGAATTCTACAATCAGCT s droRho2.KB449310 33866 18 - 65043 TGGATCTTATAATTGGGT s droFic2.KB457177 79625 18 + 995874 GGGGTCCTACTGCTCGGA a score=8502.000000 s dm6.chr2R 24348838 21 + 25286936 GGGCTTCGCCTTC-----------------------------------------------------------------------------------------TGGCTTTT s droSim1.chr2R 18695561 21 + 19596830 GAGCTTCGCACTC-----------------------------------------------------------------------------------------TGGCTTTT s droSec1.super_23 115316 21 + 989336 GGGCTTCGCAATC-----------------------------------------------------------------------------------------TGGCCTTT s droYak3.chr2R 20204507 21 + 21139217 GGGCTTTGTATTC-----------------------------------------------------------------------------------------TGGCGCTT s droEre2.scaffold_4845 21602503 21 + 22589142 GGGCTTTGTATTC-----------------------------------------------------------------------------------------TGGCTCTT s droBia2.KB462602 794852 9 + 3129309 --------TACCC---------------------------------------------------------------------------------------------CTTT s droSuz1.KI419649 12040036 21 - 14502029 AGATCTTGTACTC-----------------------------------------------------------------------------------------TGGTCTTT s droBip2.KB464407 1958445 21 + 2915140 GGGTACCGAGTTT-----------------------------------------------------------------------------------------CGTCATTA s droEug2.KB465067 599523 21 + 1515531 AGATCTTTTACTC-----------------------------------------------------------------------------------------TGGCTTTT s droEle2.KB458573 520234 21 - 5320397 AGATCTTGTTTTC-----------------------------------------------------------------------------------------TGGTTTTC s droTak2.KB461535 140016 110 - 669855 GGGCTTTACTTTCACATTAATGCCTAATGATTTGAAcacgaaattaattatttttgttatctggagacaataatatttaaaattcacttataacttattttttaaccttt s droRho2.KB449310 33884 21 - 65043 AGATCttgttttg-----------------------------------------------------------------------------------------tggttttt s droFic2.KB457177 79643 21 + 995874 GGATCTGGCCCCC-----------------------------------------------------------------------------------------TGGTTTTT a score=15224.000000 s dm6.chr2R 24348859 5 + 25286936 ACTTG s droSim1.chr2R 18695582 5 + 19596830 ACTTT s droSec1.super_23 115337 5 + 989336 ACTTT s droYak3.chr2R 20204528 5 + 21139217 ACTTT s droEre2.scaffold_4845 21602524 5 + 22589142 ACTTT s droBia2.KB462602 794861 5 + 3129309 ACTTT s droSuz1.KI419649 12040057 5 - 14502029 ACTTT s droBip2.KB464407 1958466 5 + 2915140 TCtcg s droEug2.KB465067 599544 5 + 1515531 ACTTT s droEle2.KB458573 520255 4 - 5320397 ACTT- s droTak2.KB461535 140126 5 - 669855 ttttg s droRho2.KB449310 33905 5 - 65043 aCTTT s droFic2.KB457177 79904 5 + 995874 ACCTT a score=1302.000000 s dm6.chr2R 24348864 1 + 25286936 C s droSim1.chr2R 18695587 1 + 19596830 C s droSec1.super_23 115342 1 + 989336 C s droYak3.chr2R 20204533 1 + 21139217 A s droEre2.scaffold_4845 21602529 1 + 22589142 C s droEug2.KB465067 599609 1 + 1515531 C s droRho2.KB449310 33910 1 - 65043 C s droFic2.KB457177 79909 1 + 995874 C a score=-59097.000000 s dm6.chr2R 24348865 9 + 25286936 CAC----TAGC-------------------------------GT------ s droSim1.chr2R 18695588 9 + 19596830 CAA----TAGC-------------------------------GC------ s droSec1.super_23 115343 9 + 989336 CAA----TAGC-------------------------------GT------ s droYak3.chr2R 20204534 18 + 21139217 CAA----AAGT-----TAAA-------------TGA----TTGT------ s droEre2.scaffold_4845 21602530 23 + 22589142 CAA----ACGCA----TAGAAC---------GGCGA----TTGT------ s droBia2.KB462602 794875 4 + 3129309 ----------------------------------------TTAT------ s droSuz1.KI419649 12040278 4 - 14502029 ----------------------------------------CTAT------ s droEug2.KB465067 599610 44 + 1515531 CAAATTTAAGCCCCTTTAAAATTTACTACAAAATGAGATCTGAG------ s droEle2.KB458573 520259 4 - 5320397 ----------------------------------------TCAC------ s droTak2.KB461535 140143 4 - 669855 ----------------------------------------CTAT------ s droFic2.KB457177 79910 9 + 995874 -----------------------------------------TGTGAAAGT a score=2624.000000 s dm6.chr2R 24348874 3 + 25286936 AAA s droSim1.chr2R 18695597 3 + 19596830 TTA s droSec1.super_23 115352 3 + 989336 AAA s droYak3.chr2R 20204552 3 + 21139217 AGA s droEre2.scaffold_4845 21602553 3 + 22589142 AGA s droBia2.KB462602 794879 3 + 3129309 TCT s droSuz1.KI419649 12040282 3 - 14502029 GAA s droEug2.KB465067 599654 3 + 1515531 AAA s droEle2.KB458573 520263 3 - 5320397 AGA s droTak2.KB461535 140147 3 - 669855 GAA s droRho2.KB449310 34344 3 - 65043 AAA s droFic2.KB457177 79919 3 + 995874 AAA a score=14864.000000 s dm6.chr2R 24348877 11 + 25286936 GTACAGGCTAG s droSim1.chr2R 18695600 11 + 19596830 TTGGAGGCTAG s droSec1.super_23 115355 11 + 989336 GTAGAGGCTAG s droYak3.chr2R 20204555 11 + 21139217 GTAACTGCTAG s droEre2.scaffold_4845 21602556 11 + 22589142 GTAACTGCCAG s droBia2.KB462602 794882 9 + 3129309 CTTCA--CCAG s droSuz1.KI419649 12040285 11 - 14502029 AGTAAAGCCAG s droAna3.scaffold_13266 5709684 7 - 19884421 ----AAGTTGA s droBip2.KB464407 1958471 7 + 2915140 ----aaattaa s droEug2.KB465067 599657 11 + 1515531 ATAAAAGCCAG s droEle2.KB458573 520571 11 - 5320397 GTAACAGCCAG s droTak2.KB461535 140161 11 - 669855 CTAGAAGCCAG s droRho2.KB449310 34347 11 - 65043 GTAAAAACCAG s droFic2.KB457177 79922 10 + 995874 -AACCAGCCAG a score=-196588.000000 s dm6.chr2R 24348888 71 + 25286936 TTAACGAAG--TTCCA------TAGAC-C----ACACCAAAA---TGAATG------------------------GACCACT-----------------------------------TAAAAATTGTGTATTGCTTTA------AAGTCTAA s droSim1.chr2R 18695611 69 + 19596830 TTAACGAAG--TTCCA------TAGAC-C----ACACCAAAA---TGATTG------------------------AACCACT-----------------------------------TAAAAATTCTGTATTGCTTTA------AAGTGT-- s droSec1.super_23 115366 69 + 989336 TTAACGAAG--TTCCA------TAGAC-C----ACACCAAAA---TAATTG------------------------AACCACT-----------------------------------TAAAAATTCTGTATTGCTTTA------AAGTGT-- s droYak3.chr2R 20204566 56 + 21139217 CTTACAAAG--TTCAAA-----TGGAACC----CCTCCAAAA---TGACT---------------------------CCCTT-----------------------------------TTGAGATTCAGCAt------------------t-- s droEre2.scaffold_4845 21602567 65 + 22589142 CTTGCGAAG--TTCCAT-----TAGAA-C----ACTCCGAAG---TGATTG-------------------------AACCTT-----------------------------------TTGAAGTTCAGCATTCCTC----------GCCT-- s droBia2.KB462602 794891 68 + 3129309 --GGCAGTT--TTACA------TTTat-t-------ccaaat---taaatga-----------------agTA--AAAATCC-----------------------------------AGAAAAGTGATTTctgcttta-------aattt-- s droSuz1.KI419649 12040302 71 - 14502029 GTAACAAAG--TTCCA------TAAGT-C-------CGCAAA---AAAGTAT-----------------AG----AACCCTC-----------------------------------ACCATATTCTTTATCGCTTTAT----TGGGTAG-- s droAna3.scaffold_13266 5709691 52 - 19884421 AAAGTAGAA--TCTTAT-----TAGAC-CTTCAGCTCTT------TATATG------------------------GACAATT-----------------------------------TAGAACCG--------------------------- s droBip2.KB464407 1958478 46 + 2915140 aaagtaaaa--tcttAT-----TAGAC-CTTCAATTCTTAGGACATATATG------------------------GA-----------------------------------------------A--------------------------- s droEug2.KB465067 599668 83 + 1515531 TTAATGAAGCCTCTCA------TAAGA-C----CAACCGAAA---AGCTTGTCC--CCTGCACTGTATCACTT--AATTAGG-----------------------------------TAGAAGTTCTGTTTGACCA---------------- s droEle2.KB458573 520582 101 - 5320397 TTAGCAAAG--TTCCAT-----CAGAC-C----TCACAAAAA---CGATAGAATAACTTGTTCCCCACAAATTcgaatcattttttttttgta--------------------tgtgtaaAAACTTTGTATTACCA---------------- s droKik2.KB459527 275097 73 - 1234237 TCAAAAAAC--TTCTACCTTCGTAAAC-A----TCGCCAAAC---Cgcttaattggttttttaagttaaaa----aacaaTG-----------------------------------TCTAA------------------------------ s droTak2.KB461535 140172 83 - 669855 TTGACAAAG--TTCCAT-----TAGGC-C----GCCCAAAAA---TGATAA------------------------AACACCTTGTCTTTCACAA--------------TATTCTGGGTTGCAACTCTGTATTACCA---------------- s droRho2.KB449310 34358 97 - 65043 TCAACAAAG--TTCCAT-----AAGAC-C----TCACAAAAA---TGATAG------------------------AATAACTTATCCCCCACAAATTCTTTCatacttttttttggataGAAACTCTGTATTACCA---------------- s droFic2.KB457177 79932 78 + 995874 TTTACCAAG--CTCCA------AAGGC-C----TCACGAGTG---CGATAG------------------------GATGTCTTGTCCCC----------------------------AACAAATTTTTCACTACCTTATTGGCTAA------ a score=76717.000000 s dm6.chr2R 24348959 34 + 25286936 ----------------AAAGACCGCTCCTCGACGTTTTCCCGCTC--------AAATA s droSim1.chr2R 18695680 34 + 19596830 ----------------AAAGACCGCTCCTCGACGTTTTCCCGCTC--------AAAGA s droSec1.super_23 115435 34 + 989336 ----------------AAAGACAGCTCCTCGACGTTTTCCCGCTC--------AAAGA s droYak3.chr2R 20204622 26 + 21139217 ------------------------gttttcccagttttcccgcAC--------TAAAA s droEre2.scaffold_4845 21602632 26 + 22589142 ------------------------CTCCTCCACGTTTTTCCGCAC--------AAAAA s droBia2.KB462602 795203 34 + 3129309 ----------------AAACACCGCACCTCGCCGTTTTCCCGCAG--------AAAAA s droSuz1.KI419649 12040389 34 - 14502029 ----------------AAACACCAATCCTCGACGTTTTCCCGCAG--------AAAAA s droAna3.scaffold_13266 5709743 13 - 19884421 ----------------ATAG-------------------CCGCAC--------CA--A s droBip2.KB464407 1958524 11 + 2915140 ----------------GTAG---------------------GCAC--------CA--A s droEug2.KB465067 599751 34 + 1515531 ----------------AAAGACCACTCCTCGACGTTCTCCCGCAC--------AAAAA s droEle2.KB458573 520683 34 - 5320397 ----------------AAACACCAAACTTCGACGCTTTCTCGCAG--------AAAAA s droKik2.KB459527 275172 32 - 1234237 ----------------TTAAACCACACCTCAGTGCTGTTCCGCAA--------AA--A s droTak2.KB461535 140255 42 - 669855 ----------------AAACACCACACCTCGACGTTCTCCCGcacataacaaaaaaaa s droRho2.KB449310 34455 34 - 65043 ----------------AAACACCAAACTTCGACGTTTTCCCGCAG--------AAAAA s droFic2.KB457177 80010 50 + 995874 ACAATCTGCACTACCAAAACACCACGCCTCGACGTTTTCCCGCAG--------AGAAA a score=116900.000000 s dm6.chr2R 24348993 15 + 25286936 CCAAGTCCG--GTTAGT s droSim1.chr2R 18695714 15 + 19596830 CCAAGCCCG--GTTAGT s droSec1.super_23 115469 15 + 989336 CCAAGCCCG--GTTAGT s droYak3.chr2R 20204648 15 + 21139217 CCAAGCCCG--TTTAGT s droEre2.scaffold_4845 21602658 15 + 22589142 CCAAGCCCG--TTTAGT s droBia2.KB462602 795237 14 + 3129309 CCAAG-CCA--GTTAGT s droSuz1.KI419649 12040423 14 - 14502029 CCAAG-CCA--GTTAGT s droAna3.scaffold_13266 5709756 15 - 19884421 CCAAGCCAG--TCTAGT s droBip2.KB464407 1958535 15 + 2915140 CCGATCCAG--TTTAGT s droEug2.KB465067 599785 14 + 1515531 CCAAG-CCA--GTTAGT s droEle2.KB458573 520717 15 - 5320397 CCAAGCCAG--TTTAGT s droKik2.KB459527 275204 17 - 1234237 CCAAGCCAGTTTTTAGT s droTak2.KB461535 140297 15 - 669855 ccaagccaG--TTTAGT s droRho2.KB449310 34489 15 - 65043 CCAAGCCAG--TTTAGT s droFic2.KB457177 80060 15 + 995874 CCAAGCCAG--CTTAGT s droPse3.chr3 1348072 15 - 19787792 CAAAACCCA--ATTAGT s droPer1.super_34 536919 15 - 916997 CAAAACCCA--ATTAGT s droMir2.chr3 1389176 15 - 20862834 CAAAACCCA--ATTAGT a score=74021.000000 s dm6.chr2R 24349008 13 + 25286936 TAG--ACAG--------CAGTT---------------------G- s droSim1.chr2R 18695729 13 + 19596830 TAG--ACAG--------CAGTT---------------------G- s droSec1.super_23 115484 13 + 989336 TAG--ACAG--------CAGTT---------------------G- s droYak3.chr2R 20204663 21 + 21139217 TAG--ACAGCTCATAGACAGTT---------------------C- s droEre2.scaffold_4845 21602673 13 + 22589142 TAG--ACAG--------CAGTT---------------------C- s droBia2.KB462602 795251 15 + 3129309 TAG--ACAG--------CAGTT-------------------TAT- s droSuz1.KI419649 12040437 15 - 14502029 TAG--ACAG--------Cagtt-------------------tat- s droAna3.scaffold_13266 5709771 14 - 19884421 TAG-AACAG--------CAGTT---------------------T- s droBip2.KB464407 1958550 15 + 2915140 TAGAAAcag--------cagtt---------------------t- s droEug2.KB465067 599799 13 + 1515531 TAG--ACAG--------CAGTT---------------------T- s droEle2.KB458573 520732 13 - 5320397 TAG--ACAG--------CAGTT---------------------T- s droKik2.KB459527 275221 15 - 1234237 TAG--ACAG--------CAGTT-------------------TAT- s droTak2.KB461535 140312 15 - 669855 TAG--ACCG--------CAGTT-------------------TAT- s droRho2.KB449310 34504 13 - 65043 TAG--ACAG--------CAGTT---------------------T- s droFic2.KB457177 80075 13 + 995874 TAG--ACAG--------CAGTT---------------------T- s droPse3.chr3 1348087 34 - 19787792 TAG--ACAG--------CCGTTTTATGTTTAGACATAGACCTAC- s droPer1.super_34 536934 34 - 916997 TAG--ACAG--------CAGTTTTATGTTTAGACATAGACCTAC- s droMir2.chr3 1389191 34 - 20862834 TAG--ACAG--------CAGTTTTATGTTTAGacatagacatac- s droVir3.scaffold_12875 7350303 12 + 20611582 TAG--GCAG--------CA--T---------------------TG s droGri2.scaffold_15245 899496 14 + 18325388 TAG--GCAG--------CAAGT---------------------TG a score=8285.000000 s dm6.chr2R 24349021 1 + 25286936 A s droSim1.chr2R 18695742 1 + 19596830 A s droSec1.super_23 115497 1 + 989336 A s droYak3.chr2R 20204684 1 + 21139217 A s droEre2.scaffold_4845 21602686 1 + 22589142 A s droBia2.KB462602 795266 1 + 3129309 A s droSuz1.KI419649 12040452 1 - 14502029 a s droAna3.scaffold_13266 5709785 1 - 19884421 T s droBip2.KB464407 1958565 1 + 2915140 t s droEug2.KB465067 599812 1 + 1515531 A s droEle2.KB458573 520745 1 - 5320397 A s droKik2.KB459527 275236 1 - 1234237 A s droTak2.KB461535 140327 1 - 669855 A s droRho2.KB449310 34517 1 - 65043 A s droFic2.KB457177 80088 1 + 995874 A s droPse3.chr3 1348121 1 - 19787792 A s droPer1.super_34 536968 1 - 916997 A s droMir2.chr3 1389225 1 - 20862834 a s droWil2.CH963894 1307741 1 + 2843958 a a score=189275.000000 s dm6.chr2R 24349022 62 + 25286936 T----ATG-------TT-----TA--GCAGAT-CCAAAGTGCAGCA-------A-ATGGC-TTG---ATGGCAACTTCGATAC--------G--------CGTAC---------TCCG s droSim1.chr2R 18695743 62 + 19596830 T----ATG-------TT-----TA--GCAGAT-CCAAAGTGCAGCA-------A-ATGGC-TTG---ATGGCAACTTCGATAC--------G--------CGTAC---------TCCG s droSec1.super_23 115498 62 + 989336 T----ATG-------TT-----TA--GCAGAT-CCAAAGTGCAGCA-------A-ATGGC-TTG---ATGGCAACTTCGATAC--------G--------CGTAC---------TCCG s droYak3.chr2R 20204685 62 + 21139217 T----ATG-------TT-----TA--GCAGAT-CCAAAGTGCAGCA-------A-ATGGC-TTG---ATCG-AACTTCGATAC-------TT--------CGTAC---------TTCG s droEre2.scaffold_4845 21602687 57 + 22589142 T----ATG-------TT-----TA--GCAGAT-CCAAAGTGCAGCA-------A-ATGGC-TTG---ATCG-AACTTCGATAC-------TT--------CGTA-------------- s droBia2.KB462602 795267 51 + 3129309 T----ATG-------TT-----TA--GCAGAT-CCAAAGTGCAGCA-------A-ATGGC-TTG---ATCG-AACTTCGATAC----------------------------------- s droSuz1.KI419649 12040453 56 - 14502029 t----atg-------tt-----ta--gcaGAT-CCAAAGTGCAGCA-------A-ATGGC-TTG---ATCG-AACTTCGATAC--------T--------CGTA-------------- s droAna3.scaffold_13266 5709786 39 - 19884421 TT---ATG-------AT-----TA--GCAGAT-CCAAAGTGCAACA-------ATGTGGC--------TCG-A--------------------------------------------- s droBip2.KB464407 1958566 47 + 2915140 ttttaatg-------tt-----tagtGCAGAT-CCAAAGTGCAGCA-------A-ATGGC-TCG---ATCG-A--------------------------------------------- s droEug2.KB465067 599813 51 + 1515531 T----ATG-------TT-----TA--GCAGAT-CCAAAGTGCAGCA-------A-ATGGC-TCG---ATCG-AACTTCGATTC----------------------------------- s droEle2.KB458573 520746 51 - 5320397 T----ATG-------TT-----TA--GCAGAT-CCAAAGTGCAGCA-------A-ATGGC-TTG---ATCG-AACTTCGATAC----------------------------------- s droKik2.KB459527 275237 51 - 1234237 T----ATG-------TT-----TA--GCAGAT-CCAAAGTGCAGCA-------A-ATGGC-TCG---ATCG-AACTTCGATAC----------------------------------- s droTak2.KB461535 140328 58 - 669855 T----ATG-------TT-----TA--GCAGAT-CCAAAGTGCAGCA-------A-ATGGC-TTG---ATCG-AACTTCGATAC--------T--------AGTAC---------T--- s droRho2.KB449310 34518 51 - 65043 T----ATG-------TT-----TA--GCAGAG-CCAAAGTGCAGCA-------A-ATGGC-TTG---ATCG-AACTTCGATAC----------------------------------- s droFic2.KB457177 80089 61 + 995874 T----ATG-------TT-----TA--GCAGAT-CCAAAGTGCAGCA-------A-ATGGC-TTG---ATCG-AACTGCGATAC--------T--------CGTAT---------CTCG s droPse3.chr3 1348122 88 - 19787792 T----ACGTAGATGTTT-----TA--GCAGAT-CCAAAGTGCAGCA-------ATTTGGC-TTGTATGTCGGAGTTTcgatatg------tt----tgtatgtatgtatgtacatatg s droPer1.super_34 536969 84 - 916997 T----ACGTAGATGTTT-----TA--GCAGAT-CCAAAGTGCAGCA-------ATTTGGC-TTGTATGTCGGAGTTTCGAtatg------tt--------tgtatgtatgtacatatg s droMir2.chr3 1389226 92 - 20862834 t----atgtagatgttt-----TA--GCAGAT-CCAAAGTGCAGCA-------ATTTGGC-Ttgtatgtcggagtttcgatatg------tttgtatgtatgtatgtatgtgcatatg s droWil2.CH963894 1307742 59 + 2843958 t----CTT-------TT-----TA--GCAGAT-CCAAAGTGAAATA-------T-TTGGC-TTCCATTTCA----TTCCATCCC------CC--------CGCGC------------- s droVir3.scaffold_12875 7350317 66 + 20611582 ----AGTT-------TA-ACATTA--GCAGAT-CCAAAGTGCAGAATTTTGGCC-ATGAA-TTGTC-ACTGCAAATGTAATGGG---------------------------------- s droMoj3.scaffold_6496 26145413 56 + 26866924 ----tgtg-------tg-----tA--GCAGAT-CCAAAGTG------------C-ATGAG-TCGGC-GCGGCAACGGGAGGGGGATTACG---------------------------- s droGri2.scaffold_15245 899512 68 + 18325388 ----AGTT-------TTCACATAA--GCAGTTCCCAAAGTGCAGCA-TTTGGCC-ATGAATTTGTC-ACTGCAAATGTAATGGG---------------------------------- a score=108949.000000 s dm6.chr2R 24349084 18 + 25286936 TAGTTCGTATTT---------------------------------------CGGATC s droSim1.chr2R 18695805 18 + 19596830 TAGTCCGTATTT---------------------------------------CGGATC s droSec1.super_23 115560 18 + 989336 TAGTCCGCATTT---------------------------------------CGGATC s droYak3.chr2R 20204747 18 + 21139217 TATTTCGTGTTT---------------------------------------CGGATC s droEre2.scaffold_4845 21602744 9 + 22589142 ---------TTT---------------------------------------CGGATC s droBia2.KB462602 795318 14 + 3129309 ----TCGTGTTT---------------------------------------CGGATC s droSuz1.KI419649 12040509 16 - 14502029 --TTTCGTATTT---------------------------------------CGGATC s droAna3.scaffold_13266 5709825 14 - 19884421 ----TCGAATTT---------------------------------------CGGATC s droBip2.KB464407 1958613 14 + 2915140 ----TCGATTTT---------------------------------------CGGATC s droEug2.KB465067 599864 14 + 1515531 ----TCGTATTT---------------------------------------CGGATC s droEle2.KB458573 520797 14 - 5320397 ----TCGTATTT---------------------------------------CGGATC s droKik2.KB459527 275288 14 - 1234237 ----TCGTATTT---------------------------------------CGGATC s droTak2.KB461535 140386 14 - 669855 ----TCGTATTT---------------------------------------CGGATC s droRho2.KB449310 34569 14 - 65043 ----TCGTATTT---------------------------------------CGGATC s droFic2.KB457177 80150 18 + 995874 TGCTTCGTATTT---------------------------------------CGGATC s droPse3.chr3 1348210 18 - 19787792 tacatagtatgt---------------------------------------CGGATT s droPer1.super_34 537053 18 - 916997 tacatagtatgt---------------------------------------CGGATT s droMir2.chr3 1389318 18 - 20862834 tacatagtatgt---------------------------------------cGGATT s droWil2.CH963894 1307801 53 + 2843958 ----TCGTATTTTAAAGAGAAAATTTCTTAGACAATATATTCATCAAGGGGCGGATC s droVir3.scaffold_12875 7350383 11 + 20611582 -------TTGTG---------------------------------------GTGATT s droGri2.scaffold_15245 899580 18 + 18325388 TATAGAGATATT---------------------------------------ATGATC a score=180457.000000 s dm6.chr2R 24349102 12 + 25286936 CA-----TGGCC--AATAC s droSim1.chr2R 18695823 12 + 19596830 CA-----TGGCC--AATAC s droSec1.super_23 115578 12 + 989336 CA-----TGGCC--AATAC s droYak3.chr2R 20204765 12 + 21139217 CA-----TGGCC--AATAC s droEre2.scaffold_4845 21602753 12 + 22589142 CA-----TGGCC--AATAC s droBia2.KB462602 795332 12 + 3129309 CA-----TGGCC--AATAC s droSuz1.KI419649 12040525 12 - 14502029 CA-----TGGCC--AATAC s droAna3.scaffold_13266 5709839 12 - 19884421 CA-----TGGCC--AATAC s droBip2.KB464407 1958627 12 + 2915140 CA-----TGGCC--AATAC s droEug2.KB465067 599878 12 + 1515531 CA-----TGGCC--AATAC s droEle2.KB458573 520811 12 - 5320397 CA-----TGGCC--AATAC s droKik2.KB459527 275302 12 - 1234237 CA-----TGGCC--AATAC s droTak2.KB461535 140400 12 - 669855 CA-----TGGCC--AATAC s droRho2.KB449310 34583 12 - 65043 CA-----TGGCC--AATTC s droFic2.KB457177 80168 12 + 995874 CA-----TGGCC--AATTC s droPse3.chr3 1348228 12 - 19787792 CA-----TGGCC--AATAC s droPer1.super_34 537071 12 - 916997 CA-----TGGCC--AATAC s droMir2.chr3 1389336 12 - 20862834 CA-----TGGCC--AATAC s droWil2.CH963894 1307854 19 + 2843958 TAATAGTTAGCCATATTAC s droVir3.scaffold_12875 7350395 9 + 20611582 --------GGCC--AATTG s droAlb1.JH854640 308125 12 + 406291 CG-----TGGCC--AATAG s droGri2.scaffold_15245 899598 11 + 18325388 -A-----TGGCC--ATTCG a score=1350054.000000 s dm6.chr2R 24349114 410 + 25286936 GATCTCG-CCGCTCGTTT--TGTTC-T---TGTT--TACCGCAGATAGCA--------------------GTG-TTTGTG---TTTA--T-------TAAT------------------------TTAC--------------------------ATTACATGT-----ATTTA--CG-------------TT--------------------TTTT----------GTATACTAGTCAAG--ACTC-TACTTAAAGGCGACTGTGCCATAG-C---------A------AGCTACAGCC---CC-TCCCCA-------------------------------------------GT----------------ACATC---------------------GTA--------C----T--T--CCCATAG---------------------CAATAGACCCAGTG-----------CC---------------CC-------CAGCTGCAG---------------------CTTCC--AACC-----CAGTGCCA-T-------T---C--------------TAC-----CGAACCACTAGATAAC--------------------------------TAGACC--A---------CT-------------------------------------AGAG------ACACATC----GAGACACA--TTGAGAC----------ACAGCCGAGACTGC-----TTAGTTAGTCC-TTAAAG------------------TT---------AAGCCGCAAGTGCAATAC--------------CACACACAACT-----------------------------TAGCA------------GAAG---------------TAGCAGAA--GCAGGA--------TACTTTC--------C------------GCA-A---------------GTA-------TTTG----------CTGTACAGAGTCT-A-----GAGTGTAA---ACAGCTAC-----T---G-----TGCGTT s droSim1.chr2R 18695835 418 + 19596830 GATCTCG-CCGCTCGTTT--TGTTC-T---TGTT--TACCGCAGATAGCA--------------------GTG-TTTGTG---TTTA--T-------TAAT------------------------TTAC--------------------------ATTACATGT-----ATTTA--CG-------------TT--------------------TTTT----------GTATACTAGTCAAG--ACTC-TACTTAAAGGCGACTGTGCCATAG-C---------A------AGCTACAGCC---CT-T-CCCA-------------------------------------------GT----------------ACATC---------------------GTA--------C----T--C--CCCATAG---------------------CAATAGCCCCAGTG-----------CC---------------CC-------CAGCTGCAG---------------------CTTCC--AACC-----CAGTGCCA-T-------T---C--------------TAC-----CGAACCACTAGATAAC--------------------------------TAGACC--A---------CT-------------------------------------AGAG------ACACATC----GAGACACA--TTGAGAC----------ACAGCCGAGACTGC-----TTAGTTAGTCC-TTAAAG------------------TT---------AAGCCGCAAGTGCAATAC--------------CACACACAACT-----------------tagcaga---agtagca------------gaag---------------tagcagaa--gCGGGA--------TACTTTC--------C------------GCA-A---------------GGA-------TTTG----------CTGTACAGAGTCT-A-----GAGTGTAA---ACAGCTAC-----T---G-----TGCGTT s droSec1.super_23 115590 426 + 989336 GATCTCG-CCGCTCGTTT--TGTTC-T---TGTT--TACCGCAGATAGCA--------------------GTG-TTTGTG---TTTA--T-------TAAT------------------------TTAC--------------------------ATTACATGT-----ATTTA--CG-------------TT--------------------TTTT----------GTATACTAGTCAAG--ACTC-TACTTAAAGGCGACTGTGCCATAG-C---------A------AGCTACAGTC---CC-T-CCCA-------------------------------------------GT----------------ACATC---------------------GTA--------C----T--C--CCCATAG---------------------CAATAGACCCAGTG-----------CC---------------CC-------CAGCTGCAG---------------------CTTCC---ACC-----CAGTGCCA-T-------T---C--------------TAC-----CGAACCACTAGATAAC--------------------------------TAGACC--A---------CT-------------------------------------AGAG------ACACATC----GAGACACA--TTGAGAC----------ACAGCCGAGACTGC-----TTAGTTAGTCC-TTAAAG------------------TT---------AAGCCGCAAGTGCAATAC--------------CACACACAACTtagc--------agaagtagcaga---agtagca------------gaag---------------tagcagaa--gCAGGA--------TACTTTC--------C------------GCA-A---------------GGA-------TTTG----------CTGTACAGAGTCT-A-----GAGTGTAA---ACAGCTAC-----T---G-----TGCGTT s droYak3.chr2R 20204777 448 + 21139217 GATCTCG-CCGCTCGTTT--TGTTC-T---TGTT--TACCGCAGATAGCa--------------------gtgttttgtg---ttta--t-------taat------------------------gtgt-a------------------------tttacatttac---attta--ca-------------tt--------------------tttt----------gtatacTAGTCAAG--ACTC-TACTTAAAGGCGACTGTGCCATAG-C---------A------AGCTACAGCC---CC-T-CCCA-------------------------------------------GT----------------ACATC---------------------GTA--------C----a--c--cccatagacccaatatacccaatagacccaatagacccaGTGC----------CC---------------CC-------CAGCTGCAG---------------------CTTCC--AACC-----CAGTGCCA-T-------T---C--------------TAC-----CGAaccacgagaccactagaccactagaccactagaccactagaccagtagacc--a---------ct-------------------------------------agaA------ACACATC----------------GAGAC----------ACAGCCGAGACTGC-----TTAGTTAGTCC-TTAAAG------------------TT---------AAGCCATAAGTGCAATAC--------------CACACACAACT-----------------------------------------------------------------TAGCAGGA--GCAGGA--------TACTTTC--------C------------GCA-A---------------GGA-------TTTG----------CTGTACAGAGTCT-A-----GAGAGTAA---ACAGCTAC-----T---G-----TGCGTT s droEre2.scaffold_4845 21602765 378 + 22589142 GATCTCG-CCGCTCGTTT--TGTTC-T---TGTT--TACCGCAGATAGCA--------------------GTGTTTTGTG---TTTA--T-------TAAT------------------------GTGT----------------------------------------ATTTA--CA-------------TT--------------------TTTT----------GTATACTAGTCAAG--ACTC-TACTTAAAGGCGACTGTGCCATAG-C---------A------AGCTACAGCC---CC-T-CCCA-------------------------------------------GT----------------ACATC---------------------GTA--------C----A--C--CCCATAG---------------------CAATAGACCCAGTG----------------------------CC-------CAGCTGCAG---------------------CTTCC--AATC-----CAGTGCCA-T-------T---C--------------TTC-----CGAaccactagaccac--------------------------------tagacc--a---------ct-------------------------------------agaG------ACACATC----------------GAGAC----------ACAGCCGAGACTGC-----TTAGTTAGTCC-TTAAAG------------------TT---------AAGCCATAAGTGCAATAC----------------CACACAACT-----------------------------------------------------------------TAGCAGAA--GCAGGA--------TACTTTC--------C------------GCA-A---------------GGA-------TTTG----------CTGTACAGAGTCT-A-----GAGCGTAA---ACAGCTAC-----T---G-----TGCGTT s droBia2.KB462602 795344 392 + 3129309 GATCTCG-CCGCTCGTTT--TGTTC-T---TGTT--TATCGCAGATCGca--------------------gtgttttgtg-ttttta--t-------taat-------------cGTATT-----GTGT-A------------------------ATTgtgta------attta--ca------t---t--tt--------------------tttt----------gtatactaGTCAAG--ACTCTTACTTAAAGGCGACTGTGCCATAG-C--------AA------AGCTACAGCT---CC-C-CCAA-------------------------------------------GT----------------ACACC---------------------CCA--------C----A--CA-CCCATAG---------------------CAATAGATCCACTGT----------GC---------------AT-------CAGCTGCAG---------------------CTTCC--AACC-----CAGTGCCA-T-------T---C--------------TGT-----------------------------------------------------AGAACC--A---------CT-------------------------------------AGAG------ACACATC----------------GAGAC----------ACAGCCGAGACTGCT----TTAGTTAGTCc-tttaaag---------ttaaaacttT---------AAGCCATAAGTGCAATAC--------------CACCCACAACT------------------------------------------------------------------------A--GAAGGA--------AACTTTC--------C------------GCA-A---------------AGG-------TTTG----------CTGTACAGAGTCT-A-----AAGGGTAA---ACAGCTCG-----A---G-----TGCGTT s droSuz1.KI419649 12040537 402 - 14502029 GATCTCG-CCGCTCGTTT--TGTTC-T---TGTT--TATCGCAGATCgca--------------------gtgttttgtgtttttta--t-------taat-------------------------tgt-a------------------------attgtgta------attta--ca------t---t--tt--------------------tttt----------gtatactaGTCAAG--ACTCTTACTTAAAGGCGACTGTGCCATAG-C--------AA------AGCTACAGCT---CCTC-CCAA-------------------------------------------GTACATCGT--ACGCCCCACATC---------------------CCA--------C----A--CATCCCATAG---------------------CAATAGTTCAATTGT----------GC---------------AT-------CAGCTGCAG---------------------CTTCC--AATC-----CAGTGCCA-T-------T---C--------------TAT-----------------------------------------------------AAAACC--A---------CT-------------------------------------AGAG------ACACATC----------------GAGAC----------ACAGCCGAGACTGCT----TTAGTTAgtcc-tttaaag---------ttaaaacttt---------AAGCCATAAGTGCAATAC--------------CATACACAACT------------------------------------------------------------------------A--GATGGA--------AACTTTC--------C------------GTA-A---------------AGA-------TTTG----------CTGTACAGAGTCT-A-----AAGGGTAA---ACAGCTCC-----A---G-----TGCGTT s droAna3.scaffold_13266 5709851 448 - 19884421 GATCTCG-CCGCTCGTTT--TGTTCGT---TGTT--TATCG------AAA--------------------GTGTTTTGTG---TTTG--A-------TTTT------------------------------------------------------ATTTTTTG------ATTAATGCA-------------TTAAAGCATTATTATTTACGCGTTTT----------ATTTACTAGTCAAG--ACTCTTATTTAAAGGCGACTGTGCCATAGAC---------A------AGCAACAGCT---CC-T-CCTGC-----AGCCTAT---------------TT-------------AT----------------ACATA-----------------------A--------T----T--C--CCCATAG---------------------CAATAGATCAATTG-----------TCATACACATGA-----AT-------CAGCTGCAG---------------------CTTCT--AACC-----CAGTGCCA-T-------T---C--------------TAC-----CGAACCACT---------------------------------------AGAGAC--A---------CT---------------------------------------AG------AGACATC----------------GAGAC----------ACAGCCGAGACTGCT----TTAGTTAGTCCATTTTT-------------------TT---------AAGCAATAAGTGCAATAA--------------TATTTACGAAAGAAA--------ATAAACAGAAGA---GTAAACA----TATATACGATAG---------------TACTTAGA--GGGAAA--------CTTTATC--------T------------AAAGA---------------GGA-------CTTCCTCAAGTTCGCTGTACAGAGTCT-A-----GAG---------------------T---G-----TGCGCT s droBip2.KB464407 1958639 445 + 2915140 GATCTCG-CCGCTCgttt--tgttc-t---tgtt--tatcg-------aa--------------------gtg-tttgtg---tttt--a-------tttt------------------------ttat-a------------------------tttttttg------attaat-cA-------------TTAA-----------------------------------TACTAGTCAAGACACTCTTATTTAAAGGCGACTGTGCCATAGAC---------aagctacagctacagct---cC-T-CCTGA-----AGCCtat---------------tt-------------at----------------acatata-------------------gta--------A----T--T--CCCATAG---------------------CAATAGATCAATAG-----------AT---cacatcagcatcag-------cagctgcag---------------------cttct-AAACC-----CAGTGCCA-T-------T---CTATCGAATACCGATTAC-----CGAACCACT---------------------------------------AGAGAC--A---------CT-------------------------------------AGAG------AGACATC----------------GAGAC----------ACAGCCGAGACTGCT----TTAGTTAGTCC-TTTTA-------------------AT---------AAGCAATAAGTGCAATAA--------------TATTTACAAGAGAAA----------CGATTACAGA---GTAAGCACCAGTACGTACTGTA----------------TACTGGAA--GGGGAA--------AACTTTT--------C------------CCCGA---------------GGA-------TGTC----------CTGCGAAGAGTCT-A-----AAG---------------------T---G-----TGCGCT s droEug2.KB465067 599890 432 + 1515531 GATCTCG-CCGCTcgttt--tgttc-t---tgtt--tgTCGCAGATCGCAAATCGCAGATCGtcgtgtttgtgttttgtg---tttt--g-------tgtt------------------------ttat-t------------------------aatgtgta------gttta--ca------t---t--tt--------------------tttc----------gtATACTAGTCAAG--ACTC-TACTTAAAGGCGACTGTGCCATAG-C--------AA------AGCTACAGCT---CC-T-CCCAA------------------------------------------GT----------------GCACC---------------------CCA--------G----TACC--CCCATAG---------------------CAATAGATCAATTGT---------CGC---------------AT-------CAGCTGCAG---------------------CTTCC--AATC-----CAGTGCCA-T-------T---C--------------TAC-----------------------------------------------------CGAACC--A---------CT-------------------------------------AGAG------ACACATC----------------GAGAC----------ACAGCCGAGACTGCT----TTAGTTAGTCC-TTAAAAC-----------------TT---------AAACCATAAGTGCAATAC--------------CATAGCCAGCT-----------------TAGTGGA---AGGAAGG------------GAAAGTCG---------GCCAGCTGGA--GGAGGC--------AACTTTC--------C------------GCA-A---------------AGA-------TTTG----------CTGAACAGAGTCT-A-----AAGGGTAA---ACAGCTCC-----TCCAG-----TGCGTT s droEle2.KB458573 520823 442 - 5320397 GATCTCG-CCGCTCgttt--tgttc-t---tgtt--tatcg-------ca--------------------gtgttttgtg---tttt--t-------ttat------------------------taat-t------------------------gtaatgta------attta--ca------t---t--tt--------------------tttt----------gtatactagTCAAG--ACTCTTACTTAAAGGCGACTGTGCCATAG-C--------AA------AGCTACAGCT---CC-T-CCCGTGT---AAcccatat---------tccata-------------gtccataatccatatcccaaatc---------------------cca--------t----a--t--cccatag----cccatagcctatag---CAATAGTTAAATTGT---------CGC---------------AT-------CAGCTGCAG---------------------CTTCT--AACC-----CAGTGCCA-T-------T---C--------------TAC-----------------------------------------------------CGAACC--A---------CT-------------------------------------AGAG------ACACATC----------------GAGAC----------ACAGCCGAGACTGCTTTAGTTAGTTAGTCC-TT----------------------TT---------AAACCATAAGTGCAATAC--------------CATACATACCT----------------AGAACATA---TGATACA------------TACA---------------TAACTAGA--AGGGGA--------AACTTTC--------C------------GTA-A---------------AGA-------TTTG----------CTGTACAGAGTCT-A-----AAGGGTGA---ACAGCTCC-----A---G-----TGCGTT s droKik2.KB459527 275314 437 - 1234237 GATCTCG-CCGCTCGTTT--TGTTC-T---TGTT--TACCG---ACCGCa--------------------gtgttttgtg---ttta--t-------aaat------------------------gtat---------------------------ttttttt------tttta-----------------tt--------------------tttt----------gtatactaGTCAAG--ACTCTTACTTAAAGGCGACTGTGCCATAT-C--------AA------AGCTACAGCT---CA-G-CTC--------------------------------------------CT----------------CCAT----------------------GTA--------C----A--T--CCAATAG---------------------CAATAGATCAATTGT---------CGC---------------AT-------CAGCTGCAG---------------------CTCCTAAAACC-----CAGTGCCA-T-------T---C--------------TAC-----------------------------------------------------CGAACCGAA---------CT-------------------------------------AGAGACGGACACATATC----------------GAGAC----------ACAGCCGAGACTGCT----TTAGTTAGTCC-TTTTTA------------------TT---------ACCGAGTAAGTGCAATAA--------------CATAGCTAgaggaggg----aggagtaggaggagg---agagtCA------------GAAGAGGA---------ACCACTAGAACTAGGGGA--------AACTTTC--------CCTTCCGTAAAGAATA-A---------------AGA-------TTTG----------CTGGACAGAGTCT-A-----AAGGGTAA---ACAGCTCG-----A---GTGTGCTGCGTT s droTak2.KB461535 140412 432 - 669855 GATCTCG-CCGCTCGTTT--TGTTC-T---TGTT--TATCGCAGATCgca--------------------gtgttttgtg---tttt--t-------ttat---------------taatcgtaattgt-a------------------------attgtgta------attta--ca------t---t--tt--------------------tttt----------gtatactaGTCAAG--ACTCTTACTTAAAGGCGACTGTGCCATAG-C--------AA------AGCTACAGCT---CC-T-CCCAAGT-ACATCGTACATC-------GTACATC-------------GT---------GCATCCCACGTC---------------------CCA--------C----A--T--CCCATAG---------------------CAATAGATCCAATGTCG-------CAC---------------AT-------TAGCTGCAG---------------------CTTCC--AATC-----CAGTGCCA-T-------T---C--------------TGT-----------------------------------------------------TAAACC--A---------CT-------------------------------------AGAG------ACACATC----------------GAGAC----------ACAGCCGAGACTGCT----TTAGTTAGTcc-tttaaag---ttaaagttaaaacttT---------AAGCCATAAGTGCAATAT--------------GATACACAACT------------------------------------------------------------------------A--GATGGA--------AACTTTC--------C------------GTA-A---------------AGA-------TTTG----------CTGTACAGAGTCT-A-----AAGGGTAA---ACAGCTCCAG---T---G-----TGCGTT s droRho2.KB449310 34595 425 - 65043 GATCTCG-CCGCTCgttt--tgttc-t---tgtt--tatcg-------ca--------------------gtg-tttgtg---tttt--t-------ttat------------------------taat-----------------------------gtgta------attta--ca------t---t--tt--------------------tttt----------gtatactagTCAAG--ACTCTTACTTAAAGGCGACTGTGCCATAG-C--------AA------AGCTACAGCT---CC-CACCCAA------------------------------------------GT----------------ACCAT---------------------GTACCATGTACC----A--T--CCCATAG---------------------CAATAGATCAATTGTCGCATc---acc---------------tg-------cagctgcag---------------------cttct--AACC-----CAGTGCCA-T-------T---C--------------TAC-----------------------------------------------------CGAACC--A---------CT-------------------------------------AGAG----ACACACATC----------------GAGAC----------ACAGCCGAGACTGCT----TTAGTTAGTCC-TT----------------------TT---------AAACCATAAGTGCAATACCTaccatacatatacatacataactAGATG----GGGAAAGTTGGAAAG---TCTAGTA-------------------------------GAAAAGAG--GGGGAA--------AACTTTC--------C------------GTA-A---------------AGA-------TTTG----------CTGTACAGAGTCT-A-----AAGGGCGA---ACAGCTCC-----A---G-----TGCGTT s droFic2.KB457177 80180 404 + 995874 GATCTCG-CCGCTCgttt--tgttc-t---tgtt--taccg-------ca--------------------gtg-tttgtg--tttta--t-------taat------------------------gtgtaa------------------------tttacatt------tttta--ca-----------------------------------tttt----------gtatacTAGTCAAG--ACTCTTACTGAAAGGCGACTGTGCCATAG-C--------AA------AGCTACAGCT---CC-T-CCCA-------------------------------------------------------------A-------------------------GTA--------C----A--T--CCCATAG---------------------CAATAGATCAATTGTCG--------CG---------------TC-------CAGCTGCAG---------------------CTTCT--AACC-----CAGTGCCA-T-------T---C--------------AAC-----------------------------------------------------CGAACC--A---------CT-------------------------------------AGAG------ACACAAC----------------GAGAC----------ACAGCCGAGACTGCT----TTAGATAGTCC-T-----------------------TT---------AAGCCATAAGTGCAATAC--------------CGTACATAACtagaagaaaaaggaaaaggaaaagg---gaagggg------------gaagggaa---------agtCGCTAGA--GGAGGA--------AACTTTC--------C------------GCA-A---------------AGA-------TTTG----------CTGTACAGAGTCTAA-----AAGGGTAA---ACAGCTCC-----A---G-----TGCGTT s droPse3.chr3 1348240 486 - 19787792 GATCTCG-CCGCtcgttt--tgttc-t---tgtt--tgtcg-------ca--------------------gtg-tttgtg---tgtg--tgtg----tttt------------------------ttgt--------------------------attttttgtattaatttta--ca------tta-t--tt--------------------tttttgtttatttcgtATACTAGTCAAG--ACTCTTACTTAAAGGCGACTGTGCCATAG-C--------CA------AGCTACAGCTAGCTC-T-CCCCTGACGATAGCTATAGCAGCGA-TAGCGATA-------------GT----------------ACATTCG----------------GTAGTA--------T----A--T--CCGATAG---------------------CAATAGATCAATTGTCAC-------AT---------------AC-------CAGCTGCAG---------------------CTTCT--AACC-----CAGTGCCATT-------T---C--------------TACGA-CTAGAACCACT---------------------------------------AGAACC--A---------CT-------------------------------------AGAG------ACACATC----------------GAGAC----------ACAGCCGAGACTGCT----TAAGTTAGTCC-TT----------------------TTCTTACATAGAAAACATAAGTGCAATGT---------------AAATGTAACT---------AAAAGAGTTAACAAA---AGGGGga------------gatatacat--------actatacata--gAAAGA--------TATTATA--------A------------AGA-ATCATCATTGAGAGAGGTA-------TGTG----------CTGTACAGAGTCT-A-----AAC---------------------A---G-----GGGGTA s droPer1.super_34 537083 482 - 916997 GATCTCG-CCGCTCGTTT--TGTTC-T---TGTT--TGTCG-------CA--------------------GTG-TTTGTG---TGTG--TGTG----TTTT------------------------TTGT--------------------------ATTTTTTGTATTAATTTTA--CA------TTA----TT--------------------TTTTTGTTTATTTCGTATACTAGTCAAG--ACTCTTACTTAAAGGCGACTGTGCCATAG-C--------CA------AGCTACAGCTAGCTC-T-CCCCTGACGATAGCTATAGCAGCGA-TAGCGATA-------------GT----------------ACATTCG-------------------GTA--------T----A--T--CCGATAG---------------------CAATAGATCAATTGTCAC-------AT---------------AC-------CAGCTGCAG---------------------CTTCT--AACC-----CAGTGCCATT-------T---C--------------TACGA-CTAGAACCACT---------------------------------------AGAACC--A---------CT-------------------------------------AGAG------ACACATC----------------GAGAC----------ACAGCCGAGACTGCT----TAACTTAGTCC-TT----------------------TTCTTACATAGAAAACATAAGTGCAATGT---------------AAATGTAACT---------AAAAGAGTTAACAAA---AGGGGGA------------GATATACAT--------ACTATACATA--GAAAGA--------TATTATA--------A------------AGA-ATCATCATTGAGAGAGGTA-------TGTG----------CTGTACAGAGTCT-A-----AAC---------------------A---G-----GGGGTA s droMir2.chr3 1389348 513 - 20862834 GATCTCG-CCGCtcgttt--tgttc-t---tgtt--tgtcg-------ca--------------------gtg-tttgtg---tgtg--tgtgtttttttt------------------------ttgt--------------------------attttttgtattaatttta--ca------tgatt--tt--------------------tttttgtttatttcgtATACTAGTCAAG--ACTCTTACTTAAAGGCGACTGTGCCATAG-C--------CA------AGCTACAGCTAGCTC-T-CCCCTGACGATAGCTATAGCAGCGA-TAGCGATA-------------GT----------------ACATTCG----------------ATAGTA--------T----A--T--CCGATAG---------------------CAATAGATCAATTGTCAC-------At---------------ac-------cagctgcag---------------------cttct--aACC-----CAGTGCCATT-------T---C--------------TACGa-ctagaaccact---------------------------------------agaacc--actagaaccgct-------------------------------------agaG------ACACATC----------------GAGAC----------ACAGCCGAGACTGCT----TAAGTTAGTCC-TT----------------------TTCTTACATAGAAAACATAAGTGCAATGT---------------AACTGTAACT---------AAAAGAGTTAACAAA---AGGGGga------------gatatacat--------actatacata--gaAAGA--------TATTATA--------A------------AGA-ATCATCATTGAGAGAGGTA-------TGTG----------CTGTACAGAGTCT-A-----AAC----A---TTACCCCCTGTTTA---G-----GGGGC- s droWil2.CH963894 1307873 566 + 2843958 GATCTCG-CCGctcgttt--tgttt-tatacttt--aaacg-------aa--------------------atg-ggcgtg---gcaagct-------caat------------------------ttga-aataaacaaagcaaaaaaaaaaagcattttgtttta---attta--ta--------------t--------------------agtt----------atatacTAGTCAAA--ACTT------AAAGGCAATTGTGCCATAG-CAAAACGCAAA------AGCTACagct---ct-c-tatctctctctctctatatcttTGAGTAGCCATATatagttacatatat----------------acataga----------------tttgTA--------TGGGGA--T--CCCCTCT---------------------CCAAAAATCCACCC-----------AC---------------CC-------CCCTCTCGC---------------------CTTAA--AAGCAATAGCAGTGCCA-T-------T---C--------------TGAAagcaagaac-------------------------------------------aaaaca--a---------ac-------------------------------------agaa------aaagatt----taaaagaaGTTTGAGACAGACTCACAAATAGACGAGACTGCTTTAGTTAGTTagtcg-tttcttttttttcgtgtt------cT---------AAACCATAAGtgcaatat---------------atatactata-taaaagACAATAATCAAGACAGA---TCGTTTA------------GAGATTTAttcatattaaataattgta--gGAATTGTAAAACTTATTACT--------T------------ATA-A---------------TGAAACAGATTTTG----------CTGCACAGagtct-a-----aaaaagaa---aaaacaaa-----a---c-----t----- s droVir3.scaffold_12875 7350406 473 + 20611582 GATCTCG-CCGCTCGTTT--TG----T---TGTT--TAGCG-------TA--------------------GTG-GGCGTG---GCAG--C-------TCAT---------------------------T----------------------------------------TTAAA--CA------T---A--TT--------------------TTGT----------TTATACTAGTCAAA--ACTCTTACTTAAAGGCGACTGTGCCATAG-C--------AA------AGCTACAGCT---CT-C------------------------------------------------AT----------------ATATAAA-----------TACCCATAGCA--------G----T--A--CCAATAG---------------------CCATAACTATCATATACATAT--ATAC---------------ATATATAATCAGCTGCAGCTACCTAATCAAATCGTACCGTATCG--AACC-----CAGTGCCA-T----CAAT---C--------------TCT-----AACGTTTCTACCAGA---------------------------------CAAATC--C---------CC----------GTGCAGACACCACTTGGGACACACCGAACAG------GCAAAGT----AAAGAAAA----AACAC----------ATAGCCGAGACTGCT----TTAGTTAGTCC-------------------------TT---------AAG-CATAAGTGCAATAA------AATGAATTAGCAaagaact---------agatgaactagaaga---actaaaa------------gaact--------------agaCAGAG--ACAACA--------CTC------------T------------ATA-A---------------AGA-------TTTG----------CTGCGCAGAGTCT-AC----ATAAAAAC---TTAACTAC-----A---T-----T----- s droMoj3.scaffold_6496 26145495 423 + 26866924 GATCTCGCCCGTTCATTT--TG----T---TGTT--TATCG-------CA--------------------GTG-GGCGTG---GCAG--C-------TCAT---------------------------T----------------------------------------TAAAG--CA------T---ATCTT--------------------TTGT----------TAATACTAGTCAAA--AC-CCAACTTGAAGGCGCCTGTGCCATAG-C--------AA------AGCCA-AGCC---TG-C------------------------------------------------AT----------------ACGTGG---------------CCATAGCA--------G----C--A--CCCATAG---------------------CCATAGC-------------------C---------------ATTCAGCATCGGCCGCAG----CAAATACAACCGAGCCGAGTCG--TACC-----CAGTGCCA-T----CATT---C--------------TAT-----AGCGTTTCTACCAGA---------------------------------CAACTC--T----------------------------------------CGTACCGAACAG------ACACACCTG--AAAACACG----ACCAG----------ATAGCCGAGACTGCT----TTAGTTAGTCC-------------------------TT---------AAG-GATAAGTGCAATAA-----------------ACAGAACT---------AGACGAACTGAACTA---AATGAAA-----------TGAAAT--------------GAGCAGAG--GAGTCA--------CTCTATG--------T------------ATA-A---------------TCA-------TTTG----------CTGCGCAGAGTCT-A-----ATGTAAAG---TAAACTAC-----A---T-----T----- s droAlb1.JH854640 308139 452 + 406291 GATCTCG-CCGCTCGTTTAGCG----T---TGTTGATAGCG---TTgttg--------------------gtg-ggcgtg---gcag--c-------tcat---------------------------t-c--------------------------------------ttaaa--ca----------a--tt--------------------ttgt----------ttatactaGTCAAA--ACTCTTACTTAAAGGCGACTGTGCCATAG-C--------CA------AGCTACAGTT---CT-C------------------------------------------------AT----------------ACAAATaccgatccgatccgatcccaacc--------g----a--a--cccgact---------------------ccgaactgaaccgaaccgaaccgaagc---------------ATTCA----CAACTGTAG--------------CGTAGCTTACCA--AACC-----TAGTGCCA-TTCTATATT---C--------------TAC-----AGCGTATCTAGAGAG---------------------------------TATCTC--A---------TT----------CTGAAAA------------CACTTAAGACAG------G---AGTTA--AATACAGA----AACAC----------ACAGCCGAGACTGCT----TTAGTTAGTCC-------------------------TT---------AAT-CATTAGTGCAATAC----------AAGTACTGgagagca---------acacagacagaaagacagaaagaaa------------gagag--------------agagagag--gagaga--------aacCA----------C------------ATG-A---------------TAA-------TTTG----------CTGCGCAGAGTCT-A-----------------------C-----A---T-----T----- s droGri2.scaffold_15245 899611 537 + 18325388 GATCTCG-CCGCTCGTTT--TG----T---TGTT--TAGCG-------TT--------------------GTG-GGCGTG---GCAG--C-------TCATACACATATATAAATAGATATATATTTGT----------------------------------------TTAAA--CCAACATTC---A--TT--------------------TTGT----------TGATACTAGTCAAA--ACTCTTACTTAAAGGCAACTGTGCCATAG-C--------CA------AGCTACAGCT---CT-C------------------------------------------------at----------------atatata-----------tttatgtatat--------a----t--a--gatatat---------------------atatattacatataCCCATATAGCAAT---------------ATCCATA--TAGCCATATACTTATATAACTATCGTACCGTATCG--AACC-----CAGTGCCA-T----CATTCTAC--------------TAC-----AGCGTATCGACCAGA---------------------------------AAGAAA--G---------CAAaaacaaaagacaaaaaaacaaacaaagaaatctcgaacag------acacaccgaacaaataaca----aacaC----------ATAGCCGAGACTGCT----TTAGTTAGTCC-------------------------TT---------AAG-CATAAGTGCAATAA----------AAACGTC----AACT---------AGAGGAgggggtggg---aatgggg---------atgggaat--------------gggaatgg--gggtgg--------ggCTATTAGCCAGTCT------------ATA-A---------------AGT-------TTTG----------CTGCGCAGAGTCT-ACATATATGTAAACTAATAAACTAC-----A---T-----T----- a score=7250.000000 s dm6.chr2R 24349524 5 + 25286936 TA---CGA s droSim1.chr2R 18696253 5 + 19596830 TA---CGA s droSec1.super_23 116016 5 + 989336 TA---CGA s droYak3.chr2R 20205225 5 + 21139217 TA---CGA s droEre2.scaffold_4845 21603143 5 + 22589142 TA---CGA s droBia2.KB462602 795736 5 + 3129309 TA---CGA s droSuz1.KI419649 12040939 5 - 14502029 TA---CGA s droAna3.scaffold_13266 5710299 5 - 19884421 TG---CAG s droBip2.KB464407 1959084 5 + 2915140 TG---CAG s droEug2.KB465067 600322 5 + 1515531 TA---CGA s droEle2.KB458573 521265 5 - 5320397 TA---CAA s droKik2.KB459527 275751 5 - 1234237 TA---CAA s droTak2.KB461535 140844 5 - 669855 TA---CGA s droRho2.KB449310 35020 5 - 65043 TA---CAA s droFic2.KB457177 80584 5 + 995874 TA---CGA s droPse3.chr3 1348726 5 - 19787792 AA---CAC s droPer1.super_34 537565 5 - 916997 AA---CAC s droVir3.scaffold_12875 7350887 2 + 20611582 TA------ s droAlb1.JH854640 308597 2 + 406291 TG------ s droGri2.scaffold_15245 900156 5 + 18325388 TACGA--- a score=-8906.000000 s dm6.chr2R 24349529 38 + 25286936 A------ACTTAGTTA---AAACAAG-TTG-------A-----TAGCAAAT------------------------AATA-----------------TAAAG s droSim1.chr2R 18696258 38 + 19596830 A------ACTTAGTTA---AAACAAG-TTG-------A-----TAGCAAAT------------------------AATA-----------------TAAAG s droSec1.super_23 116021 38 + 989336 A------ACTTAGTTA---AAACAAG-TTG-------A-----TAGCAAAT------------------------AATA-----------------TAAAG s droYak3.chr2R 20205230 61 + 21139217 AACTTACACTTAGTTT---AAACAAG-TTG-------A-----TAGCAAAT------------------------AATACGAGTACATGTATATGTTAAAG s droEre2.scaffold_4845 21603148 44 + 22589142 AACTTAAACTTAGTTA---AAACAAG-TTG-------G-----TAGCAAAT------------------------AGTA-----------------TAGGG s droBia2.KB462602 795741 39 + 3129309 A------ACTTAGTTA---AAACAAG-TTg-------a-----tagcaaat--------------a---------aaaa-----------------tgggg s droSuz1.KI419649 12040944 39 - 14502029 A------ACTTAGTTA---AAACAAG-TTG-------A-----tagcaaat--------------a---------aata-----------------tgaaa s droAna3.scaffold_13266 5710304 44 - 19884421 G------ACCTACATATCCTTGCAAG-TTG-------A-----TAGCAAAT--------------A-A------GGATA-----------------CAAGA s droBip2.KB464407 1959089 46 + 2915140 T------ACTTATAT----TTACAAG-TTGATAGCAAA-----TAGCAAAT--------------A-A------AGATA-----------------CAA-A s droEug2.KB465067 600327 37 + 1515531 A------ACTTAGTTA-----ACAAG-TTG-------A-----Tagcaaat--------------a---------aatg-----------------taaaa s droEle2.KB458573 521270 36 - 5320397 C------ACTTAGTTA-----CCAAGTTTG-------a-----tagcaaat--------------a---------aata-----------------caa-- s droKik2.KB459527 275756 42 - 1234237 T------ACTTAGTGA-----ACAAG-TTG-------ATATgttagcaaat--------------a---------aata-----------------aaaca s droTak2.KB461535 140849 47 - 669855 A------ACTTAGTTA---AAGCAAG-TTG-------A-----TAGCAAAT--------------A-AACAAGTAAATA-----------------TGAAA s droRho2.KB449310 35025 38 - 65043 T------ACTTAGTTA-----ACAAGTTTG-------a-----tagcaaat--------------a---------aata-----------------caaat s droFic2.KB457177 80589 35 + 995874 T------GCTTAGTTA-----GCAAGTTTG-------A-----tagcaaat--------------ata-------aata---------------------- s droPse3.chr3 1348731 39 - 19787792 G------GCCAAACAC---CCAAAAG-TTG-------T-----TGGCAAGT--------------A---------AATA-----------------AAAGT s droPer1.super_34 537570 39 - 916997 G------GCCAAACAC---CCAAAAG-TTG-------T-----TGGCAAGT--------------A---------AATA-----------------AAAGT s droMir2.chr3 1389861 19 - 20862834 -------------------------------------T-----TGGCAAGT--------------A---------AATA-----------------AAAGT s droWil2.CH963894 1308439 39 + 2843958 -------atcaACTAA---TCTTAAA-TTGT------t-----tagcaaat--------------a---------tata-----------------tacat s droAlb1.JH854640 308600 22 + 406291 -------------------------T-CTT-------A-----acttaga---------------a---------aata-----------------tatat s droGri2.scaffold_15245 900170 38 + 18325388 ------------------------TG-TTt-------a-----tattatatacatatatatatata---------gata-----------------tatat a score=-128081.000000 s dm6.chr2R 24349567 12 + 25286936 CA-----AT--AAACG--------TCG------------------ s droSim1.chr2R 18696296 12 + 19596830 CA-----AT--AGACG--------TCG------------------ s droSec1.super_23 116059 12 + 989336 CA-----AT--AAACG--------TCG------------------ s droYak3.chr2R 20205291 8 + 21139217 CA-----AT------G--------TCG------------------ s droEre2.scaffold_4845 21603192 8 + 22589142 CA-----AT------G--------TCG------------------ s droBia2.KB462602 795780 9 + 3129309 CA----CAT------G--------TCG------------------ s droSuz1.KI419649 12040983 9 - 14502029 ca----aat------g--------tCG------------------ s droAna3.scaffold_13266 5710348 10 - 19884421 GA-----GT----GCG--------TCG------------------ s droBip2.KB464407 1959135 10 + 2915140 TA-----GT----GGG--------TTG------------------ s droEug2.KB465067 600364 9 + 1515531 ca----aat------g--------tCG------------------ s droEle2.KB458573 521306 6 - 5320397 -------at------g--------tcG------------------ s droKik2.KB459527 275798 13 - 1234237 aatacaaat------g--------tcG------------------ s droTak2.KB461535 140896 8 - 669855 CA-----AT------G--------TCG------------------ s droRho2.KB449310 35063 14 - 65043 aa-----atgcaaatg--------tcG------------------ s droFic2.KB457177 80624 8 + 995874 ca-----at------g--------tCG------------------ s droPse3.chr3 1348770 16 - 19787792 CC-----AG------GGAGTGTATTCG------------------ s droPer1.super_34 537609 16 - 916997 CC-----AG------GGAGTGTATTCG------------------ s droMir2.chr3 1389880 16 - 20862834 CC-----AG------GGAGTGTATTCG------------------ s droWil2.CH963894 1308478 12 + 2843958 ac-----at--atata--------tcc------------------ s droVir3.scaffold_12875 7350936 12 + 20611582 ------------------------TAGCAAATG---------TTT s droAlb1.JH854640 308624 6 + 406291 ------------------------ttgaaa--------------- s droGri2.scaffold_15245 900229 21 + 18325388 ------------------------TAGCAAATGTTGTTTTTCTTT a score=310674.000000 s dm6.chr2R 24349579 65 + 25286936 AAGGCGCCGGCGGCCG---TTTT--------------CCT---GA------------G----------------------------TGTGAGTG---------------------------------------------------AATGC------GT------GTGT------------GATGAGCGTGCT-C--------C-GTAAAG s droSim1.chr2R 18696308 65 + 19596830 AAGGCGCCGGCGGCCG---TTTT--------------CCT---GA------------G----------------------------TGTGAGTG---------------------------------------------------AATGC------GT------GTGT------------GATGAGCGTGCT-C--------C-GTAAAG s droSec1.super_23 116071 65 + 989336 AAGGTGCCGGCGGCCG---TTTT--------------CCT---GA------------G----------------------------TGTAAGTG---------------------------------------------------AATGC------GT------GTGT------------GATGAGCGTGCT-C--------C-GTAAAA s droYak3.chr2R 20205299 93 + 21139217 AAGGCGCCGGCGGCCG---ATTT--------------CCt---ga------------g----------------------------tgtgagtgaaagcgagtgagtgtgagtgaaagtg---------------------tg--tgcgt------gt------gtgt------------gatgagcgtgCT-C--------C-GTAGAG s droEre2.scaffold_4845 21603200 71 + 22589142 AAGGCGCCGGCGGCCG---TTTT--------------CCT---GA------------G----------------------------TGTGAGTG----------------------AGTG---------------------TG--AATGC------GA------GTGT------------GATGAGCGTGCT-C--------C-GTAAAG s droBia2.KB462602 795789 89 + 3129309 AATGCGCCGGCGgccg---ttttccatttcccatttcccc---ga----------CTG----------------------------TGTGAGAG----------------------AGTG---------------------TGATGATGC------GT------GAGT------------GATGAGCGTGCT-C--------C-GTACAG s droSuz1.KI419649 12040992 87 - 14502029 AATGCGCCGGCGGccg---ttttccatttcccattttcct---ga------------G----------------------------TGTGAGAG----------------------AGTG---------------------TGATGATGC------GT------GTGT------------GATGAGCGTGCT-C--------C-GTAAAG s droAna3.scaffold_13266 5710358 107 - 19884421 AATGCGCCGGCAGCCA---TTAT--------------CCT---GC------------GAGTGTGCCGGCGTGCCAGCGCGCCAGAGTGTGAGTG----------------------AGTGAGTGTATC-------------TG--TATCT------GT------GTTT------------GATGAGCGTGCT-C--------C-ATAAAG s droBip2.KB464407 1959145 97 + 2915140 AGTGCGCCGGCGGCCA---TTAT--------------CCT---GC------------A-----TCCTGcat-------cgtgtgtgtgtgtgtg----------------------tataagtgtgtc------------gtg--tatct------gt------gtTT------------GATGAGCGTGCTCC--------C-ATAAAG s droEug2.KB465067 600373 68 + 1515531 AATGCGCCGGCGGCCA---TTT---------------CCT---GA------------G----------------------------TGAGAGAG----------------------GGTG-------------------------AATGC------GA------GTGT------------GATGAGCGTGCT-C--------C-GTAAAG s droEle2.KB458573 521312 72 - 5320397 AATGCGCCGGCGGCCGTGTTTTT--------------CCT---GA------------G----------------------------TGTGAGAG----------------------ATTG-------------------------AATGC------GT------GTGT------------GATGAGCGTGCT-C--------C-GTAAAG s droKik2.KB459527 275811 90 - 1234237 AATGCGCCGGcggcca---ttttccatttt-------cct---gaATCCCCGggtccg----------------------------tgtgtgtg----------------------tgtg---------------------tg--tttgc------ga------gTGT------------GATGAGCGTGCT-C--------A-ATAAAG s droTak2.KB461535 140904 101 - 669855 AATGCGCCGGCGgccg---ttttccatttt-------cct---ga------------g----------------------------tgtgagag----------------------agtgtgatgatgatgatcataatgatgattatgc------gt------gtgt------------gatgagcgtgCT-C--------C-GTAGAG s droRho2.KB449310 35077 69 - 65043 AATGCGCCGGCGGCCA---TTTT--------------cct---ga------------g----------------------------tgtgagtg----------------------tgtg-------------------------aaTGC------GT------GTGT------------GATGAGCGTGCT-C--------C-GTAAAG s droFic2.KB457177 80632 69 + 995874 AATGCGCCGGCGGCCG---TTTT--------------CCT---GA------------G----------------------------TGTGAGAG----------------------AGTG-------------------------AATGC------GT------GTGT------------GATGAGCGTGCT-C--------C-GTAAGT s droPse3.chr3 1348786 86 - 19787792 AATGCGCCGGCGGCCA---TTTT--------------CCTTTGga------------g----------------------------tgtaagtg----------------------tgtg---------------------tg--cgtgc------gt------gtgtgtgcgtgtgggcgATGAGCGTGCT-C--------T-TTGAAC s droPer1.super_34 537625 88 - 916997 AATGCGCCGGCGGCCA---TTTT--------------CCTTTGGA------------G----------------------------TGTAAgtg----------------------tgtg---------------------tg--cgtgcgt----gt------gtgtgtgtgtgtgGGCGATGAGCGTGCT-C--------T-TTGAAC s droMir2.chr3 1389896 92 - 20862834 AATGCGCCGGCGGCCA---TTTT--------------CCTTTGga------------g----------------------------tgtaagtg----------------------tgtg---------------------tg--tgtgcgtgtgcgt------gtgcgtgtgtgtgggcgatGAGCGTGCT-C--------T-TTGAAC s droVir3.scaffold_12875 7350948 58 + 20611582 --------------------------------------------A------------G----------------------------CGAGGCGG----------------------CGTC---------------------CG--GCGGC------CT---CCAGTGC------------GATGAGCGTGCT-CTAACCGAAC-CTAAAA s droAlb1.JH854640 308630 65 + 406291 --------------------------------------------a------------g----------------------------cGGGGCTA----------------------CGTC---------------------TG--GCGAC------CTTTCCCCGTGC---------AATGATGAGCGTGCT-CAATGCGAAcattaaat s droGri2.scaffold_15245 900250 48 + 18325388 --------------------------------------------A------------G----------------------------T--GGCGT----------------------CGGG---------------------CG--TCGGC------CT---TCAGTGC------------GATGAGCGTGCT-C------AAC---AAAA a score=59639.000000 s dm6.chr2R 24349644 12 + 25286936 TTAAGCGTAC----------------------TT s droSim1.chr2R 18696373 12 + 19596830 TTAAGCGTAC----------------------TT s droSec1.super_23 116136 11 + 989336 TTAAGCGTA-----------------------TT s droYak3.chr2R 20205392 12 + 21139217 TTAAGCGTAC----------------------TT s droEre2.scaffold_4845 21603271 12 + 22589142 TTAAGCGTAC----------------------TT s droBia2.KB462602 795879 12 + 3129309 TTAAGCGTAC----------------------TT s droSuz1.KI419649 12041080 12 - 14502029 TTAAGCGTAT----------------------TT s droAna3.scaffold_13266 5710476 12 - 19884421 ATAAGCGTAT----------------------TT s droBip2.KB464407 1959251 9 + 2915140 ATAAGCGTA------------------------- s droEug2.KB465067 600442 12 + 1515531 TTAAGCGTAT----------------------TT s droEle2.KB458573 521386 12 - 5320397 TTAAGCGTAT----------------------TT s droKik2.KB459527 275902 12 - 1234237 TTAAGCGTAT----------------------TT s droTak2.KB461535 141006 12 - 669855 TTAAGCGTAT----------------------TT s droRho2.KB449310 35148 12 - 65043 TTAAGCGTAT----------------------TT s droFic2.KB457177 80701 12 + 995874 TTAAGCGTGT----------------------TT s droPse3.chr3 1348874 10 - 19787792 TTAAGCTTA------------------------T s droPer1.super_34 537715 10 - 916997 TTAAGCTTA------------------------T s droMir2.chr3 1389990 10 - 20862834 TTAAGCTTA------------------------T s droWil2.CH963894 1308542 12 + 2843958 TTTAGCCTGA----------------------CG s droVir3.scaffold_12875 7351006 12 + 20611582 AAAATCATAT----------------------TT s droAlb1.JH854640 308695 34 + 406291 caaatcataTAGTTCTAAACTATATGCTCAACTT s droGri2.scaffold_15245 900298 12 + 18325388 CACATCTTAT----------------------TT a score=361088.000000 s dm6.chr2R 24349656 86 + 25286936 TCCAGATTCG-TTAGCCTAATGTTA---GTTGTA-----------------------TTATGTTTA--TTCGA--------TCGATCC---------GATT-------GGCTT----------TTACTGAC-----------------CCCTACTA-----ACTGGAG------TGT s droSim1.chr2R 18696385 86 + 19596830 TCCAGATTCG-TTAGCCTAATGTTA---GTTGTA-----------------------TTATGTTTA--TTCGA--------TCGATCC---------GATT-------GGCTT----------TTACTGAC-----------------CCCTACTA-----ACTGGAG------TGT s droSec1.super_23 116147 86 + 989336 TCCAGATTCG-TTAGCCTAATGTTA---GTTGTA-----------------------TTATGTTTA--TTCGA--------TCGATCC---------GATT-------GGCTT----------TTACTGAC-----------------CCCTACTA-----ACTGGAG------TGT s droYak3.chr2R 20205404 100 + 21139217 TCCAGATGCG-TTAGCCTAATGTTA---GTTGTA------TTACCGCGCTATAG---TTATGTTTA--TCCGA--------TCGATCC---------GATT-------GGCTT----------TTATTGAC-----------------CCCTACTA-----ACTGGAG------TGT s droEre2.scaffold_4845 21603283 100 + 22589142 TCCAGATTCG-TTAGCCTAATGCTA---GTTGTA------TTACCGCGCTATAG---TTATGTTTA--TCTGA--------TCGATCC---------GATT-------GGCTT----------TTATTGAC-----------------CCCTACTA-----ACTGGAG------TTT s droBia2.KB462602 795891 100 + 3129309 TCCGGGTTTGTTTAGCGTAATGTTA---GTAGTA-----TTTACCACCCTATAG---TTATGTTTA---TTGA--------TCGATCC---------AATT-------GGCTT----------TTATTGAC-----------------ACTTACTA-----ATTGGA-------TGT s droSuz1.KI419649 12041092 101 - 14502029 TCCGGGTTCGTTTAGCTTAATGTTA---GTAGTA-----TTTACCACTCTATAG---TTATGTTTA--TTTGA--------TCGATCC---------AATT-------GGCTT----------TTATTGAC-----------------ACCTACTA-----ATTGGA-------TGT s droAna3.scaffold_13266 5710488 113 - 19884421 TCCGGATTCGTTTAGCTTAATGTTA---GT-GTA-----CTTACAAGCTTATAG---TTATTTTTA--TTCGA-------------TC---------GATT-------GGCCG----------TTAGTGTCTTTTGAATCTGTTTGGCTATTACTA-----ATCGGAA------TGT s droBip2.KB464407 1959260 83 + 2915140 -----------------TAATGTTA------GTA-----CTTACCAGCTTatag---ttatgttta--tttga------------ttt---------gatt-------ggCCC----------TTAGTTACTTTGG------------CATTACTA-----ATCGGAA------TGT s droEug2.KB465067 600454 101 + 1515531 TCCGGATTCGTTTAGCCTAATGTTA---GTAGTA-----TTTACCGCCCCTTAG---TTATGTTTA---TTGA--------TCGATCC---------AATT-------GGCTT----------TTATTGAC-----------------ACCTACTA-----ATCGGAG------TGT s droEle2.KB458573 521398 102 - 5320397 TCCGGATTCGTTTAGCTTAATGTTA---GTAGTA-----TTTACCACTCTATAG---TTATGTTTA--TTTGA--------TTGATCC---------AATT-------GGCTT----------TTATTGAC-----------------ACTTACTA-----ATTGGAA------TGT s droKik2.KB459527 275914 126 - 1234237 TCCGGACTCGTTTAGCCTAATGTTA---GTAGTTTATACTTTACGACTTtgtag---ttttgttta--tttga--------ttgATCCCGCCCCTAAAATT-------GGCTTAAAGTATTTCCAACTGAC-----------------CTCTACTA-----ATTGGAA------TGT s droTak2.KB461535 141018 89 - 669855 TCCGGGTTCGTTTAGCCTAATGTTA---GTATGT-----------------TAG---TTATGTTTA--TTCGA--------TCGATCC---------AATT-------GGCTT----------TTATTGAC-----------------ACCTACTA-----ATTGGA-------TGT s droRho2.KB449310 35160 103 - 65043 TCCGGATTCGTTTAGCTTAATATTA---GTAGTA-----TTTACCACTCTACAG---TTATGTTTA--TTTGA--------TTGATCC---------AATT-------GGCTT----------TTATTGAC-----------------ACTTACTA-----ATTGGAA-----TTGT s droFic2.KB457177 80713 105 + 995874 TCCAGATTCGTCTAGCTTAATGTCATCAGTAGTA-----TTTACCGCCCCTTAG---TTATGTTTA--TTTGA--------TTGATCC---------AATT-------GGCTT----------TTATTGAC-----------------ACCTACTA-----ATTGGAA------TGT s droPse3.chr3 1348884 114 - 19787792 CCCAGAAGC--TTAGCTTAATTTTA---GAACTA-----TTTATAATTGTGAAGCTATTATGTTTA--TTTGAATTGGCTTtcgattt---------gtttatttttcgagtt----------ttatttgc-----------------attca--a-----actaaac------t-- s droPer1.super_34 537725 113 - 916997 CCCAGAAGC--TTAGCTTAATTTTA---GAACTA-----TTTATAATTGTGAAGCTATTATGTTTA--TTTGAATTGGCTTTCGATTT---------GTTTATTTTTCGAGTT----------TTATTTGC-----------------ATTCA--A-----ACTAAAC--------- s droMir2.chr3 1390000 114 - 20862834 CCCAGAAGC--TTAGTCTAATGTTA---GAGCTA-----TTTATAATTGTGAAGCTATTATGTTTA--TTTGAATTGGCTTtcgattt---------gtttatttttcgagtt----------ttatttgc-----------------attca--a-----actaaac------t-- s droWil2.CH963894 1308554 96 + 2843958 TCTGGGCCAA-TGAGCGTGCTCTAA---GTAAGA-------------------G---TTTctttaa--gttaa--------tttatgc---------aatt---------tat----------ttatacaa-----------------atctaatatatatattaaagacaCACTTT s droVir3.scaffold_12875 7351030 78 + 20611582 ----------------TGCAAACTA---TTATTA-----TTTTTTGTTTTG-------TGTGAAGA--AATGA--------TC-ATCG---------TTTT-------AGCTT------AAACTTAGCGCT-----------------ATTTATAA-----TTT------------- s droAlb1.JH854640 308764 81 + 406291 ----------------tgcatatta----tatta-----tttgttgttttgtga----tGTGAAGAACACTCA--------TC-ATCG---------TTTT-------AGCTT-------ATCTTAGcgct-----------------atttataa-----ttt------------- a score=59177.000000 s dm6.chr2R 24349742 9 + 25286936 TGCATGAGG s droSim1.chr2R 18696471 9 + 19596830 TGCATGAGG s droSec1.super_23 116233 9 + 989336 TGCATGAGG s droYak3.chr2R 20205504 9 + 21139217 TGCATGAAG s droEre2.scaffold_4845 21603383 9 + 22589142 TGCATGAAG s droBia2.KB462602 795991 9 + 3129309 TGCATGACG s droSuz1.KI419649 12041193 9 - 14502029 TGCATGACG s droAna3.scaffold_13266 5710601 8 - 19884421 TGCATGAC- s droBip2.KB464407 1959343 9 + 2915140 TGCATGACa s droEug2.KB465067 600555 9 + 1515531 TGCATGACG s droEle2.KB458573 521500 9 - 5320397 TGCATGACG s droKik2.KB459527 276040 9 - 1234237 TGCATGATT s droTak2.KB461535 141107 9 - 669855 TGCATGACG s droRho2.KB449310 35263 9 - 65043 TGCATGGCC s droFic2.KB457177 80818 9 + 995874 TGCATGACG s droPse3.chr3 1348998 6 - 19787792 ---accaaa s droPer1.super_34 537838 6 - 916997 ---AAAAAA s droMir2.chr3 1390114 6 - 20862834 ---aaaaaa s droWil2.CH963894 1308650 9 + 2843958 TGCATCGTT s droVir3.scaffold_12875 7351439 9 + 20611582 TGCATAAAA s droAlb1.JH854640 308845 9 + 406291 tacatttat a score=-228876.000000 s dm6.chr2R 24349751 19 + 25286936 AATCGCTCAGAAA-GAATC---------------------------------C------------------ s droSim1.chr2R 18696480 19 + 19596830 AATCGCTCAGAAA-GAATC---------------------------------C------------------ s droSec1.super_23 116242 19 + 989336 AATCGCTCAGAAA-GAATC---------------------------------C------------------ s droYak3.chr2R 20205523 18 + 21139217 AATCGCTCAGAAA-GAACT---------------------------------------------------- s droEre2.scaffold_4845 21603392 21 + 22589142 AAGCGCGCAGAAA-GAACT-------------------------------TCA------------------ s droBia2.KB462602 796000 21 + 3129309 AATCGCTCAGAAT-GAGTG-------------------------------CCA------------------ s droSuz1.KI419649 12041202 28 - 14502029 AATCGCTCAAAAT-GAGTG--CCAATTT----------------------CCA------------------ s droAna3.scaffold_13266 5710609 3 - 19884421 -----------------TT---------------------------------T------------------ s droBip2.KB464407 1959356 17 + 2915140 aaTCgagcttaa---aatt---------------------------------a------------------ s droEug2.KB465067 600564 17 + 1515531 AA-CGCTCAACAG-TTATC---------------------------------------------------- s droEle2.KB458573 521509 51 - 5320397 AATCGCTCAAAAC-GGACTATCCGATCTGGCTA-AATTCCAAAAAGAAACTTA------------------ s droKik2.KB459527 276049 6 - 1234237 AA-------------AGTT---------------------------------------------------- s droTak2.KB461535 141121 18 - 669855 AATCGCTCAAAAT-GATCT---------------------------------------------------- s droRho2.KB449310 35272 36 - 65043 AATCGCTCAAAAC-GGATT----------------ATCCGGATTAAGACAATC------------------ s droFic2.KB457177 80827 46 + 995874 AATTGCTCAAAAG-GATCA------TCTGGCTAGATTCCCTAGCCAGACTATC------------------ s droPse3.chr3 1349004 20 - 19787792 aaaaagacactAACAAATT---------------------------------G------------------ s droPer1.super_34 537844 20 - 916997 AAAAAGACACTAACAAATT---------------------------------G------------------ s droMir2.chr3 1390120 19 - 20862834 aaaaaggcactaa-aaatt---------------------------------g------------------ s droWil2.CH963894 1308659 13 + 2843958 TTTCGTTT------GAACC---------------------------------------------------- s droVir3.scaffold_12875 7351448 2 + 20611582 ------------------------------------------------------------AG--------- s droMoj3.scaffold_6496 26146604 19 + 26866924 ----------------------------------------------------AACCTTTAAGCCGAAACTC s droAlb1.JH854640 308854 6 + 406291 -----------------------------------------------------------------atattt a score=831982.000000 s dm6.chr2R 24349770 250 + 25286936 AGTTC---CAAAT-CG----------------CTGCGTGCAACA---T---GGCCACTTTCTACTCACATTTGAGCTGT---TTGCT--TTTCGC---------------CTT--TCTACTAATATTTATTGTACCCATACT----------------------TG-----AACCTAAATACCT----------AAATACCAAATTA-AAA---CAGCTCAAAG--CA---AGTTC--------TCT-----C---GTATCCa---------------------------------------ttttaattttatttataactta-------atgttta----------------cttCGTTAGAGA---A-----AATACTCAAGA---------------GCACGTAATTTAAAAAATGAAA----CACAC-------------------TTTTCTGTCAAACAGAA s droSim1.chr2R 18696499 242 + 19596830 AGTTC---CAAAT-TG----------------CTGCGTGCAACA---T---GGCCACTTCCTACTCACATTTGAGCTGT---TCGCT--TTTCGC---------------CTT--TCTACTAATATTTATTGTACCCATACT----------------------TG-----A--------ACCT----------AAATACCAAATTA-AGA---CAGCTCAAAG--CA---AGTTC--------TCT-----C---GTATCCA---------------------------------------TTTTAATTTTATTTATAACTTA-------ATGTTTA----------------CTTCGTTAGAGA---A-----AATACTCAAGA---------------GCACGTAATTTAAAAAATGAAA----CACAC-------------------TTTTCTGTCAAACAGAA s droSec1.super_23 116261 242 + 989336 AGTTC---CAAAT-TG----------------CTGCGTGCAACA---T---GGCCACTTCCTACTCACATTTGAGCTGT---TTGCT--TTTCGC---------------CTT--TCTACTAATATTTATTGTACCCATACT----------------------TG-----A--------ACCT----------AAATACCAAATTA-AGA---CAGCTCAAAG--CA---AGTTC--------TCT-----C---GTATCCA---------------------------------------TTTTAATTTTATTTATAACTTA-------ATGTTTA----------------CTTCGTTAGAGA---A-----AATACTCAAGA---------------GCACGTAATTTAAAAAATGAAA----CACAC-------------------TTTTCTGTCAAACAGAA s droYak3.chr2R 20205541 230 + 21139217 ---------AAGT------------------------TGCAACA---T---GGCCACTTACTACTCACATTTGAGCTGT---TTGCT--TTTCGC---------------CTT--tctactaatatttattgtaCCTATACT----------------------TA-----A--------ACCT----------AAATACCAAATTA-AAG---CAGCTCAAAG--CA---AGTTC--------TCT-----C---ATATCCc--------------------------------------ctttttattgtatttataacTTT-------ATGTTTA----------------CTTCGTTAGTGA---A-----AATACTCAACA---------------ACACGTAatttaaaaaacgaaa----cacac-------------------GTTTCTGTCAAACAGAA s droEre2.scaffold_4845 21603413 241 + 22589142 AGTTG---CAAGT-TG----------------CTGCGTGCAACA---T---GGCCACTTCCTACTCACATTTGAGCTGT---TTGCT--TTTCGC---------------CTT--TCTACTAATATTTATTGTACCTATACT----------------------TA-----A--------ACCT----------AAATACCAAATTA-AAA---CAGCTCAAAG--CA---AGTTC--------TCT-----C---GCATCCA----------------------------------------TTTAATTTTATTTTTAACTTA-------ATGTTTA----------------CTTCGTTAGAGA---A-----AATACTCAACA---------------AGACGTAATTTAGAAAACGAAA----CACGC-------------------GTATCTGTCAAACAGAA s droBia2.KB462602 796021 253 + 3129309 AGTTC---TAAAT-TA----------------CTCCGTGCAACA---C---AACCGCTAGTTACTCACCTTTGAGCTGT---TTGCTTGTTTCGC--------------TCTT--TCtactaatatttattgtac----acc----------------------ta-----a--------attt----------aaataccaaatta-aaa-agcagCTCAAAG--CA---AGTTC--------GCT-----C---GCATCAA-------------------------Aggc--------aatttacatttaatttattactta-------attttta----------------cTCCGTTAAAGA---A-----AGTACTCGACA----AG--------CacacataatttaattaccgAAA----CACAC------------------ACTTTCTGTCAAACAGAA s droSuz1.KI419649 12041230 253 - 14502029 AGTTC---CAAAT-TA----------------TTCCGTGCAACA---T---AACCGCTACTTACTCACCTTTGAGCTGT---TTGCTTGTTTCGC--------------TCTT--TCtactaatatttattgtac----atc----------------------ta-----a--------attt----------aaataccaaatta-aaa-aacagcTCAAAG--CA---AGTTC--------GCT-----C---ACATCAA-------------------------AGgc--------aatttacatttaatttattactta-------attttta----------------cTCCGTTAAAGA---G-----AATACTCGACA----AG--------CACACATAATTTAATTACCGAAA----CACAC------------------ATTTTCTGTCAAACAAAA s droAna3.scaffold_13266 5710612 217 - 19884421 TGTGG---CAACTGTG--------------------GCGACACA---GCC-GCTCAGT-------AACCTTTGAGCTGC---TCGCT--TCT-AT---------------CTC--CCTACTAATATTTATTGTAC----ATT----------------------TC-----A--------GTTA----------AAATACCAAATTA-AGA--GCAGCTCAAAG--CC---CTCTCTCACCCTATCC-----C---ACATCAA--------------------------------------ATTTAAAGTTAATTT---ATTTA-------CTTTTTA----------------TGTGTTAATTGA---A-----AGGACCTACTA-------------------------------CCGA-------TCAT-------------------GTTTCTGTCAAACAGAA s droBip2.KB464407 1959373 189 + 2915140 aatta---aaatt-ta--------------------gcGCAACA---TTTAGCGCAGTTTTACTCAACCTTTGAGCTGC---TCAAC--TTT-AT---------------CTC--TCTACtaatatttattgtat----att----------------------ta-----a--------attt----------aaataccaaATTC-AGA--GCAGCTCAAAG--CC---TCCTC--------------------------A--------------------------------------CTTAGAAG--GATCT---ACATA-------CTACTC-------------------TGTTTAGT--------------------TA-------------------------------CCGA-------TCGT-------------------GTTTCTGTCAAACAGAA s droEug2.KB465067 600581 245 + 1515531 AGTTC---CCAGT-TA----------------CTCCATGCAACA---C---GGCCGCCACCTACTCACCTTTGAGCTGT---TTGCTTGTTTCGC--------------CCTT--TCTACTAATATTTATTGTACCTATACC----------------------Ta-----a--------actt----------aaaaaccaaatta-aaa---caGCTCAAAG--CA---CGTTC--------TCT-----C---ACACcgt------------------------------------------taatttaaattattacttT-------ATGTTTA----------------CTCCATTAAAGA---A-----AACGCTCAGCA----GA--------CGCGCATAGTTTAGTTACCGAGA----CACAC-------------------TTTTCTGTCAAACAGAA s droEle2.KB458573 521560 256 - 5320397 AGTTC---CAAAT-TA----------------CTCCATGCAACA---T---AACCGCTTCTTAATCACCTTTGAGCTGT---TTGCTTATTTCGC--------------TCTT--ATtactaatatttattgtac----att----------------------tc-----a--------attt----------acataccaaatta-caaaaacagcTCAAAG--CA---AGTTC--------TCT-----C---ACATCaa-------------------------aggc--------aatttaaatttaatttattaatta-------attttta----------------cttcattaaaga---a-----aatactcAACAAGCGAG--------CacacataatttaattaccgACA-----AAAC-------------------ACTTCTGTCAAACAGAA s droKik2.KB459527 276055 225 - 1234237 ----------AAA-GA----------------CTTTGTGCAACA---T---AGCCGCCACTTACTCAACTTTGAGCTGT---TTGCT--TTACGA-------------CTCTT--TCtactaatatttattgtac----att----------------------ta-----a--------attta---------aaataccaaatta-aaa-aacagctcaaag--c--------c--------gca-----caaaaaatcaa---------------------------------------gttaaatttaatttattacccT-------ATGTTta----------------ctctctctcacacaca-----attatttaata------------------------ttaattaccgA-------TCAC-------------------ATTTCTGTCAAACAGAG s droTak2.KB461535 141139 255 - 669855 -GTTC---CAAAT-TA----------------TTCCGTGCAACA---C---AACCGCTACTTACTCACCTTTGAGCTGT---TTGCTTGTTTCGC--------------TCCT--TCtactaatatttattgtac----atc----------------------ta-----a--------attt----------aaataccaaatta-aaa-aacagcTCAAAG--CC---AGTTC--------TCT-----C---ACTTCAAA------------------------Aggc--------aatttacatttaatttattactta-------attttta----------------ctcagctaaaga---a-----aaTACTCGACA----AG--------CAcacataatttaattaccgaaa----cacac----------------acattttcTGTCAAACAGAA s droRho2.KB449310 35308 254 - 65043 AGTTC---CAAAA-CA----------------TTCCATGCAACA---T---AACCGCTACTTACTCACCTTTGAGCTGT---TTGCTTGTTTCGC--------------TCTT--Tctactaatatttattgtac----att----------------------ta-----a--------attt----------aaataccaaatta-aaaaaacagctCAAAGTTCA---AGTTC--------TCT-----C---ACATCAAa------------------------aggc--------aatttaaatttaatttattaatta-------atgttta----------------ctTCATTAAAGA---A-----AATGCTCAACA----AAC-------cacacataatttaattaccgA-------ACAC-------------------GTTTCTGTCAAACAGAA s droFic2.KB457177 80873 254 + 995874 TGCTC---CGAAT-TA----------------ATCCGTGCAACA---G---AACCGCTTTGTAC-CGCCTTTGAGCTGT---TTGCTTGACTCGC--------------TCTT--TCtactaatatttattgtac----att----------------------ta-----a--------actt----------aaataccaaatta-aaa--acagcTCAAAG--CA---AGTTC--------TCT-----C---ACagcaa-------------------------aagc--------aatttaaacttaatttattcaCTT-------ATGTTTA----------------CTGCGTTAAAGA---A-----AATACTCAAGA----AA--------CacacataatttaattaccgAACATACCGAAC-------------------GTTTCTGTCAAACAGAA s droPse3.chr3 1349024 246 - 19787792 TATTC---AAAAT-TG----------------TTG--------A---A---GACCCCCACTCAC---CCTTTGAGCTCA---CCCTCCATTCCGcgcactctctctttcgttt--tctactaatatttattgtat----att----------------------tt-----t--------attt----------agaaaccaaatta-aaa-aGCAGCTCAGAG--CT---AATTT--------CCA-----C---CACTCAA-------------------------acgc--------aatttaaatttaatttattattta-------aacttaa----------------tttcattaaata---------------caaaa----aga-------agaacttaatttaattagagA-------TCGC-------------------ATTTCTgtcaaacagaa s droPer1.super_34 537864 246 - 916997 TATTC---AAAAT-TG----------------TTG--------A---A---GACCCCCACTCAC---CCTTTGAGCTCA---CCCTCCATTCCGCGCACTCTCCCTTTCGTTT--TCTACTAATATTTATTGTAT----ATT----------------------TT-----T--------ATTT----------AGAAACCAAATTA-AAA-AGCAGCTCAAAG--CT---AATTT--------CCA-----C---CACTCAA-------------------------ACGC--------aatttaaatttaatttattattta-------aacttaa----------------tttcattaaata---------------CAAAA----AGA-------AGAACTTAATTTAATTAGAGA-------TCGC-------------------ATTTCTGTCAAACAGAA s droMir2.chr3 1390139 246 - 20862834 tattc---aaaat-tg----------------ttg--------a---a---aaaccCCACTCAC---CCTTTGAGCTCA---CCCTCCATTCCGCgcactctctcttttgttt--tctactaatatttattgtat----att----------------------tt-----t--------attt----------agaaaccaaatta-aaa-agcaGCTCAAAG--CT---AATTT--------CCA-----C---CACTCAA-------------------------acgc--------aatttaaatttaatttattactta-------aacttaa----------------tttcattaaaga---------------caaaa----aga-------agaacttaatttaattagaga-------TCGC-------------------ATTTCTgtcaaacagaa s droWil2.CH963894 1308672 291 + 2843958 ---TT---TGAGC-TG----------------CCTGTTGC-------T---CTCCCCCTCTCACTCAC------ACAGT---CTTCTC-CCTCAC---------------TCT--ATTactaatatttattgtat----att----------------------tg-----t--------ttttagttttaaagaaaaaccaaattc-tTACAGCAGCTCAAAG--Ct---tttta--------cct-----c---ttttaca-------------------------agac--------caatattttttaaatcatttccaa-------aattttaaaatttaaattgcattattttttacaaa---a-----aacaaaaaaga----aaacctaacttaaatttaaatttaaaaaggaaa----ctaatttagtttagttttttgttgttttctgtcAAACAGAA s droVir3.scaffold_12875 7351450 272 + 20611582 AAGCC---CAATT-AG----------------CAAATCGAGTCC---T---AAATTGTACTTAC---CCTTTGAGCTGC---CTGCT----------------------GCTC--TCTACtaatatttattgtat----attttt-------------------tt-----a--------atat----------aaaaaCCAAATTA-CAA-AGCAGCTCAAAG--CATATGATTC--------TTATGTGGC---ATGACAATAGATCATAGAAAATA---------AAACAATTACG-TATTTGCAAGCAGtttaataat---------attattt----------------attaattaaaGC---GTATTTAAATCATAATT--------------TCATGCTAATTTAGT----AAAG----TTTGC-------------------ATTTCTGTCaaacagaa s droMoj3.scaffold_6496 26146623 307 + 26866924 AAATC---CAACT-CG----------------CAAATCGAAT-----T---GAATCAT-CTTAC---CCTTTGAGCTGC---CTGCT----------------------TCTCTGTCTACtaatatttattgtat----atttttatgaaaattttagttaaaatt-----a--------aaaa----------GAAAACCAAATTA-CGA-AGCAGCTCAAAG--TATTTCATTC--------TTGTGTGGC---ATGACAATAGATAATAGTAAATAAAAAGGAATAAAAAATGAAGCTATTTGCAAGCAATATACTAATTATAAAGACATGTTTG----------------AAACattaaatt---aaattgaaaaattaaat--------------ta--gataatttaat----gcag----attac-------------------attTCTGTCAAACAGAA s droAlb1.JH854640 308860 271 + 406291 gtatctttcgATT-TGATTGGCTTCTTTTGTTCGATTTGATA-----C---AAAATTTACTCAC---TCTTTGAGCTGCTGTCTCAT----------------------GCTT--TTtactaatatttattgtat----attttt---------ttaattaaa-tt-----g--------atac----------ccaaaaaaaataa---a-tgcagctcaaag--cttttaattt--------c-------c---tttacaaaaaatcaagcaaaa-----------agacaa------aatACGTAA----------------------TTTTCTC----------------Gcaagttaaaat---a-atttattaattaaat--------------tcatggTAATTTAGT----GCAG----GTTGC-------------------ATTTCTGTCAAACAGAA s droGri2.scaffold_15245 900789 299 + 18325388 ATTTC---CAAAT-AG----------------CAAATCGAGCAAAAGC---AAAATGTACTTAC---CCTTTGAGCTGCTGCCTGCT----------------------GTTC--TCTACTAATATTTATTGTAT----ATTTTT-----AATTCAAACAAAAATTCGAAGA--------AAAA----------AAAAACCAAATTTGAAA-GGCAGCTCAAAG--CA--TAATTC--------TTATGTGGC---ATGACAATAGAACGTAGAACAACAAA------AGCAAAATACGTAATTTGCAAGCaatttaat------------ataattt----------------attaattacaac---ttatttaaattataatt--------------tCAAGCTAATTTAGT----GCAG----ATTGC-----------------AGATTTCTGTCaaacagaa a score=-16574.000000 s dm6.chr2R 24350020 22 + 25286936 -----------------------------A-GCCGA---------GT-------------------AATTTCTTA------------CATAC s droSim1.chr2R 18696741 22 + 19596830 -----------------------------A-GCTGA---------TT-------------------AATTTCTTA------------TATAC s droSec1.super_23 116503 22 + 989336 -----------------------------A-GCCGA---------GT-------------------AATTTCTTA------------CATAC s droYak3.chr2R 20205771 22 + 21139217 -----------------------------A-GCCGA---------GT-------------------AATTTCTTA------------AATAC s droEre2.scaffold_4845 21603654 22 + 22589142 -----------------------------A-GCCGA---------GT-------------------AATTTCTTA------------AATAC s droBia2.KB462602 796274 22 + 3129309 -----------------------------G-GCCGA---------GT-------------------AATTTCTTT------------AATAC s droSuz1.KI419649 12041483 22 - 14502029 -----------------------------G-GCCGA---------GT-------------------AATTTCTTT------------AATAc s droAna3.scaffold_13266 5710829 22 - 19884421 -----------------------------AGGCAAA---------GC-------------------AATAACTTA-------------ATCC s droBip2.KB464407 1959562 21 + 2915140 -----------------------------A-GCATT---------GC-------------------ATTAACTTA-------------ATcc s droEug2.KB465067 600826 22 + 1515531 -----------------------------A-GCCGA---------GT-------------------AATTTCTTT------------AATAC s droEle2.KB458573 521816 22 - 5320397 -----------------------------A-GCCGA---------GT-------------------AATTTCTTT------------AATAc s droKik2.KB459527 276280 27 - 1234237 -----------------------------A-GCAAAG----CAACGT-------------------AATTCTCTT------------AATAc s droTak2.KB461535 141394 22 - 669855 -----------------------------A-GCCGA---------GT-------------------TATTTCTTT------------AACAc s droRho2.KB449310 35562 22 - 65043 -----------------------------A-GCCGA---------GT-------------------AATTTCTTT------------AATAc s droFic2.KB457177 81127 22 + 995874 -----------------------------A-GCCGA---------GT-------------------AATTTCTTT------------AATAC s droPse3.chr3 1349270 40 - 19787792 -----------------------------a-acaaa---------ac-aaaaaaaaacgagaacaGAATTTCTTT------------AATAA s droPer1.super_34 538110 41 - 916997 -----------------------------A-ACAAA---------ACAAAAAAAAAACGAGAACAGAATTTCTTT------------AATAA s droMir2.chr3 1390385 41 - 20862834 -----------------------------a-acaaa---------acaaaaaaaaaaccagaacagAAATTCTTT------------AATAA s droVir3.scaffold_12875 7351722 61 + 20611582 atacaaaaaatcaaa--aaaaaaaaaaaaa-atcaaaaaacaaaCGC-------------------AATTCTCTAATA---------AATAC s droMoj3.scaffold_6496 26146930 39 + 26866924 AC-------------------AAAACAGAA-ATCAA-----AACCGC-------------------AATTCTATAATA---------AATAT s droAlb1.JH854640 309131 60 + 406291 AT-------TGCGAATGAAAGCAGCAAGAA-ACCAG-----AAAGAC-------------------AATTcgctaataataatatttaatat s droGri2.scaffold_15245 901088 65 + 18325388 gaaaaatataatgaaaagaaaaagaaaaaa-agcaaaaacaaaaCGC-------------------AATTCGCTAAAAAA-------AATAT a score=875342.000000 s dm6.chr2R 24350042 297 + 25286936 TAGTTAAA-TTTATTATT-----TAAA-GATCGT------------------------------------GAAAACGAC---------------GCAAATCCAATAACCC---------------------TAAAGCAATTTACCCAG------------TAAGCCAT-CAAC--AACA---TATGTTTA--------AA-A-----CACCACAAAat-agtat-------ctacatatcagaa-------------------------------acata------a--------atatatatatatattatttaGCGCAATATTA-CGAAATAAT-----AAACA-TA--AAACGA---------------------AC---AAAA--------------------------------------------------CC--------GGA---------G------AAC----CCAAGCATA----------------------------------------------TTTCC-------------AG------------CT----GTTTCAAGAGCA-------AGGTTAAGA-----GCACCGCGATAAGA------------------------------CTGAACCC---AG-----------------------------ACCCAACG--TTT--CCAG--TT---GCTAG----CCT----------ACCCA--------------------------CATCT----- s droSim1.chr2R 18696763 295 + 19596830 TAGTTAAA-TTTATTATT-----TAAA-GATCGT------------------------------------GCGAGCGAC---------------GCAAATCCAATAACCC---------------------TAAAGCAATTTACCCAG------------TAAGCCAT-CAAC--AACA---TATGTTTA--------AA-A-----CACCACAAAAT-AGTAT-------CTACATACCAGAA-------------------------------ACata------a----------atatatatatattatttaGCGCAATATTA-CGAAATAAT-----AAACA-TA--AAACGA---------------------AC---AAAA--------------------------------------------------CC--------GGA---------G------AAC----CCAAGCATA----------------------------------------------TTTCC-------------AG------------CT----GTTTCAAGAGCA-------AGGTTAAGA-----GCAGCGCGATAAGA------------------------------CCGAACCC---AG-----------------------------ACCCAGCG--TTT--CCAG--TT---GCTAG----CCT----------GCCCA--------------------------CATCT----- s droSec1.super_23 116525 281 + 989336 TAGTTAAA-TTTATTATT-----TAAA-GATCGT------------------------------------GCAAGCGAC---------------GCAAATCCAATAACCC---------------------TAAAGCAATTTACCCAG------------TAAGCCAT-CAAC--AACA---TATGTTTA--------AA-A-----CACC----------------------ACATACCAGAA-------------------------------ACata------a----------atatatatatattatttaGCGCAATATTA-CGAAATAAT-----AAACA-TA--AAACGA---------------------AC---AAAA--------------------------------------------------CC--------GGA---------G------AAC----CCAAGCATA----------------------------------------------TTTCC-------------AG------------CG----GTTTCGAGAGCA-------AGGTTAAGA-----GCACCGCGATAAGA------------------------------CCGAACCC---AG-----------------------------ACCCAGCG--TTT--CCAG--TT---CCTAG----CCT----------ACCCA--------------------------CATCA----- s droYak3.chr2R 20205793 341 + 21139217 tagttaaa-tttattatt-----taattgatcGTGCAATGCGCcgaagc-------------aaagcaaagcaagcGAC---------------GTAAATCGAATAACCC---------------------TAAAGCAATTTACCCAG------TAAGCCTAAGCCAT----C--AACA---TATGTTTA--------AAGA-----CACCACAAAAT-AGTAT-------CTACATACcagaa-------------------------------acata------a------------atatatatattatttagcGCAATATTA-cgaaataat-----aaaca-ta--aaacga---------------------AC---AAAA-------------------------------------CACCAAACCT---CT--------GCG---------G------TTC----CCCAACACA----------------------------------------------TTTCC-------------AG------------CT----GCTTCAAGAGCA-------AGGTTAAGA-----GCACCGCGATAAGA------------------------------CCGAACCT---ACC---------------ACCAACCT-----accca--g--ttg--ccag--tt---gccag-ttacCT----------GCCCA--------------------------CATCT----- s droEre2.scaffold_4845 21603676 321 + 22589142 TAGTTAAA-TTTATTATT-----TAAATGATCGTGCAATGCGCCG-------------------AGCAAAGCAAGCGAC---------------GTAAATCCAATAACCC---------------------TAAAGCAATTTACCCAG------------TAAGCCAT----C--AACA---TATGTTTA--------AA-A-----CACCACAAAAT-AGTAT-------CTACATACCAGAA-------------------------------ACATA------A------------ATATATATATTATTTAGCGCAATATTA-CGAAATAAT-----AAACA-TA--AAACGA---------------------AC---AAAA--------------------------------------------------CC--------GGA---------G------AAC----CCAAACATA----------------------------------------------TTTCC-------------AG------------CT----GTTTCAAGAGCA-------AGGTTAAGA-----GCACCGCGATAAGA------------------------------CCGAACCC---AGC----------------------------TCCCA--G--TTT--CCAG--TT---GCTAGCCTACCCACAACCCACAACCCA--------------------------CATCT----- s droBia2.KB462602 796296 307 + 3129309 tagttaaa-tttattatt-----taatagatCGTGCACTGCGccgcagc-------------aaa-----acaaaagac---------------gtAAATCGAATAACCC---------------------TAAAGCAATTTACCGCA------------TAAGCCat----c--aaaa---tatgttta--------aa-aaac--aaccaCAAAAT-AGTAT-------CTATGCAGAagaa-------------------------------acata------c------------atatatatattatttagcgcaatatta-taaaataat-----aaaaa-gg--aaaacg---------------------at---aaaa-----------------------------------------aaaCCA---AC--------GGA---------G------AAC----CCCAACATG----------------------------------------------TTTCC-------------AG------------CT----GTTTCAAGAGCA-------AGGTTGAGA-----GCACCGCGATAAGC------------------------------CCGAGCCC---AG-----------------------------------AG--TTT--CTAG--TT---TCTAG----CCT----------ACACA------------------------------------ s droSuz1.KI419649 12041505 287 - 14502029 tagttaaa-tttattatt-----taatagatCGTGCACTGCGCcgaagc-------------aaa-----acaaaagac---------------gTAAATCGAATAACCC---------------------TAAAGCAATTTACCGAA------------TAAGCcat----caaaaaa---tatgttta--------aa-aaac--aaccacaaaat-agtat-------ctatacaaaag---------------------------------------------------------------------------------tta-taaaataat-----aaaaa-ga--aaaaag---------------------atacaaaaa-----------------------------------------aaaaaa---cc--------gga---------G------AAC----CCAAACATA----------------------------------------------TTTCC-------------AG------------CT----GTTTCAAGAGCA-------AGGTTAAGA-----GCACCGCGATAAGC------------------------------CCGAACCC---AAA----------------------------GTTTATAG--TTT--CTAG--TT---TCTAG----CCT----------ACACA------------------------------------ s droAna3.scaffold_13266 5710851 388 - 19884421 TAGTTAAATTTTATAACT-----TAGTTGGTCGTGCAATGCGCCC------------------------------------------------------CCCAATAACCA---------------------TAAAGCAATCTATTTCA------------TAAGCAAT----C--GACA---TATGTTTA--------AA-AAAC--AACCACAAAAT-AGTAT-------CTATACGATGAGt-------------------------------atata------a--------atatatatatatattatttaGCGCAATATTA-TAAAACAAT-----AAACA-AA--AATCAACAAAACACACATTATAATATTAC---AAAA-ATTACAAAACAA--CTACA-----GAA---GTGTAATGTAAAAGTG---CC---------CG---------A------AAC----CCAAACACACT-----------------------------------CATT-----TTTTC-------------AG------------CT----ATTTCAAGAGCA-------AGGTTAAGA-----GCGTTTAGATAAGCCACGAGCTACAAGCTGCAAGCCTCCAGACTCCGAACCCCAAAA-----------------------------CCCCAAAG--TTT--CTAGTTTT---TTTAG----CCT----------ACACA------------------------------------ s droBip2.KB464407 1959583 385 + 2915140 tagttaaattttattatt-----tagttaAACGTGCAACTCG------------------------------------------------------------AATAACCATAAACCATAAACCATAAAACGTAAAGCAATTTATTTCA------------TAAGCTAT----c--gaaa---tatgttta--------aa-aaac--aacCACAAAat-agtat-------ctatacgagaagt-------------------------------atataaatatga--------atatacatatatattatttagcgcaatatta-taaaacaat-----aaaca-ga--aaacaagaaaacaca------ATTATTAC---AAAA--------------------------------TGTAATGTAAAAGTA---CC---CCAATACC---------A------AAC----CCAAACACACT-----------------------------------gaat-----ttttc-------------ag------------at----atttcaAGAGCA-------AGGTTAAGA-----GTGTTTAGATAAGCCACAGGCTGCATGCC-----CCTCCAGACTCTAGACTCCAAAA-----------------------------GCCCAAagttttt--ctagtttt---tctaG----CCT----------ACaca------------------------------------ s droEug2.KB465067 600848 370 + 1515531 tagttaaa-tttattatt-----taatagaGCGTGCAATG-GCcgaagc-------------aaa-----acaaaagac---------------gTAAATCGAATAACCC---------------------TAAAGCAATTTACCTAC------------TAAGATAt----c--gaaa---tatgttta--------aa-aaac--aacCAC-AAAT-AGTGT-------CTATACAagagaa-------------------------------acata------t----------atatatatatattatttagcgcaatatta-taaaataat-----aaaca-gt--aaacgaaaa------------------ac---gaaaaactaaaaactaa--aaacaccGACGCA---GAATAATGTAAAAGTG---CCCGCCGAGCGGA---------G------AAC----CCAAACATA----------------------------------------------TTGCC-------------AG------------CC----GTTTCAAGAGCA-------AGGTCAAGA-----GCACCGCGATAACC------------------------------CCGAaccc---aga---------------gccagagccaga-gcccaGAG--TTT--CTAG--TT------AG----CCT----------ACACA------------------------------------ s droEle2.KB458573 521838 330 - 5320397 tagttaaa-tttattatt-----taatagatCGTGCAATGCGccgaagc-------------aaa-----acaaaagac---------------gtAAATCGAATAACCC---------------------TAAAGCAATTTACCTAA------------TAAGCcat----c--aaaa---tatgttta--------aa-aaac-aaaccacaaaat-agtat-------ctatacaaaaaga-------------------------------atata------aat------atatacatatatattatttagcgcaatatta-taaaataat-----aaaca-ga--aaacaa---------------------aa---aaaa--------------------tcgacgCA---ATATAATGTAAAAGTG---CC-----------------------------C----CCAAACATA----------------------------------------------TTTCC-------------AG------------CT----GTTTCAAGAGCA-------AGGTTAAGA-----GCACCGCGATAAGC------------------------------CTAAGCCC---CGA----------------------------ACCCAAAG--TTT--CTAG--TT------AG----CCT----------ACACA------------------------------------ s droKik2.KB459527 276307 343 - 1234237 tagttaaa-tttattatt-----taatggatCGTGCAATTCGCCGAAGC-----------------------------------------------------AATAACCC---------------------TAAAGCAATTTACCCCA------------TAAGCGAT----Cgagaaa---tatgttta--------aa-aaacaaaaccacaaAAT-AGTAT-------CTACACAagaagt-------------------------------atata------aatatatgaacatatatatatattatttagcgcaatatta-taaaataat-----aaaca-ga--aaacaa---------------------ca---aaaa----------------------------------------------t---cc---------------------------gAT----ACAGGAATG----------------------------------------------TATGCTGTACGATGTAAAAG------------CT----GTTTCAAGAGCA-------AGGTTAAGA-----GCATTGAGATAAGCCCCAAAAGCCCAGACCCCGAATCCCCAGCTCCGAACCC---AG-----------------------------GTCCAACG--TTT--CTAT--TA---CTTAG----CCT----------ACACA------------------------------------ s droTak2.KB461535 141416 304 - 669855 tagttaaa-tttattatt-----taatagacCGTGCACTGCGCCGCAGC-------------GAA-----ACAAAAGAC---------------GTAAATCGGATAACCC---------------------TAAAGCAATTTACCTAA------------TAAGCCat----c-aaaaa---tatgttta--------aa-aaac--aaccacaaaat-agtat-------ctatacaaagcaa-------------------------------atata------a------------atatatatattatttagcgcaatatta-taaaataat-----aaaaagga--aaacga---------------------aa---aaaa----------------------------------------------a---cc--------ggA---------G------AAC----CCAAACATA----------------------------------------------TTTCC-------------AG------------CT----GTTTCAAGAGCA-------AGGTTAAGA-----GCACTGCGATAAGC------------------------------CCGAACCC---AA-----------------------------------AG--TTT--CTAG--TT---TCTAG----CCT----------ACACA------------------------------------ s droRho2.KB449310 35584 335 - 65043 tagttaaa-tttattatt-----taatagatCGTGCAATGCGCcgaagc-------------aaa-----acaaaagac---------------gTAAATCGAATAACCC---------------------TAAAGCAATTTACCTAA------------TAAGCCat----c--aaaa---tatgttta--------aa-aaacg-aaccacaaaat-agtat-------ctatacaaaagaa-------------------------------atata------a------------atatatatattatttagcgcaatatta-taaaataat-----aaaca-ga--aaacga---------------------aa---aaaaaaacaaaaacaaaaccaaaaccgacGCA---GAATAATGTAAAAGTG---CC-----------------------------------CAAGCATA----------------------------------------------TTTCC-------------AG------------CT----GTTTCAAGAGCA-------AGGTTAAGA-----GCACCGCGATAAGC------------------------------CCGAACCC---AA-----------------------------------AG--TTT--CTAG--TT------AG----CCT----------ACACA------------------------------------ s droFic2.KB457177 81149 355 + 995874 TAGTTAAA-TTTACTATT-----TAATAGATCGTGCAATGCGCCCAAGC-------------AGA-----ACAAAAGAC---------------GTAAATCGAATAACCC---------------------TAAAGCAATTTACCGAA------------TAAGCCat----c--aaaa---tatgttta--------aa-aaacg-AACCACAAAAT-AGTAT-------CTATACGAATGAG-------------------------------ACata------aatatatgcatatatata-atattatttagcgcaatatta-t-aaataat-----aaaca-ta--aatcga---------------------aa---aaaC------------------AACGGATGCA---GCGTAATGTAAAAGtgaaccc--------aaa------ccca------aac----ccaaacacA----------------------------------------------CTTCC-------------AG------------CT----GTTTCAAGAGCA-------AGGTTAAGA-----GCACCGCGATAAGC------------------------------CCGAACCC---AAA---------------GTTT---------ATACATAG--TTT--CTAG--TT---TCTAG----CCT----------ACACA------------------------------------ s droPse3.chr3 1349310 424 - 19787792 TAGTTAAA-TTTACTATTTATGATAAATGCTCGTGCAATCCGCAGAAAC-------------CGA---------------------------------ATCGAATAACCC---------------------TAAAACAATTTATGTTG------------taagcgaaacaaa--acaa---tatgttta--------aa-aaaca-aaccacaaaat-agtatatctaccatatataaaaaga-------------------------------gtata------t------------gcatatattttactTAGCGCAATATTA-TACattaat-----aaaca-ac--aacaaa---------------------aa---aaca-----------tagtttaaacaaaagcacacaaataATGTAAAAGTG---CC--------AGATGCTGCCGCC------AGC----CCCAACACACA-----------------------------------GATT-----TTTCC-------------AG------------CTTCCAGTTTCAAGAGCA-------AGGTTAAGA-----GCGCTA-GATAAGA------------------------------CCCATTCc---ctacccccctcccaccaTGCCGGGGCCAGCTCTCAAAAG--TCT--GTAG--TT----ATGG----CCT----------ACACAGAATGTACAGTCCACAATCCACACTCCACCA----- s droPer1.super_34 538151 424 - 916997 TAGTTAAA-TTTACTATTTATGATAAATGCTCGTGCAATCCGCAGAAAC-------------CGA---------------------------------ATCGAATAACCC---------------------TAAAACAATTTATGTTG------------TAAGCGAAACAAA--ACAA---TATGTTTA--------AA-AAACA-AACCACAAAAT-AGTATATCTACCATATATAAAAAGA-------------------------------GTATA------T------------GCATATATTTTACTTAGCGCAATATTA-TACATTAAT-----AAACA-AC--AACAAA---------------------AA---AACA-----------TAGTTTAAACAAAAGCACACAAATAATGTAAAAGTG---CC--------AGATGCTGCCGCC------AGC----CCCAACACACA-----------------------------------GATT-----TTTCC-------------AG------------CTTCCAGTTTCAAGAGCA-------AGGTTAAGA-----GCGCTA-GATAAGA------------------------------CCCATTCC---CTACCCCCCTCCCACCATGCCGGGGACAGCTCTCAAAAG--TCT--GTAG--TT----ATGG----CCT----------ACACAGAATGTACAGTCCGCAATCCACACTCCACCA----- s droMir2.chr3 1390426 425 - 20862834 TAGTTAAA-TTTACTATTTATGATAAATGCTCGTGCAATCCGCAGAAAC-------------CGA---------------------------------ATCGAATAACAC---------------------TAAAACAATTTATGTTG------------taagcgaaacaaa--acaa---tatgttta--------aa-aaaca-aaccacaaaat-agtatatctaccatatataaaaaga-------------------------------gtata------t------------gcatatattttactTAGCGCAATATTA-TACattaat-----aaaca-acaaaaaaaa---------------------aa---aaca-----------taatttaaacaaaagcacacaaataATGTAAAAGTG---CC--------AGATGCTGCCGAC------AGC----CCCAACGCCGC-----------------------------------GATT-----TTTCC-------------AG------------CTTCCAGTTTCAAGAGCA-------AGGTTAAGA-----GCGCTA-GATAAGA------------------------------CCCATTCC---CTA-CCCCCTCCCACCATGCCGGGGACAGCTCTCAAAAG--TCT--GTAG--TT----ATGG----CCT----------ACACAGAATGTACAGTCCACAATCCACACTCCACCA----- s droWil2.CH963894 1308990 342 + 2843958 tagttaaa-tttattttg-----caaaacatttaac----------------------------------acaaaaaa------------------aaaacgaaaaagac---------------------aaaaacaattta---at------------taaatgtt----a--agta---caagaaga--------ag-atga--agttaatgaatgaatat-------ctattacaaatac-------------------------------acaaa------a----------atatatatattttatttagcgcaatatta-ttacagaaa-----aaaaa-aa--aacaag---------------------aa---ataa-------------------------------------tataaaaata---at--------aat---------a------aacaaaacagaaaaaa----------------------------------------------ttaaa-------------aa------------tt----atggtAAACACATAACTAGAGATAACGATTTACGTACTTGACCAAAA------------------------------CGTAAACC---AC-----------------------------ATCCAAAT--CCTGACcag--tttgatttgt----ttt----------tctca--------GTTTTTCAGTTAAGATTCAAGAG----- s droVir3.scaffold_12875 7351786 381 + 20611582 TAGTTAAA-TTAAT--TT-----TAAATGCTTGTGC-ATTAGCTAAACA-------------AAA-----ACGAAAAAC----------AAAATACTCTTTTAAAGACAC---------------------ACAACACAAATAACCACAAGTTATTAGGCTAAGCGAA----A--GACATA-TATGTTTA--------CA-AATC-------CAATAT-AGTAA-------CTATATAAATGCa----------------------------------ta------t------------atatatattttatttagcgcaatatta-taaattaat-----aaaaa-aC--GAGAGT---------------------AA---AGAA----------------------------------TATTATAGAATTA---CC--------CAACCTCCTCCTG---ATTATC----CTTAACGCAATTTC------CCCAAAAAAAATGGGCCTCTAACTA-GTTTCACAGTTTTC-------------AA-------TTTTCAA----TTTTCAAGAGCA-------AGGTTAAGA-----GC---------TTT------------------------------ACATAACC---AGCCA------------------CACGAGCTGC---CAG--TTT--CTTG--TT------AA----CCT----------ACACG-------------------------------C---- s droMoj3.scaffold_6496 26146972 402 + 26866924 TAGTGCAA-TTAAT--TT-----TAGATGTT----------aaaaaaaa-------------gaa-----acaaaaaac-----aacaaaaaaaaaacatttaaaaa-aa---------------------aaaaaaCAATTAACAAAACGTTTTTAGCCTAAGTAAA----A--AATATATTATGTTTA--------AA-AATC-------AAATAT-AGTAA-------CTATACGAATGCACGCATGCatatatacatataaacatatatatgtgtg------t------------atatatatatTATTTAGCTCAATATTA-CAAAATAAT--AAAAAAAA-AC--AAACGT---------------------AA---AGAA----------------------------------TATTTGAAAACGA---CG--------CAAATAACTGCCGCAACTTGTG----CTCAAAG----------------AGAAGAAATGAAGCTTTTCCAACGTTTCCCAGTTTCC-------------AATTTGGAGTTTTGGC----TTTTCAAGATCA-------AGGTGAAGA-----TC----------TT------------------------------ACATAACC---A------------------------------GC---TAG--CTT--CTTG--TT------AG----CCT----------ACACG-------------------------------C---- s droAlb1.JH854640 309194 340 + 406291 tagttaaa-ttaat--tt-----aaaagctttgtGCAATTAGCTAAAAA-------------gag-----caaacatattttttaaatgaaatatatcatataaagaaaa---------------------ataacacacaaattaaa----tgataagtTAAGtgaa-tata--cacata-tatgttta---------a-actc-------caatat-agtaa-------ctatacaaatgca------------------------tatatacacata------a------------atatatattttatttagcgcaatattattataataat-----aaaca-ga--aaacat---------------------AA---ATCA----------------------------------T-----------A---CG--------CGACCGATCCTCG----TTCTC----CT--------------------------------------------GCCAGCTACTCTCG-------------GA------------AT----CGTTCAAGATCA-------AGGTTAAGA-----GC---------TGT------------------------------ACACATCA---A------------------------------GT--ATAG--TTT--CTTG--TT------AA----CCT----------ACTCT-------------------------------CAAAA s droGri2.scaffold_15245 901156 432 + 18325388 TAGTTAAA-TTAAT--GT-----ATAATGCTTGTGCAATTAGCTaaaaacaaaagcaaaaacaaa-----acaaaaaac---------aaCAAATTACTTTTAAAAAGAC---------------------ACAAAAAATAACACGAAATTTTCCTAGGCTAAGCGAA----A--GACATATTATGTTTAAAACAAAAAA-AAAA-------CAATAT-AGTAA-------CTATATAAATGCa--------------------------tatatacata------t------------ataaatattttatttagcgcaatatta-taaattaataaaaaCAAAA-AC--AAGAAT---------------------GA---AAAA----------------------------------CTCTTG------A---CT--------CGA---------G---AGTATC----CTGAACACAATTTACATCAGCCCAACAATTAAGTGCTGCCAACTA-GTTTGAGAGTTTTC-------------AG----ACTTTCCAGC----TTTTCAAGAGCA-------AGGTTAAGA-----GC-------TTTTT------------------------------ACATAACC---AGCCAGCAGTCAGCAGCCAGCCGCACGAGCTGC---CAG--TTT--CTTG--TT------AA----CCT----------ACACG-------------------------------C---- a score=-26549.000000 s dm6.chr2R 24350339 4 + 25286936 ----CA------AT s droSim1.chr2R 18697058 4 + 19596830 ----CA------AT s droSec1.super_23 116806 4 + 989336 ----CA------AT s droYak3.chr2R 20206134 7 + 21139217 ----CA---TCTAG s droEre2.scaffold_4845 21603997 7 + 22589142 ----CA---TCGAG s droPse3.chr3 1349734 2 - 19787792 ----CA-------- s droPer1.super_34 538575 2 - 916997 ----CA-------- s droMir2.chr3 1390851 2 - 20862834 ----CA-------- s droWil2.CH963894 1309332 10 + 2843958 ----CAAGGTGAAG s droMoj3.scaffold_6496 26147378 4 + 26866924 CCAT---------- s droGri2.scaffold_15245 901588 3 + 18325388 -CAA---------- a score=-95962.000000 s dm6.chr2R 24350343 12 + 25286936 C--CCATC----------------------T--A------GCAG s droSim1.chr2R 18697062 12 + 19596830 C--CCATC----------------------T--A------GCAG s droSec1.super_23 116810 12 + 989336 C--CCATG----------------------T--A------GCAG s droYak3.chr2R 20206141 14 + 21139217 CATCTATC----------------------T--A------GTAA s droEre2.scaffold_4845 21604004 10 + 22589142 C----ATC----------------------T--A------GCAA s droBia2.KB462602 796603 11 + 3129309 ---CTAGC----------------------C--T------CTAA s droSuz1.KI419649 12041792 11 - 14502029 ---CTAGC----------------------C--A------CTAA s droAna3.scaffold_13266 5711239 10 - 19884421 ---CTGAA-------------------------A------ATAA s droBip2.KB464407 1959968 10 + 2915140 ---ctgaa-------------------------a------ataa s droEug2.KB465067 601218 10 + 1515531 ---C-GGC----------------------T--G------GTAA s droEle2.KB458573 522168 10 - 5320397 ---C-GGC----------------------C--A------gtaa s droKik2.KB459527 276650 13 - 1234237 ---CCGCC----------------------GCAG------ATAT s droTak2.KB461535 141720 11 - 669855 ---CTATC----------------------C--A------CTAA s droRho2.KB449310 35919 10 - 65043 ---CGGTC-------------------------A------GTAA s droFic2.KB457177 81504 14 + 995874 ---CGGTCGGT-------------------C--T------CCAA s droPse3.chr3 1349736 14 - 19787792 ---CAATC----------------------C--A---CGCGTAA s droPer1.super_34 538577 14 - 916997 ---CAATC----------------------C--A---CGCGTAA s droMir2.chr3 1390853 14 - 20862834 ---CAATC----------------------C--A---CGCGTAA s droWil2.CH963894 1309342 18 + 2843958 C--CTACA----------------------C--ATGGCATACAG s droMoj3.scaffold_6496 26147382 27 + 26866924 ---------CTCAAAGATACTATTCAAAATG--A------AAAG s droAlb1.JH854640 309534 6 + 406291 ------------------------------G--A------gcag a score=-14993.000000 s dm6.chr2R 24350355 2 + 25286936 -T-----A s droSim1.chr2R 18697074 2 + 19596830 -T-----A s droSec1.super_23 116822 2 + 989336 -T-----A s droYak3.chr2R 20206155 7 + 21139217 -TAATCCA s droEre2.scaffold_4845 21604014 7 + 22589142 -TAATCCA s droBia2.KB462602 796614 2 + 3129309 -T-----A s droSuz1.KI419649 12041803 2 - 14502029 -T-----A s droAna3.scaffold_13266 5711249 2 - 19884421 -T-----A s droBip2.KB464407 1959978 2 + 2915140 -t-----a s droEug2.KB465067 601228 2 + 1515531 -T-----A s droEle2.KB458573 522178 2 - 5320397 -t-----a s droKik2.KB459527 276663 2 - 1234237 -T-----A s droTak2.KB461535 141731 2 - 669855 -T-----A s droRho2.KB449310 35929 2 - 65043 -T-----A s droFic2.KB457177 81518 2 + 995874 -T-----A s droPse3.chr3 1349750 2 - 19787792 -T-----A s droPer1.super_34 538591 2 - 916997 -T-----A s droMir2.chr3 1390867 2 - 20862834 -T-----A s droWil2.CH963894 1309360 2 + 2843958 -T-----G s droVir3.scaffold_12875 7352197 2 + 20611582 TT------ s droMoj3.scaffold_6496 26147419 2 + 26866924 TG------ s droAlb1.JH854640 309550 2 + 406291 tt------ a score=579962.000000 s dm6.chr2R 24350357 312 + 25286936 ATCCC---ACT-G--GCGAGTGG---GTCG---------------------------------------------------------GCTCTCCA--TGAATGAATT-------------------------------T----C-TG---ATTTCGATA-------------------CGTTCG-----------------------------TTTC------T--AT-------------------------TTTCC--TTCGATG----------TTG-----C-AAAGA---GCTTCCGCTT-----------CTTCCA------------------------------------------------------C----------------------------------------------TAGAGA------CCCCAATA---AAAGAG----TTTTGGC----------------------TGCGG-----------G------GGCTC---------------------TGTGACGTCA-T------GAC-----AAC-------------------CA--TGC---TGG---CGACGAGTTCATAAATCGATCAGAG---CCACCACTG-------G----------------------------------------------------------------------------------C-TCGTCATGCACCACCGGC---------------CAAGTCAG--------TCGG-------------------TC--------------------------------------------------CCCTCA--CTTT-------------------C-------CT-------------------------C--CCGGCTTGGCATGCAAATCGCGTTTC-TGG-CTCG---TAC-TTTTCAATG----------CCA-----------------AAAGC--------------------------------TTGGCGTAGGC s droSim1.chr2R 18697076 316 + 19596830 ATCCC---ACT-G--GCGAGTGG---GTCG---------------------------------------------------------GCTCTCCA--TGAATGAATT-------------------------------T----C-TG---ATTTCGATACGT---------------TCGTTCG-----------------------------TTTC------T--GT-------------------------TTTCC--TTCGATG----------TTG-----C-AAAGA---GCTTCCGCTT-----------CTTCCA------------------------------------------------------C----------------------------------------------TAGAGA------CCCCAATA---ACAGAG----TTTTGGC----------------------TGCGG-----------G------GGCTC---------------------TGTGACGTCA-T------GAC-----AAC-------------------CA--TGC---TGG---CGACGAGTTCATAAATCGATCAGAG---CCACCACTG-------G----------------------------------------------------------------------------------C-TCGTCATGCACCACCGGC---------------CAAGTCAG--------TCGG-------------------TC--------------------------------------------------CCCTCG--CTTT-------------------C-------CT-------------------------C--CCGGCTTGGCATGCAAATCGCGTTTC-TGG-CTCG---TAC-TTTTCAATG----------CCA-----------------AAAGC--------------------------------TTGGCGTAGGC s droSec1.super_23 116824 316 + 989336 ATCCC---ACT-G--GCGAGTGG---GTCG---------------------------------------------------------GCCTTCCA--TGAATGAATT-------------------------------T----C-TG---ATTTCGATACGT---------------TCGTTCG-----------------------------TTTC------T--GT-------------------------TTTCC--TTCGATG----------TTG-----C-AAAGA---GCTTCCGCTT-----------CTTACA------------------------------------------------------C----------------------------------------------TAGAGA------CCCCAATA---AAAGAG----TTTTGGC----------------------TGCGG-----------G------GTCTC---------------------TGTGACGTCA-T------GAC-----AAC-------------------CA--TGC---TGG---CGACGAGTTCATAAATCGATCAGAG---CCACCACTG-------G----------------------------------------------------------------------------------C-TCGTCATGCACCACCGGC---------------CAAGTCAG--------TCGG-------------------TC--------------------------------------------------CCCTCG--CTTT-------------------C-------CT-------------------------C--CCGGCTTGGCATGCAAATCGCGTTTC-TGG-CTCG---TAC-TTTTCAATG----------CCA-----------------AAAGC--------------------------------TTGGCGTAGGC s droYak3.chr2R 20206162 328 + 21139217 ATCCC---ACT-G--GCGAGTGGGTCGTCG---------------------------------------------------------GCTCTCCA--TGAATGAATT-------------------------------CGTAAC-TG---AATT---TC-------------------TGTTCG-----------------------------CTTC------G--CT-------------------------TTTCC--TTCGATG----------TTG-----C-AAAGA---GCTTCCGCTTTGTGGCT----------------------------------------------------------------------------------------------------------------------------TCCAATA---ACAGAG----TTTCGGC----------------------TGCGG-----------G------GGCTC---------------------TGTGACGTCA-T------GACAAGCAAAC-------------------CA--TGC---TGG---CGACGAGTTCATAAATCGATCAGAGCCACCACCACTG-------G----------------------------------------------------------------------------------C-TCGTCATGCACCACCGGC---------------caagtcag--------tcag-------------------tcagttcgCAGAT---------------------------------------CCCTCG--CTTT-------------------C-------CT-------------------------C--TCCGCTTGGCATGCAAATCGCGTTTC-TGG-CTCG---TAC-TTTTCAATG----------CCA-----------------AAAGC--------------------------------TTGGCGTAGGC s droEre2.scaffold_4845 21604021 335 + 22589142 ATCCC---ACT-G--GCGAGTGG---GTCG---------------------------------------------------------GCTCTCCA--TGAATGAATT-------------------------------T----C-TG---ATCTCGATA-------------------CGTTCG-----------------------------TTTCCATACGT--GT-------------------------TTTAC--TTCGATG----------TTG-----C-AAAGA---GCTTCCGCTTTGTAGCTGTAGCTTCCA------------------------------------------------------C----------------------------------------------TAGAGA------CTCCAATA---AAAGAG----TTTTGGC----------------------TGCGG-----------GGGCTCCGGCTC---------------------TGTGACGTCA-T------GAC-----AAC-------------------CA--TGC---TGG---CGACGAGTTCATAAATCGATCAGAG---CCACCACTG-------G----------------------------------------------------------------------------------C-TCGTCATGCACCACCGGC---------------CCAGTCAG--------TCGG-------------------TC--------------------------------------------------CCCTCG--CTTT-------------------C-------CT-------------------------C--CCGGCTTGGCATGCAAATCGCGTTTC-TGG-CTCG---TAC-TTTTCAATG----------CCA-----------------AAAGC--------------------------------TTGGCGTAGGC s droBia2.KB462602 796616 344 + 3129309 ATCCCAAAACT-G--GCGAGTGG---GTCG---------------------------------------------------------GCTCTCCA--TGAATGAATT-------------------------------T----G-TG---ATGTCGTTATAT---------------CTGCGTG-----------------------------TTTC------T--GT-------------------------TTTCC-TTTCGCTG----------TTG-----C-AAAGA---GCTTCCGCTT-----------CTCCCC------------------------------------------------------A----------------------------------------------TAGAGACCCGACCCCGAATG---AAAGAG---TTTTTGGC----------------------CGCGG-----------G------GGCAC---------------------TGTGACGTCA-T------GAC-----AAC-------------------AA--TGC---TGG---CGACGAGTTCATAAATCGATCAGAG---CCACCACTG-------A-----------------------------------------------------A------------T---------------C-CCGTCATGCACCAacag----------------ccagtcag--------tcagtgagCGAGT----------TC--------------------------------------------------CCCTCG--CTTT-------------------TCCGCCG-CT-------------------------T--TCgacttggcatgcaaatcGCGTTTG-TGC-CTCG---TAC-TTTTCAATG----------CCA-----------------AAAGC---T----------------------------TTGGCGTAGGC s droSuz1.KI419649 12041805 341 - 14502029 ATCCCAAAACT-G--GCGAGTGG---GTCG---------------------------------------------------------GCTCTCCA--TGAATGAATT-------------------------------T----G-TG---ATTTCGATATAT---------------CTGTGTG-----------------------------TTTC------T--GT-------------------------TTTCC-TTTCGATG----------TTG-----C-AAAGA---GCTTCCGCTT-----------CTCCCC------------------------------------------------------A----------------------------------------------TAGAGACCCGACCCCGAATG---AAAGAG--TTTTTTGGC----------------------CGCGG-----------G------GGC-T---------------------TGTGACGTCA-T------GAC-----AAC-------------------AA--TGC---TGG---CGACGAGTTCATAAATCGATCAGAG---CCACCATTG-------A-----------------------------------------------------A------------T---------------C-TCGTCATGCACCAA--------------------CAGTCAG--------TCAGTGAGTGAGT----------TC--------------------------------------------------CCCTCG--GTTT-------------------TCTCTCGCCT-------------------------T--TCGACTTGGCATGCAAATCGCGTTTG-TGG-CTCG---TAC-TTTTCAATG----------CCA-----------------AAAGC---T----------------------------TTGGCGTAGGC s droAna3.scaffold_13266 5711251 340 - 19884421 ATCTTTCAACTCG--GCGAGTGG---GCCGATCTACT-----------------------------------GCTGCTGCTGCTGCTACTCTCCA--TGAATGAA-----------------------------------------------TTCGAAG-------------------CATTCG-----------------------------TTTC------T--GT-------------------------TTTCCTTTTCAATGTTT-------TGGAAAGAA-AAAGA---GCTTCCGCTT----------------------------------------------------------------------------------------------------------------------------------CGCTGTGA---AATGCT----ATTTGGC----------------------TGCGG-----------G------GGCTTCTTT--TGGCTGGGAGGCCTGTGTGACGTCA-T------GAC-----AAC-------------------AA--AGC---CAA---CGACGAGTTCATAAATCGATCAGAG---CCACCAGAGCCACAGAG-----------------------------------------------------C------------T---------------C-TCGTCATGCACCAC-------------------CAAGTCAG--------TCA------------------------------------------------------------------------------------------------------------------------------------------C--TCCGCTTGGCATGCAAATCGCGTTTGGTGG-CTCG---TAC-TTTTCAATG----------CCA-----------------CGATACTTT----------------------------TTGGCGTAGGC s droBip2.KB464407 1959980 362 + 2915140 atctttTAACT-G--ACGAGTGG---GCCGACCTA-------------------------------------------------GCTGCTCTCCA--tgaatgaata-------------------------------t----a-tt---tttttgaag-------------------ca---------------------------------tTTC------G--GT-------------------------TTTTCATTCCTATATGT-------TTG-----T-AAAGA---GCTTCCGCTT----------------------------------------------------------------------------------------------------------------------------------CGATGTGA---AATGCT----ATTCGGC----------------------TGCGG-----------G------GGCTTCTTT------TGGGAGGCCCAAGTGACGTCA-T------GAC-----AAC-------------------AATGAAC---TGG---CGACCAGTTCATAAATCGATCAGAG---CCACCATTG-------A-----------------------------------------------------C------------T---------------C-TCGTCATGCACCAC-------------------caagtcag--------tcag-------------------tcagccagccagtcagtcagt---ccagcc----------------aTCCAAACCCCC--TTCC-------------------C-------AT-------------------------C--TCGACTTGGCATGCAAATCGCGTTTTGTGG-CTCG---TAC-TTTTCAATG----------CCA-----------------CGAATCTTT----------------------------TTGGCGTAGGC s droEug2.KB465067 601230 344 + 1515531 ATCCA--AGCT-G--GCGAGTGG---GTCG---------------------------------------------------------GCTCTCCA--TGAATGAATT-------------------------------T----C-TG---ATTTCGATA----------------------------------------------------------------T--GT-------------------------TTTCC-TTTCGATG----------TTG-----C-AAAGA---GCTTCCGCTT-----------CTCCCA-----------------------------------------------------------------------------------------------------TAGAGAC-----CCCGAATG---AAAGAG----TTTTGGC----------------------TGCGG-----------G------GGCTT-------CACCCGGGGGCTT-TGTGACGTCA-T------GAC-----AAC-------------------AA--TGC---TGG---CGACGAGTTCATAAATCGATCAGAG---CCACCATTG-------A-----------------------------------------------------A------------T---------------C-TCGTCATGCACCaacagccagt--------cagccagtcag--------tcagtttgCGAGTC--TGCGAGCTC--------------------------------------------------CCCTCG--GTTT-------------------T-------CT-------------------------C--CTGGCTTGGCATGCAAATCGCGTTTG-TGG-CTCG---TAC-TTTTCAATG----------CCA-----------------AAAGC---T----------------------------TTGGCGTAGGC s droEle2.KB458573 522180 399 - 5320397 aactt-aaact-g--GCGAGTGG---GCTG---------------------------------------------CCTTCCTCGGCGGCTCTCCA--Tgaatgaatt-------------------------------t----g-ta---ttttcg-ta-------------------ttttcgagcatatatgta----------------ttttt------t--gt-------------------------tttcc-tttcgaTATG--------TTG-----C-AAAGA---GCTTCCGCTT-----------CTCCCA-----------------------------------------------------------------------------------------------------TAGAGAC-----CCCGAATATCCAAAAAG----TTTCGTC----------------------TGCGG-----------G------GGCTT---------------------TGTGACGTCA-T------GAC-----AAC-------------------AA--TGC---TGGCGACGACGAGTTCATAAATCGATCAGAG---CCACCATTG-------A-----------------------------------------------------A------------T---------------C-TCGTCATGCACCAacag----------------ccagtcag--------tcag-------------------tcagttagtcagtcagtcagctagtcagCTTGTGAGTTTGTTGTGAGTTTGCCCCTCG--ATTT-------------------T-------CT-------------------------C--CTGGCTTGGCATGCAAATCGCGTTTG-TGG-CTCG---TAC-TTTTCAATG----------CCA-----------------AAAGC---T----------------------------TCGGCGTAGGC s droKik2.KB459527 276665 355 - 1234237 GACGA--AATC-T--GCGAGTGG---GCTG------------------------------------------------------CAACTCCTCTA--TGAATGaatt-------------------------------t----c-tg---tgtttt----------------------tattcgagcatatatatatatttttttgtcgaTCTTTTC------TGCGT-------------------------TTTCC-TCTCGATGTT--------TTG-----T-AAAGA---GCTTCCGCTT-----------CCACAG------------------------------------------------------C----------------------------------------------CGTAGA------GCTGACGG---AGTCCG----TCTTGTG----------------------TGTGG-----------G------GCC-----------------------TGTGACGCC----------AC--------------------------------------GG---CGACGAGTTCATAAATCGATCAGAG---CCACCAGGG-------GGA---------------------------------------------------C------------T---------------C-TCGTCATGCACCAACAGccat------------tcagtcag--------tcag-------------------tcggttggct------------------------------------------ccctct--tcct-------------------c----cgccG-------------------------C--TTGGCTTGGCATGCAAATCGCGTTTTGTGG-CTCG---TAC-TTTTCAATG----------CCA-----------------AAAGC-CTC----------------------------TCGGCGtaggc s droTak2.KB461535 141733 353 - 669855 ATCCA-AATCT-A--GCGAGTGG---GTCG---------------------------------------------------------GCTCTCCA--TGAATGAATT-------------------------------T----C-AG---ATTTCGTTACAT--------------GTTGTGTA-----------------------------TTTC------T--GT-------------------------TTTCC-TTTCGATG----------TTG-----C-AAAGA---GCTTCCGCTT-----------CTCCCA--------GCCG------------------------------------------A----------------------------------------------TAGAG-------CCCGaatg---aaaaag---tttttggC----------------------TGCGG-----------G------GGCTT---------------------TGTGACGTCA-T------GAC-----AAC-------------------AA--TGC---TGG---CGACGAGTTCATAAATCGATCAGAG---CCACCATTG-------A-----------------------------------------------------A------------T---------------C-TCGTCATGCACCAACAGCCAAG--------tcgtcagtcag--------tcagtttcAGCTTCAGTTCCAGTTC--------------------------------------------------CCCTCG--CTTT-------------------T-------CT-------------------------C--CCGACTTGGCATGCAAATCGCGTTTG-TGG-CTCG---TAC-TTTTCAATG----------CCA-----------------AAAGC---T----------------------------TTGGCGTAGGC s droRho2.KB449310 35931 381 - 65043 GACTCAAAACT-G--GCGAGTGG---GCTG------------------------------------------------------------CTCCA--Tgaatgaatt-------------------------------t----a-ta---ttttcgagC------------------ATATATG-----------------------------TTTC------T--GT-------------------------TTTCC-TTTCGATATG--------TTG-----C-AAAGAGTTGCTTCCGCTT-----------CTCCCA-----------------------------------------------------------------------------------------------------TAGAGAC-----GCcgcata---aaaaag--tattttggc----------------------TGCGG-----------G------GGCTT------CCACTCGGGGGCTT-TGTGACGTCA-T------GAC-----AAC-------------------AA--TGCAAAAGG---CGACGAGTTCATAAATCGATCAGAG---CCACCATTG-------A-----------------------------------------------------A------------T---------------C-TCGTCATGCACCAAcagccag------------tcagtcag--------tcag-------------------tcagttagtcagCTTGTGAGTTTCAGAGTTTGTGAGTTC-------------CCCTCG--GTTT-------------------T-------CT-------------------------C--CTGACTTGGCATGCAAATCGCGTTTG-TGG-CTCG---TAC-TTTTCAATG----------CCA-----------------AAAGC---T----------------------------TTGGCGTAGGC s droFic2.KB457177 81520 408 + 995874 ATCCC-AAGCT-G--GCGAGTGG---GCCG------------------------------------------------CGCTCCTCGGCTCTCCA--TGAAtgaatt-------------------------------t----g-tgtttttttcgagC------------------ACATatg-----------------------------tttc------t--gt-------------------------tttcc-tttcgATG----------TTG-----C-AAAGA---GCTTCCGCTT-----------CTCCCA-----------------------------------------------------------------------------------------------------TGGAGAC-----CCCgatca---aatgaaatgttttcgGC----------------------TGCGG-----------G------GGCTTCAGCCGTTGCT----------TGTGACGTCA-T------GAC-----AAC-------------------AA--TGC---CCG---CGACGAGTTCATAAATCGATCAGAG---CCACCACTG-------A-----------------------------------------------------A------------T---------------C-TCGTCATGCACCAAcagtcagtccaaccaaccatcagtcag--------tcat-------------------tcagtcagtcagttagtcagttgGCCAGCTCGCGAGTTAGTGAGTT------CCCTCGGCTTTT-------------------T-------CT-------------------------C--CTGGCTTGGCATGCAAATCGCGTTTG-CGG-CTCG---TAC-TTTTCAATG----------CCA-----------------AAAGC--TT----------------------------TTGGCGTAGGC s droPse3.chr3 1349752 450 - 19787792 ATCGCCGAATC-GGAGCGAGTGG---GCAGCccctcttctctgctctgccatgcgctgctt--------------------tgctctgctccctG--TGAATGAATT-------------------------------T----C-TG---TTTTCGAGCATA--------------TGcacata-----------------------------tttc------t--gt-------------------------ttttcctttcAACATTCGGTTGGGCTG-----T-AAAGA---GCTTCCGCTT-----------CCACAA-----------------------------------------------------------------------------------------------------TAGA--------CCTCAGCC---AAAGCA----CTGCTGC-----------------------GCGG-----------G------GGCTT--------CTTTGGGGGCCC-TGTGACGTCA-TAAGACAGAC-----AGC-----------------GGAA--TAC---GGG---CGACGAGTTCATAAATCGATCAGAG---CACCCATTG-------ACTCTCTTGTGTGTCTTGTGTGTCGTCTGGCCCG--------------------G------------T-----CTCGTCTCGGC-TCGTCATGCACCAACAGGCC-------------TCAG--AT--------CCGA-------------------Tc--------------------------------------------------cccctg--tccc-------------------c-------ctcccccctgt-cttggcttggcttggc--ttggcttggcatGCAAATCGCGTTTC-T----------TAC-TTTTCAATG----------CCA------------------AAGC---T----------------------------Atggcccgggc s droPer1.super_34 538593 479 - 916997 ATCGCCGAATC-GGAGCGAGTGG---GCAGCCCctcttctctgctctgccatgcgctgctttgccgtgcgctgctctgctctgctctgctcCCTG--TGAATGAATT-------------------------------T----C-TG---TTTTCGAGCATA--------------TGCACATA-----------------------------TTTC------T--GT-------------------------TTTTCCTTTCAACATTCGGTTGGGCTG-----T-AAAGA---GCTTCCGCTT-----------CCACAA-----------------------------------------------------------------------------------------------------TAGA--------CCTCAGCC---AAAGCA----CTGCTGC-----------------------GCGG-----------G------GGCTT--------CTTTGGGGGCCC-TGTGACGTCA-TAAGACAGAC-----AGC-----------------GGAA--TAC---GGG---CGACGAGTTCATAAATCGATCAGAG---CACCCATTG-------ACTCTCTTGTGTGTCTTGTGTGTCGTCTGGCCCGgtctcgtc----------tcg------------t-----ctcgtctcggc-tcgtcATGCACCAACAGGCC-------------TCAG--AT--------CCGA-------------------TC--------------------------------------------------CCCTT---TCCC-------------------C-------CTCACCACTGT-cttggcttggcttggc--ttggcttggcATGCAAATCGCGTTTC-T----------TAC-TTTTCAATG----------CCA------------------AAGC---T----------------------------ATGGCCCGGGC s droMir2.chr3 1390869 484 - 20862834 ATCGCCGAATC-GGAGCGAGTGG---GCAGCccctcttctctgctctgctttgccgtgcgctgccgtgcgctgctctgctctactctgctctctg--tgaatgaatt-------------------------------t----c-tg---ttttcgagcata--------------tgcacata-----------------------------tttc------t--gt-------------------------ttttcctttcaacATTCGGTTGGGCTG-----T-AAAGA---GCTTCCGCTT-----------CCACAA-----------------------------------------------------------------------------------------------------TAGA--------CCTCAGCC---AAAGCA----CTGCTGC-----------------------GCGG-----------G------GGCTT--------CTTTGGGGCCCC-TGTGACGTCA-TAAGACAGAC-----AGC-----------------GGAA--TAC---GGG---CGACGAGTTCATAAATCGATCAGAG---CACCCATTG-------Actctcttgtgggtcttgtgtgtcgtctggcccggtctcgtc----------tcg------------tctcggctcgtctcggc-tcgtcATGCACCAACAGGCC-------------TCAG--AT--------CCGA-------------------TC--------------------------------------------------CCCTT---TCCC-------------------C-------CTCACCACtgt-cttggcttggcttggc--ttggcttggcatGCAAATCGCGTTTC-T----------TAC-TTTTCAATG----------CCA------------------AAGC---T----------------------------ATGGCccgggc s droWil2.CH963894 1309362 372 + 2843958 aaaaa--aaTC-A--ATGCGTGG---GTTG---------------------------------------------------TCCATTGCTGtt----tgaatgaatt-------------------------------t----t-ca---aatt-----------------------------------------------------------tcgt------t--gt-------------------------tgtagttgtcgttg----------ttg-----taaAAGA---GCTTCCGCTA-----------TACTGG-----------------------------------------------------------------------------------------------------------------CCTATTGA---CAATTG----GTTTATC----------------------TAGGT-----------G------GGTTT---------------------TCTGTTGT----------GAC-----GTC--------------------A--CAC---TGG---CGTCGAGTTCATAAATCGATCAG-G---CAACAATtg-------c--cccatcatcatcatcaacatcaacaacattgatgttgttgttgctgtcgtcg------------t---------------cgtcgtcatgcACCATCAG----------------CTGCTTGG--------TCtg-------------------tc--------------------------------------------------ttttct--ctct-------------------c-------tctatctctgtgcTCAGACACAGTTGCC--TCCAGTTGGCATGCAAATCGCGTTTT-------CT---TACTTTTTCAATG----------CCA-----------------GAGTC---G----------------------------GAGTCGGAGTC s droVir3.scaffold_12875 7352199 432 + 20611582 ATCCA---GCT-G--GCGAGTGG---GCAG---------------------------------------------------------GCCCAGCAGCTGAATGAATTTGTATCTTTAGCCA-TTGGCTTTGGC-TGTAT----C-TG---TATCTGCATATA--------------TACGTTTG-----------------------------TATC------T--GTATCTGCTGA----------------GTTTC--ATCATTGCG--------TTG-----T-AAA-A---GCTTCCGCTT-----------GTGCTAGGTGAAGTGCCC-----------------------------------------------------------------ACTCGATG------GGCTTG----CGGAGCA-----CTGAGCGG---GGTGCT----TATGAACAATAGACTCGCTGATAACTGCATGTGGGTTTTGCGTGTG------ACGCT---------------------TGTGACGTCA-T------GA-----------------------------------------------CGAGTTCATAAATCGATCAA-----CAACAATTG-------GCTCCTCGAAGA------------------------------------------G------------T---------------C-AAGTCATGCATCAGCAG----------------TTAGCTAA-------CCCAG-------------------CT--------------------------------------------------CCGCTG--TCCC-------------------G-------CT-------------------------C--CGATCTTGGCATGCAAATCG----CG-GGCTCGCG---GCA-TTTTCAATg----------ccaggccaggccgggccgggccagC---TGCCA------------------------GTCGTGTAGGC s droMoj3.scaffold_6496 26147421 478 + 26866924 ATGCA---GCC-G--GCGAGTGG---GCAG---------------------------------------------------------GC---GCAGCTGAGTGAATTTGTATCTGTAACTGCTTGACTTTTACTTGTAT----C-TG---TATCtgtatgtatgtgtgtgagt--gtgtgtgtg-----------------------------tatc------t--gtgtTTGCATACGCTT-----------GTGCT--ATC--TGCG--------CTG-----T-TAA-A---GCTTCCGCTT-----------GTGCTATTAAAAGTGCCTGA---AGCGCTCTGCC--------------------------CGCTACGTCCGtcgactcg----actcgacgcggctcggctcgacAATAGAGC------CTCTGATA---GCCGCA----TGTAGGT----------------------TGTGC---------GTG------CTGCT---------------------TGTGACGTCA-T------GAG----------------------------C--GAC---TCG---CATCGAGTTCATAAATCGATCAA-----CAGCAATTG-------GCTCGTCCAAGA------------------------------------------G------------C---------------C-AAGTCATGCATCAGCAG----------------CTG-------------CCCT-------------------CT--------------------------------------------------CCGGCC--CCTC-------------------G-------CT-------------------------T--CCCACTTGGCATGCAAATCGCGCTCG-CACTCGCGCGCGTT-TTTTCAATgccagaccagaccaggccaggccaggccaagccagC---TGGCA------------------------GTCGCGTAGGC s droAlb1.JH854640 309552 482 + 406291 gcgca---tac-g--acgaGTGG---GCTG---------------------------------------------------------TCCT-----CTGAATGAATTTGAATCTTCCGCTTTTccgctgtatc-tgtat----cttg---tatctgAATCTGCAtctgtaaataaatatctacG-----------------------------TAGC------T--GAATTTGCCTCTGCTTGCTCATAGAGAGTTTC--GTCATTGCG--------TTG-----T-AAA-A---GCTTCCGCTT-----------GCCCCATTTGAAGTGTGCCAGAgggtgttgtgttg-------------------------tgttgtgctctgTGGCGAGAGGCACACAA------------------TAGAGT------CGATGATA---ACTGCA----TGTGGGT----------------------TTTGC-------GTGTG------ACGCT---------------------CGTGACGTCACT------GAG-----CACTCG--------------CAAC--GAG---CAG---CAGCGAGTTCATAAATCGATCAG-----CAACAATTG-------GCTCGTCCAAGA------------------------------------------G------------C---------------C-AAGTCATGCATCAGCAG----------------TTCGCTTG----CTTCCCAT-------------------CT--------------------------------------------------CCGCTT--CTCCCTCCTCTGTCTACCTGTGTG-------CT-------------------------CAGCGATCTTGGCATGCAAATCG----CG-----CGCG---GCA-TTTTCAATG------------------------------CCAGC---TGCCA------------------------GTCGCGTAGGC s droGri2.scaffold_15245 901634 492 + 18325388 ATCCA---ACA-G--GCGAGTGG---GCAG---------------------------------------------------------CCTC-TGAGCTGAATGAATT---------------------------TGTAT----C-TG---TATCTACATATAT------------TTGTATCTT-----------------------------TATC------T--TTATCTGCTCC----------------GTTTC--ATCATTGCG--------TTG-----T-AAA-A---GCTTCCGCTT-----------GTGCTATGTGAAGTGACG-----AGCGATTTCTTGGCTAttttttttctctgtttctcttcttttttttttttAGTTATGAACAATAGACA----------------CAGTGC---------TGATA---ACTGCA----TGTGGGT----------------------TTTGC---------------------------------------------GTGACGTCA-T------AAG-----CGATCGGTCGCTTGGTCGTTCGGT--CGC---TCGCT-CAACGAGTTCATAAATCGATCAA-----CAACAATTG-------GCTCGTCCAAGT------------------------------------------GCCCCATCCAAGTC---------------C-AAGTCATGCATCAGCAG----------------TTAGCCACACGCCTCCCCCC-------------------CT--------------------------------------------------ATCGCC--CCCA-------------------G-------CT-------------------------C--AGATCTTGGCATGCAAATCG----CT-GAG-CGCG---GCA-TTTTCAATG----------CCAGGC--GGCCAGGC--GGCCAGC---TGCCAgtcgtcgtcgtcgtcgtcgtcgtcgtcgCGTAGGC a score=2163.000000 s dm6.chr2R 24350669 1 + 25286936 C s droSim1.chr2R 18697392 1 + 19596830 C s droSec1.super_23 117140 1 + 989336 C s droYak3.chr2R 20206490 1 + 21139217 C s droEre2.scaffold_4845 21604356 1 + 22589142 C s droKik2.KB459527 277029 1 - 1234237 c s droPse3.chr3 1350202 1 - 19787792 t s droPer1.super_34 539072 1 - 916997 T s droMir2.chr3 1391353 1 - 20862834 t s droVir3.scaffold_12875 7352631 1 + 20611582 T s droMoj3.scaffold_6496 26147899 1 + 26866924 C s droAlb1.JH854640 310034 1 + 406291 T s droGri2.scaffold_15245 902126 1 + 18325388 T a score=-150179.000000 s dm6.chr2R 24350670 72 + 25286936 -CCACTGGCC--------------------------------------TCTTGGC-TGC---------------CCCGATGAC-GTGTGCCAC---GAT-CC--------------GAG-CCGC----A-----------GCCC--------------C-TCGC----TGCTTCTC-----CCCAT s droSim1.chr2R 18697393 68 + 19596830 -CCACTGGCC--------------------------------------TCTTGGC-TGC---------------CCCGATGAC-GTGTGCCAC---GAT-CC--------------AAG-CACC----A-----------GCCC--------------C-TCGC----TTC----C-----CCCAT s droSec1.super_23 117141 68 + 989336 -CCACTGGCC--------------------------------------TCTTGGC-AGC---------------CCCGATGAC-GTGTGCCAC---GAT-CC--------------AAG-CACC----A-----------GTCC--------------C-TCGC----TTC----C-----CCCAT s droYak3.chr2R 20206491 68 + 21139217 -CCACTGGCC--------------------------------------TCTTGGC-TGC---------------CCCGATGAC-GTGTGCCAC---GAT-CC--------------AAG-CCCC----A-----------GCCC--------------C-TCGA----TTT----C-----CCCTC s droEre2.scaffold_4845 21604357 68 + 22589142 -CCACTGGCC--------------------------------------TCTTGGC-TGC---------------CCCGATGAC-GTGTGCCAC---GAT-CC--------------AAG-CCCC----A-----------GCCC--------------C-TCGA----TTC----C-----CCCTt s droBia2.KB462602 796961 64 + 3129309 -CCACTGGCC--------------------------------------TCTTGGC-TG----------------CCCGATGAC-GTGTGCCAC---GA------------------TCG-ACTC----A-----------GCCC--------------C-CTGG----TGG----C-----CCCAT s droSuz1.KI419649 12042147 83 - 14502029 -CTACTGGCC--------------------------------------TCTTGGC-TGC---------------CCCGATGAC-GTGTGCCAC---GAT-CCCCGCCCCAATCCGCTCG-ACTC----A-----------GCCC--------------CTCTGG----CTG----C-----CCCAT s droAna3.scaffold_13266 5711592 89 - 19884421 -----TTGCCTCTTGGCTCTCGACTCTCGGATCTCGGCTGGCCTCTTGTCTTGGC-TGC---------------CCCGATGAC-GTGTGCCAC---GAT-CT----------------------------------------------------------CCTC----CGT----C-----TCCGT s droBip2.KB464407 1960343 52 + 2915140 -----TTGCC--------------------------------------TCTTGGC-TGC---------------CCCGATGAC-GTGTGCCAC---CACGAT----------------------------------------------------------CTAC----CGT----C-----TCCAT s droEug2.KB465067 601575 69 + 1515531 -CCACTGGCC--------------------------------------TCTTGGC-TGC---------------CCCGATGAC-GTGTGCCAC---GAT-CC--------------GCG-TCCC----A-----------TTCCG-------------C-TCGA----CTC----G-----CCCCT s droEle2.KB458573 522580 73 - 5320397 -CCACTGGCC------------------------------ACCAC---TCTTGGT-TGC---------------CCCGATGAC-GTGTGCCACCAAGAT-CT--------------GCG-TCCC----A-----------T-----------------T-CCGC----TCC----A-----CTCAG s droKik2.KB459527 277030 71 - 1234237 -acactgtgc--------------------------------------T-TCCAC-TGC---------------CTCGATGAC-GTGTGCCACCGCGAT-CT-------------------CCT----G-----------TACC--------------C-TCTC----TTT----CGGTGGCTCAA s droTak2.KB461535 142090 72 - 669855 -CTACTGGCC--------------------------------------TCTTGGC-TGC---------------CCCGATGAC-GTGTGCCAC---GAT-cc--------------ccgccccc----a-----------gccc--------------c-cctc----ttt----c--ttaccccg s droRho2.KB449310 36313 70 - 65043 -CTACTGGCC--------------------------------------TCTTGGT-TGC---------------CCCGATGAC-GTGTGCCAC---GAT-CT--------------GCG-TCCC----A-----------TTCCGC------------T-CCAC----TCG----A-----CCCCT s droFic2.KB457177 81929 65 + 995874 -CTACTGGCC--------------------------------------TCTTGGC-TGC---------------CCCGATGAC-GTGTGCCAC---GAT-CT--------------GCG-TCCC----A-----------T-----------------T-CCGC----TCC----A-----CTCAG s droPse3.chr3 1350203 62 - 19787792 ----ctggct----------------------------------------ctggc-tct---------------ggcggtggctgtggcccgg---gct-ct--------------ggG-TCCCGCGTA-----------GGCT--------------T-GCGC----GAT--------------- s droPer1.super_34 539073 62 - 916997 ----CCGGCT----------------------------------------CTGGC-TCT---------------GGCGGTGGCTGTGGCCCGG---GCT-CT--------------GGG-TCCCGCGTA-----------GGCT--------------T-GCGC----GAT--------------- s droMir2.chr3 1391354 62 - 20862834 ----ccggct----------------------------------------ctggc-tct---------------ggcggtggctgtggcccgG---GCT-CT--------------GGG-TCCCGCGTA-----------GGCT--------------T-GCGC----GAT--------------- s droWil2.CH963894 1309744 71 + 2843958 -ACACCAAGC--------------------------------------TCATGG----------------------CGTAGGC-TTGGGCTTC---GCT-TT--------------TGGATCTT----A-----------GTTTATGGATGACGTGTGC-GCGC----CAC--------------- s droVir3.scaffold_12875 7352632 62 + 20611582 TCATCGCATC--------------------------------------TCTTTGC-GGC----------------CCGATGAC-GTGTGCCACCGAGAG-AC--------------ACT-CTTT----T-----------CGGC--------------T-GCTC---------------------- s droMoj3.scaffold_6496 26147900 61 + 26866924 TCATGGCATC--------------------------------------GCTTAGCTGGC----------------CCGATGAC-GTGTGCCGTC--GAG-CC--------------ACT-CTTT----G-----------CGGC--------------T-GCGC---------------------- s droAlb1.JH854640 310035 75 + 406291 TCATCACATC--------------------------------------TCTTTGC-TGC----------------CCGATGAC-GTGTGCCACT--GAG-CC--------------ACT-CTTT----tttctccgtctccgtc--------------t-acgtctca------------------ s droGri2.scaffold_15245 902127 76 + 18325388 TCATCGCATC--------------------------------------TCTTAGC-AGCGACAGAGACGGCGACTGCGATGAC-GTGTGCCACT--GAG-CC--------------ACT-CTTT----T-----------CGGT--------------G-GGTC---------------------- a score=-358831.000000 s dm6.chr2R 24350742 43 + 25286936 CCGAAACcaag--ccaagccaagccaaccc--agctcaac------t------caact----c---------------- s droSim1.chr2R 18697461 45 + 19596830 CCCCAACCGAGCCCCAAGCCAAGCCAATCc--aacccagc------t------caact----c---------------- s droSec1.super_23 117209 44 + 989336 Ccccaaccaag-cccaagccaagccaatcc--aacccagc------t------caact----c---------------- s droYak3.chr2R 20206559 34 + 21139217 T-----------TCCAGTCCAGTCCAATCC--AACCcagc------t------caact----c---------------- s droEre2.scaffold_4845 21604425 37 + 22589142 cc-------ag-tccagtccaatccaatcc--aacccagc------t------caact----c---------------- s droBia2.KB462602 797025 11 + 3129309 CCCCGTCCGCA-------------------------------------------------------------------- s droSuz1.KI419649 12042230 11 - 14502029 CCCCATCCGAA-------------------------------------------------------------------- s droAna3.scaffold_13266 5711681 17 - 19884421 CTCTATCTCTG------------------------------------------CGGAT----C---------------- s droBip2.KB464407 1960395 16 + 2915140 CG-GATCTTTG------------------------------------------GTTCC----G---------------- s droEug2.KB465067 601644 2 + 1515531 CT----------------------------------------------------------------------------- s droEle2.KB458573 522653 17 - 5320397 CCCCAGTCCCT------------------------------------------CGttt----t---------------- s droKik2.KB459527 277101 26 - 1234237 CCTCAACTTGG-----------------------CGCAGC------GCA----CAGCT----C---------------- s droTak2.KB461535 142162 11 - 669855 ccccTCCAAAA-------------------------------------------------------------------- s droRho2.KB449310 36383 11 - 65043 CCTCGTTCCAC-------------------------------------------------------------------- s droFic2.KB457177 81994 8 + 995874 CC---------------------------------------------------CCCCT----T---------------- s droWil2.CH963894 1309815 41 + 2843958 ---------------TGAAAAACTTAAACCGAAACTCAAA------CTCTT-TCAATTCTGCC---------------- s droVir3.scaffold_12875 7352694 43 + 20611582 --------------------------------GACTGTGGCCCCAACAACAAACAGCT----GTCGTttcattcgtttc s droMoj3.scaffold_6496 26147961 28 + 26866924 --------------------------------CAAGCAGG------CAGCCAACAGCT----G---------TCGCTTC s droAlb1.JH854640 310110 28 + 406291 --------------------------------gactgaga------ctgcggCCAGCT----G---------TCGTTTC s droGri2.scaffold_15245 902203 18 + 18325388 ----------------------------------------------C--CAAGCAGCT----G---------TCGTTTC a score=-43404.000000 s dm6.chr2R 24350785 28 + 25286936 aactcaactca----------gctcggctcggctc---aGT s droSim1.chr2R 18697506 28 + 19596830 aactcaactca----------gctcggctcggctc---agT s droSec1.super_23 117253 28 + 989336 aacTCTACTCA----------GCTCGGCTCGGATC---AGT s droYak3.chr2R 20206593 23 + 21139217 aactcaactga---------------GCTCGACTC---AGT s droEre2.scaffold_4845 21604462 38 + 22589142 gactcaactgaactcggcttggctcggctcggctc---AGT s droBia2.KB462602 797036 13 + 3129309 GACCCAGCTCA----------------------------GT s droSuz1.KI419649 12042241 13 - 14502029 AACTCAACTCA----------------------------GT s droAna3.scaffold_13266 5711698 20 - 19884421 AGACCCTCTCT---------------------GTCTCTGGT s droBip2.KB464407 1960411 17 + 2915140 AGACCCTCTCT---------------------TTC---GGT s droEug2.KB465067 601646 16 + 1515531 -ATTCCCCCAA---------------------CTC---AGT s droEle2.KB458573 522670 18 - 5320397 tttCCAACTCA--------------------GCTC---TGT s droKik2.KB459527 277127 18 - 1234237 CACTCCAGTCA--------------------GTTC---AGC s droTak2.KB461535 142173 12 - 669855 ------ACTCA--------------------ACTC---AGT s droRho2.KB449310 36394 14 - 65043 ----CAACCCA--------------------ACTC---AGT s droFic2.KB457177 82002 18 + 995874 TTTCCAGCGCG--------------------ACTC---AGT s droWil2.CH963894 1309856 17 + 2843958 AAATCTTCTCA---------------------AGC---AGC s droVir3.scaffold_12875 7352741 23 + 20611582 -gcttcattcg-----------cttcattcAGCTC------ s droMoj3.scaffold_6496 26147993 23 + 26866924 -GACTCACTCG-----------CTTCATTCAGCTC------ a score=3581.000000 s dm6.chr2R 24350813 1 + 25286936 T s droSim1.chr2R 18697534 1 + 19596830 T s droSec1.super_23 117281 1 + 989336 T s droYak3.chr2R 20206616 1 + 21139217 T s droEre2.scaffold_4845 21604500 1 + 22589142 T s droBia2.KB462602 797049 1 + 3129309 T s droSuz1.KI419649 12042254 1 - 14502029 T s droAna3.scaffold_13266 5711718 1 - 19884421 G s droBip2.KB464407 1960428 1 + 2915140 G s droEug2.KB465067 601662 1 + 1515531 T s droEle2.KB458573 522688 1 - 5320397 T s droKik2.KB459527 277146 1 - 1234237 T s droTak2.KB461535 142185 1 - 669855 T s droRho2.KB449310 36408 1 - 65043 T s droFic2.KB457177 82020 1 + 995874 T s droWil2.CH963894 1309876 1 + 2843958 C a score=158235.000000 s dm6.chr2R 24350814 16 + 25286936 TTTCCATTCAGCATGG- s droSim1.chr2R 18697535 16 + 19596830 TTTCCATTCAGCATGG- s droSec1.super_23 117282 16 + 989336 TTTCCATTCAGCCTGG- s droYak3.chr2R 20206617 16 + 21139217 TTTCCATTCAGCATGG- s droEre2.scaffold_4845 21604501 16 + 22589142 TTTCCATTCAGCATGG- s droBia2.KB462602 797050 16 + 3129309 TTTCCATTCAGCCTGG- s droSuz1.KI419649 12042255 16 - 14502029 TTTCCATTCAGCATGG- s droAna3.scaffold_13266 5711719 15 - 19884421 GCTCCATTCAGC-TGG- s droBip2.KB464407 1960429 15 + 2915140 GCTCCATTCAGC-TGG- s droEug2.KB465067 601663 16 + 1515531 TTTCCATTCAGCATGG- s droEle2.KB458573 522689 16 - 5320397 TTTCCATTCAGCATGG- s droKik2.KB459527 277147 16 - 1234237 TTTCCATTCAGCATGG- s droTak2.KB461535 142186 16 - 669855 TTTCCATTCAGCATGG- s droRho2.KB449310 36409 16 - 65043 TTTCCATTCAGCATGG- s droFic2.KB457177 82021 16 + 995874 TTTCCATTCAGCATGG- s droPse3.chr3 1350331 16 - 19787792 TTTCCATTCAGTTCGA- s droPer1.super_34 539203 16 - 916997 TTTCCATTCAGTTCGA- s droMir2.chr3 1391474 16 - 20862834 TTTCCATTCAGTTCGA- s droWil2.CH963894 1309877 16 + 2843958 GTTTCATTCAGTTTCA- s droVir3.scaffold_12875 7352764 9 + 20611582 --------CAACTTGGA s droMoj3.scaffold_6496 26148016 8 + 26866924 --------CAAC-TGGA s droAlb1.JH854640 310141 8 + 406291 --------CAAC-TGGA a score=821208.000000 s dm6.chr2R 24350830 55 + 25286936 GCCGATGAATGAAAG--CC---------------------------------------------------AAATGTTGTGGGTGTGA--------CACCAACGCCGGCTCAGGTCA s droSim1.chr2R 18697551 55 + 19596830 GCCGATGAATGAAAG--CC---------------------------------------------------AAATGTTGTGGGTGTGA--------CACCAACGCCGGCTCAGGTCA s droSec1.super_23 117298 55 + 989336 GCCGATGAATGAAAG--CC---------------------------------------------------AAATGTTGTGGGTGTGA--------CACCAACGCCGGCTCAGGTCA s droYak3.chr2R 20206633 55 + 21139217 GCCGATGAATGAAAG--CC---------------------------------------------------AAATGTTGTGGGTGTGA--------CACCAACGCCGGCTCAGGTCA s droEre2.scaffold_4845 21604517 55 + 22589142 GTCGATGAATGAAAG--CC---------------------------------------------------AAATGTTGTGGGTGTGA--------CACCAACGCCGGCTCAGGTCA s droBia2.KB462602 797066 56 + 3129309 GCCGATGAATGAACG--CC--------------------------------------------------AAAATGTTGTGGGTGTGA--------CACCAACGCCGGCTCAGGTCA s droSuz1.KI419649 12042271 56 - 14502029 GCCGATGAATGAAAG--CC--------------------------------------------------AAAATGTTGTGGGTGTGA--------CACCAACGCCGGCTCAGGTCA s droAna3.scaffold_13266 5711734 56 - 19884421 GGCGATGAATGAAAT--CC--------------------------------------------------AAAATGTAGTGGGTGTGA--------CACCAACGCCGGTTCAGGTCA s droBip2.KB464407 1960444 56 + 2915140 GGCGATGAATGAAAG--CC--------------------------------------------------AAAATGTAGTGGGTGTGA--------CACCAACGCCGGTTCAGGTCA s droEug2.KB465067 601679 56 + 1515531 GCCGATGAATGAACG--CC--------------------------------------------------AAAATGTTGTGGGTGTGA--------CACCAACGCCGGCTCAGGTCA s droEle2.KB458573 522705 56 - 5320397 GCCGATGAATGAACG--CC--------------------------------------------------AAAATGTTGTGGGTGTGA--------CACCAACGCCGGCTCAGGTCA s droKik2.KB459527 277163 56 - 1234237 GCCGATGAATGAACG--CC--------------------------------------------------AAAATGTTGTGGGTGTGA--------CACCAACGCCGGCTCAGGTCa s droTak2.KB461535 142202 56 - 669855 GACGATGaatgaaag--cc--------------------------------------------------aaaatgttgtGGGTGTGA--------CACCAACGCCGGCTCAGGTCA s droRho2.KB449310 36425 56 - 65043 GCCGATGAATGAAAG--CC--------------------------------------------------AAAATGTTGTGGGTGTGA--------CACCAACGCCGGCTCAGGTCA s droFic2.KB457177 82037 55 + 995874 GCCGATGAATGAAA---CC--------------------------------------------------AAAATGTTGTGGGTGTGA--------CACCAACGCCGGCTCAGGTCA s droPse3.chr3 1350347 88 - 19787792 GACGATGAATGAAAG-cccccccAACAGCCAAAGAG------------------CCAACAACGAGC-CAAAGATGTTGTGGGTGTGA--------CACCAACGCCGGTTCAGGtca s droPer1.super_34 539219 87 - 916997 GACGATGAATGAAAG--CCCCCCAACAGCCAAAGAG------------------CCAACAACGAGC-CAAAGATGTTGTGGGTGTGA--------CACCAACGCCGGTTCAGGTCA s droMir2.chr3 1391490 89 - 20862834 GACGATGAATGAAAGccccccccAACAGCCAAAGAG------------------CCAACAACGAGC-CAAAGATGTTGTGGGTGTGA--------CACCAACGCCGGTTCAGGTCA s droWil2.CH963894 1309893 56 + 2843958 TTCGATGAATGAAAG--TT----------------------------------------------------------GTAGGTGTCACCAGTAACCACCAACGCCGGTTCAGGTCA s droVir3.scaffold_12875 7352773 81 + 20611582 GACGATGAATGAACG--CC-------AAGCACAACG------------------GCAGCAGGCACCACGCAAATGTTGTGGGTGTGA--------CACCAACGCCGCTTCGGGTCA s droMoj3.scaffold_6496 26148024 99 + 26866924 GACGATGAATGAACG--CC-------GAGCAcagcgcagcagcgcagcagcgcagcagcAGCTACCACGCAAATGCTGTGGGTGTGA--------CACCAACGCCGCTCCGGATCA s droAlb1.JH854640 310149 82 + 406291 GACGATGAATGAA----CC-------Aagca-agcg----------gcaa----gcggcagCCACCACGCAAATGATGTGGGTGTGA--------CACCAACGCCGCTTCAGgtca s droGri2.scaffold_15245 902278 49 + 18325388 -----------------------------------------------------------GACGACGACTGAAAGGTTGTGGGTGTGA--------CACCAACGCCGCTTCAGGTCA a score=1698.000000 s dm6.chr2R 24350885 2 + 25286936 TC- s droSim1.chr2R 18697606 2 + 19596830 TC- s droSec1.super_23 117353 2 + 989336 TC- s droYak3.chr2R 20206688 2 + 21139217 TC- s droEre2.scaffold_4845 21604572 2 + 22589142 TC- s droBia2.KB462602 797122 2 + 3129309 TC- s droSuz1.KI419649 12042327 2 - 14502029 TC- s droAna3.scaffold_13266 5711790 2 - 19884421 TC- s droBip2.KB464407 1960500 2 + 2915140 TC- s droEug2.KB465067 601735 2 + 1515531 TC- s droEle2.KB458573 522761 2 - 5320397 TC- s droKik2.KB459527 277219 2 - 1234237 tc- s droTak2.KB461535 142258 2 - 669855 TC- s droRho2.KB449310 36481 2 - 65043 TC- s droFic2.KB457177 82092 2 + 995874 TC- s droPse3.chr3 1350435 2 - 19787792 tc- s droPer1.super_34 539306 2 - 916997 TC- s droMir2.chr3 1391579 2 - 20862834 TC- s droVir3.scaffold_12875 7352854 2 + 20611582 -CA s droMoj3.scaffold_6496 26148123 2 + 26866924 -TA s droAlb1.JH854640 310231 2 + 406291 -ca s droGri2.scaffold_15245 902327 2 + 18325388 -CA a score=-48795.000000 s dm6.chr2R 24350887 35 + 25286936 --AGTTGTT-GC--GC-TACACACAAAGAAATG--------------GTTGCGT---T s droSim1.chr2R 18697608 35 + 19596830 --AGTTGTT-GC--GC-TACACACAAAGAAATG--------------GTTGCGT---T s droSec1.super_23 117355 35 + 989336 --AGTTGTT-GC--GC-TACACACAAAGAAATG--------------GTTGCGT---T s droYak3.chr2R 20206690 39 + 21139217 --AGTTGTT-GC--TC-TACACACAAAGAAATG-------------TCTCGCGTTTCT s droEre2.scaffold_4845 21604574 35 + 22589142 --AGTTGTT-GC--TC-TACACACAAAGAAATG--------------CTGGCGT---T s droBia2.KB462602 797124 35 + 3129309 --AGTTGCT-GC--TC-TACACGCgcagaaaaa--------------tgtaaat---t s droSuz1.KI419649 12042329 35 - 14502029 --AGTTGTT-GC--TC-TACACAGGCAGAAAAA--------------TGCTAAT---A s droAna3.scaffold_13266 5711792 31 - 19884421 --AGTTGTG-GC--GGTTACACCAAGCGAAACT------------------AAG---- s droBip2.KB464407 1960502 31 + 2915140 --AGTTGTG-GC--GG-TACACCAAGCAAAACA------------------AAG---T s droEug2.KB465067 601737 31 + 1515531 --AGATGTT-GC--TC-TACACTCaaaaaaaGG------------------GAG---G s droEle2.KB458573 522763 34 - 5320397 --AGTTGTT-GC--TC-TACACACAAAGAAATT--------------ATTGCCT---- s droKik2.KB459527 277221 40 - 1234237 --agttgtt-gttgtc-taCACACAAAGAAAAT--T---------ATGGTAATT---T s droTak2.KB461535 142260 36 - 669855 --AGTTGTT-GC--TC-TACACATGCAGAAAAA-------------TGTTAATC---T s droRho2.KB449310 36483 35 - 65043 --AGTTGTT-GC--GC-TACACACAAAGAAAAG--------------TATAATC---T s droFic2.KB457177 82094 47 + 995874 --AGTTGTT-GC--tc-tacacagaaagaaatt--gcGATCTCCAACAACATAA---A s droVir3.scaffold_12875 7352856 28 + 20611582 ACAAAC----AC--AA-CAAAGAAGTAGGTGTGCT----------------------- s droMoj3.scaffold_6496 26148125 31 + 26866924 ACAAAACAG-AA--AA-CACAGAAGTAGGTGTGCT----------------------- s droAlb1.JH854640 310234 22 + 406291 acagcacagcac--ag-cacacacg--------------------------------- s droGri2.scaffold_15245 902329 28 + 18325388 ACAAAC-AT-AA--AA-TACACACACAGACATT------------------------- a score=-59768.000000 s dm6.chr2R 24350922 34 + 25286936 CAC-ACCGAAAGTGAA-GGGAAA--TCGTTTAACTAAG---------------- s droSim1.chr2R 18697643 34 + 19596830 CAC-ACCGAAAGTGAA-GGGAAA--TCGTTTAACTAAG---------------- s droSec1.super_23 117390 34 + 989336 CAC-ACCGAAAGTGAA-GGGAAA--TCGTTTAACTAAG---------------- s droYak3.chr2R 20206729 34 + 21139217 TCC-ACCGAAAGTGAATGGGAAA--TCG-TCAACTAAG---------------- s droEre2.scaffold_4845 21604609 34 + 22589142 TCC-ACCGAAAGTGAA-GGGAAA--TCGTTCAACTAAG---------------- s droBia2.KB462602 797159 33 + 3129309 tgt-aCAGAAAATGAA-GGGAAA---CATCCCATCCAA---------------- s droSuz1.KI419649 12042364 34 - 14502029 TGTAACTGAAAATGAA-GGGAAA---TATTCAGCTAAG---------------- s droAna3.scaffold_13266 5711823 20 - 19884421 ----CATAAAAATAAA-----TA--TTATTC----------------------- s droBip2.KB464407 1960533 23 + 2915140 CCC-Cccgaaaatgtt-----ta--ttattc----------------------- s droEug2.KB465067 601768 29 + 1515531 TAA-CCTTAAACCGAA-----AA---TATTTCTCACAC---------------- s droEle2.KB458573 522797 34 - 5320397 TAA-ACCtcgaataaa-aagaaa--taatttaccTAAC---------------- s droKik2.KB459527 277261 33 - 1234237 TGT-AGCCTCATTTAA-AGGCAA---TATATTATAGAG---------------- s droTak2.KB461535 142296 34 - 669855 TTA-ACGGAAAATGAa-gggaag--tttttcttataaa---------------- s droRho2.KB449310 36518 34 - 65043 TGA-ATACCAAATGAA-AGGAAA--TAAGTTATCCAAC---------------- s droFic2.KB457177 82141 36 + 995874 CAC-TCTGAGAATATC-CCaaaatcttattttatttga---------------- s droAlb1.JH854640 310256 32 + 406291 ------cacaacaaag-AAGTAG--GTGTGCGGTGAGC-----GAT-------- s droGri2.scaffold_15245 902357 45 + 18325388 ------CGCAGCAAAG-AAGTAG--GTGTGCTGCCAGCTAACTGATTGACTAAG a score=-7285.000000 s dm6.chr2R 24350956 29 + 25286936 CCCT--TTTCACA-----TTTAATGGCTCTTTTGAG s droSim1.chr2R 18697677 29 + 19596830 CCCT--TTTCCCA-----TTTAATGGCTCTTTTGAG s droSec1.super_23 117424 29 + 989336 CCCT--TTTCCCA-----TTTAATGGCTCTTTTGAG s droYak3.chr2R 20206763 29 + 21139217 CCCT--TTCCACA-----TTTAATGGCTCTTTGGAG s droEre2.scaffold_4845 21604643 28 + 22589142 CCCT--TTTCAT------TTTAATGGCTCGTCTGAG s droBia2.KB462602 797192 29 + 3129309 GCCC--TTTCATA-----TCCTAGAGATCTTTTGAG s droSuz1.KI419649 12042398 29 - 14502029 ACCT--TTTTATA-----TCTTTGGCATCTTTTGAG s droAna3.scaffold_13266 5711843 26 - 19884421 CCCT--CTCCCCA-----TACCTGGGGGTGTTT--- s droBip2.KB464407 1960556 19 + 2915140 --------cTCCA-----ACTCTTGGACTA-TT--- s droEug2.KB465067 601797 23 + 1515531 AACC--TTTTACA-----TCTTTTG------TTAAG s droEle2.KB458573 522831 25 - 5320397 ACCT--CTCC-CA-----TTT---GGATATTttgag s droKik2.KB459527 277294 29 - 1234237 TATT--CGTCATA-----ACTCGATGATTTTTGGGG s droTak2.KB461535 142330 29 - 669855 CCCT--TTCATAA-----CTTCTGGGATCTTTTGAa s droRho2.KB449310 36552 31 - 65043 ACCTCATCTCACA-----TCGTTTGGATATTttgag s droFic2.KB457177 82177 33 + 995874 actc--tccaaaaaaattatttatagtttttttga- s droAlb1.JH854640 310288 29 + 406291 GCTT--ATTGACT-----TTATGATACCCTATTAAA a score=-10478.000000 s dm6.chr2R 24350985 5 + 25286936 --CGTGG s droSim1.chr2R 18697706 5 + 19596830 --CGTGG s droSec1.super_23 117453 5 + 989336 --CGTGG s droYak3.chr2R 20206792 5 + 21139217 --CGTGG s droEre2.scaffold_4845 21604671 5 + 22589142 --CGTGG s droBia2.KB462602 797221 5 + 3129309 --GGTTA s droSuz1.KI419649 12042427 5 - 14502029 --GGtta s droEug2.KB465067 601820 3 + 1515531 --AAA-- s droEle2.KB458573 522856 5 - 5320397 --aataa s droTak2.KB461535 142359 2 - 669855 --gg--- s droAlb1.JH854640 310317 4 + 406291 TTTG--- a score=-152180.000000 s dm6.chr2R 24350990 43 + 25286936 TCAG--------TA------------CACATT--------------------------AGTTTAGCACTTAAG----------ATACAATCTC-----------GACCGA-- s droSim1.chr2R 18697711 43 + 19596830 TCAG--------TA------------CACATT--------------------------AGTTCAGCACTCAAG----------ATACAATCTC-----------TTCCGA-- s droSec1.super_23 117458 43 + 989336 TCAG--------TA------------CGCATT--------------------------AGTTCAGCACTCAAG----------ATACAATCTC-----------TTCCGA-- s droYak3.chr2R 20206797 61 + 21139217 TCAGCACGAT--TGGCCAAGAAGTCCCTCTTA--------------------------CATGCAGCATTCAAG----------ATACAATCTC-----------TGGCAA-- s droEre2.scaffold_4845 21604676 55 + 22589142 TCCA--------TGTCCAAGAAGTGCCCCATA--------------------------AGTCCAGCATTCAAG----------ATACAATCTC-----------CTCCAA-- s droBia2.KB462602 797407 60 + 3129309 ---------------TTAaagcattttgtttta-------------------------aaagatataatgAAA----------TGATACTTGCTTTCGATCTaatcttga-- s droSuz1.KI419649 12042464 48 - 14502029 ---------------CTTAAGCCACCTGCTTT--------------------------AGAGATTTGATGAAA----------AGATAATTGC-----------acttca-- s droEug2.KB465067 601823 36 + 1515531 -------------------------------------------------------------TAAGTACTGAAG-CTTTGT-ATTTCCGATGGC-----------TTATCA-- s droEle2.KB458573 522861 39 - 5320397 --------------------------------ataaa------------------atatatacaatttgaaaa----------ttataattta-----------aatcta-- s droKik2.KB459527 277323 49 - 1234237 -----------------------GTCTTTATT--------------------------Tgttgagaaaataaa-agaaatcaaatgaaatcgt-----------ttctta-- s droTak2.KB461535 142361 85 - 669855 --------------ttagaaaaaatatttactgtcGAAAAAAGAGCGCTGTTGCGATATTTCTTGCATAGAAATCTATGTTTTAGACATCTTA-----------TTTAAA-- s droFic2.KB457177 82210 49 + 995874 --------attataattttgtttaaaccTTTT--------------------------GGGTGAAGAGCTAAC----------TCTCAACTCC------------------- s droAlb1.JH854640 310321 21 + 406291 --------------------------------------------------------------------------------CCAGCATTATCAC-----------TTCTAACA a score=-131932.000000 s dm6.chr2R 24351033 34 + 25286936 G--------------TGA---------------------------------------ATACACGAAGTATCGCT--GAG-------CT----------------GGCCCCGA--- s droSim1.chr2R 18697754 34 + 19596830 A--------------GGA---------------------------------------ATACACGCAGCATCGCT--GAG-------CT----------------GGCCCCGA--- s droSec1.super_23 117501 34 + 989336 G--------------TGA---------------------------------------ATACACGCAGTATCGCT--GAG-------CT----------------GGCCCCGA--- s droYak3.chr2R 20206858 10 + 21139217 G--------------------------------------------------------------------------------------T----------------GGCCCCGA--- s droEre2.scaffold_4845 21604731 34 + 22589142 T--------------TGA---------------------------------------ATGCCTGAAGTATCGCT--GGG-------CT----------------GGCCCCGA--- s droBia2.KB462602 797467 34 + 3129309 a--------------aaa---------------------------------------aaatagCCTATTTTATT--TGA-------GT----------------GACTTCGA--- s droSuz1.KI419649 12042512 34 - 14502029 a--------------caa---------------------------------------aaatattttatattatt--tga-------gt----------------GGCTTCAA--- s droEug2.KB465067 601859 43 + 1515531 A--------------AAA------------------------------------TCTAAAGATCAAAAGTGGCT--CAA-------GTCCAAGC----------CCCTCCGA--- s droEle2.KB458573 522900 81 - 5320397 a--------------cAAAGTGCTGTAACAAAGTTGGTTCTATAAAGTATTTTCGCTATATGCTTAGAAGTAGT--AAG-------CAAATAGT--------TATGCTTAAA--- s droKik2.KB459527 277372 62 - 1234237 aatattatcatGG--AAA---------------------------------------GGAAATACTTTAGTGTT--GGA-------ATAATCACAACGTTTTTCGTTTGCAA--- s droTak2.KB461535 142446 55 - 669855 GATGTGATGAAAGCAGAA---------------------------------------ACACAATACTTACTTTT--GAGTAATTCTtt----------------gtcaataa--- s droRho2.KB449310 36901 32 - 65043 -------------------------------------------------------GTGGATATCTGTAATTTTC--AAA-------CC----------------GCTTTCAA--- s droFic2.KB457177 82259 34 + 995874 -----------------------------------------------------GCCTTAATAGCAATTTGAATT--CAA-------AC----------------ACACccaa--- s droAlb1.JH854640 310342 34 + 406291 ----------------------------------------------------------TACACTTGTTGTCGCTGCGAA-------GG----------------GTATTCGACAG a score=-40602.000000 s dm6.chr2R 24351067 6 + 25286936 A-------------------------------TTCTT s droSim1.chr2R 18697788 6 + 19596830 G-------------------------------TTCTT s droSec1.super_23 117535 6 + 989336 A-------------------------------TTCTT s droYak3.chr2R 20206868 6 + 21139217 A-------------------------------TTCTC s droEre2.scaffold_4845 21604765 6 + 22589142 A-------------------------------TTCTT s droBia2.KB462602 797501 13 + 3129309 GAACTA------------------------TTTATTT s droSuz1.KI419649 12042546 13 - 14502029 GTCGAA------------------------TTTATTT s droAna3.scaffold_13266 5711869 5 - 19884421 --------------------------------TTCTT s droBip2.KB464407 1960575 5 + 2915140 --------------------------------TTCTC s droEug2.KB465067 601902 6 + 1515531 T-------------------------------TGTTT s droEle2.KB458573 522981 37 - 5320397 GCACAAACATTATTGTCAAACCCCTCACTTTTTATTT s droKik2.KB459527 277434 8 - 1234237 A-----------------------------TTTTTTC s droTak2.KB461535 142501 11 - 669855 ataata--------------------------ttttt s droRho2.KB449310 36933 6 - 65043 T-------------------------------TATTT s droFic2.KB457177 82293 8 + 995874 g-----------------------------ttttttt s droVir3.scaffold_12875 7353438 6 + 20611582 -------------------------------ATTATT s droAlb1.JH854640 310376 6 + 406291 -------------------------------ATACGT a score=30363.000000 s dm6.chr2R 24351073 11 + 25286936 TCTGTGTAGC------C s droSim1.chr2R 18697794 11 + 19596830 TCTGTGTAGC------C s droSec1.super_23 117541 11 + 989336 TCTGTGTAGC------C s droYak3.chr2R 20206874 11 + 21139217 GCAGTGTTGC------C s droEre2.scaffold_4845 21604771 11 + 22589142 ACCGTGTAGC------C s droBia2.KB462602 797514 11 + 3129309 CCTGTGTAGC------C s droSuz1.KI419649 12042559 11 - 14502029 CCTGTGTAGT------C s droAna3.scaffold_13266 5711874 10 - 19884421 GCTGTGTAGT------- s droBip2.KB464407 1960580 17 + 2915140 GCTGTGTACTTCTACTG s droEug2.KB465067 601908 11 + 1515531 CCTGTGCAGC------C s droEle2.KB458573 523018 11 - 5320397 CCTGTGTAGT------C s droKik2.KB459527 277442 11 - 1234237 CTTGTGTAAA------C s droTak2.KB461535 142512 11 - 669855 tatattttat------t s droRho2.KB449310 36939 11 - 65043 CCTGTGTTGC------C s droFic2.KB457177 82301 11 + 995874 tcggtgtagc------C s droPse3.chr3 1350437 11 - 19787792 attttgttgt------t s droPer1.super_34 539308 11 - 916997 ATTTTGTTGT------T s droMir2.chr3 1391581 11 - 20862834 atttagttgt------t s droVir3.scaffold_12875 7353448 11 + 20611582 ctgctgctgc------t s droMoj3.scaffold_6496 26148471 11 + 26866924 TTTGTGATAC------C s droAlb1.JH854640 310388 11 + 406291 TTTCCGATAT------T a score=9825.000000 s dm6.chr2R 24351084 2 + 25286936 GT s droSim1.chr2R 18697805 2 + 19596830 GT s droSec1.super_23 117552 2 + 989336 GT s droYak3.chr2R 20206885 2 + 21139217 GT s droEre2.scaffold_4845 21604782 2 + 22589142 GT s droBia2.KB462602 797525 2 + 3129309 GT s droSuz1.KI419649 12042570 2 - 14502029 GT s droBip2.KB464407 1960597 2 + 2915140 GT s droEug2.KB465067 601919 2 + 1515531 GT s droEle2.KB458573 523029 2 - 5320397 AA s droKik2.KB459527 277453 2 - 1234237 CC s droTak2.KB461535 142523 2 - 669855 tc s droRho2.KB449310 36950 2 - 65043 AA s droFic2.KB457177 82312 2 + 995874 AC s droPse3.chr3 1350448 2 - 19787792 gt s droPer1.super_34 539319 2 - 916997 GT s droMir2.chr3 1391592 2 - 20862834 gt s droVir3.scaffold_12875 7353459 2 + 20611582 gt s droMoj3.scaffold_6496 26148482 2 + 26866924 AT s droAlb1.JH854640 310399 2 + 406291 GT s droGri2.scaffold_15245 903617 2 + 18325388 GT a score=1390035.000000 s dm6.chr2R 24351086 105 + 25286936 TG-GTAGCT-G----CCTGC--CAGCTGACTGATAAAATAAAAT-CCA---TAACTCG---T-----AC-------------------CGCTGCTGCTGTAGGTCGTT------------CT--------GCCGCCGCCAACTC--------TTTGTCCA---GCCAAGGTTAAT s droSim1.chr2R 18697807 105 + 19596830 TG-GTAGCT-G----CCTGC--CAGCTGACTGATAAAATAAAAT-CCA---TAACTCG---T-----AC-------------------CGCTGCTGCTGTAGGTCGTT------------CT--------GCCGCCGCCAACTC--------TTTGTCCA---GCCAAGGTTAAT s droSec1.super_23 117554 105 + 989336 TG-GTAGCT-G----CCTGC--CAGCTGACTGATAAAATAAAAT-CCG---TAACTCG---T-----AC-------------------CGCTGCTGCTGTAGGTCGTT------------CT--------GCCGCCGCCAACTC--------TTTGTCCA---GCCAAGGTTAAT s droYak3.chr2R 20206887 105 + 21139217 TG-GTAGCT-G----CCTGC--CAGCTGACTGATAAAACAAAAT-CCA---TAACTCG---T-----AC-------------------CGCTGCTGCTGTAGGTCGTT------------CT--------GCCGCCGCCAACTC--------TTTGTCCA---GCCAAGGTTAAT s droEre2.scaffold_4845 21604784 105 + 22589142 TG-GTAGCT-G----GCTGC--CAGCTGACTGATAAAACAAAAT-CCA---TAACTCG---T-----AC-------------------CGCTGCTGCTGTAGGTCGTT------------CT--------GCCGCCGCCAACTC--------TTTGTCCA---GCCAAGGTTAAT s droBia2.KB462602 797530 105 + 3129309 TG-GTAGCT-G----ACTGC--CAGCTgactgataaaataaaat-cca---taaCTCG---T-----AC-------------------CGCTGCTGCTGTAGGTCGTT------------CT--------GCCGCCGCCAACTC--------TTTGTCCA---GCCAAGGTTAAT s droSuz1.KI419649 12042575 105 - 14502029 TG-GTAGCT-G----ACTGC--CAGCTGactgataaaataaaat-cca---taaCTCG---A-----AC-------------------CGCTGCTGCTGTAGGTCGTT------------CT--------GCCGCCGCCAACTC--------TTTGTCCA---GCCAAGGTTAAT s droAna3.scaffold_13266 5711884 110 - 19884421 ---------------CTCGC--CAGCTGACTGAC-TGATAAAAG-TCA---TAACGCG---G-----GC-----------TGT-----CGCTGCTGCTGTAGGTCGTTCTACTGCCGCCGCC--------GCCACCGCCAACTC--------TTTGTCCA---GCCAAGGTTAAT s droBip2.KB464407 1960599 111 + 2915140 TG-GCGACT-GCcagctgac--tgactgactgac-tgataAAAT-TCA---TAACCTG---G-----CC-------------------CGCTGCTGCTGTAGGTCGTTCTA---------CC--------GCCGCCGCCAACTC--------TTTGTCCA---GCCAAGGTTAAT s droEug2.KB465067 601921 105 + 1515531 TG-GTAGCT-G----CCTGC--CAGCTGactgataaaataaaat-cca---taaCTTG---T-----AC-------------------CGCTGCTGCTGTAGGTCGTT------------CT--------GCCGCCGCCAACTC--------TTTGTCCA---ACCAAGGTTAAT s droEle2.KB458573 523034 105 - 5320397 TG-GTAGCT-G----ACTGC--CAGCTGactgataaaataaaat-cca---taaCTTG---T-----AC-------------------CGCTGCTGCTGTAGGTCGTT------------CT--------GCCGCCGCCAACTC--------TTTGTCCA---GCCAAGGTTAAT s droKik2.KB459527 277461 105 - 1234237 TG-CTGGCT-G----ACTGC--CAGCTGACTTGACTGATAATAT-TCA---TAACTTG---t-----ac-------------------cgctgctgctgtaggtcgtt------------cc--------gccgccgccaactC--------TTTGTCCA---GCCAAGGTTAAT s droTak2.KB461535 142526 106 - 669855 tgtGTATCT-A----ACCGC--CAGCTgactgataaaataaaat-cca---taaCTTG---T-----AC-------------------CGCTGCTGCTGTAGGTCGTT------------CT--------GCCGCCGCCAACTC--------TTTGTCCA---GCCAAGGTTAAT s droRho2.KB449310 36955 105 - 65043 TG-GTAGCT-G----ACTGC--CAGCTGactgataaaataaaat-cca---taacTTG---T-----AC-------------------CGCTGCTGCTGTAGGTCGTT------------CT--------GCCGCCGCCAACTC--------TTTGTCCA---GCCAAGGTTAAT s droFic2.KB457177 82317 105 + 995874 TG-GTAGCT-G----ACTGC--CAGCTGactgataaaataaaat-cca---taACTTG---T-----AC-------------------CGCTGCTGCTGTAGGTCGTT------------CT--------GCCGCCGCCAACTC--------TTTGTCCA---GCCAAGGTTAAT s droPse3.chr3 1350456 120 - 19787792 tg-gaagcc------ccagcagcagctgactTGACTGATAAAAG-TCA---TGGCTGG---T-----acgcggctgctgctgc-----tgctgctgctgtaggtCGTT------------CT--------GCTGCCGCCAACTC--------TTTGTCCA---GCCAAGGTTAAT s droPer1.super_34 539327 120 - 916997 TG-GAAGCC------CCAGCAGCAGCTGACTTGACTGATAAAAG-TCA---TGGCTGG---T-----ACGCGgctgctgctgc-----tgctgctgctgTAGGTCGTT------------CT--------GCTGCCGCCAACTC--------TTTGTCCA---GCCAAGGTTAAT s droMir2.chr3 1391600 117 - 20862834 tg-gaagcc------ccagcagcagctgacttGACTGATAAAAG-TCA---TGGCTGG---T-----acgcg---actgctgc-----tgctgctgctgtaggtCGTT------------CT--------GCTGCCGCCAACTC--------TTTGTCCA---GCCAAGGTTAAT s droWil2.CH963894 1310004 107 + 2843958 TT-GTGGCT-G----TTAGC--CAGCTGACTTGACTGATAAACTACCA---AAGCTCT---C-----TT-------------------GTCTGCTGCTGTAGATCGTT------------TT--------GC--CCGCCAACTC--------TTTGTCCAGTCGCCAAGGTTAAT s droVir3.scaffold_12875 7353461 111 + 20611582 tg-ctgctTGG----TTAGC--CAGCTGACTG-----ATAAACT-TCA---TAGCTTG---TTATTGCC-------------------CGGGGCTGCTGTAGGTCGTT------------CT---CTGACACTGCCGCCAACTC--------CGAGTCCA---GCCAAGGTTAAT s droMoj3.scaffold_6496 26148484 112 + 26866924 TG-CTGCTG-------------CAGCTGACTG-----ATAAACT-TCA---TTGCTTG---TTATTGCC-------------------CGCGGCTGCTGTAGGTCGTT------------CT---CTGTCGCTGTCTCTTTCTCTTTCTCTTCCAAGCCA---GCCAAGGTTAAT s droAlb1.JH854640 310401 129 + 406291 CA-GTTACT-------------CAATTGACTG-----ATAAACC-TTAAaccttcttg---ttgttgtcatatctgtttgtttgtttgtttggctgctGTAGGTCGTT------------CTCTGCTGGCATCGCCGCCAACTC--------CAAGTCCA---GCCAAGGTTAAT s droGri2.scaffold_15245 903619 113 + 18325388 TG-GTATTT-G----TTGGC--CAGCTGACTG-----ATAAACT-TCA---TAGCTTGTTATTATTGCC-------------------TGGAGCTGCTGTAGGTCGTT------------CT---CTGACACTGCCGCCAACTC--------CGAGTCCA---GCCAAGGTTAAT a score=19110.000000 s dm6.chr2R 24351191 1 + 25286936 T s droSim1.chr2R 18697912 1 + 19596830 T s droSec1.super_23 117659 1 + 989336 T s droYak3.chr2R 20206992 1 + 21139217 T s droEre2.scaffold_4845 21604889 1 + 22589142 T s droBia2.KB462602 797635 1 + 3129309 T s droSuz1.KI419649 12042680 1 - 14502029 T s droAna3.scaffold_13266 5711994 1 - 19884421 T s droBip2.KB464407 1960710 1 + 2915140 T s droEug2.KB465067 602026 1 + 1515531 T s droEle2.KB458573 523139 1 - 5320397 T s droKik2.KB459527 277566 1 - 1234237 T s droTak2.KB461535 142632 1 - 669855 T s droRho2.KB449310 37060 1 - 65043 T s droFic2.KB457177 82422 1 + 995874 T s droPse3.chr3 1350576 1 - 19787792 T s droMir2.chr3 1391717 1 - 20862834 T s droVir3.scaffold_12875 7353572 1 + 20611582 T s droMoj3.scaffold_6496 26148596 1 + 26866924 T s droAlb1.JH854640 310530 1 + 406291 T s droGri2.scaffold_15245 903732 1 + 18325388 T a score=196167.000000 s dm6.chr2R 24351192 26 + 25286936 GCCGAC-TTGCAGTGGG-----------CTG-CTCA----------------C-----ta s droSim1.chr2R 18697913 24 + 19596830 GCCGAC-TTGCAGTGGG-----------CTG-CTCA----------------C------- s droSec1.super_23 117660 24 + 989336 GCCGAC-TTGCAGTGGG-----------CTG-CTCA----------------C------- s droYak3.chr2R 20206993 26 + 21139217 GCCGAC-TTGCAGTGGG-----------CCG-CTCG----------------C-----TG s droEre2.scaffold_4845 21604890 26 + 22589142 GCCAAC-TTGCAGTGGG-----------CTG-CTCG----------------C-----TG s droBia2.KB462602 797636 31 + 3129309 GCCGAC-TTGCAGTGGG-----------CTG-TTCG----------------CCGTGCTG s droSuz1.KI419649 12042681 31 - 14502029 GCCGAC-TTGCAGTGGG-----------CTG-TACG----------------CTCTGCTG s droAna3.scaffold_13266 5711995 15 - 19884421 GCCAAC-TTGCAGTGG-------------------------------------------- s droBip2.KB464407 1960711 25 + 2915140 GCCAAC-TTGCAGTGGG-----------TTG-TT-G----------------C-----CG s droEug2.KB465067 602027 26 + 1515531 GCCGAC-TTGCAGTGGg-----------ctg-ttcg----------------c-----cg s droEle2.KB458573 523140 26 - 5320397 GTTGAC-TTGCAGTggg-----------ctg-tttg----------------c-----tg s droKik2.KB459527 277567 26 - 1234237 GCCGAC-TTGCAGTGGG-----------CTG-AGAG----------------C-----TC s droTak2.KB461535 142633 26 - 669855 GCCGAC-TTGCAGTGGG-----------CTG-TTCG----------------C-----TG s droRho2.KB449310 37061 26 - 65043 GCCGAC-TTGCAGTGGG-----------CTG-TTCG----------------C-----TG s droFic2.KB457177 82423 26 + 995874 GCCGAC-TTGCAGTGGG-----------CCG-TTCG----------------C-----TG s droPse3.chr3 1350577 36 - 19787792 GCCATC-ATGCAGTGGGCTgttgtgcccctg-cccc----------------c-----t- s droPer1.super_34 539448 36 - 916997 GCCATC-ATGCAGTGGGCTGTTGTGCCCCTG-CCCC----------------C-----T- s droMir2.chr3 1391718 25 - 20862834 GCCATC-ATGCAGTGGG-----------CTG-CCCC----------------C-----T- s droWil2.CH963894 1310112 42 + 2843958 GTCATT-TTGCAGTGGG-----------CTG-CACGAGCTTACGAGTATTTTC-----TA s droVir3.scaffold_12875 7353573 26 + 20611582 GTCCGC-ATGCAGTGGG-----------TTG-CTCT----------------T-----TC s droMoj3.scaffold_6496 26148597 26 + 26866924 GTCCGT-TAGCAGTGGG-----------TTG-TTCT----------------T-----TC s droAlb1.JH854640 310531 28 + 406291 GCTCACATTGCAGTGGG-----------TTGTCTCT----------------A-----TC s droGri2.scaffold_15245 903733 26 + 18325388 GTCTGC-ATGCAGTGGG-----------TTG-CTCT----------------A-----Tc a score=-150566.000000 s dm6.chr2R 24351218 13 + 25286936 ----------gatagatagatac s droSim1.chr2R 18697937 11 + 19596830 ------------TAGATGGATAC s droSec1.super_23 117684 11 + 989336 ------------TAGATGGATAC s droYak3.chr2R 20207032 13 + 21139217 ----------GCTGGCTCACTAG s droEre2.scaffold_4845 21604929 13 + 22589142 ----------GCTGGCTCACTAG s droBia2.KB462602 797680 13 + 3129309 ----------GCTGGCTCACATT s droSuz1.KI419649 12042725 13 - 14502029 ----------TCTGGCTCacatt s droAna3.scaffold_13266 5712010 12 - 19884421 ----------GTTGGCCAACAT- s droBip2.KB464407 1960742 12 + 2915140 ----------GTTGGCCAACTC- s droEle2.KB458573 523169 10 - 5320397 ----------gctgtgctgt--- s droKik2.KB459527 277608 10 - 1234237 ----------GTTGGCCAAC--- s droTak2.KB461535 142684 8 - 669855 ----------GCTGGCTC----- s droRho2.KB449310 37091 8 - 65043 ----------GTTTGCCA----- s droPse3.chr3 1350613 3 - 19787792 --------------tcc------ s droPer1.super_34 539484 3 - 916997 --------------TCC------ s droMir2.chr3 1391743 3 - 20862834 --------------TCC------ s droWil2.CH963894 1310154 13 + 2843958 ----------GTTGGGCAACTTT s droVir3.scaffold_12875 7353599 6 + 20611582 AGTT--TG--------------- s droMoj3.scaffold_6496 26148623 13 + 26866924 AGTt--tgttattgt-------- s droAlb1.JH854640 310559 13 + 406291 TCTA--GAGCTCTAC-------- s droGri2.scaffold_15245 903759 15 + 18325388 tgctgctgctgctgc-------- a score=-91232.000000 s dm6.chr2R 24351231 20 + 25286936 ----------atatatacatGC-TCATGTAG s droSim1.chr2R 18697948 19 + 19596830 ----------ATATATACAAGC-TCATGTA- s droSec1.super_23 117695 19 + 989336 ----------ATATATACAAGC-TCATGTA- s droYak3.chr2R 20207045 20 + 21139217 ----------CTAGATACGTGC-CTAtgtag s droEre2.scaffold_4845 21604942 20 + 22589142 ----------ATAGATACGTGT-TCATGTAG s droBia2.KB462602 797693 19 + 3129309 ----------ATATGTGTATGC-TTACATA- s droSuz1.KI419649 12042738 19 - 14502029 ----------atatatgtatac-ttgCCTA- s droEug2.KB465067 602081 19 + 1515531 ----------aCATTTGCTGGC-TCACATT- s droEle2.KB458573 523190 18 - 5320397 ----------ACATTTGCTAGC-TCACAT-- s droKik2.KB459527 277618 20 - 1234237 ----------ACATTTGCTAAC-TCACATTA s droTak2.KB461535 142697 19 - 669855 ----------ATATATGCTCAC-TTATATA- s droRho2.KB449310 37099 20 - 65043 ----------ACATTTGCTGGC-TCacatta s droPse3.chr3 1350618 19 - 19787792 ----------ACATTTACCCGCAGTATGC-- s droPer1.super_34 539489 19 - 916997 ----------ACATTTACCCGCAGTATGC-- s droMir2.chr3 1391748 19 - 20862834 ----------ACGTTTACCCGCAGTATAC-- s droWil2.CH963894 1310183 18 + 2843958 ----------atatatatatta-ttatat-- s droVir3.scaffold_12875 7353605 12 + 20611582 ---------TATTTGTTGTTG---------- s droMoj3.scaffold_6496 26148636 21 + 26866924 tgctaatgttgttttttgtcg---------- s droAlb1.JH854640 310572 21 + 406291 CTCTAGCTCTAGCTCTAGTTG---------- s droGri2.scaffold_15245 903774 20 + 18325388 tgctgctgctg-ctgctgctg---------- a score=636359.000000 s dm6.chr2R 24351251 100 + 25286936 C-----------------------------------------TGTGTGT-----TT--CT-------------------------GGC-------TCC-GAT-------------CGAGAGTGCGATCCATC--AGT----------------------CTGCGCGGGTGT---------------------CTTGGCTACACG----------------G----------------------A-TCGCCTTCTATGG--TCGCTCACCTGCGCATCATC s droSim1.chr2R 18697967 95 + 19596830 ----------------------------------------------TGT-----TT--CT-------------------------GGC-------TCC-GAT-------------CGAGAGTGCGATCCATC--AGT----------------------CTGCGCGGGTGT---------------------CTTGGCTACACG----------------G----------------------A-TCGCCTTCTATGG--TCGCTCACCTGCGCATCATC s droSec1.super_23 117714 95 + 989336 ----------------------------------------------TGT-----TT--CT-------------------------GGC-------TCC-GAT-------------CGAGAGTGCGATCCATC--AGT----------------------CTGCGCGGGTGT---------------------CTTGGCTACACG----------------G----------------------A-TCGCCTTCTATGG--TCGCTCACCTGCGCATCATC s droYak3.chr2R 20207065 135 + 21139217 c---tgtgtgtatctgtgagatatctgtgtgtgtttgtg---tgtgtgt-----at--ct-------------------------gac-------TCC-CAT-------------CGAGAGTGCGATCCATC--AGT----------------------CTGCGCGGGTGT---------------------CTTGGCTACGCG----------------G----------------------A-TCGCCTTCTATGG--CCGCTCACCTGCGCATCATC s droEre2.scaffold_4845 21604962 110 + 22589142 C---TGTGTGTATC----------------------------TGTGTGT-----AG--CT-------------------------GGC-------TCC-GAT-------------CGAGAGTGCGATCCATC--AGT----------------------CTGCGCGGGTGT---------------------CTTGGCTACACG----------------G----------------------A-TCGCCTTCTATGG--TCGCTCACCTGCGCATCATC s droBia2.KB462602 797712 98 + 3129309 ------------------------------------------TATTCGT-----AT--CT-------------------------TGC-------T-C-CAT-------------CGAGAGTGCGATCCATC--AGT----------------------CTGCGCGGGTGT---------------------CTTGGCTACATA----------------G----------------------G-TTGCCTTCTATGG--TCGCTCACCTGCGCATCATC s droSuz1.KI419649 12042757 97 - 14502029 ------------------------------------------TAT--AT-----AT--CT-------------------------GGA-------TCC-CAT-------------CGAGAGTACGATCCATC--AGT----------------------CTGCGCGGGTGT---------------------CTTGGCTACATA----------------G----------------------A-TTGCCTTCTATGG--TCGCTCACCTGCGCATCATC s droAna3.scaffold_13266 5712022 95 - 19884421 ----------------------------------------------------------CT-------------------------CGG-------CTC-TAT-------------CGAGAGTACGATCCATCCGACT----------------------CTGCGCGGGTGT---------------------CTTTGCCACATA----------------G----------------------GCTTACCTTCTATGGTCTCACTCACCTGCGCATCATC s droBip2.KB464407 1960754 83 + 2915140 ---------------------------------------------------------------------------------------G-------CAT-TAT------------------GTGGTATC---TCGGGT----------------------CTGCGCGGGTGT---------------------CTTGGCTACATA----------------G----------------------GCTTACCTTCTATGGTCTCACTCACCTgcgcatcatc s droEug2.KB465067 602100 117 + 1515531 ------------------------ATGTATACATTTGTAAGTCGTATAT-----AC--CT-------------------------TGC-------TCC-GAT-------------CGAGAGTGCGATCCATC--AGT----------------------CTGCGCGGGTGT---------------------CTTGGCTACATA----------------G----------------------A-TCGCCTTCTATGG--TCGCTCACCTGCGCATCATC s droEle2.KB458573 523208 104 - 5320397 ------------------------------------------TATGTATATAAGAT--CT-------------------------GGC-------TCG-GAT-------------CAAGAGTGCGATCCATC--AGT----------------------CTGCGCGGGTGT---------------------TATGGCTACATA----------------G----------------------A-TTACCTTCTATGG--TCGCTCACCTGCGCATCATC s droKik2.KB459527 277638 99 - 1234237 ------------------------------------------TGTACGT-----TA--TA-------------------------TAT-------CAG-CAT-------------CGAGAGTGCGATCCATC--GAT----------------------CTGCGCGGGTGT---------------------CTTGGCTACATA----------------G----------------------A-TTACCTTCTATGG--TCGCTCACCtgcgcatcatc s droTak2.KB461535 142716 93 - 669855 ------------------------------------------------T-----AT--CT-------------------------GGC-------TCC-GAT-------------CGAGAGTGCGATCCATC--AGT----------------------CTGCGCGGGTGT---------------------CTTGGCTACATA----------------G----------------------A-TCGCCTTCTATGG--TCGCTCACCTGCGCATCATC s droRho2.KB449310 37119 112 - 65043 tgtatattaatata----------------------------tatatat-----at--ct-------------------------gac-------TCG-GAT-------------CGAGAGTGCGATCCATC--AGT----------------------CTGCGCGGGTGT---------------------CTTGGCTACATA----------------G----------------------A-TTACCTTCTATGG--TCGCTCACCTGCGCATCA-C s droFic2.KB457177 82494 105 + 995874 -----------------------------------------TTATGTATTGTAAAT--CT-------------------------GGC-------TGG-TAT-------------CGAGAGTGCGATCCATC--AGT----------------------CTGCGCGGGTGT---------------------CTTGGCTACATA----------------G----------------------A-TCGCCTTCTATGG--TCGCTCACCTGCGCATCATC s droPse3.chr3 1350637 116 - 19787792 -----------------------------------------CCGAGTAT-----AT--AT-------------------------TGC-------GTA-CAT-------------ATCTGCTCGTGTCTATC--GGT----------------------CTGCGCGGGTGT---------------------CTTGGCTATATACTCGAGACTCTGCGCCG----------------------A-TTGCCTTCTATGG--TCGCTCACCTGCGCATCATC s droPer1.super_34 539508 116 - 916997 -----------------------------------------CCGAGTAT-----AT--AT-------------------------TGC-------GTA-CAT-------------ATCTGCTCGTGTCTATC--GGT----------------------CTGCGCGGGTGT---------------------CTTGGCTATATACTCGAGACTCTGCGCCG----------------------A-TTGCCTTCTATGG--TCGCTCACCTGCGCATCATC s droMir2.chr3 1391767 116 - 20862834 -----------------------------------------CCGAGTAT-----AT--AT-------------------------TGC-------GTA-CAT-------------ATCTGCTCGTGTCTATC--GGT----------------------CTGCGCGGGTGT---------------------CTTGGCTATATACTCGAGACTCTGCGCCG----------------------A-TTGCCTTCTATGG--TCGCTCACCTGCGCATCATC s droWil2.CH963894 1310201 97 + 2843958 ---------------------------------------------atgt----------------------------------------------------------------------------atatata--tat----------------------ctgcgCGGGTGT---------------------TTTGACTATATA----------------GTCAGCATAGGCAGGCATACAACA-TTACCTTCTATGGGATCGCTCACCTGCGCATCATC s droVir3.scaffold_12875 7353617 122 + 20611582 ---------------------------------------------CTGT-----TG--CT-GTTGTTG-----------------GGC-------AAC-TTTGCGCCACTTTATACAATACTTATGTATAGC--AAA--CTAATATGCGTAGCTTTTGGCTGCGCGGGTGT--------------------------------------------------------------------------TTGCCTTCTTTGG--TCGCTCACCTGCGCATCTTA s droMoj3.scaffold_6496 26148657 146 + 26866924 ---------------------------------------------ctgc-----gg--ct-attgttgttgttgttgcttttgttgGCGTTAAGCAAC-TTTACGCCACTTTATGCAATACTTATATATAGC--AAA--GCAATATGCGTAGATTTTAGCTGCGCGGGTGT--------------------------------------------------------------------------TTACCTTCTTTGG--TCGCTCACCTGCGCATCTTA s droAlb1.JH854640 310593 145 + 406291 ---------------------------------------------CTGT-----CGTTCT-CTTGTTACTG--------------GGA-------AACTTTTTCGATGTATTATACAACGATTATGTATAGC--AAACTCTCGTAATCACATCTCTTGGCTGCGAGGGTGT---------------------TTTGACTATATA----------------G---------------------CA-TTACCTTCTATGG--TCGCTCACCTGCGCATCACA s droGri2.scaffold_15245 903794 162 + 18325388 ---------------------------------------------ctgc-----tg--ctgGTTGTTGTTG--------------GGC-------AAC-TTTGCGCCACTTTATACAATACTTATGTATAGC--AAA--CTAATATGCGTATATTTTATCTGCGCGGGTGTTTCTTTACTTTGTCTGCTTCTTTTTACTATAGA----------------T---------------------CA-TTACCTTCTTTGG--TCGCTCACCTGCGCATCTTA a score=-43609.000000 s dm6.chr2R 24351351 12 + 25286936 ATCCC------------AGCCGCC------ s droSim1.chr2R 18698062 12 + 19596830 ATCCC------------AGCCGCC------ s droSec1.super_23 117809 12 + 989336 ATCCC------------AGCCGCC------ s droYak3.chr2R 20207200 12 + 21139217 ATCCC------------AGCCGCC------ s droEre2.scaffold_4845 21605072 12 + 22589142 ATCCC------------AGCCGCC------ s droBia2.KB462602 797810 20 + 3129309 ATCTAAA----CATCTGAACCGCC------ s droSuz1.KI419649 12042854 20 - 14502029 ATCTAAA----CATCTGAACCGCC------ s droAna3.scaffold_13266 5712117 17 - 19884421 ATTCA-------AGCCACGCCGCC------ s droBip2.KB464407 1960837 15 + 2915140 atc---------atccaagCCGCC------ s droEug2.KB465067 602217 12 + 1515531 GTCCG------------AACCGCC------ s droEle2.KB458573 523312 12 - 5320397 ATCTA------------AGCCGCC------ s droKik2.KB459527 277737 24 - 1234237 atcatcatcatcatccaaaCCGCC------ s droTak2.KB461535 142809 20 - 669855 ATCTA----AACATCTGAAACGCC------ s droRho2.KB449310 37231 12 - 65043 ATCTA------------AACCGCC------ s droFic2.KB457177 82599 11 + 995874 ACCG-------------AACCGCC------ s droPse3.chr3 1350753 10 - 19787792 TCC--------------ATTCGCC------ s droPer1.super_34 539624 10 - 916997 TCC--------------ATTCGCC------ s droMir2.chr3 1391883 10 - 20862834 TCT--------------ATTCGCC------ s droVir3.scaffold_12875 7353739 12 + 20611582 ------------------AACGCCCACGCC s droMoj3.scaffold_6496 26148803 12 + 26866924 ------------------AACGCCAACGCC s droAlb1.JH854640 310738 6 + 406291 ------------------AACGCC------ s droGri2.scaffold_15245 903956 12 + 18325388 ------------------AACGCCAACGCC a score=252845.000000 s dm6.chr2R 24351363 61 + 25286936 CACG-------------------------AAGCCCGACCAGTAAAAA------C-----------------TGCGAGTTTGTTGGCTTCTGCGAT--T-----CGTATTTATTTCA----- s droSim1.chr2R 18698074 61 + 19596830 CACG-------------------------AAGCCCGACCAGTAAAAA------C-----------------TGCGAGTTTGTTGGCTTCTGCGAT--T-----CGTATTTATTTCA----- s droSec1.super_23 117821 60 + 989336 CACG-------------------------AAGCCCGACCAGTAAAAA------C-----------------TGCGAGTTTGTTGGCTTCTGCGAT--T------ATATTTATTTCA----- s droYak3.chr2R 20207212 61 + 21139217 CACG-------------------------AAGTCGAAGCAGTAAGAA------A-----------------TGCGAGTTTGTTGGCTTCAACGAC--T-----CGTGTTTATTTCA----- s droEre2.scaffold_4845 21605084 61 + 22589142 CACG-------------------------AAGCCCGAGCAGTAAGAA------A-----------------TGCGAGTTTGTTGGCTTTTACGAT--T-----CGTGTTTATTTCA----- s droBia2.KB462602 797830 64 + 3129309 CACG-------------------------AAGCCCAGCCAGTGAAAA------AG-G--------------CGCAAGTTTGTTGGCTTTtacgat--t----ttgtttttatttca----- s droSuz1.KI419649 12042874 64 - 14502029 CACG-------------------------AAGACCAACCAGTAAAAA------AG-G--------------TGCAAGTTTGTTGGCTTTTATGAT--T----Tcgtatttatttca----- s droAna3.scaffold_13266 5712134 72 - 19884421 CAC----------------------------TCCCAACCAGCCGAAA------TA-AA---ACAAAATATCTGCAAGTTTGTTGGCTTTTATGAT--T----TCGTATTTATTCAA----- s droBip2.KB464407 1960852 74 + 2915140 CAC----------------------------TCCAAGACAgtcgaaa------ta-aa---acaaaatagctgcaagtttgttggcttttatgattat----ttctatttatttaa----- s droEug2.KB465067 602229 65 + 1515531 CACG-------------------------AAGCCCCGCCAGTAAGAA------AA-GC-------------TGCAAGTTTGTTGGCTTTTACgat--t----tggtatttatttca----- s droEle2.KB458573 523324 68 - 5320397 CACG-------------------------AAACCCATCCAGTAAAAA------CT-AA---AGC-------TGTAAGTTTGTTGGCTTTTACGAT--T----Tcgtatttattaca----- s droKik2.KB459527 277761 77 - 1234237 CACG-------------------------TGGCCcaaccaataaaaa------at-aaca-ataaaaacactgcaagtttgttggcttttatgat--t----ttgtatttatttca----- s droTak2.KB461535 142829 66 - 669855 CACG-------------------------AAGCCCAACCAGTaaaaa------aa-GC-------------TGCAAGTTTGTTGGCTTGTatgac--t---tttgtttttatttca----- s droRho2.KB449310 37243 65 - 65043 CACG-------------------------AAGCCCAGCCAGTaaaaa------aa-GC-------------TGCAAGTTTGTTGGCTTTTACGAT--T----tcgtatttatttca----- s droFic2.KB457177 82610 66 + 995874 CACG-------------------------GAGCCCAACCATTGAAAA------AACGC-------------TGCAAGTTTGTTGGCTTTTGCgat--t----tcgtatttatttcg----- s droPse3.chr3 1350763 90 - 19787792 CACTACTTCTACATTTTCTATGATcccccagcctcagcccccaGAAA------AG-CA-------------CGCaagtttgttggcttttataat--t----tcgtttttatttca----- s droPer1.super_34 539634 90 - 916997 CACTACTTCTACATTTTCTATGATCCCCCAGCCTCAGCCCCCAGAAA------AG-CA-------------CGCAAGTTTGTTGGCTTTTATAAT--T----TCGTTTTTATTTCA----- s droMir2.chr3 1391893 89 - 20862834 CACTACTTCTACATTTTCTATGat-ccccagcctcagcccccagAAA------AG-CA-------------CGCAagtttgttggcttttataat--t----tcgtttttatttca----- s droVir3.scaffold_12875 7353774 50 + 20611582 ---------------------------------------CACAAAAT------AC-AAA--ATGT------TGTAAGTTTATTGGCTTTAGC--T--T------------TTATTAGTAT- s droAlb1.JH854640 310779 50 + 406291 ---------------------------------------aataaaatgagtaaaa-aaaTCATGT------TTGTAGTTTGTTGGCTTC------------------------TGAGCAt- s droGri2.scaffold_15245 903976 65 + 18325388 ---------------------------------------AATAAAAA------AC-ACAACATGT------TGTAAGTTTATTGGCTTTAGC--T--CAGTTTTATTTTATTTTAAATGTC a score=43986.000000 s dm6.chr2R 24351424 7 + 25286936 AAATTTT s droSim1.chr2R 18698135 7 + 19596830 AAATTTT s droSec1.super_23 117881 7 + 989336 AAATTTT s droYak3.chr2R 20207273 7 + 21139217 AAACTTT s droEre2.scaffold_4845 21605145 7 + 22589142 AAATTTG s droBia2.KB462602 797894 7 + 3129309 acattta s droSuz1.KI419649 12042938 7 - 14502029 aaattta s droAna3.scaffold_13266 5712206 7 - 19884421 TAATTTT s droBip2.KB464407 1960926 7 + 2915140 taattca s droEug2.KB465067 602294 7 + 1515531 aaatttg s droEle2.KB458573 523392 7 - 5320397 aaatttg s droKik2.KB459527 277838 7 - 1234237 aaatttt s droTak2.KB461535 142895 7 - 669855 acatttt s droRho2.KB449310 37308 7 - 65043 aaatttg s droFic2.KB457177 82676 7 + 995874 gAATTTG s droPer1.super_34 539816 7 - 916997 GGATTGT s droVir3.scaffold_12875 7353824 6 + 20611582 -ACTTTT s droAlb1.JH854640 310829 6 + 406291 -gctttt s droGri2.scaffold_15245 904041 6 + 18325388 -GCTTTT a score=28689.000000 s dm6.chr2R 24351431 3 + 25286936 ATT s droSim1.chr2R 18698142 3 + 19596830 ATT s droSec1.super_23 117888 3 + 989336 ATT s droYak3.chr2R 20207280 3 + 21139217 ATT s droEre2.scaffold_4845 21605152 3 + 22589142 ATT s droBia2.KB462602 797901 3 + 3129309 att s droSuz1.KI419649 12042945 3 - 14502029 att s droAna3.scaffold_13266 5712213 3 - 19884421 ATT s droBip2.KB464407 1960933 3 + 2915140 agA s droEug2.KB465067 602301 3 + 1515531 att s droEle2.KB458573 523399 3 - 5320397 att s droKik2.KB459527 277845 3 - 1234237 att s droTak2.KB461535 142902 3 - 669855 att s droRho2.KB449310 37315 3 - 65043 att s droFic2.KB457177 82683 3 + 995874 ATG s droPer1.super_34 539823 3 - 916997 ATG s droAlb1.JH854640 310855 3 + 406291 att s droGri2.scaffold_15245 904047 3 + 18325388 ATT a score=-86975.000000 s dm6.chr2R 24351434 32 + 25286936 CAAGATGTT----ATGCTTCAAAGTTATCAACTATA s droSim1.chr2R 18698145 31 + 19596830 CAAGATGTT----ATAC-TCAAAGTTATGAACTATA s droSec1.super_23 117891 32 + 989336 CAAGATGTT----ATACTTCAATGTTATCAGCTATA s droYak3.chr2R 20207283 24 + 21139217 CAAGATACA----TTACTTCAGCTTTAT-------- s droEre2.scaffold_4845 21605155 32 + 22589142 CAAGATACA----TTACTTCAGTCTTGCGCATCAGC s droBia2.KB462602 798123 28 + 3129309 caatttgTT----TTGATCTAAAATAACCTTT---- s droAna3.scaffold_13266 5712222 32 - 19884421 TTAGTGAGT----TTGCATAACAGTTTTTCTCTGAC s droBip2.KB464407 1960941 32 + 2915140 ttAGTGATT----TTACATAACAGTTCTATGCTTGG s droEug2.KB465067 602304 18 + 1515531 ---tgtgtt----tAGCGTTGACAT----------- s droEle2.KB458573 523629 32 - 5320397 CACGTTCTT----TGGCTTGAACTTTAGTTTCATTG s droKik2.KB459527 277848 27 - 1234237 -----tgtt----ttgcgtgattagttttCAACAAA s droTak2.KB461535 142905 32 - 669855 tgcgTTGCG----TAGCGTtgacataatttaattta s droRho2.KB449310 37318 32 - 65043 tgtgttGCT----TAGCGTTAACATGATTTCAAagg s droFic2.KB457177 82686 22 + 995874 --------------TGCGTTGACATGATTTCAAAGA s droPer1.super_34 539827 32 - 916997 AAGATTCTT----TTGCGATTAATTTACCTTTACGA s droAlb1.JH854640 310858 34 + 406291 GTGAACTTTCGAACTGAGACAGTTTCagacaata-- s droGri2.scaffold_15245 904050 20 + 18325388 TTGAGTGTT----TTGAGTCTGCT------------ a score=3276.000000 s dm6.chr2R 24351466 1 + 25286936 T s droSim1.chr2R 18698178 1 + 19596830 T s droSec1.super_23 117925 1 + 989336 T s droEre2.scaffold_4845 21605189 1 + 22589142 T s droEle2.KB458573 523663 1 - 5320397 t s droTak2.KB461535 143244 1 - 669855 t s droRho2.KB449310 37360 1 - 65043 t s droPer1.super_34 539877 1 - 916997 T s droAlb1.JH854640 310892 1 + 406291 t a score=-20449.000000 s dm6.chr2R 24351467 5 + 25286936 AAA----TG s droSim1.chr2R 18698179 9 + 19596830 AAACATTTT s droSec1.super_23 117926 9 + 989336 AAACATTTT s droYak3.chr2R 20207307 1 + 21139217 -------T- s droEre2.scaffold_4845 21605190 2 + 22589142 A------T- s droBia2.KB462602 798151 5 + 3129309 ----AATTG s droSuz1.KI419649 12043271 5 - 14502029 ----GGATA s droEle2.KB458573 523664 6 - 5320397 ---aaattt s droPer1.super_34 539878 5 - 916997 AAATA---- s droAlb1.JH854640 310893 5 + 406291 aaaaa---- a score=-335414.000000 s dm6.chr2R 24351472 34 + 25286936 CTCTTTTAA-------------------------ATGAT----TGTTG---------------CATGTGTGTATGTAC----------------------------- s droSim1.chr2R 18698188 34 + 19596830 CTCTTTTTC-------------------------ATGAT----TGTTG---------------CATGTGTGTATGTGC----------------------------- s droSec1.super_23 117935 32 + 989336 CTCTTTTTC-------------------------ATGAT----TGTTG---------------CA--TGTGTATGTGC----------------------------- s droYak3.chr2R 20207308 11 + 21139217 -------------------------------------------------------------------TGTGTGCATGC----------------------------- s droEre2.scaffold_4845 21605192 11 + 22589142 -------------------------------------------------------------------TGTGTATTTGC----------------------------- s droBia2.KB462602 798156 51 + 3129309 CTGTTCCTCCCTGCATACCTGCATAT-------TAAACT----ACTCA---------------GATAAAT-CACTTTC----------------------------- s droSuz1.KI419649 12043276 23 - 14502029 CTCTTCTTC-------------------------AAACT----TGTTA--------------------------CTTC----------------------------- s droAna3.scaffold_13266 5712254 28 - 19884421 ------------------------AA-------TTTCAA----TTCTA---------------AATTTAATTATTTTT----------------------------- s droBip2.KB464407 1960973 19 + 2915140 ------------------------A--------------------TCG---------------CATTTAATAGTTTCT----------------------------- s droEle2.KB458573 523670 37 - 5320397 cttttcata---------------aa-------catagt----ttttt---------------tcttttttcggaTGT----------------------------- s droKik2.KB459527 277877 31 - 1234237 ------------------------------------GAG----GGTTGAGAGC-------GATTAAGTGTTTAGATAT----------------------------- s droTak2.KB461535 143245 45 - 669855 ------------caatactcaactaaat--attttttat----ttttt---------------tccccgtGTTCTCCC----------------------------- s droRho2.KB449310 37361 46 - 65043 ------------aaatggtaAATAAAGTG-AGTAGTGCT----GCTCT---------------GACATGTACAAATTA----------------------------- s droFic2.KB457177 82725 10 + 995874 --------------------------------------------------------------------AGCtgtgtta----------------------------- s droPse3.chr3 1351090 32 - 19787792 ----------------------------CTCTTcaaaata---gttta---------------tttttattcaaacaT----------------------------- s droPer1.super_34 539908 35 - 916997 ----------------------------ATCTCTAAAATGTACTCCTC---------------TTTCCGTTTAAATTT----------------------------- s droAlb1.JH854640 310898 59 + 406291 ----------------------------------------atatacaaagaaaTTAGCATGGATCCAAATTAGGATCGCATT--------TATAATGTAGTATATAA s droGri2.scaffold_15245 904070 64 + 18325388 -------------------------------------------TGCTAATCGCTTACAGTGGTGACCCTTTTGACTTTCATTTTTTGCTCTTTGGTACAGTTTCTGC a score=-445357.000000 s dm6.chr2R 24351506 44 + 25286936 TAA-TA-------------------------------G--------CCGAATGAAAT-----T-----------ACTGT-AGCTTGGCA-ATGACTATCTTT s droSim1.chr2R 18698223 39 + 19596830 TAA-TA-------------------------------T--------CCGAATGAAAT---------------------T-GGCTTAGAA-ATGTTTATCTTT s droSec1.super_23 117968 39 + 989336 TAA-TA-------------------------------T--------CCGAATGAAAT---------------------T-GGCTTAGCA-ATGTTTATCTTT s droYak3.chr2R 20207320 25 + 21139217 TAT-TA-------------------------------T--------ACAAATGAAAT-------------------------------------TAGCCGCT s droEre2.scaffold_4845 21605204 46 + 22589142 TAA-AC-------------------------------T--------CCGAATGAAATG---GT-----------TCTTT-CCCTCACGA-TAGCCAGCCGCT s droBia2.KB462602 798208 72 + 3129309 TAA-TATACTCTTTTACCAccttgttattgcctgatga--------AACAGTAAAGT-------------------TAC-AGTATTCCA-TAGAGCATCCCT s droSuz1.KI419649 12043300 40 - 14502029 TGA-TA-------------------------------A--------AGCAGTAAAAT-------------------TTC-AGT-TCCCT-AAGGAAATCCTT s droAna3.scaffold_13266 5712286 41 - 19884421 TAA-TG-------------------------------C--------CGCAACCCATT-------------------TAT-GGCTTGATT-AATTTCCTTCCA s droBip2.KB464407 1960993 37 + 2915140 TAA--------------------------------------------GAAATTCAAT-------------------TCTAaacttgatt--atttttttgtg s droEug2.KB465067 602322 42 + 1515531 -----------------------------------------------GATATTAGTT-----TCAC------TATCCCT-GAGTTGGCA-AACTCTGTTTGT s droEle2.KB458573 523708 63 - 5320397 TGC-CATCGTTttat----------------------t--------cccaaaaaaataaatgtgta------tattCAT-AGAATTTCT-ATGGGTGCCTGC s droKik2.KB459527 277909 81 - 1234237 TAA-CAGTTTTCATAGTTCTGAACTGATTTACTGGGGA--------Actattacaat----atata------ttgTCAA-GGTTGATTA-GGCGAAGTCTCT s droTak2.KB461535 143291 45 - 669855 TGa-catt-----------------------------t--------ccaaataaaat-----------------agtaa-agtTCCACT-CGAGTTTATAGT s droRho2.KB449310 37408 58 - 65043 TGATTA-------------------------------G--------ATGAATCAATTGGTTGTCTAC---TTCaagctt-aatttttta-aaccataatATC s droFic2.KB457177 82736 55 + 995874 taa-aa-------------------------------t--------aacattcagtc-----tattttaatctttattc-ATTCTTTGT-ATGCTTATTTGT s droPse3.chr3 1351127 40 - 19787792 ----------------------------------------------TCAAATGGAAC---------------TAGTTCC-AGTTTCCCATAGTGTTTCCTCT s droPer1.super_34 539949 48 - 916997 --------------------------------GAACCAA------ATCCAATGGAAC---------------TAGTTCC-AGTTTCCTATAGTGTTTCCCCT s droMir2.chr3 1392223 46 - 20862834 --------------------------------TAATCT--------CCAAATGGAAC---------------TAGTTCC-AGTTTCCTCTAGGGTTTCCTCT s droAlb1.JH854640 310957 44 + 406291 --------------------------------------TTGGGGTAGAGAGTGAGCA---------------TGAATAC-GC-TTCTct-actttaattt-- s droGri2.scaffold_15245 904134 50 + 18325388 --------------------------------------TTAGGTTAAATAGCCGATC------------TTTTAAATAT-ATATTGTCA-ACTATCTTTTAT a score=-73959.000000 s dm6.chr2R 24351550 14 + 25286936 TAGTACTGTACTGA s droSim1.chr2R 18698262 14 + 19596830 TACTACTGTACTAA s droSec1.super_23 118007 14 + 989336 TACTACTGTACTAA s droYak3.chr2R 20207345 14 + 21139217 GACTACTGTACTAA s droEre2.scaffold_4845 21605250 14 + 22589142 TACTACTGTACTAA s droBia2.KB462602 798280 6 + 3129309 GAGTTC-------- s droSuz1.KI419649 12043340 6 - 14502029 GAGTTC-------- s droAna3.scaffold_13266 5712327 14 - 19884421 AGCTGTTGAAAAGA s droBip2.KB464407 1961030 14 + 2915140 taatgcCGCATCCC s droEug2.KB465067 602364 6 + 1515531 GATTAC-------- s droEle2.KB458573 523771 9 - 5320397 AATTATTTG----- s droKik2.KB459527 277990 10 - 1234237 GGAAATTTCA---- s droTak2.KB461535 143336 8 - 669855 TCACGTTG------ s droRho2.KB449310 37466 7 - 65043 CGCAATC------- s droFic2.KB457177 82791 14 + 995874 ACCTTTCATATTAA s droPse3.chr3 1351167 14 - 19787792 TTGTACCCTTCTCC s droPer1.super_34 539997 14 - 916997 TTGTACCCTTCTCC s droMir2.chr3 1392269 14 - 20862834 TTGTACCCTTCTCC s droGri2.scaffold_15245 904184 11 + 18325388 GGTTGTATTAA--- s anoGam1.chr3L 3987825 14 + 41284009 TAATGCTGTACTGC a score=-19145.000000 s dm6.chr2R 24351564 8 + 25286936 ACACCTTG--- s droSim1.chr2R 18698276 5 + 19596830 ATACT------ s droSec1.super_23 118021 5 + 989336 ATACT------ s droYak3.chr2R 20207359 5 + 21139217 ATACT------ s droEre2.scaffold_4845 21605264 5 + 22589142 GTACC------ s droBia2.KB462602 798286 5 + 3129309 ATAGT------ s droSuz1.KI419649 12043346 5 - 14502029 ATAGT------ s droAna3.scaffold_13266 5712341 3 - 19884421 TTG-------- s droBip2.KB464407 1961044 3 + 2915140 ATA-------- s droFic2.KB457177 82805 5 + 995874 GTTGT------ s droPse3.chr3 1351181 5 - 19787792 ATACA------ s droPer1.super_34 540011 5 - 916997 ATACA------ s droMir2.chr3 1392283 5 - 20862834 ATACA------ s droAlb1.JH854640 311001 4 + 406291 attg------- s anoGam1.chr3L 3987839 8 + 41284009 ACACC---CGT a score=-82645.000000 s dm6.chr2R 24351572 15 + 25286936 TC--------------TTTGTCATCTT---TC s droSim1.chr2R 18698281 15 + 19596830 TC--------------TTTGTCATCTT---TC s droSec1.super_23 118026 15 + 989336 TC--------------TTTGTCATCTT---TC s droYak3.chr2R 20207364 15 + 21139217 TC--------------TTTGTGATGTT---TT s droEre2.scaffold_4845 21605269 14 + 22589142 TC---------------TTGTGATCCT---TT s droBia2.KB462602 798291 17 + 3129309 TGA------------GTTTGTCAAGCC---TT s droSuz1.KI419649 12043351 17 - 14502029 TGA------------GTTTGTCAAGTT---TT s droBip2.KB464407 1961047 18 + 2915140 --TAT---------GGTTTGATTAATT---TC s droEug2.KB465067 602370 13 + 1515531 ----------------TTCTCAAACTT---AG s droEle2.KB458573 523780 22 - 5320397 ----TATT------GATGTGACCTCTCTGATT s droKik2.KB459527 278000 24 - 1234237 -----ACTGATTAAAAGTTGGCCTAAT---TG s droTak2.KB461535 143344 12 - 669855 -----------------TCAACCTTTT---TT s droRho2.KB449310 37473 15 - 65043 --------------agcttaatatatt---tt s droFic2.KB457177 82822 15 + 995874 --------------TGTTTCTTAACCT---CC s droPse3.chr3 1351196 15 - 19787792 --------------TTCTTTTCGCGTT---CT s droPer1.super_34 540026 15 - 916997 --------------TACTTTTCGCGTT---CT s droMir2.chr3 1392298 15 - 20862834 --------------TACTTTTGGCGTT---CT s droAlb1.JH854640 311005 12 + 406291 -----------------ttgctgaAAT---CT s anoGam1.chr3L 3987847 15 + 41284009 --------------TTCACGTCATCTT---TC a score=-5630.000000 s dm6.chr2R 24351587 1 + 25286936 C--- s droSim1.chr2R 18698296 1 + 19596830 C--- s droSec1.super_23 118041 1 + 989336 C--- s droYak3.chr2R 20207379 1 + 21139217 C--- s droEre2.scaffold_4845 21605283 1 + 22589142 C--- s droBia2.KB462602 798308 1 + 3129309 C--- s droSuz1.KI419649 12043368 1 - 14502029 C--- s droBip2.KB464407 1961065 1 + 2915140 C--- s droEug2.KB465067 602383 1 + 1515531 C--- s droEle2.KB458573 523802 1 - 5320397 C--- s droKik2.KB459527 278024 1 - 1234237 C--- s droTak2.KB461535 143356 1 - 669855 C--- s droRho2.KB449310 37488 1 - 65043 c--- s droFic2.KB457177 82837 1 + 995874 C--- s droPse3.chr3 1351211 1 - 19787792 G--- s droPer1.super_34 540041 1 - 916997 G--- s droMir2.chr3 1392313 1 - 20862834 G--- s droAlb1.JH854640 311017 4 + 406291 GTGC a score=13150.000000 s dm6.chr2R 24351588 15 + 25286936 CTGGCAAATCTAGTG s droSim1.chr2R 18698297 15 + 19596830 CTGGCAAATCTAGTG s droSec1.super_23 118042 15 + 989336 CTGGCAAATCTAGTG s droYak3.chr2R 20207380 15 + 21139217 TGCTCGAATCTAGTG s droEre2.scaffold_4845 21605284 15 + 22589142 TGCTCGAACCTAGTG s droBia2.KB462602 798309 15 + 3129309 TGGTCAAAAGTAATG s droSuz1.KI419649 12043369 15 - 14502029 TGATCAAAACAAATG s droBip2.KB464407 1961066 13 + 2915140 T--TCTAAGCTGTTG s droEug2.KB465067 602384 15 + 1515531 TGATCAAAACTAAGG s droEle2.KB458573 523803 15 - 5320397 TGGTCCAAAGTAATG s droKik2.KB459527 278025 15 - 1234237 TTAACAAAGTTAAGG s droTak2.KB461535 143357 15 - 669855 Ggatcaaaactaatt s droRho2.KB449310 37767 15 - 65043 CTGGTCCACCTAATG s droFic2.KB457177 82838 15 + 995874 TGCAACAAACTTATG s droPse3.chr3 1351218 15 - 19787792 CCTTCAATCCCTGCA s droPer1.super_34 540048 15 - 916997 CCTTCAATCCCTGTA s droMir2.chr3 1392320 15 - 20862834 CCTTCAATCCCTGTA s droAlb1.JH854640 311021 15 + 406291 TCCGCGAACTTATAG a score=-4196.000000 s dm6.chr2R 24351603 13 + 25286936 CTGTGAACTCT-AC s droSim1.chr2R 18698312 13 + 19596830 CTGTGAACTCT-AG s droSec1.super_23 118057 13 + 989336 CTGTGAACTCT-AG s droYak3.chr2R 20207395 14 + 21139217 CTTTGAACCTTGGC s droEre2.scaffold_4845 21605299 13 + 22589142 CTGTGAACCTT-AC s droBia2.KB462602 798324 13 + 3129309 CTCTGATCCCT-GC s droSuz1.KI419649 12043384 13 - 14502029 TTCTGATCCCT-AC s droAna3.scaffold_13266 5712372 11 - 19884421 --CTATGTAGT-TT s droBip2.KB464407 1961085 11 + 2915140 --TTGAATAGT-Tg s droEug2.KB465067 602399 13 + 1515531 TTCTGATCTTA-AC s droEle2.KB458573 523818 13 - 5320397 TGCTGATCTTT-AC s droKik2.KB459527 278058 13 - 1234237 CTTCTTACTTT-GT s droTak2.KB461535 143372 13 - 669855 ttctgATCCCA-AC s droRho2.KB449310 37782 13 - 65043 TTGTGATCCTT-AC s droFic2.KB457177 82853 13 + 995874 TTCTGATTATT-AC s droPse3.chr3 1351233 6 - 19787792 -------CAAT-AC s droPer1.super_34 540063 6 - 916997 -------CAAT-AC s droMir2.chr3 1392335 6 - 20862834 -------CAAT-AC s droAlb1.JH854640 311036 10 + 406291 --CCAATCACG-A- a score=-313474.000000 s dm6.chr2R 24351616 91 + 25286936 CCCC--AG-----------------------TTCCTC-----------ATCAT-TA---------------------------CGTTTTC-TACC-----GAATTAGCTGGAATAGAAAACCCGAGGCA-GAAACAA---------AGACC-----AAACCTCT-GGCCCCGG-------CTTC s droSim1.chr2R 18698325 91 + 19596830 CCCC--AG-----------------------TTCCTC-----------ATCAT-TA---------------------------CGTTTTC-CACC-----GAATTAGCTGGAATAGAAAACCCGAGGCA-GAAACAA---------AGACC-----AAACCTCT-GGCCCCGG-------CTTC s droSec1.super_23 118070 91 + 989336 CCTC--AG-----------------------TTCCTC-----------ATCAT-TA---------------------------CGTTTTC-CACC-----GAATTAGCTGGAATAGAAAACCCGAGGCA-GAAACAA---------AGACC-----AAACCTCT-GGCCCCGG-------CTTC s droYak3.chr2R 20207409 72 + 21139217 CCCC--AA-----------------------TTCCTC-----------ATCAT-TA-----------------------------------------------------GGTATAGAAAAGCCAAGGAAGGAAACAA---------AGACC-----AAACCTCT-GGCCCcgc-------cctc s droEre2.scaffold_4845 21605312 92 + 22589142 CCCC--AA-----------------------TTCCTC-----------ATCAT-TA---------------------------CGTTCTC-CACC-----AAATTAGCTGGCATGGAAAACCCGAGGAATGAAACAA---------AGACC-----GAACCTCT-GGCCCTGG-------CCTC s droBia2.KB462602 798337 84 + 3129309 CCTCCTAA-----------------------TACCTC-----------ATCAT-G-----------------------------GGTCCT-TAGC--------------Agcaggcaaaaacaaaaa---gaaataagcC------AAATT-----GAACCTCT-GGCCCAGGT------TTTC s droSuz1.KI419649 12043397 84 - 14502029 CCTCTTAA-----------------------TACCTC-----------ATCAT-T-----------------------------GGTCTT-TACC--------------AGCAGGCAAAATCTAAAA---GAAACAAGCC------AAACT-----GAACCTCT-GGCCCAGCT------TTTC s droAna3.scaffold_13266 5712383 69 - 19884421 TTCC--TA-----------------------CAATCT------GTACTATTTG-TA---------------------------CTTTTTC-TG--------------------------------------AAGCTA---------ATTTT-----GTAGCTCT--GCTGCAGTCCTTA-TTTC s droBip2.KB464407 1961096 83 + 2915140 cttg--aa-----------------------taaattaaa-gaaaactagGTT-TA---------------------------TTTTCCC-TGC------------------------AATCTGCT----AAAGCTA---------ATTTT-----GTACCTCT-GGCCCCAATCCT---TTGG s droEug2.KB465067 602412 81 + 1515531 CTTTTCAA-----------------------TGACCC-----------ATCAT-TG---------------------------AGCCTTCTTACC-----CATTTacctaaaagaaaaaacc--------aaaatga---------------------accACT-GGCCCAAGT------TCCC s droEle2.KB458573 523831 95 - 5320397 CCTCTTGC-----------------------CACCTC-----------ATCAG-GG----G----------------------ACCTTTC-TGTT-----GAATTACCTGCAAGCAGAAATAAGAC----CAAACAAAGG------AAGTC-----GAACCTCT-GGCCCAAGT------TTTC s droKik2.KB459527 278071 144 - 1234237 Tccc--aaattaaacaaaaaaccctttagtttttctt-----------agttt-tg----gCTGTACTACTTCTTCCCACCTCTTGTTTC-TGCCTTCTGAAGTCATCccagctaaaaaataaaata---aaaaccatccT-----AAATT-----GAACCTCT-GGCCCTGT-------TTTT s droTak2.KB461535 143385 85 - 669855 CCCCTAAA-----------------------TACCTC-----------ATCAT-TG----------------------------GCCTTA-AGCA--------------gccagcaaaaaacaaaac---gaaataaaCC------AAATC-----GAACCTCT-GGCCCAGGT------TTTC s droRho2.KB449310 37795 95 - 65043 CCTCTTGC-----------------------CACCTC-----------ATCAG-GG----G----------------------TCTTTTC-TGCT-----GAATTACCTGCAAGCTGAAATAAGAC----AAAACAAACC------CAATC-----GAACCTCT-GGGCCAAGT------TTTC s droFic2.KB457177 82866 90 + 995874 TCTCTTAC-----------------------CACCTC-----------CTCATGTG---------------------------ACTTTTC-TGCC-----GGTCTACCTGCaggagaaaca---------aaaacaaaac------aaggc-----GAACTTCT-GGCCCAAGT------TTCT s droPse3.chr3 1351239 114 - 19787792 CCTC--GG-----------------------CAACTCCAATTTGTTCGAACGC-TG----ATT--------------------CATTTTC-CAGC-----GAACCAGCTCCCGAACCGATCCT-------GAAGCGATCCTCTAGCAATCCCCCAGCAACCTCC-GGCCCGCtc------ttcc s droPer1.super_34 540069 120 - 916997 CCTC--TG-----------------------CAACTCCAATTTGTTCGACCGC-TG----ATT--------------------CATTTTC-CAGC-----GAACCAGCTCCCGAACCGATCCT-------GAAGCGATCCTCTAGCAATCCCCCAGCAACCTCC-GGCCCGCTCCTCCAGCTCC s droMir2.chr3 1392341 114 - 20862834 CCTC--TG-----------------------CAACTCCAATTTGTTCGACCGC-TG----ATT--------------------CATTTTC-CAGC-----GAACCAGCTCCCGAACCGATCCT-------GAAGCGATCCTCTAGCAATCCCCCGGCAACCTCC-TGcccgctc------ctcc s droVir3.scaffold_12875 7354308 93 + 20611582 CCCA--AA-----------------------GTCCAC-----------CTCCT-CGCGCCGCA--------------------ACTCCTC-CAAC-----TGCTTAGCTCTTGTCCACAAACACATACA-CACACGG---------ACACA-----CATGTTCTTGGCCCC------------- s droAlb1.JH854640 311046 66 + 406291 -AGC--GA-----------------------GTTCgc-----------tcaat-tg-----------------------------------caat-----tgcttaaCCGGTAGC----------TCCA-CTCGCTG---------CCCTC-----cggcttct--gcttc------------- a score=22946.000000 s dm6.chr2R 24351707 22 + 25286936 CTCCTC------------------------------GG---CGGTGGGAGCAC-------GG- s droSim1.chr2R 18698416 22 + 19596830 CTCCGC------------------------------GG---CGGTGGGAGCAC-------GG- s droSec1.super_23 118161 22 + 989336 CTCCGC------------------------------GG---CGGTGGGAGCAC-------GG- s droYak3.chr2R 20207481 52 + 21139217 ctcctcctcctccacctcctcctgctcctcggcAGTGG---AAGCGGGAGCAC-------GG- s droEre2.scaffold_4845 21605404 22 + 22589142 CTCCTC------------------------------GG---CAGTGGGAGCAC-------GG- s droBia2.KB462602 798421 22 + 3129309 CTCCAC------------------------------GG---CAGTGGGAGCAC-------GG- s droSuz1.KI419649 12043481 22 - 14502029 CTCCAC------------------------------GC---CAGTGGGAGCAC-------GG- s droAna3.scaffold_13266 5712452 22 - 19884421 TTTCCT------------------------------CG---AAGGGGCCACGG-------GG- s droBip2.KB464407 1961179 22 + 2915140 TTTTCT------------------------------GG---AAGGGGCCACGG-------GG- s droEug2.KB465067 602493 8 + 1515531 CTCCTC------------------------------------------------------GG- s droEle2.KB458573 523926 22 - 5320397 CTCCAC------------------------------GG---CAGTGGGAGCAC-------GG- s droKik2.KB459527 278215 28 - 1234237 CTACTC-------------------------CTGAGAA---GAGTGGGAGCCCT------GG- s droTak2.KB461535 143470 22 - 669855 CTCCAC------------------------------GC---CAGTGGGAGCAC-------GG- s droRho2.KB449310 37890 22 - 65043 CTCCTC------------------------------GG---CAGTGGGAGCAC-------GG- s droFic2.KB457177 82956 22 + 995874 CTCCGC------------------------------GG---CAGTGGGAGCAC-------GG- s droPse3.chr3 1351353 25 - 19787792 agctcc------------------------------agctacagagGGAGCAC-------GA- s droPer1.super_34 540189 25 - 916997 AGCTCC------------------------------AGCTACAGAGGGAGCAC-------GA- s droMir2.chr3 1392455 25 - 20862834 agctcc------------------------------agctacagagGGAGCAC-------GA- s droVir3.scaffold_12875 7354406 23 + 20611582 CGGATC------------------------------GA---ACCTGGGCACAC-------TAA s droMoj3.scaffold_6496 26149499 30 + 26866924 CCCCTC------------------------------GT---GGCTGTGCGCACTGTACAGTAA s droAlb1.JH854640 311118 23 + 406291 gaCTTC------------------------------GG---CTTCGGTTGGCC-------AAA a score=229389.000000 s dm6.chr2R 24351729 11 + 25286936 GTGCATATCAG s droSim1.chr2R 18698438 11 + 19596830 GTGCATATCAG s droSec1.super_23 118183 11 + 989336 GTGCATATCAG s droYak3.chr2R 20207533 11 + 21139217 GTGCATATCAG s droEre2.scaffold_4845 21605426 11 + 22589142 GTGCATATCAG s droBia2.KB462602 798443 11 + 3129309 GTGCATATCAG s droSuz1.KI419649 12043503 11 - 14502029 GTGCATATCAG s droAna3.scaffold_13266 5712474 11 - 19884421 GTGCATATCAG s droBip2.KB464407 1961201 11 + 2915140 GTGCATATCAG s droEug2.KB465067 602501 11 + 1515531 GTGCATATCAG s droEle2.KB458573 523948 11 - 5320397 GTGCATATCAG s droKik2.KB459527 278243 11 - 1234237 GTGCATATCAG s droTak2.KB461535 143492 11 - 669855 GTGCATATCAG s droRho2.KB449310 37912 11 - 65043 GTGCATATCAG s droFic2.KB457177 82978 11 + 995874 GTGCATATCAG s droPse3.chr3 1351378 11 - 19787792 GTGCATATCAG s droPer1.super_34 540214 11 - 916997 GTGCATATCAG s droMir2.chr3 1392480 11 - 20862834 GTGCATATCAG s droVir3.scaffold_12875 7354429 11 + 20611582 GTACATATCAG s droMoj3.scaffold_6496 26149529 11 + 26866924 ATACATATCAG s droAlb1.JH854640 311141 11 + 406291 GTACATATCAG s droGri2.scaffold_15245 904945 11 + 18325388 GTACATATCAG a score=4787529.000000 s dm6.chr2R 24351740 411 + 25286936 TTTGAGAAATTAAAAGCATTTTGCGGTTTCGCT--GACTATCGA----CGCTGCGTGCCGCT----------------------------CGAGCCT-------------------CTAACGACATTTCAATGATTtgctgcttggc---tctgg-c---------------------------tgcagttg----ctg--------ttgctgcggc---------tgctg---ct---------------------------------g------ctgctgcG------CCTGT------AACA-TGGCCACGTGCGCAGCACAAGAC------------------GCA------------------------GGC---------------G------------------GA-------GGACA-------------------------------------------------------CAA-----GCATTTGCA---ATGCTCGT----------------------------CGATTACGTACGAGGGCGACCTCTGT-----CAGGCAGC--------------------------------------------------GTCCA-------------------------G---CT----GT----CC--GAA--AGCCACCAACAACGC------------AGCCACGCAAGGAATC-------------------------------------------TC------------------------------------------------------C-------TCCGC------------------GG----------------------------ATTT------------------------------------------------------------------------TG-TGT-TTAAGCCGCCGC----T--------------GCGAGTTCTAACCGCATGCCGCCACAATGTCCTCTTAATTTCCT----A-------------------------G---CC--CGC-GC----------TCACCACGCGATGATATCGCCGG------CGATCCACT--------------GGA---------GGGAC-------CCC s droSim1.chr2R 18698449 423 + 19596830 TTTGAGAAATTAAAAGCATTTTGCGGTTTCGCT--GACTATCGA----CGCTGCGTGCCGCT----------------------------CGAGCCT-------------------CTAACGACATTTCAATGATTTGCTGCTTGGC---TCTGG-C---------------------------CGCAGTtg----ctg--------ttgctgctgc---------tgttg---ttgc---------------------ggctgctgctg------ctgctgcG------CCTGC------AACA-TGGCCACGTGCGCAGCACAAGAC------------------GCA------------------------GGC---------------G------------------GA-------GGACA-------------------------------------------------------CAA-----GCATTTGCA---ATGCTCGT----------------------------CGATTACGTACGAGGGCGACCTCTGT-----CAGGCAGC--------------------------------------------------GTCCA-------------------------G---CT----GT----CC--GAA--AGCCACCAACAACGC------------AGCCACGCAAGGAATC-------------------------------------------TC------------------------------------------------------C-------TCCGC------------------GG----------------------------ATTT------------------------------------------------------------------------TG-TGT-TTAAGCCGCCGC----T--------------GCGAGTTCTAACCGCATGCCGCCACAATGTCCTCTTAATTTCCT----A-------------------------G---CC--CGC-GC----------TCACCACGCGATGATATCGCCGG------CGATCCACT--------------GGA---------GGGAC-------CCC s droSec1.super_23 118194 414 + 989336 TTTGAGAAATTAAAAGCATTTTGCGGTTTCGCT--GACTATCGA----CGCTGCGTGCCGCT----------------------------CGAGCCT-------------------CTAACGACATTTCAATGATTTGCTGCTTGGC---TCTGG-C---------------------------CGCAGTtg----ctg--------ttgctgctgc---------tgttg---ttgc---------------------g---------g------ctgctgcG------CCTGC------AACA-TGGCCACGTGCGCAGCACAAGAC------------------GCA------------------------GGC---------------G------------------GA-------GGACA-------------------------------------------------------TAA-----GCATTTGCA---ATGCTCGT----------------------------CGATTACGTACGAGGGCGACCTCTGT-----CAGGCAGC--------------------------------------------------GTCCA-------------------------G---CT----GT----CC--GAA--AGCCACCAACAACGC------------AGCCACGCAAGGAATC-------------------------------------------TC------------------------------------------------------C-------TCCGC------------------GG----------------------------ATTT------------------------------------------------------------------------TG-TGT-TTAAGCCGCCGC----T--------------GCGAGTTCTAACCGCATGCCGCCACAATGTCCTCTTAATTTCCT----A-------------------------G---CC--CGC-GC----------TCACCACGCGATGATATCGCCGG------CGATCCACT--------------GGA---------GGGAC-------CCC s droYak3.chr2R 20207544 471 + 21139217 TTTGAgaaattaaaagcattttgcGGTTTCGCT--GACTATCGA----AGCTGCGTGCCGCT----------------------------CGAGCCT-------------------CTAACGACATTTCAATGATttgctgcttggc---tctgg-c---------------------------tgcagttg----cag--------ttgctgctgt---------tgcgg---ctgctgttgcagttgctgctgt---tgcggctgctgttgcgactgctgcg------gctgc------AACA-TGGCCACGTGCGCAGCACAAGAC------------------GCAGG---------------------CGGC---------------G------------------GA-------GGACA-------------------------------------------------------CAA-----GCATTTGCA---ATGCTCGT----------------------------CGATTACGTACGAGGGCGACCTCTGTCAGCACAGGCAGC--------------------------------------------------GTCCA------------------GCTGTCCG---CT----GT----CC--AAA--AGCCACCAACAACGC------------AGCCACGCAAGGAATC-------------------------------------------TC------------------------------------------------------C-------TCCGC------------------GG----------------------------ATTT------------------------------------------------------------------------TG-TGT-TTAAGCCGCCGC----T--------------GCGAGTTCTAACCGCATGCCGCCACAATGTCCTCTTAATTTCCT----A-------------------------G---CC--CGC-GC----------TCACCACGCGATGATATCGCCGG------CGATCCTCT--------------GGAAGCCGAGGGGGGAC-------tcc s droEre2.scaffold_4845 21605437 422 + 22589142 TTTGAGAAATTAAAAGCATTTTGCGGTTTCGCT--GACTATCGA----AGCTGCGTGCCGCT----------------------------CGAGCCT-------------------CTAACGACATTTCAATGATTtgctgct-----------------------------------------tgcagttg----cgg--------ttgctgctgt---------tgcgg---ctgc---------------------tgcggctgctg------ctgctgcG------CCTGC------AACA-TGGCCACGTGCGCAGCACAAGAC------------------GCAGG---------------------CGGC---------------G------------------GA-------GGACA-------------------------------------------------------CAA-----GCATTTGCA---ATGCTCGT----------------------------CGATTACGTACGAGGGCGACCTCTGT-----CAGGCAGC--------------------------------------------------GTCCA-------------------------G---CT----GT----CC--AAA--AGCCACCAACAACGC------------AGCCACGCAAGGAATC-------------------------------------------TC------------------------------------------------------C-------TCCGC------------------GG----------------------------ATTT------------------------------------------------------------------------TG-TGT-TTAAGCCGCCGC----T--------------GCGAGTTCTAACCGCATGCCGCCACAATGTCCTCTTAATTTCCT----A-------------------------G---CC--CGC-GC----------TCACCACGCGATGATATCGCCGG------CGATCCTCT--------------GGAAGCCCCTGCAGG----------CC s droBia2.KB462602 798454 459 + 3129309 TTTgagaaattaaaagcattttgcgGTTTCGCT--GACTATCGA----AGCTGCGTGCCGCT----------------------------CGAGCCT-------------------CTAACGACATTTCAATGATttgctgcttggctgttgttg-c---------------------------tgctgttg----ctg--------ctgatgttgctgccgtgcttgctg---ttgc-----------gagttgc---tgctgctgctg------ctgctgcggctgctgctgc------aaca-tgGCCACGTGCGCAGCACAAGAC------------------GCA------------------------GGC---------------G------------------GA-------GGACA-------------------------------------------------------AAA-----GCATTTGCA---ATGCTCGT----------------------------CGATTACGTACGAGGGCGACCTCTGT-----CAGCCAGC--------------------------------------------------GTCCA-------------------------G---CT----GT----CC--AAA--AGCCACCAACAACGC------------AGGAACCCGAGGAATC-------------------------------------------TC------------------------------------------------------C-------TCTGC------------------GG----------------------------ATTT------------------------------------------------------------------------TG-TGT-TTAAGCCGCCGC----A--------------GCGAGTTCTAACCGCATGCCGCCACAATGTCCTCTTAATTTCCTAGTGA-------------------------G---CG--CGG-GC----------TCACCACGCGATGATATCGCCGG------CGATCCTCC--------------AGAGccccca--ggaac-------ccc s droSuz1.KI419649 12043514 441 - 14502029 TTTGAgaaattaaaagcattttgcGGTTTCGCT--GACTATCGA----AGCTGCGTGCCGCT----------------------------CGAGCCT-------------------CTAACGACATTTCAATGATttgctgtttggc---tgttg-c---------------------------tgctgctg----ctg--------ctgatgttgc---------tgctg---ttgc-----------aagttgc---tgctgctgctg------ctgctgcg------gctgc------aaCA-TGGCCACGTGCGCAGCACAAGAC------------------GCA------------------------GGC---------------G------------------GA-------GGACA-------------------------------------------------------AAA-----GCATTTGCA---ATGCTCGT----------------------------CGATTACGTACGAGGGCGACCTCTGT-----CAGCCAGC--------------------------------------------------GTCCA-------------------------G---CT----GT----CC--AAA--AGCCACCAACAACGC------------AGGAACCCAAGGAATC-------------------------------------------TC------------------------------------------------------C-------TCTGC------------------GG----------------------------ATTT------------------------------------------------------------------------TG-TGT-TTAAGCCGCCGC----A--------------GCGAGTTCTAACCGCATGCCGCCACAATGTCCTCTTAATTTCCTAGTGA-------------------------G---CG--CGG-GC----------TCACCACGCGATGATATCGCCGG------CGATCCTCC--------------AGAGCCCCCA--GAAAC-------CCC s droAna3.scaffold_13266 5712485 538 - 19884421 TTTGAGAAATTAAAAGCATTTTGCGGTTCTCCT--GACTATCGA----TGCTGCGTGCCGCT----------------------------CGAGCCT-------------------CTAACGACATTTCAATGATTTGCTGTTTGGT---TGTTG-C---------------------------T-----------------CCTGCTTGCTACTCC---------TGGTG---CTCC-----------------------------TGG------CTGGCGCG------TCACC------AACA-TGGCCACGTGCGCAGCAC------------------------CA------------------------GGC---------------G------------------GA-------GGACAAAGGCAACAACAAGAGGAGGCACCAACGCAAAAGCAAAACCAAAAAGCTAAACCAAAA-----GCATTTCCA---ATGCTCGT----------------------------CGATTACGTACGAGGGCGACCTCTGT-----CAGGCAGC--------------------------------------------------GTCCA-------------------------G---CT----GT----CC--AAA--AGCCACCAACAACGC------------AGCCACGCAAGGAATC------TTATGCTGCAGTCCATCTGTATATCCGTGTGTGTGTGCC------------------------------------------------------T-------CTTGC------------------GG----------------------------ATTT------------------------------------------------------------------------TG-TGT-TTAAGCCGCCGC----T--------------GCAAGTTCTAACCGCATGCCGCCACAATGTCCTCTTAATTTCCT----AGCC-------GCAGCAGCAGC---TG---CG--CGC-GCGCCTTCTCT-TCTATACGCGATGATATCGCAGA------TCCACCTCCTCCTCCTCCAT---GGACTACCCA--GGAAC-------CTG s droBip2.KB464407 1961212 533 + 2915140 TTTGAgaaattaaaagcattttgCGGTTCTGCT--GACTATCGA----TGCTGCGTGCCGCT----------------------------CGAGCCT-------------------CTAACGACATTTCAATGATTtgctgttttgc---tgttg-c---------------------------tgctgctg----ctgctgcctgctgcctgctcc---------tgttg---ctCC------TTCTGTTGTGGT---TGTGGCTGTGG------CAGGCGCG------TCACC------AACA-TGGCCACGTGCGCAGCAC------------------------CA------------------------GGC---------------G------------------GA-------GGACAAAGCCAACAACA----------------------------CAAGAGCTCCAAGCTCAA-----GCATTTGCA---ATGCTCGT----------------------------CGATTACGTACGAGGGCGACCTCTGT-----CAGGCAGC--------------------------------------------------GTCCA-------------------------G---CT----GT----CC--AAA--AGCCACCAACAACGC------------AGCAACGCAAGGAATC-----TTTGTGCCACAG--------------AGTCAGTATATGCC------------------------------------------------------T-------CTTGC------------------GG----------------------------ATTT------------------------------------------------------------------------TG-TGT-TTAAGCCGCCGC----T--------------GCAAGTTCTAACCGCATGCCGCCACAATGTCCTCTTAATTTCCT----AGCC-------GCAGCAGCTgc----g---cg--cgc-gcgcTTCTTCTCTCTATACGCGATGATATCGCAGA------ACcacctccttctcctccttcgATGACTACCCA--AGAAC-------CAG s droEug2.KB465067 602512 421 + 1515531 TTTGAgaaattaaaagcattttgcGGTTTCCCT--GACTATCGA----AGCTGCGTGCCGCT----------------------------CGAGCCT-------------------CTAACGACATTTCAATGATttgctgcttggc---ttttg-c---------------------------t---gttg----ctg--------ttgctgctgc---------tgctg---ctgc---------------------------tgtgc------ttgcAACA------GTTGC------AACA-TGGCCACGTGCGCAGCACAAGAC------------------GCA------------------------GGC---------------G------------------GA-------GGACA-------------------------------------------------------AAA-----GCATTTGCA---ATGCTCGT----------------------------CGATTACGTACGAGGGCGACCTCTGT-----CAGCCAGC--------------------------------------------------GTCCA-------------------------G---CT----GT----CC--AAA--AGCCACCAACAACGC------------AGCCACGCAAGGAATC-------------------------------------------TC------------------------------------------------------C-------TCCGC------------------GG----------------------------ATTT------------------------------------------------------------------------TG-TGT-TTAAGCCGCCGC----T--------------GCGAGTTCTAACCGCATGCCGCCACAATGTCCTCTTAATTTCCT----A-------------------------G---CC--CGC-GC----------TCACCACGCGATGATATCGCCGG------CGATCCTCC--------------AGAGCCCCCA--GGAAC-------TGC s droEle2.KB458573 523959 445 - 5320397 TTtgagaaattaaaagcattttgcgGTTGCGCT--GACTATCGA----TGCTGCGTGCCGCT----------------------------CGAGCCT-------------------CTAACGACATTTCAATGATttgctgtttgct---tgttg-c---------------------------tgctgttg----ctg-------cttgctgctgc---------ttatg---ttgc------tgctgatgccgc--ttgctgttgctg------ctgctgcg------tcaGC------AACA-TGGCCACGTGCGCAGCACAAGAC------------------GCA------------------------GGC-------TGGCTGGAG------------------GA-------GGACA-------------------------------------------------------AAA-----GCATTTGCA---ATGCTCGT----------------------------CGATTACGTACGAGGGCGACCTCTGT-----CAGCCAGC--------------------------------------------------GTCCA-------------------------G---CT----GT----CC--AAA--AGCCACCAACAACGC------------AGCCACGCAAGGAATC-------------------------------------------TC------------------------------------------------------C-------AGTGC------------------GG----------------------------ATTT------------------------------------------------------------------------TG-TGT-TTAAGCCGCCGC----T--------------GCAAGTTCTAACCGCATGCCGCCACAATGTCCTCTTAATTTCCT----A-------------------------G---CC--CGC-GC----------TCACCACGCGATGATATCGCCGG------CGATCCTCC--------------AGT---------GGAGC-------CCC s droKik2.KB459527 278254 500 - 1234237 TTTGagaaattaaaagcattttgcGGTTTCGTT--GACTATCGA----GGCTGCGTGCCGCT----------------------------CGAGCCT-------------------CTAACGACATTTCAATGATTtgctgtttggc---tgccg-t---------------------------tgctgctc----ctg--------ctcctgctcc---------cgctc---ctgt---------------------ctctgcttctg------ctgctgct------cctactGGGGGGATG-TGGCCACGTGCGCAGCACAAGAC------------------GCA------------------------GATGCAGACGCAGACGAAG------------------GA-------GGACA-------------------------------------------------------AAA-----GCATTTGCA---ATGCTCGT----------------------------CGATTACGTACGAGGGCGACCTCtgt-----cagccagca---------gcagccg-cggcAGCGTCCAGATGTCCACAT---------GTCCA-------------------------G---CT----GT----CC--GAA--AGCCACCAACAACGC------------AGCCACGCAAAGAATC-------------------------------------------TT------------------------------------------------------TCGGCCAGTTTGC------------------GG----------------------------ATTT------------------------------------------------------------------------TG-TGT-TTAAGCCGCCGC----T--------------TCAAGTTCTAACCGCATGCCGCCACAATGTCCTCTTAATTTCCT----AGTC-------GCCGCAGCTgcgcgcg---cg--cgc-gc----------TCTCCACGCGATGATATCGCCGA------CGATCCTCC--------------TGCA--------GGGGC-------CA- s droTak2.KB461535 143503 408 - 669855 TTTGAgaaattaaaagcattttGCGGTTTCGCT--GACTATCGA----AGCTGCGTGCCGCT----------------------------CGAGTCT-------------------CTAACGACATTTCAATgat------------------------------------------------------------------------ttgctgttgc---------t------------------------------------------g------ctgctgcg------cctgc------aACA-TGGCCACGTGCGCAGCACAAGAC------------------GCAGGA--------------------AGGC---------------G------------------GA-------GGACA-------------------------------------------------------AAA-----GCATTTGCA---ATGCTCGT----------------------------CGATTACGTACGAGGGCGACCTCTGT-----CAGCCGGG------------------TTCCAGGCTCCAGGTTCCAGCTTCCA------GTCCA-------------------------G---CT----GT----CC--AAA--AGCCACCAACAACGC------------AGGAACCCAAGGAATC-------------------------------------------TC------------------------------------------------------C-------TCTGC------------------GG----------------------------ATTT------------------------------------------------------------------------TG-TGT-TTAAGCCGCCGC----T--------------GCGAGTTCTAACCGCATGCCGCCACAATGTCCTCTTAATTTCCTAGTGA-------------------------G---CG--CGG-GC----------TCACCACGCGATGATATCGCCGG------CGatcctcc--------------agaatcccc------------------ s droRho2.KB449310 37923 433 - 65043 TTTGagaaattaaaagcattttgcGGTTTCGCT--GACTATCGA----AGCTGCGTGCCGCT----------------------------CGAGCCT-------------------CTAACGACATTTCAATGATttgctgtttggctgttcttg-t---------------------------tggagttg----ctg--------ctgctgctgg---------tgatg---ttgc------tgctgtgcttgcaactgttgctgctg------ctgctgcg------tcaGC------AACA-TGGCCACGTGCGCAGCACAAGAC------------------GCA------------------------GGC---------------G------------------GA-------GGACA-------------------------------------------------------AAA-----GCATTTGCA---ATGCTCGT----------------------------CGATTACGTACGAGGGCGACCTCTGT-----CAGCCAGC--------------------------------------------------GTCCA-------------------------G---CT----GTCCAGCC--AAA--AGCCACCAACAACGC------------AGCCACGCAAGGAATC-------------------------------------------TC------------------------------------------------------C-------TTCGC------------------GG----------------------------ATTT------------------------------------------------------------------------TG-TGT-TTAAGCCGCCGC----T--------------GCAAGTTCTAACCGCATGCCGCCACAATGTCCTCTTAATTTCCT----A-------------------------G---CC--CGC-GC----------TCACCACGCGATGATATCGCCGG------AGatcctc------------------------------------------ s droFic2.KB457177 82989 430 + 995874 TTTGagaaattaaaagcattttgcgGTTTGGCT--GACTATCGA----AGCTGCGTGCCGCT----------------------------CGAGCCT-------------------CTAACGACATTTCAATGATttgctgttcggc---tgttg-c---------------------------tgctgcgg----ctg--------ccgatgttgc---------tgctgtgcctgc---------------------aacagttgctg------ctgctgcg------tcagC------AACA-TGGCCACGTGCGCAGCACAAGAC------------------GCA------------------------GGC---------------G------------------GA-------GGACAAAGGCA-------------------------------------------------CAG-----GCATTTGCA---ATGCTCGT----------------------------CGATTACGTACGAGGGCGACCTCTGT-----CAGGCAGC--------------------------------------------------GTCCA-------------------------G---CT----GT----CC--AAA--AGCCACCAACAACGC------------AGCCACGCAAGGAATC-------------------------------------------TC------------------------------------------------------C-------AGTGT------------------GG----------------------------ATTT------------------------------------------------------------------------TG-TGT-TTAAGCCGCCGC----T--------------GCGAGTTCTAACCGCATGCCGCCACAATGTCCTCTTAATTTCCT----A-------------------------G---CC--CGC-GC----------TCACCACGCGATGATATCGCCGG------CGatcctcc--------------agaggtccc------------------ s droPse3.chr3 1351389 538 - 19787792 TTTGAgaaattaaaagcattttGCGGTTCCGCT--GACTATCGA----TGCTGCGTGCCGCT----------------------------CGAGCCT-------------------CTAACGACATTTCAAtgatttgctg--ttgc---tgttg-c---------------------------tgttgctg----ttg--------ctgctgctgc---------tgctg---ctgt---------------------tgcggcagCAA------CAGACGCG------TCACC------AAGT-TAGCCACGTGCGCAGCACAAgac------------------gcaggagcagcaggcggaggaggtggagga---------------g------------------ga-------gtaca-------------------------------------------------------AAA-----GCATTCGCA---ATGCTCGT----------------------------CGATTACGTACGAGGGCGACCTCTGT-----CAGGCATC--------------------------------------------------GTCCA-------------------------G---CT----GT----CC--AAA--AGCCACCAACAACGC------------AGCCACGCAAGGAATCTTGGCTTTGGGTTaacttctttctctctctctctctctctctctctctctgtgtgtgcgtg-------------------------tgtgtgtgtgt--c-------ttggc------------------GG----------------------------ATTT------------------------------------------------------------------------TG-TGT-TTAAGCCGCCGC----T--------------GCAAGTTCTAACCGCATGCCGCCACAATGTCCTCTTAATTTCCT----AGCCCCCAAcgtcagcagctgct---g---cg--cgC-GC----------TCTCCACGCGATGATATCGTCGC------CGG--CTTC--------------AGATCC------AGAAC-------GAG s droPer1.super_34 540225 531 - 916997 TTTGAGAAATTAAAAGCATTTTGCGGTTCCGCT--GACTATCGA----TGCTGCGTGCCGCT----------------------------CGAGCCT-------------------CTAACGACATTTCAATGATTTGCTGTTTtgc---tgttg-c---------------------------tgttgc-------tg--------ctgctgctgc---------tgctg---ctgt---------------------tgcGGCAGCAA------CAGACGCG------TCACC------AAGT-TAGCCACGTGCGCAGCACAAGAC------------------GCAGGAGCAGCAGGCGGAGGAGGTGGAGGA---------------G------------------GA-------GTACA-------------------------------------------------------AAA-----GCATTCGCA---ATGCTCGT----------------------------CGATTACGTACGAGGGCGACCTCTGT-----CAGGCATC--------------------------------------------------GTCCA-------------------------G---CT----GT----CC--AAA--AGCCACCAACAACGC------------AGCCACGCAAGGAATCTTGGCTTTGGGTTAACTtctttctctctctctctctctctctgtc------tGTGTGTGCG-------------------------TGTGTGTGTGT--C-------TTGGC------------------GG----------------------------ATTT------------------------------------------------------------------------TG-TGT-TTAAGCCGCCGC----T--------------GCAAGTTCTAACCGCATGCCGCCACAATGTCCTCTTAATTTCCT----AGCCCCCAACGGCAGCAGCTGCT---G---CG--CGC-GC----------TCTCCACGCGATGATATCGTCGC------CGG--CTTC--------------AGATCC------AGAAC-------CAG s droMir2.chr3 1392491 535 - 20862834 TTTGAgaaattaaaagcattttgcGGTTCCGCT--GACTATCGA----TGCTGCGTGCCGCT----------------------------CGAGCCT-------------------CTAACGACATTTCAATgatttgctgttttgc---tgttg-c---------------------------tgt----------tg--------ctgctgctgc---------tgctg---ctgt---------------------tgcggcagcaa------cagacgCG------TCACC------AAGT-TAGCCACGTGCGCAGCACAAgac------------------gcaggagcagcaggcggaagaggtggagga---------------g------------------ga-------gtaca-------------------------------------------------------aAA-----GCATTCGCA---ATGCTCGT----------------------------CGATTACGTACGAGGGCGACCTCTGT-----CAGGCATC--------------------------------------------------GTCCA-------------------------G---CT----GT----CC--AAA--AGCCACCAACAACGC------------AGCCACGCAAGGAATCTTGGCTTTGGGTTaacttctttttctctctctctctctctctctc------tctgtgtgcg-------------------------tgtgtgtgtgt--c-------ttggc------------------GG----------------------------ATTT------------------------------------------------------------------------TG-TGT-TTAAGCCGCCGC----T--------------GCAAGTTCTAACCGCATGCCGCCACAATGTCCTCTTAATTTCCT----AGCCCccaacggcagcagctgct---g---cg--cgC-GC----------TCTCCACGCGATGATATCGTCGC------CGG--CTTC--------------AGATCC------AGAACcaggtctcag s droWil2.CH963894 1311555 588 + 2843958 TTTGAgaaattaaaagcattttgcGGTTCGAATACGACTATCGAAAGCAGCCGCgtgccaccgccaccgccaccaccgccgACGAGGAGAAGAGCCTACTCctgctcctccttctcctAACGACATTTCAATGATTTGCTGCT-GCC---TGTTGCC---------------------------TGTTGTTGTTCCCTG--------TTGC--CCGC---------TGCTAT--TTGG---------------------GGTCGCCGCCG------CCGTCATG------AGGCT------TACGTTGGCCACGTGCGAAGCACAAGAC------------------GCA-------------------------------------------------------------------------CA-------------------------------------------------------AAA-----GCATTTGCA---AtcctcgtcgtcgttgtcgtcatcgtcgtcggcCAACGATTACATACGAGGGCGACCTCTGT-----CAGGCAACAGTCCGTTTGGTAGCTGCTAGCAGTggccagttgccagttgccagtttGTGTCCA-------------------------GGTTGT----GT----CCGAAAA--AGCCACCAACAACGC------------AGCAACGCCAAGAATC-------------------------------------------TT-------GAATCAGCC-------------------------TGGAACTGAGA--C-------TTGGCTCCGATGGGTTTTCTGCTgg----------------------------attt----------------------------------------------------------------------tgtg-tgt-ttaagCTGCCGC----CGcagatcagcagcagcaagttcTAACCACATGCCGCCACAATGTCCTCTTAATTTCCT----A------------GGCAGCTGC----G---GC--TGC-GC----------T------GCGATGATATCGT----------------------------------------------------------- s droVir3.scaffold_12875 7354440 494 + 20611582 TTTGAGAAATTAAAAGCATTTTGCGGTTCGGCT--GACTATCGT----AGCCGCGTGCCGCT----------------------------CGAGCCT-------------------CTAACGACATTTCAATGATTtgctgc--------ccctg-t---------------------------tgcggctg----ctg--------ctgctgctgt---------tgctg---ctgt---------------------tgTTTTTGGGG------CCAA-GCG------TCACC------AAGT-TGGCCACGTGCGCAGCACAAGGCAGCGC------------GACA------------------------GGC---------------G------------------AAACAGACGGCACA-------------------------------------------------------AAA-----GCATTTGCA---ATGCTCGC----------------------------CGATTACGTACGAGGGCGACCTCTGT-----CAG-TGGC--------------------------------------------------CGGCC---------------AGTGGCGGTTG---CC----AT----CG--CGAGCCGCCACCAACAACGC------------AACAACGCAAAGAATC-------------------------------------------TT-------GCGTGGCCCGAACCCAGCGACTGCGTCTGCAGCATGGAGCTGGAC--G-------GCTGC------------------GGTTGCGGCTGTAGCTGGAGCTGGAGCTGGATTT------------------------------------------------------------------------TG-TGT-TTAAGCCGCCGCGC--G--------------TTGAGTTCTGACCACATGCCGCCACAATGTCCTCTTAATTTCCT----A-------------------------G---GC--CGCAGC----------T----GTGCGATGATATCGTCGC-------G------------------------------------------------ s droMoj3.scaffold_6496 26149540 515 + 26866924 TTTGAGAAATTAAAAGCATTTTGCGGTTCGGCT--GACTATCTT----GGCCGCGTGCCGCT----------------------------CGAGCCT-------------------CTAACGACATTTCAATGATTTTCTGA--------CCctg-ttgctgctgctgcccccgatgttgctgctgctgctg----ctg--------ctgctgctgc---------tgctg---ttgt---------------------tgTGTTTGGGG------CCAA-GCG------TCACC------AAGT-TGGCCACGTGCGCAGCAGAAGGCAGCGC------------GACG------------------------GAC---------------G------------------AAACAGACGGCTCA-------------------------------------------------------AAA-----GCATTCGCA---GCGCTCGC----------------------------CGATTACGTACGAGGGCAACCTCTGT-----CAG-TGgc--------------------------------------------------gagtcgcgagtcgggagtcgggagtcgggag---tcgggagt----cg--ccagtcgcCACCAACATCGC------------AACAACGCCAAGAATC-------------------------------------------TT-------GCGTGGCCCCAACC--------------------TGGAGCTGAGT--A-------GCTGC------------------AA----AGCTGCA----GAGCTGTAGCTGGATTC------------------------------------------------------------------------TG-TGT-TTAAGTTGCCGCAC--G--------------TTGAGTTCTAACCACATGCCGCCACAATGTCCTCTTAATTTCCT----A-------------------------G---GC--CGCAGC----------T----GTGCGATGATATCGTCGCCA----GC------------------------------------------------ s droAlb1.JH854640 311152 495 + 406291 TTTGagaaattaaaagcattttgcgGTTCGCCT--GACTATCGC----AGCCGCGTGCCGCC----------------------------CGAGCCT-------------------CTAACGACATTTCAATGAtttgctgc--------cgcag-t---------------------------tgctgttg----ctg--------ttgctgttgc---------tgctg---tagt---------------------tgtttttgGGG------CCAA-GCG------TCACC------AAGT-TGGCCACGTGCGCAGCACAAGGCAAAGCAAGGCAGC-TCAGACA------------------------GGC----------------------------------AAACAGACGGCACA-------------------------------------------------------AAA-----GCATTTGCGAATGTGCTCGC-------------------------CGACGATTACGTACGAGGGCGACCTCTGT-----CA---GGC------------------------------------------------------------------------------------------AT----CG--CAAGTCGCCACCAACAACGCGCAGCACAGCGAAGCAACGCAAAGAATC-------------------------------------------TT-------GCGTGGCATGAAC---------------------TGGACTCGGTCTTG-------TCTGT------------------GGCTGTAGCTGTGGCT-AGCCAGCCATTGGATTT------------------------------------------------------------------------CGTTGT-TTAAGCCGCCGCGCGAG--------------CTAAGTTCTAACCACATGCCGCCACAATGTCCTCTTAATTTCCT----A-------------------------GGTCGT--CGCAGC----------T----GCGCGATGAtatcgtcgccgtcgctg------------------------------------------------ s droGri2.scaffold_15245 904956 579 + 18325388 TTTGAGAAATTAAAAGCATTTTGCGGTTCGGCT--GACTATCGG----AGCCGCGTGCCGCT----------------------------CGAGCCT-------------------CTAACGACATTTCAATGATTTGCTGCT-------TGCTG-C--TTGCTGCTGCTTGCGGCT-------TGTTGTTG----TGG--------TTTGTATTTT---------TGTTG---TTTT---------------------TTTTTTTGGGG------CCAA-GCG------TCACC------AAGT-TGGCCACGTGCGCAGCACAAGGCAACAGACAGAGGCAGCAGACA------------------------GAC---------------GGACAGTGGGACGGACAGAGAACAGACGGCACA-------------------------------------------------------AAAGCAATGCATTTGCA---ATGCTCTA-------------------------CGACGATTACGTACGAGGGCGACCTCTGT-----CAG-CGGT--------------------------------------------------TTTCA-------------------GCGTTTG---CC----GT----CG-------CGCCACCAACAACGC------------AACAACGCCAAGAATC-------------------------------------------TT-------GCGTGGCCCC------------------------TGGAC---ATC--G-------AATTC------------------GG----GACGG------GTCTCTCGGCTGCAACTGAACCTGGAACCGAACCTGGATACACtgtgtgtgtgtgcttgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg-tgtgtTAAGCCGCC------G--------------TTAAGTTCTAACCGCATGCCGCCACAATGTCCTCTTAATTTCCT----A-------------------------G---GCCGCGCAGC----------T--GCGCGCGATGATATCGTCGT------TG------------------------------------------------ a score=-279506.000000 s dm6.chr2R 24352151 24 + 25286936 ------------------------GTCT--CCCCGTCtccccattcc-----------cat s droSim1.chr2R 18698872 10 + 19596830 ------------------------GTCT--C--------------CC-----------CAT s droSec1.super_23 118608 10 + 989336 ------------------------GTCT--C--------------CC-----------CAT s droYak3.chr2R 20208015 10 + 21139217 ------------------------atct--c--------------cc-----------cct s droEre2.scaffold_4845 21605859 9 + 22589142 ------------------------GAGG--C--------------AC-----------CC- s droBia2.KB462602 798913 7 + 3129309 ------------------------atcc--c--------------cc-------------- s droSuz1.KI419649 12043955 5 - 14502029 ------------------------ATCc--c------------------------------ s droAna3.scaffold_13266 5713023 18 - 19884421 ------------------------GAAT--A--------------CTGGGGGATA---CCC s droBip2.KB464407 1961745 21 + 2915140 ------------------------GGAT--A--------------CTGGGATATATACTCC s droEug2.KB465067 602933 7 + 1515531 ------------------------AGAA--C--------------CC-------------- s droKik2.KB459527 278765 10 - 1234237 ------------------------GGCT--C--------------CC-----------CTC s droTak2.KB461535 143911 15 - 669855 -----------------------------------cacccccagtcc-----------cct s droRho2.KB449310 38356 8 - 65043 --------------------------ct--c--------------cc-----------ctt s droFic2.KB457177 83419 16 + 995874 ----------------------------------agaaccccatccc-----------cat s droPse3.chr3 1351927 21 - 19787792 ------------------------GTCT--C---AGGTCTCAGGTCC-----------CAG s droPer1.super_34 540756 21 - 916997 ------------------------GTCT--C---AGGTCTCAGGTCC-----------CAG s droMir2.chr3 1393026 21 - 20862834 ------------------------gtct--c---aggtctcaggtcc-----------cag s droWil2.CH963894 1312157 8 + 2843958 ------------------------GTTT--C--------------CC-----------C-- s droVir3.scaffold_12875 7354934 30 + 20611582 TTGTCCTCGCAGCTATCTCCCTCTTGCTAC------------------------------- s droMoj3.scaffold_6496 26150055 23 + 26866924 GCATCCTCG-----ATCCCTTTCTAGCT--------------------------------- s droAlb1.JH854640 311647 17 + 406291 ttgtCCTCG-----------CTCGATCT--------------------------------- s droGri2.scaffold_15245 905535 27 + 18325388 TCCTGCTCA-CTCCAtctctctctgtct--------------------------------- a score=4720439.000000 s dm6.chr2R 24352175 743 + 25286936 ccccatcccaa---------------tccacagcc--acaaccccagtccccaatccgaatcccatccAGAC--GTC-GTCC----------TCTGTCTG---TGCGCTCGTTTTTTAATTCAACTGATTGTAC--TGCAGCTTCTGGAATTCGGCATTTCTTAAAGC-----C-TTTGC-G---CACACACATTGT----------------GAGTCGGC-AACTTCTGGCGATCCA---AGTCGCTG-----------------GGTACTTGG-TACTTGGCCACTT---GG------CCA---------------TCGAC---------------------AA--------------CC---TCCAACTCCTGAAGCCGctgctcctgctc----------------ctgctgctgctgctgc----tc--c-----------------------tgcGCCGCCGCCTTCGCAATCTG-------------AAAAG---------------------------GTTAAGAAATGACAATTTGTGAGCGTTtttt-ct--------tttc---------------tttcgtttcgtt-----tcgattcgtttt------------gtatt-tctgtgtattg----ttt--tg-----------gttttg--------tcgtttc---------t--------tCG-------T---------TTTT-G-CC----------AGTTGG-----------------CCAGTTGTGG-CTG----------------------TC-----------------TTGCTTTTGGCCCTG-TTGCTTTCATTGTGATTATTTAAAAGCC----------------------------------------------AG--AC-------------------------------------------------------------------------TGA---G------------------------GCCTTAACGAGGCG--CTT--TTGGCCT--TTCAGCAGGACTCAC-------------ATTTAGTTAAGCAATTATTGGGCC-GCAAT-GCAAACAAATAATGC-----GTACATTGTG--TGC--CTCAGAGTCT--ATCTGCCTCGGTGGTTTC--CCGC----------------------------------------------------------------------------------------CCG---CC-AGT-----------CC------------------------GAC------------CCGACTTACTCCACTGATTTTCCAAGTTAATCAAAATTCTTGGCTATCCA-CG-----------------------TCG--AAATCTCTGCGAC-----CTTC--C---------------CCGCCCGC-------------------C-CAGTCCC------------------C-TCTTCCATGGC--------TCTT-----C--TAGCGCCG---C-C-------------------------------G-----------AGC---------------------CACGCCC s droSim1.chr2R 18698882 709 + 19596830 CCCAATCCCAA---------------TCCACAGCC--ACATCCCCAGTCCCCAATCCGAATCCCATCCAGAC--GTC-GTCC----------TCTGTCTG---TGCGCTCGTTTTTTAATTCAACTGATTGTAC--TGCAGCTTCTGGAATTCGGCATTTCTTAAAGC-----C-TTTGC-G---CACACACATTGT----------------GAGTCGGC-AACTTCTGGCGATCCA---AGTCGCTG-----------------GGTACTTGG-TACTTGGCCACTT---GG------CCA---------------TCGAC---------------------AA--------------CC---TCCAACTCCTGATGCCGCTGCTCCTGCTG----------------CTGCTCCT-----------------------------------------CCGCCGCCGCCTTCGCAATCTG-------------AAAAG---------------------------GTTAAGAAATGACAATTTGTGAGCGTTTttt-ct--------tttc---------------tttcgtttcgtt-----tcgattcgtttt------------gtATT-TCTGTGTATTG----TTT--TG-----------GTTTAG--------TCGTTTC---------T--------TCT-------T---------TTTT-G-CC----------AGTTGG-----------------CCAGT--TGG-CTG----------------------TC-----------------TTGCTTTTGGCCCTG-TTGCTTTCATTGTGATTATTTAAAAGCT----------------------------------------------AG--AC-------------------------------------------------------------------------TGA---G------------------------ACCTTAACGAGGCG--CTT--TTGGCCT--TTCAGCAGGACTCAC-------------ATTTAGTTAAGCAATTATTGGGCC-GCAAT-GCAAACAAATAATGC-----GTACATTGTG----------------------TGCCTCGGTGGTTTC----------------------------------------------------------------------------------------------CCG---CC-AGC-----------CC------------------------GAC------------CCGACTTACTCCACTGATTTTCCAAGTTAATCAAAATTCTTGGCTATCCA-CG-----------------------TCG--AAATCTCTGCGAC-----CTTC--C---------------CCGACCGC-------------------C-CAGCCCC------------------C-TCTTCCGTGGC--------TCTT-----C--TAGCGCCG---C-C-------------------------------G-----------AGC---------------------CACGCCC s droSec1.super_23 118618 743 + 989336 CCCAATCCCAA---------------TCCACAGCC--ACATCCCCAGTCCCCAATCCGAATCCCATCCAGAC--GTC-GTCC----------TCTGTCTG---TGCGCTCGTTTTTTAATTCAACTGATTGTAC--TGCAGCTTCTGGAATTCGGCGTTTCTTAAAGC-----C-TTTGC-G---CACACACATTGT----------------GAGTCGGC-AACTTCTGGCGATCCA---AGTCGCTG------------------------GG-TACTTGGCCACTT---GG------CCA---------------TCGAC---------------------AA--------------CC---TCCAACTCctgatgccgctgctcctgctg----------------ctgctgctcctg------------c-----------------------GCCGCCGCCGCCTTCGCAATCTG-------------AAAAG---------------------------GTTAAGAAATGACAATTTGTGAGCGTTTttt-ct--------tttc---------------tttcgtttcgtt-----tcgattcgtttt------------gtATT-TCTGTGTATTG----TTT--TG-----------GTTTAG--------TCGTTTC---------T--------TCG-------T---------TTTT-G-CC----------AGTTGG-----------------CCAGT--TGG-CTG----------------------TC-----------------TTGCTTTTGGCCCTG-TTGCTTTCATTGTGATTATTTAAAAGCC----------------------------------------------AG--AC-------------------------------------------------------------------------TGA---G------------------------ACCTTAACGAGGCG--CTT--TTGGCCT--TTCAGCAGGACTCAC-------------ATTTAGTTAAGCAATTATTGGGCC-GCAAT-GCAAACAAATAATGC-----GTACATTGTG--TGC--CTCAGAGTCT--ATCTGCCTCGGTGGTTTC--CCGCCA-----------GCCCG-----------AT----------------------------------CC-----------------CCGTCCG---CC-AGC-----------CC------------------------GAC------------CCGACTTACTCCACTGATTTTCCAAGTTAATCAAAATTCTTGGCTATCCA-CG-----------------------TCG--AAATCTCTGCGAC-----CTTC--C---------------CCGACCGC-------------------C-CAGCCCC------------------C-TCTTCCGTGGC--------TCTT-----C--TAGCGCCG---C-C-------------------------------G-----------AGC---------------------CACGCCC s droYak3.chr2R 20208025 769 + 21139217 actcatctcca---------------tccacatgc--acatccccaatccgc-atccgaatcccatccaGAC--GTC-GTCC----------TCTGTCTG---TGCGCTCGTTTTTTAATTCAACTGATTGTAC--TGCGGCTTCTGGAATTCGGCATTTCTTAAAGCCTTTGC-TTTGC-G---CACACACATTGT----------------GAGTCGGC-AACTTCTGGCGA-CTT---GGATGCTG----GGTACT------TGGTACTTGG-TACTTGGCCACTT---GG------CCA---------------TCGAC---------------------AA--------------CC---TCCAACTCCCGATGCCT----------------------------CTGCTCCT-----------------------------------------GCGCCGCCGCCTTCGCAATCTG-------------AAAAG---------------------------GTTAAGAAATGACAATTTGTGAgcgtttttt-ct--------tttc---------------tttcatttcgtt-----tctttttgtttt------------gtatt-tctttgtattg----ttt--tg-----------gttttg--------tcgtttc---------t--------tcg-------t---------tttt-g-cc----------agttgg-----------------ccagt--tgg-ctggttggctcgTTGGCCGtcttgctt-----------------ttgcttttggccctG-TTGCTTTCATTGTGATTATTTAAAAGCC----------------------------------------------AG--AC-------------------------------------------------------------------------TGA---G------------------------ACCTTAACGAGGCG--CTT--TTGGCCT--TTCAGCAGGACTCAC-------------ATTTAGTTAAGCAATTATTGGGCc-gcaat-gcaaacaaataatgC-----GTACATTGTG--TGC--CTCACAGTCT--ATCTGCCTCGGTGGCTCC--TATCCAC--------ATCCCCT-----------CC----------------------------------GA-----------------ATCTCCA---cc-aaccccaaccccaacc------------------------GAA------------CCGACTTACTCCACTGATTTTCCAAGTTAATCAAAATTCTTGGCTATCCA-CG-----------------------TCG--AAATCTCGGCGAC-----CTTA--C---------------CC-----------------------------CCTCC------------------C-TCTTCCGTGGC--------TCTT-----C--TAGCGCCG---C-C-------------------------------G-----------GGC---------------------CACGCCC s droEre2.scaffold_4845 21605868 740 + 22589142 ---CATCCCCA---------------TCCACATCC--ACATCCCCA-------ATCCGAATCCCATCCAGAC--GTC-GTCC----------TCTGTCTG---TGCGCTCGTTTTTTAATTCAACTGATTGTAC--TGCGGCTTCTGGAATTCGGCATTTCTTAAAGC-----C-TTTGC-G---CACACACATTGT----------------GAGTCGGC-AACTTCTGGCGA-CTT---GGACGCTG----GGTACT------TGGTACTTGG-TACTTGGCCACTT---GG------CCA---------------TCGAC---------------------AA--------------CC---TCCAACTCCTGGTGCCTCTGCTCCTGCTG----------------CTGCTCCT-----------------------------------------GCGCCGCCGCCTTCGCAATCTG-------------AAAAG---------------------------GTTAAGAAATGACAATTTGTGAGCGTTtttt-ct--------tttc---------------tttcgtttcgtt-----tc-----gtttt------------gtatt-tctttgtattg----ttt--tg-----------gttttgtCGTTTCTTCGTTTC---------T--------TCG-------T---------TTTT-G-CC----------AGTTGG-----------------CCAGT--TGG-CTG----------------------TC-----------------TTGCTTTTGGCCCTG-TTGCTTTCATTGTGATTATTTAAAAGCC----------------------------------------------AG--AC-------------------------------------------------------------------------TGA---G------------------------ACCTTAACGAGGCG--CTT--TTGGCCT--TTCAGCAGGACTCAC-------------ATTTAGTTAAGCAATTATTGGGCC-GCAAT-GCAAACAAATAATGC-----GTACATTGTG--TGC--CTCAGAGTCT--ATCTGCCCCGATGGCTTC--CCTCCGA--------ATGCCCT-----------GC---------------------------------------------------------CCG---CC-AAC-----------CC------------------------GAC------------CCGACTTACTCCACTGATTTTCCAAGTTAATCAAAATTCTTGGCTATCCA-CG-----------------------TCG--AAATCTCTGCGAC-----CTTC--C---------------CCGCCCGC-------------------C-CTACCCC------------------C-TCTTCCGTGAC--------TCTT-----C--TAGCGCCG---C-C-------------------------------G-----------GGC---------------------CACGCCC s droBia2.KB462602 798920 699 + 3129309 ----atccgca---------------tccccatcc--ccatctcca--tccgagtccgaatcccatccaGCC--GTC-GGCC----------TCTGTCTG---TGCGCTCGTTTTTTAATTCAACTGATTGTAC--TGCAGCTTCTGGAATTCGGCATTTCTTAAAGC-----C-TTCGC-G---CACACACATTGT----------------GAGTCGGC-AACTTCTGGCGA-CTT--------CTG-----------------GACGCTTGGCCACTTGGCCACTT---GG------CCA---------------TCGG----------------------AA--------------CC---TCCGACTCCTGGTGCCTCTGCTTCtgc--------------------gccgct-------------------------------------------gccgccgccttcgCAATCTG-------------AAAAG---------------------------GTTAAGAAATGACAATTTGTGAgcgtttttt-ct--------tttc---------------tttcgtttc--------------------------------gtatt-tctttgtattg----ttt--tg-----------gttttt--------gctgttt---------t---cccctccg-------t---------tttt---------------tttttg-----------------ctggt--tGGCCTG----------------------TC-----------------TTGCTTTTGGCCCTG-TTGCTTTCATTGTGATTATTTAAAAGCC----------------------------------------------AG--AC-------------------------------------------------------------------------TGA---G------------------------ACCTTAACGAGGCG--CTT--TTGGCCT--TTGAGCAGGACTCAC-------------ATTTAGTTAAGCAATTATTGGGCC-Gcaat-gcaaacaaataatGC-----GTACATTGTG--CGC--TCTGGAGTCT--ATCTGCCTCAGTGGTTTC--TTGCCCA--------ATCCCCC-----------GC---------------------------------------------------------------CC-TGT-----------CC------------------------CCG------------CCGACTTACTCCAATGATTTTCCAAGTTAATCAAAATTCTTGGCTATCCA-CG-----------------------TCG--AAATCTCTGCGAC-----CTTC--C------------------------------------------C-CCGCCCC--------------------CTTTCCATGGC--------TCTT-----C--TAGCGCCG---C-C-------------------------------G-----------AGC---------------------CACGCCC s droSuz1.KI419649 12043960 707 - 14502029 -------------------------------------------caa--tccgaatccgaatcccaTCCAGCC--GTC-GTCC----------ACTGTCTG---TGCGCTCGTTTTTTAATTCAACTGATTGTAC--TGCAGCTTCTGGAATTCGGCATTTCTTAAAGC-----C-TTTGC-G---CACACACATTGT----------------GAGTCGGC-AACTTCTGGCGA-CT----------CG-----------------GATACTTGGATACTTGGCCACTT---GG------CCACTGGCCATTGGCAACTTGG----------------------AA--------------CC---TCCGACTCCTGGTGCTTCTGCTTCTgc--------------------gccgct-------------------------------------------gccgccgccttCGCAATCTG-------------AAAAG---------------------------GTTAAGAAATGACAATTTGTGAgcgtttttt-ct--------tttc---------------tttcgtttc--------------------------------gtatt-tctttgtattg----ttt--tg-----------gttttg--------ttttttt---------ttcccccctctg-------t---------tttttt-tc----------tttttg-----------------cgaGT--TGGCCTG----------------------TC-----------------TTGCTTTTGGCCCTG-TTGCTTTCATTGTGATTATTTAAAAGCC----------------------------------------------AG--AC-------------------------------------------------------------------------TGA---G------------------------ACCTTAACGAGGCG--CTT--TTGGCCT--TTCAGCAGGACTCAC-------------ATTTAGTTAAGCAATTATTGGGcc-gcaat-gcaaacaaataacGC-----GTACATTGTG--CGC--TTTGGAGTCT--ATCTGCCTCAGTGGTTTC--TTTCCCA--------ATCCCAA-----------A---------------------------------------------------------------------------------CC------------------------CCG------------CCGACTTACTCCAATGATTTTCCAAGTTAATCAAAATTCTTGGCTATCCA-CG-----------------------TCG--AAATCTCTGCGAC-----CTTC--C---------------CTCCCAGCCCC------------GCCAC-CCGCCCC------------------T-TTTTCCATGGC--------TCTT-----C--TAGCGCCG---C-C-------------------------------G-----------AGC---------------------CACGCCC s droAna3.scaffold_13266 5713041 785 - 19884421 CCTTATCCTCC---------------C---CTCAC--ATGTACTCGGTTATC-CCCAGAAGATC--CCAGCC--GTC-GTCC----------TCTGTCTG---TGCGCTCGTTTTTTAATTCAACTGATTGTAC--TGCAGCTTCTGGAATTCGGCATTTCTTAAAGC-----CGCGCGCGG---CACACACATTGT----------------GAGTCGGC-AACTTCTGGCGA-C-------TGGCCG-----------------------CGGCCAGCTTGCAACTC---GC------CAA---------------CTTGC---------------------AA--------------CC---TC---CTGCCACTGCCACTGCCGCCGCCGCCTCCTGTTGAATCCTCTGCTTCT--------------------------------------------GCGCCGCCTTCGCAATCTG-------------AAAAG---------------------------GTTAAGAAATGACAATTTGTGAGCGTTTTTT-TC---tttagtttcg----gtac-----gtttcgtttcgta-----tcgttttgtttTT--------CTCTTATT-TCTTTGTATTG----TGT--TG---------------TG--------TTTTTTG---------T--------TTG-------T---------TGTG-T-GT----------AGCCAG-----------------CTAGT--GGC-CTG----------------------TC---------------------------------TTGCTTTCATTGTGATTATTTAAAAGCCCGGCTCAGAGGATCTTTGGCTCTTTGGCTCAGAGCCTCTGTGACTGAG--AC-------------------------------------------------------------------------TGA---G------------------------ACCTTAACGAGGCG--CTT--TTGGCCT--TT---CAGGACTCAC-------------ATTTAGTTAAGCAATTATT-GGCT-GCAAT-GCAAACAAATAATGC-----GTACATTGTG--TGC--CTTG----CC--TCATGCCTCA-TGCCACA--TGCCCCA--------ACCCCTT-----------GC---------------------------------------------------------CCT---TCTTAC-----------CC------------------------TGT------------C-GACTTACTCCAATGATTTTCCAAGTTAATCAAAATTCTTTTCTATCCACCG-----------------------ATG--AAATCTCTGCGACTGCGACTGC--C---------------ACTGCGAC-------------------C-TTCCCCC------------------TGACTACGGTGGCATCCA-CTTCTT-----C--TAGCGCCG---CTT-------------------------------G-----------AGC---------------------CACGCCC s droBip2.KB464407 1961766 749 + 2915140 TCTTATCCCCC---------------TGCACATGT--ATGTACTTGGTTATC-CCCCGAAGATC--CCAGCC--GTC-GTCC----------TCTGTCTGTGCTGCGctcgttttttaattcaacTGATTGTAC--TGCAGCTTCTGGAATTCGGCATTTCTTAAAGC-----CGCGCGCGG---CACACACATTGT----------------GAGTCGGCAAACTTCTGGCGG-CGA---CTTGGCCA---------------------------CAGCTCGCAACTC---GCCATTCGCAA---------------CTTGC---------------------AA--------------CC---TC---CTCCAG--------------GCGGTAGCCCGTTGAATCCTCTGCTTCT--------------------------------------------GCGCCGCCTTCGCAATCTG-------------AAAAG---------------------------GTTAAGAAATGACAATTTGtgagcgtttttt-ttttgtttagtttcg----gtac-----gtttcgtttcgta-----tcgttttgttttt--------cttttatt-tcattgtattg----tgt-------------------tg--------ttttttg---------t--------ttg-------t---------tgtg-t-gt----------AGCCTG-----------------GTAGT--GGC-CTG----------------------TC---------------------------------TTGCTTTCATTGTGATTATTTAAAAGCCCGACTCTGAGGCTCTTTGGATCTTTGGCT-----TCTCGG-----GAG--AC-------------------------------------------------------------------------TGA---G------------------------ACCTTAACGAGGCG--CTT--TTGGCCT--TT---CAGGACTCAC-------------ATTTAGTTAAGCAATTATT-GGTT-GCAAT-GCAAACAAATAATGC-----GTACATTGTG--TGT--CTTG----CC--TCATGCCT-----------------CA--------ATACCTC-----------GC---------------------------------------------------------CCT---TC-TAC-----------CC------------------------TGT------------CGGACTTACTCCAATGATTTTCCAAGTTAATCAAAATTCTTTGCTATCCA-CG-----------------------ATG--AAATCTCTGCGAC-----CTTC--C---------------CCCTCGAC-------------------C-GTC------------------------GCGACGGTGGCATCTA-CTTCTT-----C--TAGCGCCG---CTT-------------------------------G-----------GGC---------------------CACGCCC s droEug2.KB465067 602940 753 + 1515531 --------------------------------------CATCCCCA-------ATCCGAATCCCATCCAGCC--GTC-GTCC----------TCTGTCTG---TGCGCTCGTTTTTTAATTCAACTGATTGTAC--TGCGGCTTCTGGAATTCGGCATTTCTTAAAGC-----C-TTTGC-G---CACACACATTGT----------------GAGTCGGC-AACTTCTGGCGA-CCGCC-GACCGCCGACCGGCCACTG-----GGATACTTGTATACTTGGCCACTT---GGCCGTTTCCA---------------TTGGC---------------------AACTCGGAG-------CC---TCCGACTCccgatgctgatgctgatgctt----------------ctgcttctgcttctgc----gc--c-----------------------gctgccgccgccttCGCAATCTG-------------AAAAG---------------------------GTTAAGAAATGACAAtttgtgagcgtttttt-ct--------tttc---------------tttcgtttc--------------------------------gtatt-tctttgtattg----tgt---------------gttttt--------ttttcca---------a--------tct-------t---------tttt--------------------G-----------------CGAGT--TGGCCTG----------------------TC-----------------TTGCTTTTGGCCCTG-TTGCTTTCATTGTGATTATTTAAAAGCC----------------------------------------------AG--AC-------------------------------------------------------------------------TGA---G------------------------ACCTTAACGAGGCG--CTT--TTGGCCT--TTCAGCAGGACTCAC-------------ATTTAGTTAAGCAATTATTGGGCC-gcaat-gcaaacaaataatGC-----GTACATTGTGTGTGC--TTTAGAGTCT--ATCTGCCTCGGTGGTTTG--TTGCCCA--------ATCCCCT-----------TC----------------------------------CCAATACCAGTACCAA-TGCCAATCC---CG-ATC-----------CC------------------------CCG------------CCGACTTACTCCAATGATTTTCCAAGTTAATCAAAATTCTTGGCTATCCA-CG-----------------------TCG--AAATCTCTGCGAC-----CTTC--C---------------CCCTCTTC-------------------CACTTTTCC------------------C-CTTCCCATGGC--------TCTT-----C--TAGCGCCG---C-C-------------------------------G-----------GGC---------------------CACGCCC s droEle2.KB458573 524428 810 - 5320397 ccccatctcca---------------tccccaatc--ccaatccccatccccaatcccaatcccatccaGCC--GTC-GTCC----------ACTGTCTG---TGCGCtcgttttttaattcaacTGATTGTAC--TGCAGCTTCTGGAATTCGGCATTTCTTAAAGC-----C-TTTGC-G---CACACACATTGT----------------GAGTCGGC-AACTTCTGGCGG-CGACCGGCAAACTG-----------------GCCACTTGGCCACTTGGCCGCTT---GG-------CA---------------tcctc---------------------ca--------------ac---tccaactcctgatgctgatgctactgctt----------------ctgcttctgcttctgc----gcCGC-----------------------TTCTTCGCCGCCTTCGCAATCTG-------------AAAAG---------------------------GTTAAGAAATGACAATTTGTGagcgtttttt-ct--------tttc---------------tttcgtttcgttttgtatcgttttgttttc--------ttcttatt-tctttgtattg----tgt--tt-----------ttgtat--------ttgcttt---------t--------ttg-------t---------tttt---tt----------tttctt-----------------ctggc--AAG-TTG----------------------TC-----------------TTGCTTTTGGCCCTG-TTGCTTTCATTGTGATTATTTAAAAGCC----------------------------------------------AG--AC-------------------------------------------------------------------------TGA---G------------------------ACCTTAACGAGGCG--CTT--TTGGCCT--TTCAGCAGGACTCAC-------------ATTTAGTTAAGCAATTATTGGGCc-gcaat-gcaaacaaataatgC-----GTACATTGTG--TGC--TTTAGAGTCT--ATCTGCCTCAGTGGTTTGTGTTTCCCA--------ATCTCaa-----------tc----------------------------------ccaaacccaaacccaa-tcccaatcG---CA---------------GC------------------------GAG------------CCGACTTACTCCAATGATTTTCCAAGTTAATCAAAATTCTTTGCTATCCA-CG-----------------------TTG--AAATCTCTGCGAC-----CTTC--CCGCCCGCTTGCCTacccaccacc-------------------c-cccaccc------------------c-TTTGCCATGGC--------TCTT-----C--Tagcaccg---c-c-------------------------------g--ccgccgcctagC---------------------CACGCCC s droKik2.KB459527 278777 668 - 1234237 ---------------------------------CT--CCCTCTCTA---------CCCATTCCCGGCCAGCC--GTC-GTCC----------TCTGTCTG---TGCGCTCGTTTTTTAATTCAACTGATTGTAC--TGCAGCTTCTGGAATTCGGCATTTCTTAAAGC-----C-CGCGC-G---CACACACATTGT----------------GAGTCGGC-AACTTCTGGCGA-CCG-------ATCG-----------------GCCACTGGG-CAACTTGCAACT----GG------CAA---------------CTTGC---------------------AA--------------CC---TCcaactccttctcctcctggtgctgctc----------------ctgccgct-----------------------------------------TCTGCGCCGCCTTCGCAATCTG-------------AAAAG---------------------------GTTAAGAAATGACAATTTGTGAGCGCttttt-tc--------tttggttcagttc----ggtttcgtttcgtt-----ttgttttgttttt------cccttttattccctgtgtattg----tgt----------------tttta--------tttattt---------t--------ttg-------t---------ttgt---------------------------------------------agc-CTG----------------------TC------------------------CGGCCCGGCCCGCTTTCATTGTGATTATTTAAAAGCC----------------------------------------------AG--TC-------------------------------------------------------------------------TGAG-GG------------------------ACCTTAACGAGGCG--CTT--TCGGCCT--TT---CAGGACTCAC-------------ATTTAGTTAAGCAATTATT-GGCc-gcaat-gcaaacaaataatgC-----GTACATTGTG-------------------------CCTGCTCGTTCC--TCTTCT--------------------------------------------------------------------------------------CCT---CC-CGG------------------------------------------------------GACTTAGTCCAATGATTTTCCAAGTTAATCAAAATTCTTTGCTATCCA-CG-----------------------TTG--AAATCTCAGCGAC-----CTTC--C---------------TCCTCATCTCC----------------C-CTGTGTC------------------T-GTGTCTAGAGC--------TCTT-----C--TAGCGCCG---C-T-------------------------------G-----------AGC---------------------CACGCCC s droTak2.KB461535 143935 741 - 669855 -----ccacca---------------ttcccaatc--caaatccca---------tcccatcccatccagCC--GTC-GTCC----------TCTGTCTG---TGCGCTCGTTTTTTAATTCAACTGATTGTAC--TGCAGCTTCTGGAATTCGGCATTTCTTAAAGC-----C-TTTGC-G---CACACACATTGT----------------GAGTCGGC-AACTTCTGGGGA-CTC----------G-----------------GGTACTTGGATACttggccactt---gg------cca---------------ttggccattggccattggcAACTTGGAA--------------CC---TCCGACTCCTGATTCTGATGCTgatgctt----------------ctgcttct------------gcgcc-----------------------gctgccgccgccttcGCAATCTG-------------AAAAG---------------------------GTTAAGAAATGACAATTTGTGagcgtttttt-ct--------tttc---------------tttcgtttcgtt-----tc----------------------gtatt-tctttgtattg----ttt--tg-----------gttttg--------ttatttt---------t--------ttg-------tcctccgttctgtt-t-tt----------tttttg-----------------cgagt--TGGCCTG----------------------TC-----------------TTGCTTTTGGCCCTG-TTGCTTTCATTGTGATTATTTAAAAGCC----------------------------------------------AG--AC-------------------------------------------------------------------------TGA---G------------------------ACCTTAACGAGGCG--CTT--TTGGCCT--TTCAGCAGGACTCAC-------------ATTTAGTTAAGCAATTATTGGGCC-GCAAT-GCAAACAAATAATGC-----GTACATTGTG--CGCGTTTTAGAGTCT--ATCTGCCTCAGTGGTTTG--TTTCCCA--------ATCCACA-----------GT----------------------------------CC---------------------CCTATCCC-AAT-----------CC------------------------CCG------------CCGACTTACTCCAATGATTTTCCAAGTTAATCAAAATTCTTGGCTATCCA-CG-----------------------TTG--AAATCTCTGCGAC-----CTTC--C------------------------------------------C------CC------------------C-TTTTCCATGGC--------TCTT-----C--TAGCGCCG---C-C-------------------------------G-----------TGC---------------------CACGCCC s droRho2.KB449310 38374 757 - 65043 -----ccccgagaat-----------cccagagcc--gcatcccca-------tccccaatcccatccaGCC--GTC-GTCC----------TCTGTCTG---TGCGCTCGTTTTTTAATTCAACTGATTGTAC--TGCAGCTTCTGGAATTCGGCATTTCTTAAAGC-----C-TTTGC-G---CACACACATTGT----------------GAGTCGGC-AACTTCTGGCGA-CCG---GCAAACTG-----------------GCCACTTGGCCACTTGGCAACCT---CC------CAG---------------TCCAA---------------------GT--------------CCAGGTCCAACTCCTGATGCctctgctt----------------------ctgcttct-----------------------------------------gcgCCGCCGCCTTCGCAATCTG-------------AAAAG---------------------------GTTAAGAAATGACAATTTGTGAgcgtttttt-ct--------tttc---------------tttcgtttcgtt-----tcgtatcgttttg---ttttcctcttatt-tctttgtattg----tgt----------------gtgtg--------tttcttt---------t--------ttg-------t---------tttt-g-tt----------tttttg-----------------cccTG--TCG-CTG----------------------GC-----------------TTGCTTTTGGCCCTG-TTGCTTTCATTGTGATTATTTAAAAGCC----------------------------------------------AG--AC-------------------------------------------------------------------------TGA---G------------------------ACCTTAACGAGGCG--CTT--TTGGCCT--TTCAGCAGGACTCAC-------------ATTTAGTTAAGCAATTATTGGGCC-gcaat-gcaaacaaataatgC-----GTACATTGTG--TGC--TTTAGAGTCT--ATCTGCCTCAGTGGTTCG--ATCGCTG--------ccccccc-----------T----------------------------------------------------------CTC---CC-CTC-----------CC------------------------GCA------------CCGACTTACTCCAATGATTTTCCAAGTTAATCAAAATTCTTGGCTATCCA-CG-----------------------TCG--AAATCTCTGCGAC-----CTtc--c---------------cttcccctccccctccccgtactgccac-ccacccc------------------c-tTTTCCATGGC--------TCTT-----C--TAGCGCCG---C-C-------------------------------G--------CCTGGC---------------------CACGCCC s droFic2.KB457177 83441 768 + 995874 ccgcttcttca---------------tccccatcc--ccatccgccatccac-agcccaatcccatccaGCC--GTC-GTCC----------TCTGTCTG---TGCGCtcgttttttaattcaacTGATTGTAC--TGCAGCTTCTGGAATTCGGCATTTCTTAAAGC-----C-TTTGC-G---CACACACATTGT----------------GAGTCGGC-AACTTCTGGCGA-cc----ggcaactg-----------------gcaactgg--caaccggCCACTT---GG------CCA---------------TTGGC---------------------AACTTGCAACCGGGTCCC---TCCAACTCCTGGTGCCtccgcttctgctg----------------ctgctgctgctcctgcttctgcttc-----------------------tgcgcCGCCGCCTTCGCAATCTG-------------AAAAG---------------------------GTTAAGAAATGACAATTTGTGagcgtttttt-ct--------tttc---------------ttgcgtttcgta-----tcgttttgttttt--------ctcttatt-tctttgtattg----tgttttg-----------tgtttt--------tttcttt---------t--------tcggattgttt---------tttt-t-tt----------ggtttg-----------------cgaGT--TGGCCTG----------------------TC----------------------GCTGGGCCTG-TTGCTTTCATTGTGATTATTTAAAAGCC----------------------------------------------AGGCAC-------------------------------------------------------------------------TGA---G------------------------ACCTTAACGAGGCG--CTC--TTGGCCT--TTCAGCAGGACTCAC-------------ATTTAGTTAAGCAATTATTGGGCC-gcaat-gcaaacaaataatgC-----GTACATTGTG----C--TTCGG----------TGCTTCAGTGGCTGG--CT------------------------------------------------------------------------------------------TCC---CA-ATC-----------CC------------------------CCG------------CCGACTTACTCCACTGATTTTCCAAGTTAATCAAAATTCTTGGCTATCCA-CG-----------------------TCG--AAATCTCTGCgac-----cttc--c---------------ccttccccttccccaccttc-------c-gcccacc------------------c-cttGCCACGGC--------TCTT-----C--TAGCGCCG---C-C-------------------------------G-----------GGC---------------------CACGCCC s droPse3.chr3 1351949 849 - 19787792 TCCAGGCCCTG---------------GACACAGCC--ACATCTaca-------------gccacatcca--c--gtc-GTCT----------TCTGTCTG---TGCGCTCGTTTTTTAATTCAACTGATTGTAC--TGCGGCTTCTGGAATTCGGCATTTCTTAAAGC-----C-Cgcgc-ggcacacacacattgtgcGGCTGGGGAGCGC-GCGTCGGC-AACTTCTGGCGA-CT----GCCAACTG------------------------------CTGGCCGCC-----A------CCA-----------------------------------------CA--------------TC---Tcctcctgctgatgctgatgctgctgctg----------------ctgctgcaactccTGTTGGGGCTgcc---------------------ggccgccgccgccttcgCAATCTG-------------AAAAG---------------------------GTTAAGAAATGACAATTTGTGagcgtttctt-tt--------tgtt-----gttgtttgtgttttgtttttgt-----tcaattcgtttttgtttctctctcgtatt-gctttgtattg----ttt--tttgtttggtttggtttgg--------ttggtt-------------------tCg-------t---------ctgg-c-cc----------cgcctggcctggtctgaactggcctggcc-tggcctg----------------------tcctgtctctcctgtcctgttgctcttggccctg-tTGCTTTCATTGTGATTATTTAAAAGCCCGAACACTGGACTCT-------------------------------GG--ACgatgc-----------------ctgctgcctgctg-----------------------------------ct-tgagAGG------------------------ACCCTAACGAGGCG--CTT--TCGGCCT--TT---CGGTACTCAC-------------ATTTAGTTAAGCAATTATTGGGCCtgcaat-gcaaacaaataatgCGTATTGTACATTGTG--TGC--CCCTCCATCTcgccctgcctccctgcctgc--ctgccg-----------ctctA-----------CC----------------------------------CC---------------------TTT---AC-TTT-----------Cg------------------------ggg------------gggACTTACTCCAATGATTTTCCAAGTTAATCAAAATTCTTTGCTATCCA-CG-----------------------ATG--AAATCTCAAcgac-----cttc--t------------------------------------------c-ctcctcc------------------t-gccgccgTGAC--------TCCT-----CTATAGCGCCGTCAC-C-------------------------------G-----------AGC---------------------CACGCCC s droPer1.super_34 540778 827 - 916997 TCCAGGCCCTG---------------GACACAGCC--ACATCTACA-------------GCCACATCCA--C--GTC-GTCT----------TCTGTCTG---TGCGCTCGTTTTTTAATTCAACTGATTGTAC--TGCGGCTTCTGGAATTCGGCATTTCTTAAAGC-----C-CGCGC-GGCACACACACATTGTGCGGCTGGGGAGCGC-GCGTCGGC-AACTTCTGGCGA-CT----GCCAACTG------------------------------CTGGCCGCC-----A------CCA-----------------------------------------CA--------------TC---TCCTCctgctgatgctgatgctgctactg----------------ctgctgcAACTCCTGTTGGGGCTGCC---------------------GGCCGCCGCCGCCTTCGCAATCTG-------------AAAAG---------------------------GTTAAGAAATGACAATTTGTGAGCGtttctt-tt--------tgtt-----gttgtttgtgttttgtttttgt-----tcaattcgtttttgtttCTCTCTCGTATT-GCTTTGTATTG----TTT--TTT----------GTTTGG--------TTGGTT-------------------TCG-------T---------ctgg-c-cc----------ggcctggcctggtctgaa-----ctggcc-tggcctg----------------------tcctgTCTCTCCTGTCCTGTTGCTCTTGGCCCTG-TTGCTTTCATTGTGATTATTTAAAAGCCTGAACACTGGACTCT-------------------------------GG--AC------------------------GCTGCCTGCTG-----------------------------------CT-TGAGAGG------------------------ACCCTAACGAGGCG--CTT--TCGGCCT--TT---CGGTACTCAC-------------ATTTAGTTAAGCAATTATTGGGCCTGCAAT-GCAAACAAATAATGCGTATTGTACATTGTG--TGC--CCCTCCATCTCGCCCTGCCTCCCTGCCTGC--CTGCCT-----------CTCTA-----------CC----------------------------------CC---------------------TTT---AC-TTT-----------CG------------------------GGG------------GGGACTTACTCCAATGATTTTCCAAGTTAATCAAAATTCTTTGCTATCCA-CG-----------------------ATG--AAATCTCAACGAC-----CTTC--T------------------------------------------C-CTCCTCC------------------T-GCCGCCGTGAC--------TCCT-----CTCTAGCGCCGTCAC-C-------------------------------G-----------AGC---------------------CACGCCC s droMir2.chr3 1393048 846 - 20862834 tccaggcccTG---------------GACACAGCC--ACATCTACG-------------GCCACATCCA--C--GTC-GTCT----------TCTGTCTG---TGCGCTCGTTTTTTAATTCAACTGATTGTAC--TGCGGCTTCTGGAATTCGGCATTTCTTAAAGC-----C-Cgcgc-ggcacacacacattgtgcGGCTGGGGAGCGC-GCGTCGGC-AACTTCTGGCGA-CT----GCCAACTG------------------------------CTGGCCGCC-----A------CCA-----------------------------------------CA--------------tc---tcctcctgctgatgctgatgctgctgctg----------------ctgctgcaactcctGTTGGGGCTgcc---------------------ggccgccgccgccttcgCAATCTG-------------AAAAG---------------------------GTTAAGAAATGACAAtttgtgagcgtttctt-tc--------tgtt-----gttgtttgtgttttgtttttgt-----tcaattcgtttttgtttctctctcgtatt-gctttgtattg----ttt--ttt-----gtttggtttgg--------ttggtt-------------------tcg-------t---------ctgg-c-ccggcctggcctggcctggcctggtctgaactggcctggcc-tggcctg----------------------tcctgtctctcctgtcctgttgctcttggccctg-tTGCTTTCATTGTGATTATTTAAAAGCCCGAACACTGGACTCT-------------------------------Gg--acgctgc-----------------ctgctgcctgctg-----------------------------------ct-tgagAGG------------------------ACCCTAACGAGGCG--CTT--TCGGCCT--TT---CGGTACTCAC-------------ATTTAGTTAAGCAATTATTGGGCctgcaat-gcaaacaaataatgCGTATTGTACATTGTG--TGC--CCCTCCATCTcgccctgcctccctgcct---------------------ctctA-----------CC----------------------------------CC---------------------TTT---AC-TTT-----------Cg------------------------ggg------------gggACTTACTCCAATGATTTTCCAAGTTAATCAAAATTCTTTGCTATCCA-CG-----------------------ATG--AAATCTCAACgac-----cttc--t------------------------------------------c-ctcctcc------------------t-ggcgcCGTGAC--------TCCT-----CTCTAGCGCCGTCAC-C-------------------------------G-----------AGC---------------------CACGCCC s droWil2.CH963894 1312165 628 + 2843958 ------------------------------------------------------CCATACCCCCATCCAGTG--GTCTGTccagagtgtgtgtgtgtgtg---tgtgctcgtTTTTTAATTCAACTGATTGTAC--TGTAGCTTCTGGAATTCGGCATTTCTTAAAGC----AC-ATTGT-G---C---------------------------GAGCCTCC-GCTCT-----GA-CT---------CCG------------------------------------ACTC---CA------GCA---------------T-------------------------CA--------------AC---TCCAA---------------CTCCTGCAC----------------TCGCTCCC-----------------------------------------------------TCGCAATCTG-------------AAAAG---------------------------GTTAAGAAATGACAATTTgtgagcttttttt-tt--------tttg------------------------------------------------------------t-tttttaagttt----ctt--tt-----------ctttcg--------tctgttt---------g--------ttt-------g---------ttct-g-tt----------ggctgg-----------------ttact--tgg---g----------------------tt-----------------tttgtttgtgtattg-tttttgccattgcGATTATTTAAAAGCCCCAGCG----------------------------------------AG--AC----------------------TCTTTTCTTGTGG-----------------------------------TTGTGG---A------------------------GCCCTAACGAGACGCTCTT--TTGGCCT--TTCGGCAGGATTCAC-------------ATTTAGTTAAGCAATTATTGGCCC---ATG-GCCAACAAATAATGC-----GTACATTGTA--TGC--GTTG--------Atctgttcctgctgctgc--tt--ctg--------ctgcctG-----------CC----------------------------------CC---------------------CCA---CT-CCA-----------TC------------------------ATT------------TTGACTTACTCCAATGATTTTCCATGTTaatcaaaattctttgctatcCA-CT-----------------------ATGAAAAATCTCAACGAC-----CTTC--C------------------------------------------C-C-CCGTC------------------T-CCTGCcaaagcaaaagttttcct-----C--TAGCG------C-C-------------------------------G-----------AAC---------------------CACGCCC s droVir3.scaffold_12875 7354964 818 + 20611582 ------------CACCCTGCCACCCGctctcgctc--tcgctctgg-------ctctctctctctctcgctccgtct-g-tc----------tctgtctG---TGGGCTGT-TTTTTAATTCAACTGATTGTAC--TGCAGCTTCTGGAATTCGGCATTTCTTAAAGC-----C-------G-------CACATTGT-------------GC-GCGTCGGC-AACATCTTGAGG-CTG---AACTGTTG--ATGCCACCGCTGGTAGGCAGCAAGGTACCTGAACTGCG---AC------TCG---------------CTTGC---------------------AA--------------CT---TCTTGTGGCCGTT--------TGCCGCCAGCCAG-----------CAGCCGCCT---------------------------------------------GCCGCCTTCGCAATCTGCAAAACA------GAAAG--------------AAAAAAAGTAAAGTTTAAGAAATGACAATTTGTGAGCTTCTTTT-tg--------ctga---------------tgttgttgttgt-----tgttg-------------------ctgct-gttgt-tgctgctgttgt--tg-----------tttttg--------tgtattgttTTTTGTTT--------TTT-------T---------TTTG-C-TT----------GACTTG-----------------TCTGC--AGT-CCG----------------------TT-----------------TTG----TGTGCCTC-TTGCTTTCATTGTGATTATTTAAAGGCC----------------------------------------------AA--AACCCGC-----------------------------------------------------------------CA-GGC---G------------------------GCCTTAACGAGGCG--CTT--GT-GCCT--TT---CAGAACTCCT------TTGGCGCATTTAGTTAAGCAATTATT-GTTG-GCAAT-GCAAACAAATAATGC-----GTACATTGTA--TGC--------------AACTGTCTAAGCAGCGAT--TGTGCAA--------CTGTGcaca---------acacaacacacatacaaacacaca------------caacacacacgcggtacacacacCCG---CC-GCT-----------CCCT----------------------TGT------------CTGACTTACTCCAATGATTTTCCAAGTTAATCAAAATTCTTTGCTATCCA-CT-----------------------ATG--AAATCTCAACGAC-----CTTA--C---------------CCCCCAGG-------------------C-GTGCCCG------------------T-CT-------GC--------CTTT---TGC--TAGCGCCA---T-G-------------------------------T-----------GGCAACATGCGCTC-----CCCGCCACGCCC s droMoj3.scaffold_6496 26150078 838 + 26866924 --------------------------ctctcgctc--tccctctcc-------ctctcactctcactcGTGC--GCC-G-CG----------TCTGCCTG---TGGGCTCG-TTTTTAATTCAACTGATTGTAC--TGCAGCTTCTGGAATTCGGCATTTCTTAAAGC-----C-------G-------CGCATTGT-------------GC-GCGTCGGC-AACATCTTGAGG-CTG---G-----------------------CAGCAGGGAGGTACCTGAACCGCAGTCGC------CAG---------------CTTGT---------------------AA--------------CT---CCTTGTGGCCGTTGCCgc--ctgctgcctgctgc-----------ctgctgcctctagcctcctgcctcctgcTGCCTTCTCCCAGCTGCCGGTTGGCCGCCGCCTTCGCAATCTGCAAGAGA------AAAAG---------------TAAAAAGCAAAGTTTAAGAAATGACAATTTGTGAGCTTCTTTTctg--------ctgc---------------tgctgattctcc-----tcttg-------------------ctgct-gcttc-tgctg----tgc--tg-----------cATTTG--------TGTATTG--------TT--------TTT-------G---------CTTG-G-CT----------GAGTTG-----------------TCTGC--CGT-CCG----------------------TT-----------------TTG----TTCGCCTC-TTGCTTTCATTGTGATTATTTAAAGGCC----------------------------------------------GA--AACCCGCCAA--------------------------------------------------------------CA-GGC---G------------------------GCCCTAACGAGGCG--CTT--CT-GCCT--TT---CAGAACTCCT------TCGGCGCATTTAGTTAAGCAATTATT-GTTG-GCAAT-GCAAACAAATAATGC-----GTACATTGTA--TGC--------------AACTGTCTAAGCAGCGAT--TGTGCAATAC-----CCTcacacacacacacacac-----acatacTCAGGGATAGT------------AGACTGCCCTGCCGGA-------TTG---CC-GCT-----------CCCT----------------------CGT------------CTGAGCTACTCCAATGATTTTCCGAGTTAATCAAAATTCTTCGCTATCGA-CT-----------------------ATG--AAATCTCAACGAC-----CTTA------------------CCCCCGGG-------------------C-GAGCCCG------------------T-CT-------GC--------TTTT--AGGC--TAGCGCCA---T-G-------------------------------TGC----GACGGGGCAACATGCGCCTGTCCGCCTGCCACGCCC s droAlb1.JH854640 311664 964 + 406291 --------------------------CTTTCACTCCGCCGctgtat-------ttctctctctcactctccc------------------------gaTG---TGGGCTCGTTTTTTAATTCAACTGATTGTAC--TGCAGCTTCTGGAATTCGGCATTTCTTAAAGC-----C-------G-------CACATTGT-----------GCGC-GCGTCGGC-AACATCTTGA-A-CTG---C-----------------------CACTGCGGAGGTACCTGAGCTTCG---AC------TTG------------CGACTTGC---------------------AA--------------CT---TTTTGTGGCCGTTGCCGC--CTGCCGCCTACCTC-----------CTGTTGCCTGTCGCCT--------------------------------------GCCGCCTTCGCAatctgcaaaaca------aaaaac---------aaaaaaaaaaaaaaaagtttaagaaATGACAAtttgtgagcttctttt-tg--------ttgt---------------tgctttcgtttt-----ttgtt-------------------gttct-gttttgttttg----ttt--tg-----------t-tttg--------tgtattg--------------------t-------t---------tttg-c-tt----------gacttg-----------------tctgc--tg--cca----------------------tt------------------------tgtgcctc-ttgctttCATTGTGATTATTTAAAGGCC----------------------------------------------AA--AACCCGCAAAGCAGCCCAACCAACTGTCCGTCTGCTGGTCTGTTGGTCTCTTGGTCTGCCAGGATGGTCTTCGA-GGA---G------------------------CCCCTAACGAGGCG--CTT--GT-GCCT--TT---CAGAACGTCC------TC-GCGCATTTAGTTAAGCAATTATT-Gttg-gcaat-gcaaacaaataatgc-----GTACATTGTA--TGC--------------AACTGTCTAAGAAACGAT--TGTGCAACTCTCCTACTGTGCAAATGTGCA---ACAGTGCctcgactttgacttcgacttcgactgtgccaacacacacacacgcccccCAATTG---CC-GCT-----------CCCTTTGAtgttcatgttgctgttgctgttgctttgctttgctgacTTACTCCAATGATTTTCCAAGTTAATCAAAATTCTTTGCTACCga-actcagctcaactcaacccAACGGAATG--AAATCTGAACGAC-----CTTA------------------CCCCCAGG-------------------C-ATG-CCG------------------T-CT-------GC--------TTTT---TAC--TAGCGCCA---T-GTGGCAGCagattttgctgttgccgttgccattgctgttgctgtggc----tgtggctgttgccgTATCACGCCC s droGri2.scaffold_15245 905562 821 + 18325388 --------------------------cactcgctc--tctctctgt-------ctctgtctcCTGTGTTGTT--GTT-GTTG----------TTTTTTTG---TCG------TTTTTAATTCAACTGATTGTACTGTGCAGCTTCTGGAATTCGGCATTTCTTAAAGC-CCCGC-------A-------CACATTGT-------------GCGGCGTCGGC-AACATCTTGGGG-CAG---TATAGTTG--TAGC----------TGGGCAGAAGGTACCTGA---------AC------TCA---------------ACGGC---------------------CA--------------CC---GCTTCTTGTCTTC--------------------------------------------------------------------------------------GCCGCCTTCGCAATCTGCAATACAGTGGAGAAGAGCAAGAGAATAAAAAATAAAACAAAAACTTTAAGAAATGACAATTTGTGAGCTGCTTTT-tg--------ctgc---------------tgcggctgctgc-----tgctg-------------------ctgct-gctgc----------tgt--tg-----------ctgctg--------TGTATTG------------------TTT-------T---------TTAG-CTTT----------GACTTG-----------------TCTGC--TGC-TCG----------------------TT-----------GGGGTTTTG----TTTGCCTC-TTGCTTTCATTGTGATTATTTAAAGGCC----------------------------------------------AA--AACCCGC-------------------------CGCTGG----------------------------------CA-GGC---GACTGCAGCTGTAGCTGTAGCTGGAGCCTTAACGAGGCG--CTTCAGT-GCCTCCTT---CAGGACTCTCATCGCATCGTCGCATTTAGTTAAGCAATTATT-GTTG-GCAATGGCAAACAAATAATGC-----GTACATTGTA--TGC--------------AACTGTCTAAGCAGCGAT--TGTGCAA--------CTGTGCA-----------AC-----ACAAACACACACCCCAT------------CGATCATCCCGCCCGCTCCA---CCA---CC-GCT-----------CTCT----------------------GGA------------CAGACTTACTCCAATGATTTTCCAAGTTAATCAAAATTCTTTGCTATCGA-CT-----------------------ATG-AAAATCTCAACGAT-----CTTTTAC---------------CCCCCAGG-------------------C-GTGCCCGTGTCTGGCTTCTCTTTCTT-CT-------TC--------TTTTTGTTAC--TAGCGCCA---T-G-------------------------------T-----------GGCAACATG--------------CCACGCCC a score=461924.000000 s dm6.chr2R 24352918 94 + 25286936 AT---GCAAC---GCCCCTTCAGTGGAGCGTGGCGGAGGCAGCGA----TTTGG------AGGAAACTTATGG-------------CTTTCCGC--------------------------CGTACCGCT-CCCGCCT---G-------------------GGA----------TACTTATAT s droSim1.chr2R 18699591 94 + 19596830 AT---GCAAC---GCCCCTTCAGTGGAGCGTGGCGGAGGCAGCGA----TTTGG------AGGAAACTTATGG-------------CTTTCCGC--------------------------CGTACCGCT-CCCGCCT---G-------------------GGA----------TACTTATAT s droSec1.super_23 119361 94 + 989336 AT---GCAAC---GCCCCTTCAGTGGAGCGTGGCGGAGGCAGCGA----TTTGG------AGGAAACTTATGG-------------CTTTCCGC--------------------------CGTACCGCT-CCCGCCT---G-------------------GGA----------TACTTATAT s droYak3.chr2R 20208794 94 + 21139217 AT---GCAAC---GCCCCTTCAGTGGAGCGTGGCGGAGGCAGCGA----TTTGG------AGGAAACTTATGG-------------CTTTCCGC--------------------------CGTACCGCT-CCCGCCT---G-------------------GGA----------TACTTATAT s droEre2.scaffold_4845 21606608 92 + 22589142 AT---GCAAC---GCCCCTTCAGTGGAGCGTGGCGGAGGCAGCGA----TTTGG------AGG-AACTTATGG-------------CTTTCCGC--------------------------CGTACCGCT-CCCGCCT-----------------------GAA----------TACTTATAT s droBia2.KB462602 799620 97 + 3129309 AT---GCAAC---GCCCATCCAGTGGAGCGTGGCGGAGGCAGCGA----TTTGG------AGGAAACTTATGG-------------CTTTTCGC--------------------------CGTACCGCG-CCCCGCTTTGT-------------------AGC----------TACTTATAT s droSuz1.KI419649 12044668 98 - 14502029 AT---GCAAC---GCCCATTCAGTGGAGCGTGGCGGAGGCAGCGA----TTTGG------AGGAAACTTATGG------------CCTTTTCGC--------------------------CGTACCGCT-CCCCGCTTTAT-------------------AGC----------TACTTATAT s droAna3.scaffold_13266 5713827 86 - 19884421 AT---GCAAC---GCCCATTCACTGGAGCGTGGC------------------AT------AGGAAACTTATGG--------GCCTTTCTTCCGC--------------------------CGATCCGCTCCCCGCCT---T-------------------AGC----------TACTTATAT s droBip2.KB464407 1962516 86 + 2915140 AT---GCAAC---GCCCATTCACTGGAGCGTGGC------------------AT------AGGAAACTTATGG--------GCCTTTCTTCCGC--------------------------CGATCCGCTCCCCGGCT---T-------------------AGC----------TACTTATAT s droEug2.KB465067 603694 96 + 1515531 AT---GCAAC---GCCCATTCAGTGGAGCGTGGCGGAGGCAGCGA----TTTGG------AGGAAACTTATGG------------CTTTTTTGC--------------------------CGTACCGCTCCCCGCCT---T-------------------AGC----------TACTTATAT s droEle2.KB458573 525239 96 - 5320397 AT---GCAAC---GCCCATCCAGTGGAGCGTGGCGGAGGCAGCGA----TTTGG------AGGAAACTTATGG------------TTTTTGCGC--------------------------CATACCGCTCCCCGCCT---T-------------------AGC----------TACTTATAT s droKik2.KB459527 279446 102 - 1234237 AT---GCAAC---GCCCATTCAGTGGAGCGTGGC------------------AG------AGGAAacttatag-------------ttttttatttg--gattttccTATAGC---CAAGCTTACCGCTCCCCGCCT---T-------------------AGC----------TACTTATAT s droTak2.KB461535 144678 98 - 669855 AT---GCAAC---GCCCATTCAGTGGAGCGTGGCGGAGGCAGCGA----TTTGG------AGGAAACTTATGG------------CTTTTTCGC--------------------------CGTACCGCTCCCCGCTT-TGC-------------------AGC----------TACTTATAT s droRho2.KB449310 39132 96 - 65043 AT---GCAAC---GCCCATCCACTGGAGCGTGGCGGAGGCAGCGA----TTTGG------AGGAAACTTATGG------------TTTATTCGC--------------------------CGTACCGCTCCCCGCCT---T-------------------AGC----------TACTTATAT s droFic2.KB457177 84210 96 + 995874 AT---GCAAC---GCCCATTCAGTGGAGCGTGGCGGAGGCAGCGA----TTTGG------AGGAAACTTATGG-------------CTTTCCAC--------------------------CGTACCGCTCCCCGCCT--TT-------------------AGC----------GACTTATAT s droPse3.chr3 1352799 134 - 19787792 ATGCAGCAAC---GCCCATTCACTGAAGCGTGGCAGAGGCAACAAACATTTCAG------TTGAAGCTcatag-------------ttttttgtgtg---ttttttttgtagcttgTAGCtggtccccc-tccccct---t-------------------gaCATCCCCACAGCACTTATat s droPer1.super_34 541606 137 - 916997 ATGCAGCAAC---GCCCATTCACTGAAGCGTGGCAGAGGCAACAAACATTTCAG------TTGAAGCTCATAG-------------TTTTTTGTGTGTGTTTTTTTTTGTAGCTTGTAGCTGTTCCCCC-TCCCCCT---T-------------------GCCATCCCCACAGCACTTATAT s droMir2.chr3 1393895 135 - 20862834 ATGCAGCAAC---GCCCATTCACTGAAGcgtggcagaggcaacaaaCATTTCAG------TTGAAGCTcatag-------------ttttttgtgtg--ttttttttagtagCTTGTAGCtgttccccc-tccccct---t-------------------gccATCCCCACAGCACTTATat s droVir3.scaffold_12875 7355782 108 + 20611582 -------AAA---GCTCTGCCACTGAAGCgtggcagaggcggcga----caacggcaacaacggcggcaacgg-cggcaacggcggcaacTTAG--------------------------AGACAGCCG-CTTACGT---A-------------------GGT----------TTTTTTTTC s droMoj3.scaffold_6496 26150916 123 + 26866924 ------AAAA---GCACCGCCACTGGAGCGTGGCAGAGGCGGCGA----CGTCG------ACGTTGACAAGAGTTTACAAAGGttttcttctgt--------------------------ttattttct-tttatat---gtatttttatttatttatttaat----------ttttttttt s droAlb1.JH854640 312628 78 + 406291 -------AAA---ACGCTGCCACTGAAGCGT------GGTGGCCA----CATAG------------------G-AAACTATAGTAGACTTTTA-----------------------------------T-TATACGT---GTAG----------------AAA----------ATGTTTTCC s droGri2.scaffold_15245 906383 65 + 18325388 -------AAAAATGTGCTGCCACTGAAGCGTGGCAGAGGCGGCGG----CAAAC-------------TAACAGTCAA-----------------------------------------------------------------------------------AGT----------TGTTTTTGT a score=785125.000000 s dm6.chr2R 24353012 45 + 25286936 AGGCACAGGCAGCTC-----CGCTTCACTGACCAATTTATGGCTGGGAAT s droSim1.chr2R 18699685 45 + 19596830 AGGCACAGGCAGCTC-----CGCTTCACTGACCAATTTATGGCTGGGAAT s droSec1.super_23 119455 45 + 989336 AGGCACAGGCAGCTC-----CGCTTCACTGACCAATTTATGGCTGGGAAT s droYak3.chr2R 20208888 45 + 21139217 AGGCACAGGCAGCTC-----CGCTTCACTGATTAATTTATGGCTGGGAAT s droEre2.scaffold_4845 21606700 45 + 22589142 AGGCACAGGCAGCTC-----CGCTTCACTGACCAATTTATGGCTGGGAAT s droBia2.KB462602 799717 45 + 3129309 AGGCAGAGGCAGCTC-----CGCTTCACTGGCCAATTTATGGCTGGGAAT s droSuz1.KI419649 12044766 45 - 14502029 AGGCAAAGGCAGCTC-----CGCTTCACTGACCAATTTATGGCTGGGAAT s droAna3.scaffold_13266 5713913 45 - 19884421 AGGCAAAGGCAGCTC-----CGCTTCACTGACCAATTTATGGCTGAGAAT s droBip2.KB464407 1962602 45 + 2915140 AGGCAAAGGCAGCTC-----CGCTTCACTGACCAATTTATGGCTGAGAAT s droEug2.KB465067 603790 45 + 1515531 AGGCAAAGGCAGCTC-----CGCTTCACTGACCAATTTATGGCTGGGAAT s droEle2.KB458573 525335 45 - 5320397 AGGCAAAGGCAGCTC-----CGCTTCACTGACCAATTTATGGCTGGGAAT s droKik2.KB459527 279548 45 - 1234237 AGGCAAAGGCAGCTC-----CGCTTCACTGACCAATTTATGGCTgagaat s droTak2.KB461535 144776 45 - 669855 AGGCAAAGGCAGCTC-----CGCTTCACTGACCAATTTATGGCTGGGAAT s droRho2.KB449310 39228 45 - 65043 AGGCAAAGGCAGCTC-----CGCTTCACTGACCAATTTATGGCTGggaat s droFic2.KB457177 84306 45 + 995874 AGGCAAAGGCAGCTC-----CGCTTCACTGACCAATTTATGGCTGGGAAT s droPse3.chr3 1352939 45 - 19787792 aggcagaggcagctc-----cGCTTCACTGGCCATTTTATGGCTGAGAAT s droPer1.super_34 541755 45 - 916997 AGGCAGAGGCAGCTC-----CGCTTCACTGGCCATTTTATGGCTGAGAAT s droMir2.chr3 1394036 45 - 20862834 aggcagaggcagctc-----cGCTTCACTGGCCATTTTATGGCTGAGAAT s droWil2.CH963894 1312915 50 + 2843958 AGGCAGAAGCAGCTCCTCTGCGCTTGACTGCCCATTTTATGGCTGAGAAT s droVir3.scaffold_12875 7355890 39 + 20611582 ------TTTTAGCCT-----CGCTTCACTGCGCATTTTATGGCTGAGAAT s droMoj3.scaffold_6496 26151039 39 + 26866924 ------tttttGACT-----CGCTTCACTGCGCATTTTATGGCTGAGAAT s droAlb1.JH854640 312706 33 + 406291 ------------GCT-----CGCTTCACTGCGCATTTTATATCTGAGAAT s droGri2.scaffold_15245 906448 39 + 18325388 ------ATCTTTACT-----CGCTTCACTGCGCATTTTATGGCTGAGAAT a score=-6958.000000 s dm6.chr2R 24353057 45 + 25286936 ATTTC-------------------TT--TTT----------AC-------------AA----GTCT-----------GGTTGC----------------CACAT--AG--TGTGGATTT-TTCA-A s droSim1.chr2R 18699730 45 + 19596830 ATTTC-------------------TT--TTT----------AC-------------AA----GTCT-----------GGTTGC----------------CACAT--AG--TGTGGATTT-TTCA-G s droSec1.super_23 119500 45 + 989336 ATTTC-------------------TT--TTT----------AC-------------AA----GTCT-----------GGTTGC----------------CACAT--AG--TGTGGATTT-TTCA-G s droYak3.chr2R 20208933 62 + 21139217 ATTTC-------------------TTC-TTT----------AC-------------CA----GTCT-----------GCTTGCCACAAAGCTGCATAGTCACAT--AG--TGTGGATTT-TTCA-G s droEre2.scaffold_4845 21606745 45 + 22589142 ATGTC-------------------TT--TCT----------AC-------------AA----GTCT-----------GGTTGC----------------CACAT--AG--TGTGGATTT-TTCA-G s droBia2.KB462602 799762 44 + 3129309 GATTC--------------------T--TTT----------TC-------------GA----GTCT-----------GGTTGC----------------CTCAT--AG--TGTGGATTT-TTCT-G s droSuz1.KI419649 12044811 47 - 14502029 GATTC-------------------TT--TTT----------TC-------------GA----GTCT-----------GGTTGC----------------CTCATAGAG--TGTGGATTT-TTCT-A s droAna3.scaffold_13266 5713958 42 - 19884421 ATTTC-------------------TTTCCCT----------CC-------------CA----ACC----------------------------------CTCAT--AGTCTGTGCATGT-TTGC-A s droBip2.KB464407 1962647 38 + 2915140 ATTTC-------------------TTG-CCT----------CA-------------CA----GTG----------------------------------TTTAT--G---TTTGAATGT-TTGC-A s droEug2.KB465067 603835 48 + 1515531 ATTTC----------------TCCTT--TTC----------CC-------------GA----GTCT-----------GGTTGC----------------CTCAT--AG--TGTGGATTC-TCCT-A s droEle2.KB458573 525380 49 - 5320397 ATCTC-------------------tt--tttttCC------CC-------------GA----GTCT-----------GGTTGC----------------CTCAT--AG--TGTGTATTT-TTCT-A s droKik2.KB459527 279593 59 - 1234237 atttc-------------------tt--ttttttctttccacc-------------GATGTCTTTT-----------GGTTGC----------------CTCAC--AG--CGTGGATTT-TTGT-A s droTak2.KB461535 144821 49 - 669855 AATTC-----------------TCTT--TTT----------TC-------------GA----GTCT-----------GGTTGC----------------CTCAT--AGTGTGTGGATTT-TTCT-A s droRho2.KB449310 39273 46 - 65043 atttc-----------------tttt--ttt----------tc-------------ga----gtCT-----------GGTTGC----------------CTCAC--AG--TGTGGAT-T-TTCT-A s droFic2.KB457177 84351 46 + 995874 ATTTC-------------------TTA-GTT----------TC-------------GA----GCCT----------CGGTTGC----------------CTAAT--AG--TGTGGAT-T-TTCT-A s droPse3.chr3 1352984 66 - 19787792 CTCTCGtg----------ccttcttt--ctt----------tctttatttgtgtCGGA----GT-------------GGTTGC----------------CTCAT--AG--ACGGGATTTATTAT-A s droPer1.super_34 541800 66 - 916997 CTCTCGTG----------CCTTCTTT--CTT----------TCTTTATTTGTGTCGGA----GT-------------GGTTGC----------------CTCAT--AG--ACGGTATTTATTAT-A s droMir2.chr3 1394081 58 - 20862834 CTCTCGTG----------CCTTCTTT--ATT----------TC--------TGTCGGA----GT-------------GGTTGC----------------CTCAT--AG--ACGGGATTTATTAT-A s droWil2.CH963894 1312965 71 + 2843958 TTGTTGtagatacttttttttttgtt--ttt----------gt-------------gt----gtctgCTTTTGCTTTGATTGC----------------TTCAT--AA--ATGAGATTT------A s droVir3.scaffold_12875 7355937 45 + 20611582 GTTTC-------------------TT--TTT----------TT-------------TG----GAGT-----------GGCTTCT---------------TTCAT--AG--ATTAGATTT-ATTA-- s droMoj3.scaffold_6496 26151081 39 + 26866924 ------------------------AT--CTT----------TT-------------CG----GAAT-----------GGTCTC----------------TTCAT--AG--ATTAGATTT-ATTA-- s droGri2.scaffold_15245 906487 41 + 18325388 -TAGC-------------------CT--TTT----------TT-------------TG----GAGT-----------GCTCCC-------------------CT--AG--ATTAGATTT-ATTAA- a score=128594.000000 s dm6.chr2R 24353102 11 + 25286936 CGGAGATG-----CTT s droSim1.chr2R 18699775 11 + 19596830 CGAAGATG-----CTT s droSec1.super_23 119545 11 + 989336 CGAAGATG-----CTT s droYak3.chr2R 20208995 11 + 21139217 CGGAGATG-----CTT s droEre2.scaffold_4845 21606790 11 + 22589142 CGGAGATG-----CTT s droBia2.KB462602 799806 11 + 3129309 TGAAGACG-----TTT s droSuz1.KI419649 12044858 11 - 14502029 TGAAGACG-----TTT s droAna3.scaffold_13266 5714000 11 - 19884421 TGAAGATG-----TCT s droBip2.KB464407 1962685 11 + 2915140 TGAAGATG-----TCT s droEug2.KB465067 603883 11 + 1515531 TGAAGATG-----TTT s droEle2.KB458573 525429 12 - 5320397 TGAAGATGT----TTT s droKik2.KB459527 279652 16 - 1234237 TGAAGATGTTTGCTTT s droTak2.KB461535 144870 11 - 669855 TGAAGACG-----TTT s droRho2.KB449310 39319 11 - 65043 TGAAGATG-----TTT s droFic2.KB457177 84397 11 + 995874 TGAAGATG-----TTT s droPse3.chr3 1353050 11 - 19787792 TGAAGATG-----TTT s droPer1.super_34 541866 11 - 916997 TGAAGATG-----TTT s droMir2.chr3 1394139 11 - 20862834 TGAAGATG-----TTT s droWil2.CH963894 1313036 11 + 2843958 TAGAGAAA-----TTA s droVir3.scaffold_12875 7355982 8 + 20611582 ---AGCTG-----TTT s droMoj3.scaffold_6496 26151120 8 + 26866924 ---AGATG-----TTT a score=22394.000000 s dm6.chr2R 24353113 4 + 25286936 GCCT- s droSim1.chr2R 18699786 4 + 19596830 GGCT- s droSec1.super_23 119556 4 + 989336 GCCT- s droYak3.chr2R 20209006 4 + 21139217 GCCT- s droEre2.scaffold_4845 21606801 4 + 22589142 GCCT- s droBia2.KB462602 799817 4 + 3129309 GCCT- s droSuz1.KI419649 12044869 4 - 14502029 GCCT- s droAna3.scaffold_13266 5714011 4 - 19884421 GCCT- s droBip2.KB464407 1962696 4 + 2915140 GCCT- s droEug2.KB465067 603894 4 + 1515531 GCCT- s droEle2.KB458573 525441 4 - 5320397 GCCT- s droKik2.KB459527 279668 4 - 1234237 GCCT- s droTak2.KB461535 144881 4 - 669855 GCCT- s droRho2.KB449310 39330 4 - 65043 GCCT- s droFic2.KB457177 84408 4 + 995874 GCTT- s droPse3.chr3 1353061 1 - 19787792 ---T- s droMir2.chr3 1394150 1 - 20862834 ---T- s droWil2.CH963894 1313048 4 + 2843958 GCCA- s droVir3.scaffold_12875 7355990 4 + 20611582 -TCTG s droMoj3.scaffold_6496 26151128 4 + 26866924 -TCCT a score=34398.000000 s dm6.chr2R 24353117 14 + 25286936 AATTGT-------GCCGG-------GAA s droSim1.chr2R 18699790 14 + 19596830 AATTGT-------GCCGG-------AAA s droSec1.super_23 119560 14 + 989336 AATTGT-------GCCGG-------AAA s droYak3.chr2R 20209010 14 + 21139217 AATTGT-------GCCAG-------GAA s droEre2.scaffold_4845 21606805 14 + 22589142 AATTGT-------GCCAG-------GAA s droBia2.KB462602 799821 14 + 3129309 AATTGT-------GCCGG-------GAA s droSuz1.KI419649 12044873 14 - 14502029 AATTGT-------GCCAG-------GAA s droAna3.scaffold_13266 5714015 14 - 19884421 AATTGT-------GCTGG-------CAA s droBip2.KB464407 1962700 14 + 2915140 AATTGT-------GCTGG-------CAA s droEug2.KB465067 603898 14 + 1515531 AATTGT-------GCCAC-------AAA s droEle2.KB458573 525445 17 - 5320397 AATTGTTG----GAATGA-------AAA s droKik2.KB459527 279672 21 - 1234237 AATTGT-------GGCAGCGTTAACGAA s droTak2.KB461535 144885 14 - 669855 AATTGT-------GAAAG-------AAA s droRho2.KB449310 39334 14 - 65043 AATTGT-------GCAAG-------GGA s droFic2.KB457177 84412 21 + 995874 AATTGT-------GCCAGCGGTAAGAAA s droPse3.chr3 1353062 9 - 19787792 GATT---------ACCAA---------- s droMir2.chr3 1394151 9 - 20862834 GATT---------ACCAA---------- s droWil2.CH963894 1313052 14 + 2843958 gctttt-------gaaaa-------caa s droVir3.scaffold_12875 7355997 14 + 20611582 -------ATGCAAGCCGG-------CAA a score=12245.000000 s dm6.chr2R 24353131 16 + 25286936 --------ATGTTGGGATGAAATA s droSim1.chr2R 18699804 16 + 19596830 --------ATGTTGGGATGAAATA s droSec1.super_23 119574 16 + 989336 --------ATGTTGGGATGAAATA s droYak3.chr2R 20209024 15 + 21139217 --------ATGTTGGG-TGAAATA s droEre2.scaffold_4845 21606819 16 + 22589142 --------ATGTTGGGATTGAATG s droBia2.KB462602 799835 16 + 3129309 --------AGGTTCCGATAAAGTA s droSuz1.KI419649 12044887 16 - 14502029 --------GGGTTGGGATAAAGTA s droEug2.KB465067 603912 16 + 1515531 --------ATGTTGCGATAACATA s droEle2.KB458573 525462 1 - 5320397 -----------------------A s droKik2.KB459527 279693 16 - 1234237 --------AAGTTGATGGAAACTA s droTak2.KB461535 144899 16 - 669855 --------ATGTTGGGATAAAATA s droRho2.KB449310 39348 16 - 65043 --------ATGTTGGGATCTAGAA s droFic2.KB457177 84433 11 + 995874 --------ATGCTGGGATA----- s droPse3.chr3 1353071 16 - 19787792 --------ATGTTTGGGCAACCCG s droMir2.chr3 1394160 15 - 20862834 --------ATGTTTGGGC-ACCCA s droWil2.CH963894 1313069 16 + 2843958 --------atgcTTCTATTAAGAT s droVir3.scaffold_12875 7356011 19 + 20611582 TCTCTTCAATGTCTGATTA----- a score=-3685.000000 s dm6.chr2R 24353147 8 + 25286936 ----GCTACAAG s droSim1.chr2R 18699820 8 + 19596830 ----GCTACAAG s droSec1.super_23 119590 8 + 989336 ----GCTACAAG s droYak3.chr2R 20209039 8 + 21139217 ----GCTACAAG s droEre2.scaffold_4845 21606835 8 + 22589142 ----GCTACAAG s droBia2.KB462602 799851 8 + 3129309 ----TCTAGAGA s droSuz1.KI419649 12044903 8 - 14502029 ----ACTAGAAA s droEug2.KB465067 603928 8 + 1515531 ----ACTAGAAA s droEle2.KB458573 525463 8 - 5320397 ----TCTGGAAA s droTak2.KB461535 144915 8 - 669855 ----ACTAGAAA s droRho2.KB449310 39365 8 - 65043 ----CCTACAAG s droFic2.KB457177 84444 8 + 995874 ----GCAAGAAA s droPse3.chr3 1353095 7 - 19787792 ----GCGAAGG- s droMir2.chr3 1394183 7 - 20862834 ----GCGAAGG- s droWil2.CH963894 1313088 6 + 2843958 ----ATGATA-- s droVir3.scaffold_12875 7356030 11 + 20611582 TCTCGCATCAT- a score=-6995.000000 s dm6.chr2R 24353155 15 + 25286936 --TTACCATTTAAACAA s droSim1.chr2R 18699828 15 + 19596830 --TTACCATTTGAACAA s droSec1.super_23 119598 15 + 989336 --TTACCATTTAAACAA s droYak3.chr2R 20209047 2 + 21139217 --TT------------- s droEre2.scaffold_4845 21606843 13 + 22589142 --TTACCA--GGGAGAA s droBia2.KB462602 799859 15 + 3129309 --TTAGCTAGGATAAAA s droSuz1.KI419649 12044911 15 - 14502029 --TTAACTAGTGGAAAA s droEug2.KB465067 603936 15 + 1515531 --TTAACGAGAGAAAGA s droEle2.KB458573 525471 15 - 5320397 --TTAACTAAGAGAAAA s droTak2.KB461535 144923 15 - 669855 --TTAACTAGGAAACAA s droFic2.KB457177 84452 15 + 995874 --TTATCTTAAAGAAAA s droPse3.chr3 1353102 15 - 19787792 --TTCCCATTCCCACAA s droMir2.chr3 1394190 15 - 20862834 --TTCCCactcccacaa s droWil2.CH963894 1313097 12 + 2843958 --TCACCTAtcaaa--- s droVir3.scaffold_12875 7356041 15 + 20611582 TTCCAGCTTTTATAT-- a score=-197709.000000 s dm6.chr2R 24353170 44 + 25286936 CGTGGA----------------------------------------------------TT------------CGTAGTTAA-------------------GCTAC-----------GACTTAAAT--TAT----------------------CTGTGTAAGA s droSim1.chr2R 18699843 36 + 19596830 CGTGGA----------------------------------------------------TT------------CGTAGTTAA-------------------GCTAC-----------GATTTGAAT--------------------------------TCAAA s droSec1.super_23 119613 36 + 989336 CGTGGA----------------------------------------------------TT------------CGTAGTTAA-------------------GCTGC-----------GATTTGAAT--------------------------------TCAAA s droYak3.chr2R 20209049 23 + 21139217 ------------------------------------------------------------------------AGTTGTTAA-------------------GCTTT-----------GATTTGAAT------------------------------------- s droEre2.scaffold_4845 21606856 46 + 22589142 ATTGCA----------------------------------------------------TTGG----------AAATACCCA-------------------GCTTT-----------GATTTGAAT--CAT----------------------CCACAGGGAA s droBia2.KB462602 799874 47 + 3129309 ------------------------------------------------------------------------CGCATTACG-------------------GCTATATGTTTCTGTAGATGAGAAT--TAT----------------------TTTCTTGGTA s droSuz1.KI419649 12044926 47 - 14502029 ------------------------------------------------------------------------CGCATTACA-------------------GCTATACGTTTTTGAagatcaaaat--tat----------------------tttcgtGATA s droEug2.KB465067 603951 49 + 1515531 CGCATAAA-------------------------------------------------TTC------------TATATTCTA-------------------ACATT-----------TAGTCGGACATGAT----------------------TTTCTTAGTA s droEle2.KB458573 525486 124 - 5320397 AGCATACAA------CTTTTATGCAGttcaaaatgaatttctttttcctattattttctt------------atcaatTAAAGACTTAAAAGTTACAATTGCTATTACTGCCATGCAATAAAAAC--TAT------------------GTAGTTTCTTTGAA s droTak2.KB461535 144938 93 - 669855 CACAttaaaacaattcaatttcataaatcaaaattattttctttatacctt-------tt------------tttgataaa-------------------actaC-----------AGTTTTTAT--GGT------------------ATGATTTCTTAATC s droFic2.KB457177 84467 65 + 995874 CACAT-----------------------------------------------------TA------------Aatgtttcg-------------------gtttc-----------agttagaaa--ttttaatccattaaatgtgtttaaaCTTTAGAAGA s droMir2.chr3 1394205 28 - 20862834 ---------------------------------------------------------------------------------------------------------------aaaaaagtgagaat-gaat----------------------ttccataaaa s droWil2.CH963894 1313109 45 + 2843958 ---------------------------------------------------cataaattt------------tgtattata-------------------aatat-----------taatcaaaG--CAC----------------------TTGGAAAAGG s droVir3.scaffold_12875 7356056 44 + 20611582 ------------------------------------------------------------CGTAGTTTCGGAGATTGTTCA-------------------GATAA-----------GGTTATAAA--TAA----------------------ATGTAT---- a score=-119610.000000 s dm6.chr2R 24353214 26 + 25286936 TA---CAATCAATGTCTAA-----------------------------------------------TGGCCAGATA s droSim1.chr2R 18699879 59 + 19596830 TA---CAATCAATGTCTAATCTC------GTCGT-----ACATTCCATCTTTCATTTCTTTTG---TTGCCAGGCA s droSec1.super_23 119649 59 + 989336 TA---CAATCAATGTCTAATCTC------GTCGT-----ATATTCCATCTTTCATTTCTTTTA---TTGCCAGGCA s droYak3.chr2R 20209072 48 + 21139217 ---------CAATGTCTTATCTC----------------ATTTGCCAACTTTCATTGCACCTA---TCGCCAGATA s droEre2.scaffold_4845 21606902 69 + 22589142 TA---CAGGCAATGTC-CATCTCCCTAACGTCTTTAATTCCTTGTAAACTTGCATTGCTTCTG---TCGCCAGACA s droBia2.KB462602 799951 41 + 3129309 taagttaatcaATATC-------------------------Actcgattttaaatttctt----------cagcta s droEug2.KB465067 604003 27 + 1515531 ------------------------------------------TCTTTTCCTCAAAATCTTTTG-------AAAATG s droEle2.KB458573 525633 33 - 5320397 ----------------------------------------TGCAACAAACTCTGTTAACCTTG---tagttaaaaa s droTak2.KB461535 145043 31 - 669855 ------------------------------------------taattattttactctcactaa---tttcaaaata s droFic2.KB457177 84532 18 + 995874 -------------------------------------------------------Cacttttg---ttgaaaaaaa s droMir2.chr3 1394233 12 - 20862834 --------------------------------------------------tatagTACACTT-------------- s droWil2.CH963894 1313154 16 + 2843958 -----------------------------------------------TCTTAAAAGCGATTTA------------- s droVir3.scaffold_12875 7356100 22 + 20611582 -----------------------------------------------------ATTGCCTTTGAACTTGCAAAAA- a score=-274894.000000 s dm6.chr2R 24353240 51 + 25286936 TTACTA----------AATCGAA-----------------ATTTATACCAAATGTT--------------------------------------TTAGAAATAGCTAAGAAA------------ATTA s droSim1.chr2R 18699938 31 + 19596830 TAACTA----------AATCAAA-----------------ATTTATAGCAAAT-TT---------------------------------------------------------------------TTA s droSec1.super_23 119708 32 + 989336 TAACTA----------AATCAAA-----------------ATATATAGCAACTATT---------------------------------------------------------------------TTA s droYak3.chr2R 20209120 74 + 21139217 TAAATA----------CATCTAT-----------------ATTTATAGCATCTATTGCTC---------------CAAAATGGTGTAAAGTCGTTTAGAAAAAGTTGTGAAA------------ATTG s droEre2.scaffold_4845 21606971 68 + 22589142 TAAATG--------------TAA-----------------ATTTATAGCAGCTATTTTTCT--------------CAAAATATTGT-TAGTCGCTTAGAAAAAGTTGTG--A------------ATTA s droBia2.KB462602 800001 86 + 3129309 aaaata----------aaacaagtgtTA-----AAATGCTGCTTTCAGCAAAT-TT-CACC--------------AACGatggaatatttatatttaaacagaaCTTCGAAA-----------GGATG s droSuz1.KI419649 12045148 74 - 14502029 aaaaCA----------ATAGTAGtaaca-----aaaaa--gttt---ataaat-tc---ct--------------aaaaaggttttttttatctcCATGCACCTATTCCAGA---------------- s droEug2.KB465067 604032 50 + 1515531 --------------------------------------------GCAGCAATGCTT---------------------------TCTGAATCTGACCCTACATAGTTTCTAGTTTT-------CTACTA s droEle2.KB458573 525666 68 - 5320397 -----------------------------------ttactttgtatattatatttt-------------------------gtgcTTTGCAATGTCAgggacatttttaaaaatttgcaggCCAAATA s droTak2.KB461535 145085 115 - 669855 taaatattatttaattagtcAATCTTCAAGGTTAATTACAATTTCtggtaaaa-ttgttttatagttTAGACAGAAAGAAAGTGTTAAGAATATTAATAACTTGTGACTAAA------------AATA s droFic2.KB457177 84568 55 + 995874 -----------------------------------TTCCTAAGAttaccatat-tt-------------------------attttgagtaTGACTTGAAATCTGTGAAAAC------------ATAA s droMir2.chr3 1394245 38 - 20862834 -------------------------------------------TGGAGTAAAACCT-------------------ACAAACAAGCGATAGATATCCAGAA---------------------------- s droWil2.CH963894 1313170 49 + 2843958 -----------------------------------TTTGTGAAGATGGAAAGTTTT-------------------TAAACAgttgtttcaaaaatttaaatca------------------------- s droVir3.scaffold_12875 7356122 50 + 20611582 ----------------------------ATATTTTCTTATGTTTATATTAGGACTT-------------------CTTGAAAAGGCAAATAGCACCA------------------------------- a score=-2726.000000 s dm6.chr2R 24353291 6 + 25286936 CTTAGA s droSim1.chr2R 18699969 6 + 19596830 ATTAGA s droSec1.super_23 119740 6 + 989336 CTTAGA s droYak3.chr2R 20209194 6 + 21139217 CTAAGA s droEre2.scaffold_4845 21607039 6 + 22589142 CTAAGA s droBia2.KB462602 800087 6 + 3129309 TTTGGA s droEug2.KB465067 604082 6 + 1515531 CCTCAG s droEle2.KB458573 525734 6 - 5320397 TTTGGC s droTak2.KB461535 145200 6 - 669855 CCTAGA s droRho2.KB449310 39744 6 - 65043 ctcaGA s droFic2.KB457177 84630 6 + 995874 CTCACA s droMir2.chr3 1394283 4 - 20862834 -TGAG- s droWil2.CH963894 1313219 6 + 2843958 gttAGT s droVir3.scaffold_12875 7356172 1 + 20611582 C----- a score=79188.000000 s dm6.chr2R 24353297 39 + 25286936 TTTCCGCTTCT---------------AGTT----------------------GTTTGTT------TAAT--TAATGGCTTTCAA s droSim1.chr2R 18699975 39 + 19596830 TTTCCGCTTCT---------------AGTT----------------------GTTTGTT------TAAT--TAATGGCTTTCAA s droSec1.super_23 119746 39 + 989336 TTTCCGCTTCT---------------AGTT----------------------GTTTGTT------TAAT--TAATGGCTTTCAA s droYak3.chr2R 20209200 39 + 21139217 TTTCTGCTTCT---------------AGTT----------------------GTTTGCT------TAAT--TAATGGCTTTCAA s droEre2.scaffold_4845 21607045 39 + 22589142 CCTCCGCGTCT---------------GGTT----------------------GTTTGCT------TAAT--TAATGGCTTTCAA s droBia2.KB462602 800098 54 + 3129309 TTTTctcctttaaaaaaataataaaaaact----------------------gtttGAT------TAAT--TAATGGCTTCGAA s droSuz1.KI419649 12045222 39 - 14502029 TTTTCGCTTCT---------------AGTT----------------------GTTTGTT------TAGT--TAATGGTTTTCAA s droEug2.KB465067 604088 39 + 1515531 ATTCCACTGCT---------------Agtt----------------------gtttgtt------taat--taatggttttcaa s droEle2.KB458573 525744 47 - 5320397 TTTAATCTGAC---------------AATC----------------------TTTTATTACCTCCTAGTCCTAATGGTTTTCAA s droKik2.KB459527 280078 38 - 1234237 TTCCCACTTAT---------------ggtt-----------------------ttccct------taaa--aaatgtttttcct s droTak2.KB461535 145206 61 - 669855 TTTTCTAGTTT---------------AGTTCCTCCTCAGATTTTCGACCCTAGTTTGTC------TAAT--TAATTGGCTTCAA s droRho2.KB449310 39750 39 - 65043 ACTTCGCTcct---------------attt----------------------gtttgtt------taat--taatggtTTTCAA s droFic2.KB457177 84655 30 + 995874 TTTCCTTTTTT---------------AGCa----------------------gtttgtt------taat--aaat--------- s droMir2.chr3 1394287 36 - 20862834 ACTCGGCgact---------------tctc----------------------tttctct------tact--TTCTACTTTT--- s droWil2.CH963894 1313225 23 + 2843958 -----------------------------------------------------CTTTTT------AAAT--GGCTTATTTTGGA s droVir3.scaffold_12875 7356173 28 + 20611582 --------------------------ATTT----------------------GTTTGTG------TTAT--CGACGAATTCAAA a score=225975.000000 s dm6.chr2R 24353336 117 + 25286936 ---TGAGCTTCGAAATAACAAGC-TTGGCTCATAAAGTGTT---GA---CAAATATTG-TT-GAAACTTTTCCCGC------TGACTAGAAAGTTTCCGCCA-TT------CAA-----GGGTGTA--------TCTATAAATTTGTATCAAGTT s droSim1.chr2R 18700014 117 + 19596830 ---TGATCTTCCAAATAACAAGC-TTGGCCCATAAAGTGTT---GA---CAAATATTG-TT-GAAACTTTTCCCGC------TGACTAGAAACTTTCCGGAA-CT------TAA-----GGGTGTA--------TCTATAAATTTGTAGCAAGTT s droSec1.super_23 119785 117 + 989336 ---TGATCTTCCAAACAACAAGC-TTGGCCCATAAAGTGTT---GA---CAAATATGG-TT-GAAACTTTTCCCGC------TGACTAGAAACTTTCCGGAA-CT------TAA-----GGGTGTA--------TCTATAAATGTGTAGCAAGTT s droYak3.chr2R 20209239 106 + 21139217 ---TGATCTTCCGAATAACAAGC-TTGGCCAATAAAGTgtt---ga---caaatattt-tt-gaaacttTTCACGC------TGACTGGAAACTTT-----------------------GCTTCTA--------TCTATAAATTTGTAGCAAGTT s droEre2.scaffold_4845 21607084 115 + 22589142 ---TGATCTTCCAAATAACAAGC--TGGCCAATAAAGTGTT---GA---CAAATATTT-TT-GAAACTTTTCACGC------TGACTGGAAACTTTGCGGCA-TC------C-A-----GCTTCCA--------TCTACAAATTTGTAGCAAGTT s droBia2.KB462602 800152 115 + 3129309 ---AGATCTTTCAAATAACAAGC------CAATAAAAAGTT---GA---CAAATATGG-AA-CAAACTTCCTGCAA------TGATTATAAACttcgcttcc-tt------ctac--ctccTTGCA--------CATCTGAATTGATAGCCAGTT s droSuz1.KI419649 12045261 116 - 14502029 ---AGATTTTCCAAATAACAAGC------CAATAAAGAGTT---GA---CATATATTG-TC-CAAACTTTCTTGAA------TGATTATAAACTTTTCTCCTGCT------CTAC--CTTTTTGCA--------CATCTGAATTGATAGCAAGTT s droEug2.KB465067 604127 119 + 1515531 ---caattttccaaataaCAAGC-GAGGTCAATAAAGTGTT---GA---CAAATATTG-TC--AAACTTTTTGCAA------TGATTACAAACTTGGCTGCC-TT------CCC-----AGCTCTG-----GGCCATCTAAATCTGTGGCAAGTT s droEle2.KB458573 525791 108 - 5320397 ---TGATTTTCCAAATAACAAGC------CCATAAAGTgtt---ga---caaatattt-tc-tcaACATTAACCAA------TGACTGAAAACTTTGCCAGG-T---------------TTTTGCA--------CATCTAAATTGATAGCAAGTT s droKik2.KB459527 280116 132 - 1234237 ---tgCTTTTCCAAATAACAAGCTTTAGCCAATAAACTGTT---GA---CAAATACTG-TG-GAAACTTTATCTGctaaaaatgattataaacTTTCAAGTT-TCTCTTGGCAA-----GCTTCTT------GCCATCTAAATCTGTGGCAAGTT s droTak2.KB461535 145267 120 - 669855 ---TGACTTTTCAAATAACAAGC-TTGGCCCATAAAGTGTT---GA---CAAATATTG-CC--AAACTTTACCCAG------TGATTATAAACTTTGCTGCT-TC------CTTT----ACTTTTG-----GGTAATCTAAATTTGTACCAAGTT s droRho2.KB449310 39789 122 - 65043 ---TGATTGTCCAAATAACAAGC-TGGGCCAATAAAGTGTT---GA---CAAATATTG-TCAAAAACTTTATCCGA------TGACTGTAAACTTTGCTGCT-TC------CCCAG-CTTTTTGCA--------CATCTGAATTTGTAGCAATTC s droFic2.KB457177 84685 102 + 995874 --------tttcaaataacaaGA------CAATAAAGCGTT---GA---CAAATATTG-TC-CAGACTTCATCGAA---------------AGTTTGCTCCT-TA------CGCAG-CTTTTTGCT--------CATCTTAGTTTGTGGCAAGTT s droMir2.chr3 1394323 131 - 20862834 ------GTCGCAAATTTCCTCGC-ATTTCTCATTGAGTTTTTAGAA---CAAATATTGATT-GAAACTTTACCAAC------TTCCGCGAGGCGAGTCGCTC-GT------TGCAGCTTGTTTTTATCAGAAAGTAGCTAAATTTGTTACAAGTT s droWil2.CH963894 1313248 109 + 2843958 ATTTAATCCCTACTAGGATAGAT-TTGTTCcataaattttt---gcttttaccTCTTT-CA-AAAAAGTTGT----------TGACCATCAAAATAAGTATC-AT------CAAA----Tgttgta---------ttttaaattt---------- a score=83499.000000 s dm6.chr2R 24353453 24 + 25286936 CG---AGCTG-AACTCCAGGCAAACTGT s droSim1.chr2R 18700131 24 + 19596830 CG---AGCTG-AACTCCAGGCAAACTGT s droSec1.super_23 119902 24 + 989336 CG---AGCTG-AACTCCAGGCAAACTGT s droYak3.chr2R 20209345 24 + 21139217 CG---AGCAG-AACTCCAGGCAAACTGT s droEre2.scaffold_4845 21607199 24 + 22589142 CG---AACAG-AACTCCGGGCAAACTGT s droBia2.KB462602 800267 25 + 3129309 CCT--AAAAG-AACTCCTGGCAAACTGT s droSuz1.KI419649 12045377 27 - 14502029 CCGTAAAAAG-AACTCCAGACAAACTGT s droEug2.KB465067 604246 24 + 1515531 CC---GGCAG-AACTCCGGCCAAACTGT s droEle2.KB458573 525899 25 - 5320397 ATT--GACAG-AACTCCAGACCAACTGT s droKik2.KB459527 280248 25 - 1234237 CC---AGCTGAAACTCCGGCCAAACTGT s droTak2.KB461535 145387 27 - 669855 CCTTGGAAAG-AACTCACGTAAAACTGT s droRho2.KB449310 39911 24 - 65043 TT---GGCAG-AACTTCAGACAAACTGT s droFic2.KB457177 84787 24 + 995874 CG---AGCGG-AACTCCAGGCAAACTGT s droWil2.CH963894 1313357 19 + 2843958 --------ag-aaacTATAGAAAACAGA a score=3741.000000 s dm6.chr2R 24353477 4 + 25286936 ACTT- s droYak3.chr2R 20209369 4 + 21139217 ACTT- s droEle2.KB458573 525924 4 - 5320397 ACTT- s droKik2.KB459527 280273 4 - 1234237 ACTT- s droTak2.KB461535 145414 4 - 669855 ACTT- s droRho2.KB449310 39935 4 - 65043 Actt- s droWil2.CH963894 1313376 4 + 2843958 -TTTT a score=755.000000 s dm6.chr2R 24353481 1 + 25286936 T s droYak3.chr2R 20209373 1 + 21139217 T s droEle2.KB458573 525928 1 - 5320397 T s droTak2.KB461535 145418 1 - 669855 T s droRho2.KB449310 39939 1 - 65043 t s droWil2.CH963894 1313380 1 + 2843958 C a score=-1959.000000 s dm6.chr2R 24353482 2 + 25286936 -At s droYak3.chr2R 20209374 2 + 21139217 -AC s droTak2.KB461535 145419 1 - 669855 --C s droWil2.CH963894 1313381 2 + 2843958 AA- a score=-2159.000000 s dm6.chr2R 24353484 12 + 25286936 gttc-----acacatga s droTak2.KB461535 145421 17 - 669855 GAGCGGAAAACACATGT s droWil2.CH963894 1313383 11 + 2843958 ----GTTTAATATCA-- a score=256.000000 s dm6.chr2R 24353496 10 + 25286936 acacgaatat s droWil2.CH963894 1313394 10 + 2843958 CTACAAAAAT a score=0.000000 s dm6.chr2R 24353506 8280 + 25286936 atttaaagacttacaattttgggctccgttcatatcttatgtaaatgaatcgagagcgataaattatatttaggattttgttatctaaggcgacatgggtgcattgctcaaaaacatgtaatttaagtgcacactacatgagtcagtcacttgagatcgttccccgcctcctaaaatagtcccttagtgggagaccacagataaggtcctcgccgctcaagataggcagatgtgcccgagcgtgggacctcgataaggcggggactatttacttaggcctctgcgtaggccatttactttaagatgcgattctcatgtcacctatttaaaccgaagatatttccaaataaaatcagttttcttacaaaaactcaacgagtaaagtcttcttatttgggattttacatttggtcaatcaagcctttaatcgactctgcagtttccccctaccaaaggtaaggaactcagagaaaggccagctcctttaagcatcttacagctaaaggtagcaaaaataagtgactcttgtttccccctaccaaaggtaaggaacagagtataaatataaaaagcaaaagatacaaaagaatcttttatgttttaaaacaagcaccttatagtctatagctaaaggttgctttgtgtaccattataaattgtggtaaggcgtgcttgaggccatacatcagcaattgtgaaattaaaaagtgcataacaaaagtgccttataaatgctctaatagcattaaatcagctcataaatagagtgcagtgtatatgccataagagcataaattaaataaaaagtgcctgaaaacagtgccttataaatgctctaatagcattaaatcagctcataaatagagtgcagtgtatatgccaaaagagcataaatgccgaaataaatggctaaaaaacaaaaaatctgactggactacaaaaataataaaacgtgcaaaaaaaaaaaaaaaaaaaaaaaaatcatctttaaacatcgacggagccttaaagaagagaaggaagtcaaattcaaaggagcctctaccagcagcagaagcagcaacaacagcagcagcagaagcagcaacagcagtagcaacagcagcaacaacagcagcaacagcagcagcaacaacaacgacatcagctaagtcaaaacaagaattttctgtttatccaaacacacatatatatataaatacatataaaatacatatacacgtactatatatattaagaaattacaaaaaattttcaaaatgatgtcagaaaagactattcaattccttaagaagcagtccgaaattattttggaaattagaaagttggaagtaaaaccaacattaacagatgtagaaattctaaaattaaatgagcttcaaaaatgtttcattgctaatcatagcaatttgttaaagatcggcgttgtcgatcatgaatattttaacgcgaagcagtatgatttaataatgatggtgttagaaaaaattaaaaataaaaatgaaaaaattaagggcgagtcggtagaaaacactttccctaaatcaaacactgtccctaaatcaaaccctccccctacattaaaccttgaaatgcgtggtcaccctgaaaaagagggtatagcacaaaacaacgctttaaaagtagagcaggcatttcgtaataatgttggccaatttcgagtatatctagaagatacgtctaaactaatagacagtagtccagatttccttaaaataaggaaaaataaaattgaatttttatggcataaaatagataacctgattgaacaggtgaatagtcattttgagagttcgctattcgaagaagaaattagcgaacttgaatttgacaaacaaaatattcttacagccattaatagtcgactcagtggcacaataaataaagctgaaatgtcgacggttgttaaggcggaggagttaccaaccctgcctaaaatacagattcccaccttctttggtgattccaaagaatgggatctttttaatgaactctttacagagctcatacatgtgagagaggatctcagtccttctctcaaatttaattatctaaagtcagcattaaaaggagaagccagaaatgtggttactcatttactgctcggctctggagaaaattatgaagccacttgggagtttttgaccaagcgatatgagaataaaagaaacatattctcagatcatatgaataggcttatggatatgccaaatttaaatttagaatccaataagcaaataaagacatttattgacacgattaacgagtcaatttatattataaaattaaaggcacaattaccagaagatgtggatgcaattttcgctcacataattcttcggaaattcaataaagaatcactcaatttatatgaaagccatgttaaaaagacaaaagaaatacaggcactttctgatgtcatggactttttagagcaaaggctcaattctatatcatcattctcacaggaagtaaaacctgtaaagaaaatgattaataataacaagaataaaaattatagtgacaattgtgcatattgcaaactaccagggcattatttaattcaatgccataaatttaaaataatgaatccagcagaacggtctgactgggtaagaaaaaatgggatttgcctaagatgtctgaggcatccgtttggtaaaaaatgtataagcgagcagctttgttcgacttgtcgtaaacctcaccacacgttacttcactttgcaggtcataatccagaaaaagtgaatacgtgtagaacaacaggtcaagccttgttggccacggccttgattcaagtaaagtcgaggtatggaggctttgaacaattaagagcattgattgatagtggctctcaaagcacaattatttcagaagagtctgcacagattctaaaattgaaaaaatttcggtctcatactgaaataagtggagtatcttccacaggaacgtgcatctccaagcacaaagcggttatttcgataagaaattctccgaaaaatttagaaattgaagcaattattctcccaaaacttatgaaggcacttccagtcaacacgattaatgttgatcagaaaaaatggaagaactttaaattagccgaccccgattttaataaaccgggtcgcattgatttaatcattggagcagacgtatatactcacattctgcaaaatggagttataaaaatagacggtctccttgggcaaaaaactgatttcgggtggatagtttctggatgtaaaaaatccaaaggaaaagaaaccattgtagccacaacaatagaaataaaagagttagatcgctactgggaagtggaagaagaagaaaaagatgatatcgagtctgaaatctgtgaaaataaatttatcaaaacgacaaaaaaagattcagatgggcgatacattgtgtcaattccattcaaggaggatgtcaccttaggagattcaaagaaacaagcgatagctcgttacatgaatctggagaaaaaactaaaaagaaatgaaaaacttaaggttgactacactaaattcatgaatgaatacatggatttaggacacatgattgaagtgagtgatgaaggcaaatattttttaccgcaccaggcagtgattagagattcaagccttacgaccaaattgagagtagtttttgatgcttcagcaaaaactacgaataacaaaagtttgaacgacataatgtgggttgggccacgagttcaaaaagatatttttgacattattattaaatggagaaaatgggaatttgttgtttcggcagacattgaaaagatgtaccgacaaattaaaatagataataatgatcaaaaatatcaatatattttatggagaaattctccaaaagaaaaaattaaaacatataaattaaccacagtcacttacggaactgcatctgcaccatatttggctaccagggttctggtagatattgcagataaatgtaaaaaccaagttattagtgcaataattaggaatgatttctatatggatgacctaatgactggagctgattcggtagaagaagctaataaattaataacattaattccccatgaattgcagaaagttggattcaacttaaggaaatggatttccaacaattccaaaatattaaccactgtggaggacacaggggacaataaggttctcaatattatcgaaaatgaatgtgttaaaactttaggactaaaatgggaacctcaaaaggatttatttaagttcagcgtaaattgtaatgatgaatcaaaaaatataaataagcgcgttgtgttatcaacgctagcaaaaatatttgatccgttaggatggttggcaccagtcacggtttcaggaaaactttttattcaaaaactttggataaataaaagtgaatgggatcaggaattatccatagaagataaaaattattgggaaaaatataaagaaaatttattattgttagagaatattcgaatcccaaggtggattaattcaaacagttcttcagtcattcagattcacggatttgcggacgcctccgaaaaagcatatgctgcagtagtctatgctaaagtaggacctcatgttaatataatagctagcaaaagtagagtcaaccctataaaaaataggaagacaattcccaaactcgagctgtgtgcagctcacctgcttagtgaattaatccaaagactaaaaggatcaattgacaatataatggagatctatgcttggagtgattccacgattaccttagcatggattaacagtggtcaaagtaagatcaaatttataaaaagaagaacggatgacattcggaaattaaaaaatactgaatggaatcatgttaagtcagaggataatccagcagatttagcatccaggggagtggattctaaccagttgatcaactgtgatttttggtggaaaggtccgaaatggctagcagacccaaaagaactttggcctcggcagcagtctgtagaagaacctgtcttaataaatacggtattaaatgacaaaatagatgatcctatttacgaattaatagaaaggtattccagtatagaaaaacttatacgtataatagcatacataaatagattcgtgcagatgaaaacaagaaataaagcctattcatcaattatttcagtaaaggagataagaatagcggaaacagttgttattaagaaacaacaagaataccagtttaggcaagagataaagtgccttaaaatcaaaaaggaaatcaagacaaataataaaatattgtcattgaatccatttttggacaaggatggggttctaagagttggaggaagattgcaaaattccaatgcagaatttaatgttaaacatccaatcattttagaaaaatgccacctaacaagcttattaataaaaaatgctcataaggaaacattgcatggagggataaacctaatgcgaaactatatccaaagaaagtattggattttcgggttgaaaaattcgttgaaaaagtatttaagagaatgtgtaacgtgtgcaaggtataaacaaaatacagctcagcaaataatgggtaacttgccaaaatatagagtgacgatgacattcccgtttcttaatactggaatagattacgcaggtccttattatgttaaatgttcaaaaaatcgtggccaaaaaacatttaaaggatacgttgctgtattcgtttgcatggccaccaaagccatacacttagaaatggtaagcgatctaacttcagacgcatttttagcagcactcagaagatttattgctagacggggaaaatgttccaatatctattcagacaacggaacaaattttgtaggagctgcaagaaaattagatcaagagttatttaatgcaatacaagaaaatataacgattgcagcgcagcttgaaaaggacaggattgattggcattttattcccccggcaggacctcacttcggaggtatttgggaagctggagttaagtcaatgaaataccatttaaagcgtataatcggcgacactattttgacttacgaagaaatgtcaactcttttatgtcaaatagaagcatgcttaaattcaaggccattatacactatagttagtgagaaggaccaacaagaagttttaacaccaggtcattttttaattggaagaccacctttagaaatagtcgaaccaatggaagatgaaaaaatcggaaatttggataggtggagacttatccaaaaaatgaagaaagatttctgggttaagtggaaaagtgaatatttgcatacgctccagcaaaggaataaatggaaaaaggaaattcctaatatagaagaagggcaaatagttttattaaaggatgagaattgtcatcctgcaagatggcctttaggaaaggtggaaaaggtgcataaggggaatgatgataaggtccgagtggctaaagtaaagatgcaggaaggatatatcactagacccattactaaaatttgtcccttggaaggaataaagtctgttgacaaaaatgaggctgaccaagagccaaaaagacgaactagagcgacatcgggaatgtccaagatcggaatcattatggcaatgttgttgtttgtgttaagttgtcaagtttctagcgcattacctaaagatatagcaccaagatattctatagacaaaataaataaaacctcagcaatatatctagacccgctaggagatgttgagattgtgagtacttcttggaatttggttatctattataaaatggatccatattttaaaatgttaacaaagggtaatgcgcttatacaaagtatgaggaaagtttgcgaaagacttcatagctttgaagagcaatgtagtctagtcttagataatatgcaaagtcagttatcggaacttgaagaaaacaataaattgtttatgatacagtctagatctagaagcaagcgtgctcctttcgaatttatgggttccttgtatcatattttatttggtataatggatgaagatgatagagagcaattagaaaagaaaagtagttggttgtttaaggttcctgcgaattcaaaagtccgtctgcaatgtactggctctcaaattgaattgtttgatttgcctcagcaaggagttttaagcattgcgccatattgtacggcaagaaccgacgataaaattctagttgcccaccataacattcagtccgaaagtgaagaattattatcaacaccttatataggagaagttagtggagtgccgaagattatttgggatccgctgaaactatcaatattaaatcatactgaggaatttgaacgattgaataatgaaattaaatttatgaaagagaaccatcaaaaattgaaagatttacatttccatcatatttccggacatgctggattaattattgctttaatactaatgatagtattaataatatatttcatacggaaatgtgctgtgcaacaaagaatgcaagcaataacctttgcaggtccgttgccagtactataaatatcaatagtaaataaacaataaaataatataacaaataaaaatatacagtccactatatcgttgtttaatagaaaatgtacttctacatagaaaaagcaaaatgtttaaaataagttaattgagtacaaattgttgaattaaaaataatataaaccataattgtaatccaataaaattaaaagccagaaaaactaggcccattgaaatcttagttgcaaaataaatgaacatatatcaaataaatacagtccactactgttataaatgcaactaatatactaatgtacatctcagcttgctggccctttggcagaatgttcacacatgaacacgaatatatttaaagacttacaattttgggctccgttcatatcttatgtaaatgaatcgagagcgataaattatatttaggattttgttatctaaggcgacatgggtgcattgctcaaaaacatgtaatttaagtgcacactacatgagtcagtcacttgagatcgttccccgcctcctaaaatagtcccttagtgggagaccacagataaggtcctcgccgctcaagataggcagatgtgcccgagcgtgggacctcgataaggcggggactatttacttaggcctctgcgtaggccatttactttaagatgcgattctcatgtcacctatttaaaccgaagatatttccaaataaaatcagtttcttacaaaaactcaacgagtaaagtcttcttatttgggattttac a score=11494.000000 s dm6.chr2R 24361786 5 + 25286936 aCTTT s droSim1.chr2R 18700155 5 + 19596830 ACTTT s droSec1.super_23 119926 5 + 989336 ACTTT s droEre2.scaffold_4845 21607223 5 + 22589142 ACTTT s droBia2.KB462602 800292 5 + 3129309 ACtta s droSuz1.KI419649 12045404 5 - 14502029 ACTTT s droEug2.KB465067 604270 5 + 1515531 ACttt s droFic2.KB457177 84811 5 + 995874 ACTTT a score=1577.000000 s dm6.chr2R 24361791 1 + 25286936 A s droSim1.chr2R 18700160 1 + 19596830 A s droSec1.super_23 119931 1 + 989336 A s droEre2.scaffold_4845 21607228 1 + 22589142 A s droBia2.KB462602 800297 1 + 3129309 a s droSuz1.KI419649 12045409 1 - 14502029 A s droEug2.KB465067 604275 1 + 1515531 g s droKik2.KB459527 280303 1 - 1234237 a s droFic2.KB457177 84816 1 + 995874 G a score=2818.000000 s dm6.chr2R 24361792 1 + 25286936 A s droSim1.chr2R 18700161 1 + 19596830 A s droSec1.super_23 119932 1 + 989336 A s droEre2.scaffold_4845 21607229 1 + 22589142 A s droBia2.KB462602 800298 1 + 3129309 a s droSuz1.KI419649 12045410 1 - 14502029 A s droEug2.KB465067 604276 1 + 1515531 a s droEle2.KB458573 525929 1 - 5320397 G s droKik2.KB459527 280304 1 - 1234237 g s droRho2.KB449310 39940 1 - 65043 a s droFic2.KB457177 84817 1 + 995874 A a score=9174.000000 s dm6.chr2R 24361793 3 + 25286936 AAG s droSim1.chr2R 18700162 3 + 19596830 AAG s droSec1.super_23 119933 3 + 989336 AAG s droYak3.chr2R 20209376 3 + 21139217 AAG s droEre2.scaffold_4845 21607230 3 + 22589142 AAG s droBia2.KB462602 800299 3 + 3129309 aag s droSuz1.KI419649 12045411 3 - 14502029 AAG s droEug2.KB465067 604278 3 + 1515531 aga s droEle2.KB458573 525931 3 - 5320397 AGA s droKik2.KB459527 280306 3 - 1234237 aga s droRho2.KB449310 39942 3 - 65043 aga s droFic2.KB457177 84818 3 + 995874 GAG a score=29380.000000 s dm6.chr2R 24361796 20 + 25286936 AAAGAAAACA---TGGGTAGTAA---- s droSim1.chr2R 18700165 15 + 19596830 -AAGAAAACA---TGGGT----A---- s droSec1.super_23 119936 15 + 989336 -AAGAAAACA---TGGGT----A---- s droYak3.chr2R 20209379 15 + 21139217 -AGGAAAACA---TGTGT----A---- s droEre2.scaffold_4845 21607233 15 + 22589142 -AAGAAAACA---TGTGT----G---- s droBia2.KB462602 800302 14 + 3129309 -aggaaaaca---caTGT--------- s droSuz1.KI419649 12045414 14 - 14502029 -TGGAAAACA---CATGC--------- s droEug2.KB465067 604281 15 + 1515531 -agaaaaaca---tgTGT----A---- s droEle2.KB458573 525934 15 - 5320397 -AGAAAAACA---TGTGT----A---- s droKik2.KB459527 280309 15 - 1234237 -aaaaaaaca---tatct----G---- s droRho2.KB449310 39945 15 - 65043 -agaaaaaca---tGTGT----A---- s droFic2.KB457177 84821 15 + 995874 -AAGAAAACA---TGGGT----A---- s droPse3.chr3 1353385 20 - 19787792 ---aaaaacattttgagT----AATAA s droPer1.super_34 542201 20 - 916997 ---AAAAACATTTTGAGT----AATAA s droMir2.chr3 1394473 20 - 20862834 ---aaaaacattttgagt----AATAA a score=2334.000000 s dm6.chr2R 24361816 1 + 25286936 G s droSim1.chr2R 18700180 1 + 19596830 G s droSec1.super_23 119951 1 + 989336 G s droYak3.chr2R 20209394 1 + 21139217 G s droEre2.scaffold_4845 21607248 1 + 22589142 T s droBia2.KB462602 800316 1 + 3129309 G s droSuz1.KI419649 12045428 1 - 14502029 G s droEug2.KB465067 604296 1 + 1515531 G s droEle2.KB458573 525949 1 - 5320397 G s droKik2.KB459527 280324 1 - 1234237 G s droTak2.KB461535 145438 1 - 669855 G s droPse3.chr3 1353405 1 - 19787792 A s droPer1.super_34 542221 1 - 916997 A s droMir2.chr3 1394493 1 - 20862834 A a score=111276.000000 s dm6.chr2R 24361817 53 + 25286936 TAGCCAAAGTTTGTAGGC---AAAA--CTTTGAGCTGGcg--att-------------------gcgattgc------------------------gactgtg----------------- s droSim1.chr2R 18700181 53 + 19596830 TAGCCAAAGTTCGTAGGC---AAAA--CTTTGAGCTGGCG--ACT-------------------GCGATTGC------------------------GACTGTG----------------- s droSec1.super_23 119952 53 + 989336 CGGCCAAAGTTTGTCGGC---AAAA--CTTTGAGCTGGCG--ACT-------------------GCGATTGC------------------------GACTGTG----------------- s droYak3.chr2R 20209395 41 + 21139217 TAGCCAAAGTTTGTAGGC---AAAA--CTTTGAAC---------------------------------TGGC------------------------GACTGTG----------------- s droEre2.scaffold_4845 21607249 62 + 22589142 TAGCCAAAGTTTGTAGGC---AAAA--CTTTGAGCTGGCG--TTT-------G---TTTTGCTGGCGATGGC------------------------GACTGTG----------------- s droBia2.KB462602 800317 84 + 3129309 TTGTGATAAACTCTGGGC---AAAG--CTCTGAGCTGACC--TTT-------G---TTTTGCTCGCGATTGCCGT--GTGCTATGTGTGCTAGAGTGAATGTG----------------- s droSuz1.KI419649 12045429 77 - 14502029 TTGTCATAAATTCTGGGC---AAAA--CTTTGAGCTGGCTGGTTT-------G---TTTTGCTCGCGATTGCTAC--GTGCTAT---------AGTGATTGTG----------------- s droBip2.KB464407 1962878 72 + 2915140 TAGCAATAAATTGTAAGCTAAAAAA--CTTTGAACTAGGT--TCTaggttggg---ttttttttttcattgt------------------------gATTGTG----------------- s droEug2.KB465067 604300 56 + 1515531 ------CAAATTCTAGGC---AAAA--CTTTGAGCTGGCG--TCT-------G---CTTAGCTTGGGACTGC------------------------GATTGTG----------------- s droEle2.KB458573 525954 57 - 5320397 -------AAATTCTAGGC---AAAAAGTTTTGAGCTggcg--ttt-------g---ttttgtttgcgattgc------------------------gattgtg----------------- s droKik2.KB459527 280335 62 - 1234237 TAGGCAAAAACTTTGGGCC--AAAG--CTGGCGGCTGGCG--TCT-------G---GTTTATTTGTGATTGC------------------------G-TTGTG----------------- s droTak2.KB461535 145439 54 - 669855 TAGCAATAAATTCTGGGC---AAAA--CTTTGAGCTGGCG--TTT-------G---TTTTGCTTGCGACTG------------------------------------------------- s droRho2.KB449310 39965 55 - 65043 -------AAATTCTAGGT---AAAA--CTTTGAGCTGgcg--ttt-------g---ttttgtttgcgaTTGC------------------------GATTGTG----------------- s droFic2.KB457177 84841 55 + 995874 -------AAATTCTAGGC---GAAA--CTTGGAGCtggcg--ttt-------g---ttttgtttgcgattgc------------------------gattgtg----------------- s droPse3.chr3 1353406 73 - 19787792 ----------TTCTAAGC---TAAA--CTttgagcttgag--ctt-------gagcttCAGct-------gtggatggtg----------------gatggtgggggATGCTGGTGTGTG s droPer1.super_34 542222 80 - 916997 ----------TTCTAAGC---TAAA--CTTTGAGCTTGAG--CTT-------GAGCTTCAGCTgtggatggtggatggtg----------------gatggtggGGGATGCTGGTGTGTG s droMir2.chr3 1394494 80 - 20862834 ----------TTCTAAGC---TAAA--CTttgagcttgag--ctt-------gagcttCAGCTGTCGacggtggatggtg----------------gatggtgggggATGCTGGTGTGTG a score=25211.000000 s dm6.chr2R 24361870 23 + 25286936 cccatctc-------------ccgaatccgaaaccg s droSim1.chr2R 18700234 23 + 19596830 CCCATCTC-------------CCGAATCCGAATCCG s droSec1.super_23 120012 23 + 989336 CCCATCTC-------------CCGAATCCGAATCCG s droYak3.chr2R 20209443 23 + 21139217 TCCATCTC-------------CCGAATGCGATTCCA s droEre2.scaffold_4845 21607318 36 + 22589142 TCCATCTCCCATCTCCCGAAACCGAATCCGAATCCG s droBia2.KB462602 800401 11 + 3129309 CCCATCTC-------------------------CCA s droSuz1.KI419649 12045506 11 - 14502029 CCCATCTC-------------------------CCa s droEug2.KB465067 604356 12 + 1515531 CCCATCTC-------------CCAA----------- s droEle2.KB458573 526011 12 - 5320397 CCCATCTC-------------CCAA----------- s droKik2.KB459527 280397 16 - 1234237 CCCATCTC-------------CCATCTCC------- s droTak2.KB461535 145493 22 - 669855 -CTATGTG-------------CTATATAGTGATTGT s droRho2.KB449310 40020 12 - 65043 CCCATCTC-------------CCAA----------- s droFic2.KB457177 84896 12 + 995874 CCCATCTC-------------CGAA----------- s droPse3.chr3 1353479 13 - 19787792 CCCATCTC-------------CCAGA---------- s droPer1.super_34 542302 13 - 916997 CCCATCTC-------------CCAGA---------- s droMir2.chr3 1394574 13 - 20862834 CCCATCTC-------------CCAGA---------- a score=1209050.000000 s dm6.chr2R 24361893 189 + 25286936 attccaattccgattccgatCCATTATATAATGAAGCACACGCGGACTTCCCACATGGAA---------------CGC-GGCAAAAGCCGAC---TCTACCCACAGTCCA---------------------------CAGCA---CGG-----CCAACAAAAGTT-AACAACAATCGATGTTCGGCT--------------GCTCAGCTCATTTCCTGCCCACAATG-------AAATGTTGAAATCTG--------------TTG-------------------A-----GACG-TAC----ATA-----------TG s droSim1.chr2R 18700257 189 + 19596830 ATTCCAATTCCGATTCCGATCCATTATATAATGAAGCACACGCGGACTTCCCACATGAAA---------------CGG-GGCAAAAGCCGAC---TCTACCCACAGTCCA---------------------------CGGCA---CGG-----CCAACAAAAGTT-AACAACAATCGATGTTCGGCT--------------GCTCAGCTCATTTCCTGCCCACAATG-------AAATGTTGAAATCTG--------------GTG-------------------A-----GACG-TAC----GTA-----------TG s droSec1.super_23 120035 189 + 989336 ATTCCAATTCCGATTCCGAACCATTATATAATGAAGCACACGCGGACTTCCCACATGAAA---------------CGG-GGCAAAAGCCGCC---TCTACCCACAGTCCA---------------------------CGGCA---CGG-----CCAACAAAAGTT-AACAACAATCGATTTTCGGCT--------------GCTCAGCTCATTTCCTGCCCACAATG-------AAATGTTGAAATCTG--------------GTG-------------------A-----GACG-TAC----GTA-----------TG s droYak3.chr2R 20209466 183 + 21139217 ATTTtaattccgattccgattcatTATATAATGAAGCACACGCGGACTGCCCACATGAAG---------------CGG-GGCAACAGCCGCC---TCTACCCACAGTCC------------------------------GCA---CGG-----CAAACAAAAGTT-AACAACAATCGATGTTTGGCT-------------GGCTCAGCTCATTTCCTGCCCAcaaca-------aaatgttgaaatCTG--------------GCA-------------------A-----GAT---------GTA-----------TG s droEre2.scaffold_4845 21607354 188 + 22589142 ATTCCAATTCCGATTCCGATTCATTATATAATGAAGCACACGCGGACTTCCCACATGAAA---------------CGG-GGCAAGAGCCGAC---TCTACCCACAGTCC------------------------------GCA---CGG-----CTAACAAAAGTT-AACAACAATCGATGTTCGGCT-------------GGCTCAGCTCATTTCCTGCCCACAATA-------AAATGTTGAAATCT---------------GTG-------------------A-----GATA-CAC--TCGTA-----------TG s droBia2.KB462602 800412 191 + 3129309 ATTccgattccaattccaatCCATTATATAATGAAGCACACGCGGTCTTCCCACATGAAA---------------CGG-GGCAAAAGCCGAC---TCTACCCACAGTCC------------------------------GCA---CGG-----TTAACAAAAGTT-AACAACAATCGAT----------------------GTTCAGCTCATTTCCTGCccacaata-aaatc-aaatgttGAAATCCACACAGCTTTT----Gtg-------------------a-----tac---at----aca-----------ta s droSuz1.KI419649 12045517 193 - 14502029 gttccaattccaattccaattcatTATATAATGAAGCACACGCGGACTTCCCACATGAAA---------------CGG-GGCAAAAGCCGAC---TCTACCCACAGTCC------------------------------GCA---CGG-----TTAACAAAAGTT-AACAACAATCGAT----------------------GTTCAGCTCATTTCCTGCccacaata-aaatc-aaatgttGAAATCCACACAACTTTT----atg-------------------a-----taca-tat----ata-----------ta s droBip2.KB464407 1962976 204 + 2915140 AGCCCATCTCC----CCAATTCATTATATAATGAAGCACACGCGGACTTCCCACA--------------------CGG-GGCGA------CT---TCTGCCCACTGCCAG---------------------------TCGCCAGTCGG-----TTAACAAAAGTT-AACAACAATCGATGTTCGGCT------------TGGTTCAGCTCATTTCCTGCccacaata-aaatcaaaatgttgaaaTCAACACAACTT------ATG-------------------C-----GACT-GAT----ATACTGTACAGTGTTG s droEug2.KB465067 604368 188 + 1515531 -------------TTCCaattcattatataatgaagCACACGCGGACTTCCCACATGAAG---------------CGG-GGCAAAAGCCGAC--TTCTACCCACAGTCC------------------------------GCA---CGG-----TTAACAAAAGTT-AACAACAATCGATGTTCGGCT-------------GGTTCAGCTCATTTCCTGCCcacaata-aaatc-aaatgttGAAATCCACACAGCTTCG----GTG-------------------A-----TAC---AT----TTA-----------AG s droEle2.KB458573 526023 183 - 5320397 -------------------TTCATTATATAATGAAGCACACGCGGACTTCCCACACGGA----------------CGG-GGCAAAAGCCGAC--TTCTACCCACAGTCC------------------------------GCA---CGG-----TTAACAAAAGTT-AACAACAATCGATGTTCGGCT-------------GGTTCAGCTCATTTCCTGCccacaata-aaatc-aaatgttgAAATCAACACAATCTAT----GTG-------------------A-----TACA-TAT----GTG-----------TG s droKik2.KB459527 280413 207 - 1234237 ----------------CGATTCATTATATAATGAAGCACACGCGGACTTCCCACACGGGC---------------CAGTGGCAA--GCCGAC--TTCTACCCACAGTCCG--------------------------TCCGCA---CGG-----TTAACAAAAGTT-AACAACAATCGATGTTCGGCTGTGTCTCtggctcagctcagctcattTCCTGCCCACAATA-AAGTC-AAATGTTGAAATCAACACAACTTAT----GTG-------------------A-----GAGt-tactatacta-----------ta s droTak2.KB461535 145515 199 - 669855 GCCCATCTCCCAATTCCAATTCATTATATAATGAAGCACACGCGGACTTCCCACATGAAA---------------CGG-GGCAAAAGCCGACTTTTCTACCCACAGTCC------------------------------GCA---CGGTTAACTTAACAAAAGTT-AACAACAATCGAT----------------------GTTCAGCTCATTTCCTGCccacaata-aaatc-aaatgttgAAATCCACACAACTTTT----GTG-------------------A-----TAT---AT----ATG-----------TG s droRho2.KB449310 40032 183 - 65043 -------------------TTCATTATATAATGAAGCACACGCGGACTTCCCACACGGA----------------CGG-GGCAAAAGCCGAC--TTCTACCCACAGTCC----------------------------ATGCG---CGG-----TTAACAAAAGTT-AACAACAATCGATGTTCGGCT-------------GGTTCAGCTCATTTCCTGCCcacaata-aaatc-aaatgttgAAATCAACACAGCCCAT----GTG-------------------A-----TAC---AT----ATG-----------TG s droFic2.KB457177 84908 178 + 995874 -------------------TTCATTATATAATGAAGCACACGCGGACTTCCCACACGGC------------------G-GGCAAAAGCCGAC--TTCTACCCACAGTCC------------------------------GCA---CGG-----TTAACAAAAGTT-AACAACAATCGATGCTCGGCT-------------GGTTCAGCTCATTTCCTGCccacaata-aaatc-aaatgttgAAATCCACACAACCAC-----GTG-------------------A-----TAC---AT----ATA-----------TG s droPse3.chr3 1353492 238 - 19787792 --------------GTCGATTCATTATATAATGAAGCACACGCGGACATCCCACACGGgtagccagagt------cag-agccagagccgcc--tTCTGCCCACAGAcct------------ccagccagccagcgaccGTG---CGG-----CTAACAAAAGTGAAACAACAATCGAT----------------------GTTCAGCTCATTTCCTGCCCacaatcgaaatcgaaatgtTGAAATCCACACAAATTGTACCAGTGTATGTACTGTATCGCTTATATACagcatc-tat----gta-----------tg s droPer1.super_34 542315 252 - 916997 --------------GTCGATTCATTATATAATGAAGCACACGCGGACATCCCACACGGGTAGCCAGAGTCAGAGCCAG-AGCCAGAGCCGCC--TTCTGCCCACAGACCTccagccagccagccagccagccagcGACCGTG---CGG-----CTAACAAAAGTGAAACAACAATCGAT----------------------GTTCAGCTCATTTCCTGCCCACAATCGAAATCGAAATGTTGAAATCCACACAAATTGTACCAGTGTATGTACTGTATCGCTTATA-----TACAGCAT----CTA-----------TG s droMir2.chr3 1394587 228 - 20862834 --------------GTCGATTCATTATATAATGAAGCACACGCGGACATCCCACACGggtagc------------cag-agccagagccgcc--ttctgcccacagagcc----------agccagccagccagcgaccGTG---CGG-----CtaacaaaagtgaaacaacAATCGAT----------------------GTTCAGCTCATTTCCTGCCCacaatcgaaatcgaaatgttGAAATCCACAcaaattgtac--gagtatgtactgTATCGCTTATA-----TACAGCAT----CTA-----------TG a score=-111445.000000 s dm6.chr2R 24362082 59 + 25286936 TG-A--ATAGTAATTCGCATATAACAT-------------------TCTCTAAA----ACTTAGGC--------TT--GT-----TGGCCC-------AGAACCATA s droSim1.chr2R 18700446 59 + 19596830 TG-A--ATAGTAATTCGCATATAACAT-------------------TCTCTAAA----ACTTAGGC--------TT--GT-----TGGCCC-------AGAACCATG s droSec1.super_23 120224 59 + 989336 TG-A--ATAGTAATTCGCATATAACAT-------------------TCTCTAAA----ACTTAGGC--------TT--GT-----TGGCCC-------AGAACCATG s droYak3.chr2R 20209649 64 + 21139217 TG-A--ATAGTAATTCGCATATCACAT-------------------TCTCTTTA----ACCTGGGC--------TT--GTTGGCCTGGCCC-------AGAACTAAG s droEre2.scaffold_4845 21607542 54 + 22589142 TG-A--ATAGTAATTCGCATATAACAT-------------------TCTC-TAA----ACCTAGGC--------TT--GT-----TGGCCC-------AGAAC---- s droBia2.KB462602 800603 48 + 3129309 ta-a----------tc--ACATATTTT-------------CTAGG-CTTCTTAA----ACGTGGAA------------GA-----TGGTGC-------AGAAC---- s droSuz1.KI419649 12045710 50 - 14502029 ta-a----------tcatatatatttt-------------caacg-CTTCTCAA----ACTTGAAA------------GA-----TGGTGC-------AGAAC---- s droBip2.KB464407 1963180 57 + 2915140 TG-A--GTATATAatcagaaataaaat-------------------------aa----aatcatgcCATGGTTATG--GC-----TCTCCT-------AGAAC---- s droEug2.KB465067 604556 71 + 1515531 TA-A-------CATTGGAATATACATT-------CTCTCTCTCCG-CTTCCTAAGCCTACCTAAGA--------TTGCGC-----TGGACG-------AGAACCTAG s droEle2.KB458573 526206 73 - 5320397 TA-A--TCATTTCtacctatatgatata----tacATTCTCTTCG-CTTCctaa----atttgaaa----gttttc--GC-----TGGGAA-------TGAAC---- s droKik2.KB459527 280620 80 - 1234237 ta-g--accttatatactatatattagaCGTGTACATTCATTGGT-TCctgaaa----acttaaaa-agaGTTTGG--GG-----TAGGCT-------AGACC---- s droTak2.KB461535 145714 56 - 669855 TA-A------TCATTCGCATATACATT-----------CTCTACg-cttcttaa----atttaaaa------------gc-----tggTCC-------Acaac---- s droRho2.KB449310 40215 62 - 65043 TA-A------TCATTCGTATATACATT-----------CTCTTCG-CTTCCTAA----ACTTGAAA----GTTTTC--GC-----TGGGCC-------AGAAC---- s droFic2.KB457177 85086 69 + 995874 TA-ATCATAACCATTCGAAAACACATT-----------CTCTTCGCTTCCTAAA----AGTTGAGA----GTTTTC--GC-----TCGGCC-------AGAAC---- s droPse3.chr3 1353730 66 - 19787792 tata--gtatcTACTTTGAAATGTTCT-----------CCCAAAT-ATTCTGAG----ATTTATTT-----CTTCT--GC-----CAAACG-------AAAGT---- s droPer1.super_34 542567 66 - 916997 TATA--GTATCTACTCTGAAATGTTCT-----------CCCAAAT-ATTCTGAG----ATTTATTT-----CTTTT--GC-----CAAACG-------AAAGT---- s droMir2.chr3 1394815 66 - 20862834 TATA--GTATCTACTCTGAAATGTTCT-----------CCCAAAT-ATTCTGag----atttattt-----ctttt--gc-----caAACG-------AAAGT---- s droWil2.CH963894 1314632 68 + 2843958 TG-A--AGATGATTTTGCGAAATAGTT-------------------AACCTTAA----CCCTATAA--GTGTTGTT--GT-----TAACTCCttcagaaaaac---- a score=-9540.000000 s dm6.chr2R 24362141 25 + 25286936 CC----GTAATACCACGTTCCCGCTC------GGC s droSim1.chr2R 18700505 25 + 19596830 CC----GTAATACCACGTTCCCACTC------GGC s droSec1.super_23 120283 25 + 989336 CC----GTAATACCACGGTCCCACTC------GGC s droYak3.chr2R 20209713 29 + 21139217 CACTAGTAAGTGCCACGTTGCCGCTC------GGC s droEre2.scaffold_4845 21607596 23 + 22589142 ------CTAATGCCACGTTCCCTCTT------GGC s droBia2.KB462602 800651 28 + 3129309 ------GTAGTACTGCTGCACAACTTGCCTT-GGC s droSuz1.KI419649 12045760 29 - 14502029 ------CTAGTACTACTATACAATTTCCCCTGGGC s droBip2.KB464407 1963237 23 + 2915140 ------TTAATTCCATACTTCAACTT------GGC s droEug2.KB465067 604627 25 + 1515531 TA----CGCGTACCGCGATGCCACTT------GGC s droEle2.KB458573 526279 23 - 5320397 ------TTAATGCCATCATACCAGAC------GGC s droKik2.KB459527 280700 24 - 1234237 ------CTAATGGCACGTTTCTTTCTG-----GGC s droTak2.KB461535 145770 23 - 669855 ------ttaataataaaattccccTT------GGT s droRho2.KB449310 40277 24 - 65043 ------TTAATACCACGATTTCAGTTT-----GGC s droFic2.KB457177 85155 23 + 995874 ------TCGATGCCAAAGTTCCACTT------GGC s droPse3.chr3 1353796 28 - 19787792 ------TTTGAGGTTCTCCTCTCCTTGGCTG-GGC s droPer1.super_34 542633 28 - 916997 ------TTTGAGGTTCTCCTCTCCTTGGCTG-GGC s droMir2.chr3 1394881 28 - 20862834 ------TTTGATGTTCTCCTCTCCTTGGCTG-GGC s droWil2.CH963894 1314700 12 + 2843958 ------aaaattctg-----------------cAC s droMoj3.scaffold_6496 26152927 25 + 26866924 CC----GGAATACCCTGTAAACGCTG------AGC a score=14499.000000 s dm6.chr2R 24362166 2 + 25286936 GC s droSim1.chr2R 18700530 2 + 19596830 GC s droSec1.super_23 120308 2 + 989336 GC s droYak3.chr2R 20209742 2 + 21139217 GC s droEre2.scaffold_4845 21607619 2 + 22589142 GC s droBia2.KB462602 800679 2 + 3129309 GC s droSuz1.KI419649 12045789 2 - 14502029 GC s droBip2.KB464407 1963260 2 + 2915140 GC s droEug2.KB465067 604652 2 + 1515531 GC s droEle2.KB458573 526302 2 - 5320397 GC s droKik2.KB459527 280724 2 - 1234237 GC s droTak2.KB461535 145793 2 - 669855 GC s droRho2.KB449310 40301 2 - 65043 GC s droFic2.KB457177 85178 2 + 995874 GC s droPse3.chr3 1353824 2 - 19787792 TC s droPer1.super_34 542661 2 - 916997 TC s droMir2.chr3 1394909 2 - 20862834 TC s droWil2.CH963894 1314712 2 + 2843958 TT s droVir3.scaffold_12875 7357901 2 + 20611582 GT s droMoj3.scaffold_6496 26152959 2 + 26866924 CT a score=558859.000000 s dm6.chr2R 24362168 30 + 25286936 TAATGAAAGTGCCATAAATTTTCAATTAA--A s droSim1.chr2R 18700532 30 + 19596830 TAATGAAAGTGCCATAAATTTTCAATTAA--A s droSec1.super_23 120310 30 + 989336 TAATGAAAGTGCCATAAATTTTCAATTAA--A s droYak3.chr2R 20209744 32 + 21139217 TAATGAAAGTgccataaattttcaattaaaga s droEre2.scaffold_4845 21607621 29 + 22589142 TAATGAAAGTGCCATAAATTTTCAATTA---A s droBia2.KB462602 800681 30 + 3129309 TAATGAAAGTgccataaattttcaattaa--a s droSuz1.KI419649 12045791 30 - 14502029 TAATGAAAGTGccataaattttcaattaa--a s droBip2.KB464407 1963262 30 + 2915140 TAATGAAAGTgccataaattttcaattaa--a s droEug2.KB465067 604654 30 + 1515531 TAATGAAAGtgccataaattttcaattaa--a s droEle2.KB458573 526304 30 - 5320397 TAATGAAAGTgccataaattttcaattaa--a s droKik2.KB459527 280726 30 - 1234237 TAATGAAAGTgccataaattttcaattaa--a s droTak2.KB461535 145795 30 - 669855 TAATGAAAGTgccataaattttcaattaa--a s droRho2.KB449310 40303 30 - 65043 TAATGAAAGTgccataaattttcaattaa--a s droFic2.KB457177 85180 30 + 995874 TAATGAAAGtgccataaattttcaattaa--a s droPse3.chr3 1353826 30 - 19787792 TAATGAAAGTgccataaattttcaattaa--a s droPer1.super_34 542663 30 - 916997 TAATGAAAGTGCCATAAATTTTCAATTAA--A s droMir2.chr3 1394911 30 - 20862834 TAATGAAAGTgccataaattttcaattaa--a s droWil2.CH963894 1314714 30 + 2843958 TAATGAAAgtgccataaattttcaattaa--a s droVir3.scaffold_12875 7357903 30 + 20611582 TGATGAAAGTGCCATAAATTTTCAATTAA--A s droMoj3.scaffold_6496 26152961 30 + 26866924 TGATGAAAGTGCCATAAATTTTCAATTAA--A s droGri2.scaffold_15245 907814 30 + 18325388 TGATGAAAGTGCCATAAATTTTCAATTAA--A a score=-8233.000000 s dm6.chr2R 24362198 2 + 25286936 GC s droSim1.chr2R 18700562 2 + 19596830 GC s droSec1.super_23 120340 2 + 989336 GC s droYak3.chr2R 20209776 2 + 21139217 CT s droEre2.scaffold_4845 21607650 2 + 22589142 TC s droBia2.KB462602 800711 2 + 3129309 ct s droSuz1.KI419649 12045821 2 - 14502029 ct s droBip2.KB464407 1963292 2 + 2915140 ct s droEug2.KB465067 604684 2 + 1515531 ct s droEle2.KB458573 526334 2 - 5320397 cc s droKik2.KB459527 280756 2 - 1234237 cc s droTak2.KB461535 145825 2 - 669855 ct s droRho2.KB449310 40333 2 - 65043 ct s droFic2.KB457177 85210 2 + 995874 gc s droPse3.chr3 1353856 2 - 19787792 cc s droPer1.super_34 542693 2 - 916997 CC s droMir2.chr3 1394941 2 - 20862834 cc s droWil2.CH963894 1314744 2 + 2843958 ct s droMoj3.scaffold_6496 26152991 1 + 26866924 C- s droGri2.scaffold_15245 907844 1 + 18325388 C- a score=-90052.000000 s dm6.chr2R 24362200 2 + 25286936 C--------------------------T s droSim1.chr2R 18700564 2 + 19596830 C--------------------------T s droSec1.super_23 120342 2 + 989336 C--------------------------T s droYak3.chr2R 20209778 2 + 21139217 C--------------------------A s droEre2.scaffold_4845 21607652 2 + 22589142 C--------------------------C s droBia2.KB462602 800713 2 + 3129309 c--------------------------T s droSuz1.KI419649 12045823 2 - 14502029 c--------------------------T s droBip2.KB464407 1963308 2 + 2915140 C--------------------------T s droEug2.KB465067 604686 2 + 1515531 c--------------------------T s droEle2.KB458573 526336 2 - 5320397 c--------------------------T s droKik2.KB459527 280758 22 - 1234237 cAAAGatgcagttttat--tttt----t s droTak2.KB461535 145827 2 - 669855 c--------------------------G s droRho2.KB449310 40335 2 - 65043 c--------------------------t s droFic2.KB457177 85212 2 + 995874 c--------------------------T s droPse3.chr3 1353858 26 - 19787792 ttatgctgctgatgctg--cttgAAAAT s droPer1.super_34 542695 26 - 916997 TTATGCTGCTGATGCTG--CTTGGAAAT s droMir2.chr3 1394943 26 - 20862834 ttatgctgctgatgctg--cttgGAAAT s droWil2.CH963894 1314746 28 + 2843958 tCAGTAGGCTTCTGCCTGCCCTGTTGTT s droGri2.scaffold_15245 907846 2 + 18325388 --------------------------CT a score=-229131.000000 s dm6.chr2R 24362202 6 + 25286936 GGCCAA-------------------------------------------------------------------------------------- s droSim1.chr2R 18700566 6 + 19596830 GGCCAG-------------------------------------------------------------------------------------- s droSec1.super_23 120344 6 + 989336 GGTCAG-------------------------------------------------------------------------------------- s droYak3.chr2R 20209780 6 + 21139217 AGGCAA-------------------------------------------------------------------------------------- s droEre2.scaffold_4845 21607654 6 + 22589142 GGCCAA-------------------------------------------------------------------------------------- s droBia2.KB462602 800715 23 + 3129309 GGGCAA--------------AGTAA-------------------------------------------------------AGCCTTAGTCTC s droSuz1.KI419649 12045825 28 - 14502029 GGGTAA--------------AGTAATTCGC--------------------------------------------------AACCTTAGTTTC s droBip2.KB464407 1963310 43 + 2915140 GGCTGCTGGACTCTAGAGTTAGTAGAGCCC-------------------------------------------------TGACCCTGTCCCT s droEug2.KB465067 604688 37 + 1515531 GGCCAA--------------AGTTATTTTT--------------CGTGGG---------------------------CCCAACCTTAGCCCC s droEle2.KB458573 526338 66 - 5320397 GGGTAA--------------AGTCATTTTTT------CTTACTCCCTAGACCGAGATGCAG-----ACAGGC-GAACCCAAGCCTTGGCCTC s droKik2.KB459527 280780 28 - 1234237 gtacag--------------aCTCTCCTCC--------------------------------------------------AGACTGAGGAGA s droTak2.KB461535 145829 44 - 669855 GGgtaa--------------agcaatatttt------tttcttcttgaacCC----------------------------AACCTTAGTCTC s droRho2.KB449310 40337 65 - 65043 gggtaa--------------agtcattttttgtaACGCTCCAGACTGAGATGCAGACGGTG-----GAACCC--------AACCCTAGTCTC s droFic2.KB457177 85214 65 + 995874 GGGCCA--------------AGCCATTTTT-------TGTGATCCCGCGGACCGAGATGCA-----GACAGT-CGAACCCAACCTCAGTCCC s droPse3.chr3 1353884 57 - 19787792 TGACAA--------------ACTTCTtc------------------cagacgcagacgcagtc---gcagacacagacccaACCTTAGTGGC s droPer1.super_34 542721 63 - 916997 TGACAA--------------ACTCCTTCca------------gacgcagacgcagacgcagtc---gcagacacagacCCAACCTTAGTGGC s droMir2.chr3 1394969 57 - 20862834 TGACAA--------------ACTTCTtc------------------cagacgcagacgcagtc---gcagacacagacccaaCCTTAGTGGC s droWil2.CH963894 1314774 59 + 2843958 ATGCAA--------------TCTTCttcatttt-------------------cagtttcagtcTAGACATATGGAGGCCCAACCTTAGTTTG a score=17029.000000 s dm6.chr2R 24362208 4 + 25286936 AC---CC s droSim1.chr2R 18700572 4 + 19596830 AC---CC s droSec1.super_23 120350 4 + 989336 AC---CC s droYak3.chr2R 20209786 4 + 21139217 AC---CC s droEre2.scaffold_4845 21607660 4 + 22589142 AC---CC s droBia2.KB462602 800738 4 + 3129309 AT---CG s droSuz1.KI419649 12045853 4 - 14502029 AT---CG s droBip2.KB464407 1963353 4 + 2915140 AC---CT s droEug2.KB465067 604725 4 + 1515531 AT---CG s droEle2.KB458573 526404 4 - 5320397 AT---CG s droKik2.KB459527 280808 7 - 1234237 ACCTACG s droTak2.KB461535 145873 4 - 669855 AT---CT s droRho2.KB449310 40402 4 - 65043 AT---CG s droFic2.KB457177 85279 4 + 995874 GT---CC s droPse3.chr3 1353941 4 - 19787792 AT---CG s droPer1.super_34 542784 4 - 916997 AT---CG s droMir2.chr3 1395026 4 - 20862834 AT---CG s droWil2.CH963894 1314833 4 + 2843958 TT---TG s droVir3.scaffold_12875 7358094 4 + 20611582 AT---CG a score=168281.000000 s dm6.chr2R 24362212 46 + 25286936 T-------CTGATTGGCAACGATTAAGTTA-----TC-----------CAGCGAGGCT-----------------------------------------------------------------------------CACTTCGCAG---------C------------- s droSim1.chr2R 18700576 46 + 19596830 T-------CTGATTGGCAACGATTAAGTTA-----TC-----------CAGCGAGGCT-----------------------------------------------------------------------------CACTTCGCAG---------C------------- s droSec1.super_23 120354 46 + 989336 T-------CTGATTGGCAACGATTAAGTTA-----TC-----------CAGCGGGGCT-----------------------------------------------------------------------------CACTTTGCAG---------C------------- s droYak3.chr2R 20209790 46 + 21139217 T-------CTGATTGGCAGCGATTAAGTTA-----TC-----------CAGCGAGGCT-----------------------------------------------------------------------------CACTTCGCAG---------C------------- s droEre2.scaffold_4845 21607664 45 + 22589142 T-------CTGATT-GCAACGATTAAGTTA-----TC-----------CAGCGCGGCT-----------------------------------------------------------------------------CACTTCGCAG---------C------------- s droBia2.KB462602 800742 52 + 3129309 T-------CTGATTGGCAGCGATTAAGCCA-----TCCCATC-----GCGAGGAGAC------------------------------------------------------------------------------CTTTTCGAAG--------CC------------- s droSuz1.KI419649 12045857 52 - 14502029 T-------CTGATTGGCAGCGATTAAGCCA-----TCCCAG------ACAACGAGGCT-----------------------------------------------------------------------------TTTTTCGAAG--------CC------------- s droBip2.KB464407 1963357 52 + 2915140 TCCTCCGACTGATTGGCGCCGATTAAGAAA-----TT-----------CAACGGGGTT-----------------------------------------------------------------------------GGCTCTCCAA----------------------- s droEug2.KB465067 604729 46 + 1515531 T-------CTGATTGGCAACGATTAAGCCA-----TC-----------CGACGAGGCT-----------------------------------------------------------------------------CTC-CCGAAG--------CC------------- s droEle2.KB458573 526408 47 - 5320397 T-------CTGATTGACTGCGATTAAGCAA-----TC-----------CAACGAGTGT-----------------------------------------------------------------------------ATTTTCGTAG--------CG------------- s droKik2.KB459527 280815 55 - 1234237 T-------CTGATTGGCGCCGATTAAGCAA-----TT-----------CAGCGAGAGA-----------------------------------------------------------------------------CTTTTCgcggggctgctgct------------- s droTak2.KB461535 145877 58 - 669855 T-------CTGATTGGCAGCGATTAAGCCA-----TCCCATCCCCAACCAACGAGCCT-----------------------------------------------------------------------------CTTTTCGAAG--------CC------------- s droRho2.KB449310 40406 47 - 65043 T-------CTGATTGACGACGATTAAGCAA-----TC-----------CAGCGAGGGT-----------------------------------------------------------------------------ATTTTCGTGG--------CT------------- s droFic2.KB457177 85283 47 + 995874 T-------CTGATTGGCGACGATTAAGCCA-----TC-----------CAGCGAGGGT-----------------------------------------------------------------------------TTTCTCGAAG--------CT------------- s droPse3.chr3 1353945 122 - 19787792 T-------CTGATTGGCGCCGATTAAGCAA-----TC-----------CAACGAGGCATCAAGCCCCAGCCTCTGCCCCACTTggagagggggaaaaaaatgggGAACGGCGACAGGGACGGCGACGCTATGGCGTTTTTCGTGG----------------------- s droPer1.super_34 542788 122 - 916997 T-------CTGATTGGCGCCGATTAAGCAA-----TC-----------CAACGAGGCATCAAGCCCCAGCCTCTGCCCCACTTGGAGAGGGGGAAAAAAATGGGGAACGGCGACAGGGACGGCGACGCTATGGCGTTTTTCGTGG----------------------- s droMir2.chr3 1395030 122 - 20862834 T-------CTGATTGGCGCCGATTAAGCAA-----TC-----------CAACGAGGCATCAAGCCCCAGCCTCTGCCCCACTtggagagggggaaaaaaatgggGAACGGCGACAGGGACGGCGACGCTATGGCGTTTTTCGTGG----------------------- s droWil2.CH963894 1314837 61 + 2843958 T-------CTGATTGGCGCCGATTAAGCAACAACTTg-----------ctgcgagagagagagac----------------------------------------------------------------------ttcTTCGCAT------TATT------------- s droVir3.scaffold_12875 7358098 59 + 20611582 T-------GTGATTGGCGCCGATTAAGCAA-----TC-----------CAGGCAAAAA-----------------------------------------------------------------------------CTTTGCATAA---------TGTTGCGCGTGTGG s droMoj3.scaffold_6496 26153196 59 + 26866924 T-------CTGATTGGCGCCGATTAAGCCA-----TC-----------CAGGCGAGTA-----------------------------------------------------------------------------CTTTGCATAA---------TGTTGGCAGTGTGC s droAlb1.JH854640 315100 54 + 406291 T-------TTGATTGGCGCCGATTAGGCAA-----TC-----------CAGTC--GTA-----------------------------------------------------------------------------GTTTGCATAA---------TGTTCAGAA---GA a score=4524199.000000 s dm6.chr2R 24362258 612 + 25286936 TTCGCTG-----------CAATTATTTGCGAATTAACATTTAT---AACACTTGATCC---TGTG---CGTA------------------------------TATCCGTTGA-------AA----G-------------CTGGG--CT------GA-CTT--GACGCTTCAGCGCATTTAAAAAGTATTTTT-GT--GCCACTGCCACCAT--------------------------CTGCAGCAGCAGCAA-------CCAAGTGGCG--------------GAGTGCAGCGG-C--------------A----AGAA---------ATA-TTTGCCGCATT----TTA---AG-----A-GTCtcggtccg------cccgtccgtcccagc---gtctgtccgt--TTG---------TTGTATGTCTGTTATGCGGATTCATTGCAACCGC---------AGCCACTTGTTGCGA------GTtgc----tg--------------c-------tgctg-ctgctgctgc-tgcagttg-----c---------gctgttgc------------------------tgc----tgc-cgttc------c-tgctgctgc---tgctgTTGTGCTAAATTTCACACCGACAATGAGCGCGAGCCAACAATGAATG-AAAATTactg---------------------------------------ggcc----------gaactgaactga------actg----agccgaagtgaCGGAC----------TGGGA------TGGCCAAA----------------------------------------CGGCCAGCG----------ACCGCAGGCTAAATCGATACCTTAATTCAAAGGCACGCCAGACCGCATTTTTGGATAATATA------------------CTCCA------------GCTC-----------CATCCGCTCCAGTGAGC-----TGA----TGTGCTC-AC---------TTCAACTGCAACTT--TAGC-----------------------------GC--TGGTGGCACGCGTGAGATTTCCTGTCT-GCAG-TTTT-----GGG s droSim1.chr2R 18700622 609 + 19596830 CTCGCTG-----------CAATTATTTGCGAATTAACATTTAT---AACACTTGATCC---TGTG---CGTA------------------------------TATCCGTTGA-------AA----G-------------CTGGG--CT------GA-CTT--GACGCTTCAGCGCATTTAAAAAGTATTTTT-GT--GCCACTGCCACCAT--------------------------CTGCAGCAGCAGCAA-------CCAAGTGGCG--------------GAGTGCAGCGG-C--------------A----AGAA---------ATA-TTTGCCGCATT----TTA---AG-----A-GTCTCGGTC-------------CCGTCCGTCC---GTCTGTCCGT--TTG---------TTGTATGTCTGTTATGCGGATTCATTGCAACCGC---------AGCCACTTGTTGCGA------GT-------tg--------------c-------tgctg-ctgctgctgt-----gagg-----t---------gatgttgc------------------------tgc----tgc-cgctcctgctgc-tgctgctgc---tgctgttgTGCTAAATTTCACACCGACAATGAGCGCGAGCCAACAATGAATG-AAAATTactg---------------------------------------ggcc-----gaactgaactgaactga------actg----agccgaagtgaCGGAC----------TGGGA------TGGCCAAA----------------------------------------CGACCAACG----------ACCGCAGGCTAAATCGATACCTTAATTCAAAGGCACGCCAGACCGCATTTTTGGATAATATA------------------CTCCA------------GCTC-----------CATCCGCTCCAGTGAGC-----TGA----TGTGCTC-AC---------TTCGACTGCAACTT--CAGC-----------------------------GC--TGGTGGCACGCGTGAGATTTCCTGTCT-GCAG-TTTT-----GGG s droSec1.super_23 120400 605 + 989336 CTCGCTG-----------CAATTATTTGCGAATTAACATTTAT---AACACTTGATCC---TGTG---CGTA------------------------------TATCCGTTGA-------AA----G-------------CTGGG--CT------GA-CTT--GACGCTTCACCGCATTTAAAAAGTATTTTT-GT--GCCACTGCCACCAT--------------------------CTGCAGCAGCAGCAA-------CCAAGTGGCG--------------TAGTGCAGCGG-C--------------A----AGAA---------ATA-TTTGCCGCATT----TTA---AG-----A-GTCtccgcccg------tccatccgtccgtcc---atctgtccgt--TTG---------TTGTATGTCTGTTATGCGGATTCATTGCAACCGC---------AGCCActtgttgcga------gttgc----tg--------------c-------tgctg-ctgctgctgt-----gagg-----t---------gatgttgc------------------------tgc----tgc-cgctc----------ctgctgc---tgctgttgtgctAAATTTCACACCGACAATGAGCGCGAGCCAACAATGAATG-AAAATTactg---------------------------------------ggcc----------gaactgaactga------actg----agccgaagtgaCGGAC----------TGGGA------TGGCCAAA----------------------------------------CGACCAACG----------ACCGCAGGCTAAATCGATACCTTAATTCAAAGGCACGCCAGACCGCATTTTTGGATAATATA------------------CTCCA------------GCTC-----------CATCCGCTCCAGTGAGC-----TGA----TGTGCTC-AC---------TTCGACTGCAACTT--CAGC-----------------------------GC--TGGTGGCACGCGTGAGATTTCCTGTCT-GCAG-TTTT-----GGG s droYak3.chr2R 20209836 631 + 21139217 TCGGCTG-----------CAATTATTTGCGAATTAACATTTAT---AACACTTGATCC---TGTG---CG--------------------------------TATCCGTTGA-------AA----G-------------CTGGG--CTCTTGGCCA-CTT--GACGCTTCAGCgcatttaaaaagtattttt-gt--gccactgccacaacaaca---------------------gcagcagcagcaacaa-------caaagtggCA--------------GAGTGCAGCGG-C--------------A----AGAA---------ATA-TTTGCCGCATT----TTA---AG-----A-GACGCGCA--------------GAGTCCGTCC---CTCTGTCCGT--TTG---------TTGTATGTCTGTTATGCGGATTCATTGCAGCCGC---------AGCCACttgttgcga------gttgc----tt--------------c-------tgctg-ctgctgctga-tgttgctg-----ctgcagttgcgctgttgc------------------------tgc----tgc-cgctcctgttgc-tgttgctgc---tgctgttgtgctAAATTTCACACCGACAATGAGCGCGAGCCAACAATGAATG-AAAATTACTG---------------------------------------GGCCcaaccgaactgaactgaactga------agtG----AACCGAAGTGACGGAC----------TGAGA------TGGCCAAA-----------------------------------------------CG----------ACCGCAGGCTAAATCGATACCTTAATTCAAAGGCACGCCAGACCGCATTTTTGGATAATATA------------------CTCCA------------GCTC-----------CATCCGCTCCAGTGAGC-----TGA----TGTGCcg-atgcaac----tgcaactgcaact------------------------------------gc--tggTGGCACGCGTGAGATTTCCTGTCT-GCAg-tttt-----ggg s droEre2.scaffold_4845 21607709 604 + 22589142 TCAGCTG-----------CAATTATTTGCGAATTAACATTTAT---AACACTTGATCC---TGTG---CG--------------------------------TATCCGTTGA-------AA----G-------------CTGGG--CT------GA-CTT--GACGCTTCAGCGCATTTAAAAAGTATTTTT-GT--GCCACTGCCACAACGA------------------------CAGCAGCAGCACCAA-------CAAAGTGGCA--------------GAGTGCAGCGG-C--------------A----AGAA---------ATA-TTTGCCGCATT----TTA---AG-----A-GTCTCG------------------GTCCGTCC---GTCCGTCCGT--TTG---------TTGTATGTCTGTTATGCGGATTCATTGCAACCGC---------AGCCACTTGTTGCGA------gctgc----tg--------------c-------agctc-ctgctgttgc-tgctgctg-----ct--------gctgttgc------------------------tgc----tgt-tgctgctgctgc-tgctgcggc---tgctgttgTGCTAAATTTCACACCGACAATGAGCGCGAGCCAACAATGAATG-AAAATTACTG---------------------------------------GGCC---------------GAACTAA------ACTG----AACCGAAGTGACGGAC----------TGAGA------TGGCCAAA-----------------------------------------------CG----------ACCGCAGGCTAAATCGATACCTTAATTCAAAGGCACGCCAGACCGCATTTTTGGATAATATA------------------CTCCA------------GCTC-----------CATCCGCTCCAGTGAGC-----CGA----TGTGCTG-ATGTGCCGATGTGCCGCTGCAACTT--CTGC-----------------------------GC--TGGTGGCACGCGTGAGATTTCCTGTCC-GCAG-TTTT-----GGG s droBia2.KB462602 800794 569 + 3129309 TCCGCTG-----------CAATTATTTGCGAATTAACATTTAT---AACACTTGATCC---TGTG---CG--------------------------------TATCCGTTGA-------AA----G-------------CTGGG--CT------GA-CTT--CATGCTTCGGcgcatttaaaaagtattttt-aa--agc-------------------------------------tgcCGGC---------------CAAAGTGG-----------------AGTGCAAGag-t--------------a----agaa---------atattttgcCGCATT----TTA---GAGCCTCA-GTCCCA-----------------------------GTCCGTCGCT--TTG---------CTGTATGTCTGTTATGCGGATTCATTGCAACCGCAG-------AGCCACttgttgcgatgttgtgatgt----tg--------------c--------gatg-ttgctgctgtgtgccgatg-----t---------gctgctgc------------------------tgc----tgc-tgctgctgcagt-gcccgatgttgctgctgttgtgctAAATTTCACACCAACAATGAGCGCGCGCCAACAATGAATG-AAAATGACTG---------------------------------------AACC--------------------GA------GCTG----AACCGAACTGACGGAC----------CGGGA------TGACCAAA-----------------------------------------------CG----------ACCGCAGGCTAAATCGATACCTTAATTCAAAGGCACGCCAGACCGCATTTTTGGATAATAta------------ctccatctcca------------tctc-----------catccgCTCCAGTGAGc-----cga----tgt----------------tgccgctgttgcc------------------------------------gC--TGGTGGCACGCGTGAGATTTCCTGTCT-GCAG-TTTT-----GGG s droSuz1.KI419649 12045909 560 - 14502029 TTCGCTG-----------CAATTATTTGCGAATTAACATTTAT---AACACTTGATCC---TGTG---CG--------------------------------TATCCGTTGA-------AA----G-------------CAGGG--CT------GA-CTT--CATGCTTCGGcgcatttaaaaagtattttt-aa--agc-------------------------------------tgGCAGC---------------TAAAGTGG----------------------CCGag-t--------------a----agaa---------atattttgccgCATT----TTA---AG-----A-GTCTCA-----------------------------GTCCGTCTGT--TTG---------TTGTATGTCTGTTATGCGGATTCATTGCAACCGCAG-------AGCCACttgttgc--------gatgt----tg--------------c--------gatg-ttgctgctgtgtgccgatg-ttgct---------gctgctgc------------------------tgc----tgc-tgctgctgcagt-ggccgatgt---tgctgttgtgctAAATTTCACACCAACAATGAGCGCGCGCCAACAATGAATG-AAAATGActg---------------------------------------aacc--------------------ga------actg----aactgaactgacgGAC----------TGGGA------TGACCAAA-----------------------------------------------CG----------ACCGCAGGCTAAATCGATACCTTAATTCAAAGGCACGCCAGACCGCATTTTTGGATAATAta------ctccatctccatctcca------------tctc-----------catccgCTCCAGTGAGC-----CGA----TGT----------------TGCCGCTGTTGCC------------------------------------GCGATGGTGGCACGCGTGAGATTTCCTGTCT-GCAG-TTTT-----GGG s droBip2.KB464407 1963409 582 + 2915140 GTGGCTG-----------CAATTATTTGCGAATTAACATTTAT---AACACTTGATCC---TGTGCCCCG--------------------------------TATCCGCTGG-------AAAGCCG-------------TTGAA--AG------GAGCTT--GACGCTTCAGTgcatttaaaaagtattttc-gt--GCCACAAGAACAA---------------------------CAGCAGCGGCGGTCT-------CT-----------------------GGTGCGGCAG-C--------------A----AGAA---------ATA-TTTGCCGCATT----TTA---AG------------------------------------TCC---GTCCGTCCGT--TTG---------TTGTATGTCTGTTATGCGGATTCATTGCAACCGC---------AGTCACttgttgct-------gcagt----tg--------------c-------tgttg-cttctgccac--------------t---------gatgttgc------------------------tgc----ttc-tgcca----------ctgatgt---tgctgttgtgctAAATTTCACACCGACAATGAGCGCGCGCCAACAATGAATG-AAAATGACTGAC--------------------------------GAGTTGACC----------------AGCCAA------CCCC----AGAAGGAgt--tggtt----------ttgtt------tggccCGATG-------------------------------------TTGGGCCAAG----------ACTG--GGCTAAATCGATACCTTAATTCAAAGGCACGCCAGACCGCATTTTTGGATAATATA------------------CTTCA------------GCTT-----------CATCCGCTCCAGTGAGC-----CAAGTGTTGCACTC-GTGCTGC----TGC-ACTGCTGCCC--TGCT-----------------------------GC-CTGGTGGCACGCGTGAGATTTCCTGTCT-TCAGTTTTT-----GGA s droEug2.KB465067 604775 585 + 1515531 TTCGCTG-----------CAATTATTTGCGAATTAACATTTAT---AACACTTGATCC---TGTG---CG--------------------------------TATCCGTTGA-------AA----G-------------CTGGG--CT------GA-CTT--GACGCTTCAGCgcatttaaaaagtattttt-gt--ggCACAACAAcggcg-------------------------cagcagcagc------------taaagTGGCA--------------GAGTGCGGCAGCC--------------G----AGAA---------ATATTTTGCCGCATT----TTA---AG-----A-GTTtca----------------------gtcc---gtccgtccgt--ttg---------tTGTATGTCTGTTATGCGGATTCATTGCAACCGC---------AGCCACttgttgc--------gatgt----tg--------------t--------gatg-ttgctgctgtgtgctg-tg-----t---------gctgatgt------------------------tgc----tgc-tgcagttgcagt-tgc-gacgt---tgctgttgtgctgAATTTCACACCAACAATGAGCGCGAGCCAACAATGAATG-AAAATGACTG---------------------------------------GACT----------GGACTGAACTCA------ACTC----AACTGAACTGACGGAC----------TGGGA------TGAC---------------------------------------------------CG----------ACCGCAGGCTAAATCGATACCTTAATTCAAAGGCACGCCAGACCGCATTTTTGGATAATATA------------------CTCCA------------GCTC-----------CATCCGCTCCAGTGGGC-----CGA----TGC----------------TGCCgctggtggctggtagct--ggtg----------------------gc--tggtggcACGCGTGAGATTTCCTGTCT-GCAGTTTTT-----GGG s droEle2.KB458573 526455 561 - 5320397 GCCGCTG-----------CAATTATTTGCgaattaacatttat---aacaCTTGATCC---TGCG---CG--------------------------------TATCCGTTGA-------AA----G-------------CTGGG--CT------GA-CTT--GACGCTTCAGCGcgtttaaaaagtattttt-gttgGCCACAACAA------------------------------CGGCGGCAAC------------TAAAGTGGCACTG----------CCAGAGCAACag-c--------------a----agaa---------atattttgccGCATT----TTA---AG-----A-GTCTCG-----------------------------GTCCGTCCGT--TTG---------TTGTATGTCTGTTATGCGGATTCATTGCAACCGC---------AGCCActtgttgct-------gatgt----tg--------------c-------tgccgtttgctgatgt-tgctgccgtttgct---------gatgttgc------------------------tgctgtgtgc-tgctgctgctct-tgctgctgt---tgctgttgtgctaAATTTCACACCAACAATGAGCGCGCGCCAACAATGAATG-AAAAtgactg---------------------------------------aact----------------------------------------gaactgacgGA------------GAGA------TGACCACCGC-------------------------------------TTGGTCCGCT----------GGCCTGGGCTAAATCGATACCTTAATTCAAAGGCACGCCAGACCGCATTTTTGGATAATATA------------------CTTCA------------GCTC-----------CATCCGCTCCAGTGAGC-----CGA----TGT----------------T------------------------------------------------GC--CGGTGGCACGCGTGAGATTTCCTGTCT-GCAG-TTTT-----GGG s droKik2.KB459527 280870 542 - 1234237 gctgctg-----------caattatttgtgaattaacatttat---aacACTTGATCC---TGTG---CG--------------------------------TATCCGCTGA-------AA----G-------------CTGGGTCTT------GA-CTT--GACGCTTCAGcgcatttaaaaagtattttt-gt--gccacaacaa------------------------------cagcagcagcagaag-------c--agcagca---------------aaggcagcag-cCACCGAGGCaactaa----agaa---------ata-tttgCCGCATT----TTA---AA-----A-GTCTCG-----------------------------GTCCGTCCGT--TTG---------TTGTATGTCTGTTATGCGGATTCATTGCAACCGC---------AGCCACttgtt----------gccgc----tg--------------c-------ggctg-ttgctgctgc------atg-----t---------gatgttgc------------------------tgc----tg-----------------ctgctgt---tgctgctgtgctaAATTTCACACCAACAATGAGCGCGCGCCAACAATGAATG-AGAATGACTGACG-------------------------------GAGATGACC-----------AACTGCCAGGA------GCAG----CTTTGGGCTTTCAGCC----------TCAGC------TG-----------------------------------------------------GG----------GGCCTGGGCTAAATCGATACCTTAATTCAAAGGCACGCCAGACCGCATTTTTGGATAATATA------------------CTCGA------------GCTC-----------CATCCGCTCCAG-----------------TGC-----------------------------------------------------------------AC--T-GTGGCACGCGTGAGATTTCCTGTCT-GCAC-TTTC-----GGG s droTak2.KB461535 145935 573 - 669855 TTCGCTG-----------CAATTATTTGCGAATTAACATTTAT---AACACTTGATCC---TGAG---CG--------------------------------TATCCGTTGA-------AA----G-------------CTGGG--CT------GA-CTT--CATGCTTCGGcgcatttaaaaagtattttt-at--ag--------------------------------------caGCAACTAAAGTGG-------CCGAATGGCC--------------GAGTGCAACag-c--------------a----agaa---------atattttgccgCATT----TTA---AG-----A-GTCGCA--------------GTCCGTCTCCAT---CTCCGTCTGT--TTG---------TTGTATGTCTGTTATGCGGATTCATTGCAACCGCAGAAGTCCCAGCCACttgttgc--------gatgt----tg--------------c-------tgctg-ttgcagttgc--------------c---------gatgttgc------------------------cgt----t--------------------gatgt---tgctgttgtgctaAATCTCACACCAACAATGAGCGCGCGCCAACAATGAATG-AAAATGACTg---------------------------------------agctgaactgaactgaagtGAACCAA------ACTG----AACCGAAGTGACGGAC----------TGGGA------TGACCAAA-----------------------------------------------CG----------ACCGCAGGCTAAATCGATACCTTAATTCAAAGGCACGCCAGACCGCATTTTTGGATAATATA------CTCCATCTCCAGCTCCA------------TCTC-----------CATCCGCTCCAGTGagc-----cga----tgt----------------tgct---------------------------------------------gc--tggtggcaCGCGTGAGATTTCCTGTCT-GCAG-TTTT-----GGG s droRho2.KB449310 40453 576 - 65043 GCCGCTG-----------CAATTATTTGCGaattaacatttat---aacaCTTGATCC---TGTG---CG--------------------------------TATCCGTTGA-------AA----G-------------CTGGG--CC------GA-CTT--GACGCTTCAGcgcatttaaaaagtattttt-gttggccacaacaacag---------------------------cagcagcagcagcaa------ctaaagtggcaagac---------caacagcaacag-c--------------a----agaa---------ATATTTTGCCGCATT----TTA---AG-----A-GTCTCA-----------------------------GTCCGTCCGT--TTG---------TTGTATGTCTGTTATGCGGATTCAttgcaaccgc---------agccacttgttgct-------gctgc----tg--------------cagttagctgatg-ttgctgctgt-----gtgc-----t---------gatgttgc------------------------tgt----tgtgtgttgctgctgtgtgctgttgc---tgctgttgtgctAAATTTCACACCAACAATGAGCGCGCGCCAACAATGAATG-AAAATGACTG---------------------------------------AACT---------------------------------------------GACGGA------------GAGA------TGACCGCT----------------------------------------TGGTCCGCT----------GGCCTGGGCCAAATCGATACCTTAATTCAAAGGCACGCCAGACCGCATTTTTGGATAATAtactccatctccatctccaacTCCA------------GTTC-----------CATCCGCTCCAGTGAGC-----CGA----TGT----------------T------------------------------------------------GC--CGGTGGCACGCGTGAGATTTCCTGTCT-GCAG-TTTT-----GGG s droFic2.KB457177 85330 555 + 995874 GCCGCTG-----------CAATTATTTGCGAATTAACATTTAT---AACACTTGATCC---TGTG---CG--------------------------------TATCCGTTGA-------AA----G-------------CTGGG--CT------GA-CTT--GACGCTTCAGCGcacttaaaaagtattttt-gt--gccgcaacaacagcggca---------------------gcagcagcaacagcagcagcagctaaagtggcaagca-----acagcaacagcaagag-c--------------a----agaA---------ATATTTTGCCGCATT----TTA---AG-----A-GTCGCA-----------------------------GTCCGTCCGT--TTG---------TTGTATGTCTGTTATGCGGATTCATTGCAACCGC---------AGCCacttgttgcc-------gctgcagagtg--------------c-------tgatg-ttgctgctgc--------------t---------gctgttgc------------------------tgc----tgc-----------gt-ggccaatgt---tgctgttgtgctAAATTTCACACCAACAATGAGCGCGCGCCAACAATGAATG-AAAACGAGCG---------------------------------------AACT---------------------------------------------GACGGAC----------TGGGA------TGACCGCC----------------------------------------TGGTCCGCT----------GGCCTGGGCTAAATCGATACCTTAATTCAAAGGCACGCCAGACCGCATTTTTGGATAATATA------------------CTCCA------------GCTC-----------CATCCGCTCCAGTGAGC-----CGA----TGT----------------T------------------------------------------------GC--CAGCGGCACGCGTGAGATTTCCTGTCT-GCAG-TTTT-----GGG s droPse3.chr3 1354067 672 - 19787792 -CTGCTG-----------CAATTATTTGCGAATTAACATTTAT---AACACTTGATCC---TGTG---CG--------------------------------TATCCGTTGA-------AA----GCAGAAAGCTCTGCCTGGG--CTTTGCCTTA-CTT--GACGCTTCAGCGCgtttaaaaagtattttt-gt--gccacaacaacg------------------------------gcagcagcagcag---------aagtggcagcggcagcaacagcaacagcaacaa-c--------------g----cgAA---------ATATTTTGCCGCATT----TTA---AG-----AGGTCTTCGAGTG------TCCGTCCGTGTGGCTGGGGTCTGTCCGTGCTGG---------TTGTATGTCTGTTATGCGGATTCATTGCAACCGC---------AGTCACttgtt----------gcttc----tg--------------t-------ggctg-ccactgatgt--------------t---------gctgttgc------------------------tgt----tgc--------------------tgt---tgctgctgtgctaAATTTCACACCAACAATGAGCGCGAGCCAacaatgaatg-aaaatgaCTGACGAACGG-------------------------AGAGATGACC------------------------------------AGCCCAGGAGCCCGAC----------CAGCC------TGCTCTTGCT--------------CAtgctcttggtcttgg------tctggctctg----------gctctgcacTAAATCGATACCTTAATTCAAAGGCACGCCAGACCGCATTTTTGGATAATATA------------------CTTCA------------ACTC-----------CATCCGCTCCAGTGA-C-----CGC----TCCGCTC-GC---------TTCTGCTGCCACTCCATGGCTCCACTGCTCCACTACTCCACTACTCCATGT--TGGTGGCACGCGTGAGATTTCCTGTCT-TCAG-TTGTTCAAGGAT s droPer1.super_34 542910 688 - 916997 -CTGCTG-----------CAATTATTTGCGAATTAACATTTAT---AACACTTGATCC---TGTG---CG--------------------------------TATCCGTTGA-------AA----GCAGAAAGCTCTGCCTGGG--CTTTGCCTTA-CTT--GACGCTTCAGCGCGTTTAAAAAGTATTTTT-GT--gccacaacaacg---------------------------gcagcagcagcagcag---------aagtggcagcggcagcaacagcaacagcaacaa-c--------------g----cgaa---------ataTTTTGCCGCATT----TTA---AG-----AGGTCTTCGAGTG------TCCGTCCGTGTGGCTGGGGTCTGTCCGTGCTGG---------TTGTATGTCTGTTATGCGGATTCATTGCAACCGC---------AGTCACTtgtt----------gcttc----tg--------------t-------ggctg-ccactgatgt--------------t---------gctgttgc------------------------tgt----tgc--------------------tgt---tgctgctgtgctaaatttCACACCAACAATGAGCGCGAGCCAACAATGAATG-AAAATGACTGACGAACGG-------------------------AGAGATGACC------------------------------------AGCCCAGGAGCCCGAC----------CAGCC------TGCTCTTGCTTG-------AGGGGCATGCTCTTGGTCTTGGTCTGGCTCTGGCTCTG----------GCTCTGCACTAAATCGATACCTTAATTCAAAGGCACGCCAGACCGCATTTTTGGATAATATA------------------CTTCA------------ACTC-----------CATCCGCTCCAGTGA-C-----CGC----TCCGCTC-GC---------TTCTGCTGCCACTCCATGGCTACACTGCTCCACTACTCCACTACTCCATGT--TGGTGGCACGCGTGAGATTTCCTGTCT-TCAG-TTGTTCAAGGAT s droMir2.chr3 1395152 700 - 20862834 -CTGCTG-----------CAATTATTTGCGAATTAACATTTAT---AACACTTGATCC---TGTG---CG--------------------------------TATCCGTTGA-------AA----GCAGAAAGCTTTGCCTGGG--CTTTGCCTTA-CTT--GACGCTTCAGCGCgtttaaaaagtattttt-gt--gccacaacaacggcagcagcagcagcagcagcagcagcagcagcagcagcagcag---------aagtggcagcggcagcaacagcaacagcaacaa-c--------------g----cgAA---------ATATTTTGCCGCATT----TTA---AG-----AGGTCTTCGAGTG------TCCGTCCGTGTGTCTGGGGTCTGTCCGTGCTGG---------TTGTATGTCTGTTATGCGGATTCATTGCAACCGC---------AGTCACttgtt----------gcttc----tg--------------t-------ggctg-ccactgatgt--------------t---------gctgttgc------------------------tgt----tgc--------------------tgt---tgctgctgtgctaAATTTCACACCAACAATGAGCGCGAGCCaacaatgaatg-aaaatgacTGACGAACAG-------------------------AGAGATGACC------------------------------------AGCCCAGGAGCCTGAC----------CAGCC------TGCTCTTGCTTAtgctctt--------------ggtcttggtctggctctggctctg----------gctctgcacTAAATCGATACCTTAATTCAAAGGCACGCCAGACCGCATTTTTGGATAATATA------------------CTTCA------------ACTC-----------CATCCGCTCCAGTGA-C-----CGC----TCCGCtc-gc---------ttctgctgccactccATGGCTCCACTG--------CTCCACTACTCCATGT--TGGTGGCACGCGTGAGATTTCCTGTCT-TCAG-TTGTTCAAGGAT s droWil2.CH963894 1314898 692 + 2843958 ATTGCTGGCAGTTACCTACAATTATTTGCgaattaacatttataaaaacaCTTGATCCTTGTACG---CG--------------------------------TATCCGTTGG-------------G-------------ATGGA--AA------GC-ATTGAGACGCTTCAGCgcatttaaaaagtattttt-gt--gctgctgcagcagcaa------------------------cagcagcagcaacag-------c--aacaacaaacacagcaacaacaccaacaagag-c--------------aaTGCAGAA---------ATATTTTGCAGCATT----TCG---AA-----A-A----------------------------------GCCTTCAAGT--CTGC--------TTGTATGTCTGTTATGCGGATTCATTGCAACCGC---------AATCacttgttgct-------gatgt----tg--------------c-------agttg-tttctgttgc--------------t---------gttgctgc------------------------tgc----tgc-tac----------tgctacttc---tgatgttgtgctAAATTTCACACCAACAATGAGCGCGCGCCAACAATGAATG-AAAACGACAGACGACTgacaatgacgatgacgatggcgatggcaaAGGCAACC------------ACTGAACTGACGATTTGCTGGAGCAGGCAAGATGACCGTCTATATGTACTTAGTC------TGACCACT------------------------------------ACCGCGACCTGCT----------GGCAAAGGCTAAATCGATACCTTAATTCAAAGGAACGCCAGACCGCATTTTTGGATAATACA------------------CTCCA------------ATTCCATTCATCTCTCATCCGCTCCAGTGAACGAACTcta----tgtatttaat---------ttttgttgttgttgtctgagTC---------------------------GC--TTTTGGCACGCGTGAGATTTCCTGTCC-CAAG-TTTC-----AAG s droVir3.scaffold_12875 7358177 552 + 20611582 CTGCCTG-----------CAATTATTTGTGAATTAACATTTAT---AACACTTGATCC---T----------------------------------------TGGTTGCTGG----CAGAA----G-------------GTAGA--AAGCGTTGCG-CTT--GACGCTTCGCTGCATTTAAAAAGTATTTTTCGT--GCC-------------------------------------TTGCTGCTGCAACGG-------------------------------------CGAGT-C--------------A----AGAA---------ATA-TTTGCTGCAGCAGCAGTA---AG-----A-GC-TCTGCCCCAGG---TCTGTCCAATTGCAC---ATTTGTCCAT--TTGG--------TTGTATGTCTGTTATGCGGATTCATTGCAACCGC---------AGCCACttgttcaa-------gctgc----ca--------------c---------atg-ctgcagctac--------------t---------gctgttgctgttgtttttgttgttaatggtgttgt----tgc--------------tgctgctgc---tgttgctgtgctaaatttCACACCAACAATGAGCGCGCGCC-ACAATGAATG-AAAATGAATGACG------------------------------------CGCC----------ACATTGCGTTGC------ACTT------------------------------TGGCT------TGGTCTTT-----------------------------------------------TGCCTGGCTGGCAGTCCCGGCTAAATCGATACCTTAATTCAAAGGCACGCCAAACCGCATTTTTGGATAATCAA---------------------CA------------ACGC-----------G--------------TC-----CGC----TGC----------------TC-----------------------------------------------AA--TTGTGGCACGCGTGAGATTTCCTGTCA-CAGG-TTTC-----AAG s droMoj3.scaffold_6496 26153271 548 + 26866924 CTGCCTG-----------CAATTATTTGTGGATTAACATTTAT---AACACTCGATCC---TTGT---TG-------------------TTGTTGCT-TGGCTGTTTGTTGA----TAAAA----G-------------GTGGA--AAGCGTTGCG-CTT--GACGCTTGGCTGCATTTAAAAAGTATTTTTCGT--GCC-------------------------------------TTGCTGCAGCGGCAG-------------------------------CAGCAACGAGT-C--------------A----AGAA---------ATA-TTTgcagcagcagcagca---ac-----a-gcagcagcaAATGC---TCTGTCCAGTCGGAC---AGTTGTGCAT--TTGGCCGTACGTCTGTATGTCTGTTATGCGGATTCATTGCAACCGC---------AGCCACttgttgct-------gttgc----ca--------------c---------atg-ctgcagctac--------------a---------acagttga------------------------tgt----tgc--------------tgctgtggc---tgctgctgcGCTAAATTTCACACCAACAATGAGCGCGCGCC-ACAATGAATG-AGAATGAGCGACG------------------------------------CGTC----------GAATTGCGTTGC------ACTT------------------------------CGGCT--------GGCCGT-----------------------------------------------TG----------AGAGCTGGCTAAATCGATACCTTAATTCAAAGGCACGCCAGACCGCATTTTTGGATAATCAA---------------------CA------------GCGC-----------G--------------TC-----CGC----TGC----------------TC-----------------------------------------------CG--TTGTGGCACGCGTGAGATTTCCTGTCA-GTGG-TTTC-----AAG s droAlb1.JH854640 315162 582 + 406291 -CGACTG-----------CAATTATTTGTGAATTAACATTTAT---AACACTTGATCC---TGTG---CGTATCCAATG--------GATCGCTGGA-TGAATCGTTGCTGGATGTTGCAA----G-------------GTAGA--AAGCGACCTG-TTT--GACGCTTCGCTGCatttaaaaagtgtttttcGT--GCC-------------------------------------TTG-------------------------------------------------CGAGT-C--------------G----AGAAATATTTGCCata-gtagcaacaacagcagca---gc-----a-gcagcaacacttggttatctgtc---------------tgtccat--ttGG--------CCGTATGTATGTTATGCGGATTCATTGCAACCGC---------AGTCACTTGTTAAA-------GTTGC----CACTCGTCgcttgaagc---------ttg-ttgcagctac--------------t---------gttgccgctgttgctgttgc------------tgt----ttc--------------tgctgctgc---tgttgttgtgctaaaTTTCACACCAACAATGAGCGCACGCc-acaatgaatg-aaaatgagtgACG------------------------------------AACC----------AGA--AGAGTGG------ACTT------------------------------TGGCTCAgagtttgccttt-----------------------------------------------tg---------ttggcCAGGCTAAATCGATACCTTAATTCAAAGGCACGCCAGACCGCATTTTTGGATAATCAA---------------------CT------------GTCC-----------GG-TGGCAGT-TTTATC-----CGT----TGC-----G----------TA-----------------------------------------------CT--TTGTGGCACGCGTGAGATTTCCTGTCA-CTGG-TCTC-----AAG s droGri2.scaffold_15245 908095 589 + 18325388 TTCCCTG-----------CAATTATTTGTGAATTAACATTTAT---AACACTTGATCC---TGTG---TTGAGTGGTTGTttgttgttgttgttgctgttgttgttTGTTGG----TAGAA----G-------------GTAGA--AAGCGTTGCG-CTT--GACGCTTCGCTGCATTTAAAAAGTATTTTTCTT--GCC-------------------------------------TTGTTGTTGCAACTGCAACTGCCACAGCAACAGCAA----------CAGCAGAGAGT-C--------------G----AGAA---------ATA-TTTGCAGCAGCAGCAGCAAACAG-----A-GAAACAGCG--------TCTGTCCAATTGGAC---ATTTGTCCAT--TTGG------TTGTGTATGTCTGTTATGCGGATTCATTGCAACCGC---------AGCCACTTGTTCAA-------GTTGC----CA--------------C---------ATG-CTGCAGCTAC--------------------------------------------------------TGT----T-----------------------GT---TGTTATTGTGCTAAATTTCACACCAACAATGAGCGCGCGCC-ACAATGAATGAAAAATGAGTGACG------------------------------------CGCC----------GCATTGCGTTGC------AAGG------------------------------CACTT------TAGTCTCT-----------------------------------------------GG---------------ACTCTAAATCGATACCTTAATTCAAAGGCACGCCAGACCGCATTTTTGGATAATCAA---------------------CACAGACGGAGCTGGTGC-----------AGCTCGAGAC-TTCATC-----CGC----TGC-----GC---------CG-----------------------------------------------AG--TTGTGGCACGCGTGTGATTTCCTGTCAGCAGG-TCTC-----AAG a score=119168.000000 s dm6.chr2R 24362870 76 + 25286936 ACATTTCATATCGGATTGCAGCCAAATTT-GGTGTCC-TT--TGTGGCACG--------------------------------CGGGGTCAA-----------------AGAT-------------------------ATAC--------------------------ACACAT-----------------------AAA------------------------------------------------CAT-------------------- s droSim1.chr2R 18701231 76 + 19596830 ACATTTCATATCGGATTGCAGCCAAATTT-GGCGTCC-TT--TGTGGCACG--------------------------------CGGGGTCAA-----------------AGAT-------------------------ATAC--------------------------ACACAT-----------------------AAA------------------------------------------------CAT-------------------- s droSec1.super_23 121005 76 + 989336 ACATTTCATATCGGATTGCAGCCAAATTT-GGCGTCC-TT--TGTGGCACG--------------------------------CGGGGTCAA-----------------AGAT-------------------------ATAC--------------------------ACACAT-----------------------AAA------------------------------------------------CAT-------------------- s droYak3.chr2R 20210467 84 + 21139217 acatttcatATCGGATTGCAGCCAAATTT-GGCGTCC-TT--TGTGGCACG--------------------------------CGGGGTTAA-----------------AGAT-------------------------ATATGTACGCAT------------------ACACAC-----------------------AAA------------------------------------------------CAT-------------------- s droEre2.scaffold_4845 21608313 80 + 22589142 ACATTTCATATCGGATTGCAGCCAAATTT-GGCGTCC-TT--TGTGGCACG--------------------------------CGGGGTTAA-----------------AGAT-------------------------ATATGTAC----------------------ACGTAT-----------------------AAA------------------------------------------------CAT-------------------- s droBia2.KB462602 801363 93 + 3129309 ACATTTCATATCGGATTGCAGCCAAATTT-GGCATCC-TT--TGTGGCACG--------------------------------CGGGGTTAA-----------------AGATAC-----------------------ACACATAAACAC-----------CGTACAGATACAT-----------------------TAA------------------------------------------------CAT-------------------- s droSuz1.KI419649 12046469 91 - 14502029 ACATTTCATATCGGATTGCAGCCAAATTT-GGCAGCC-TT--TGTGGCACG--------------------------------CGGGGTTAA-----------------AGAT-------------------------ACACATAAACAT-----------CGTATATATACAT-----------------------TAA------------------------------------------------CAT-------------------- s droBip2.KB464407 1963991 102 + 2915140 ACATTTCATATCGGATTGCAACCAAATTT-GGCATCCTTT--TGCGGTTCG--------------------------------AAAGGTTaa-----------------cgcttttattttttttgtggctctcTCGGATAT--------------------------ACAAAT-----------------------AAA------------------------------------------------CAT-------------------- s droEug2.KB465067 605360 74 + 1515531 ACATTTCATATCGGATTGCAGCCAAATTT-GGCATCC-TT--TGTGGCACG--------------------------------CGGggttaa-------------------at-------------------------atac--------------------------atataa-----------------------aaa------------------------------------------------caT-------------------- s droEle2.KB458573 527016 103 - 5320397 ACATTTCATATCGGATTGCAGCCAAATTT-GGCATCCTTT--TGTGGCACG--------------------------------CGGGGTTAA-----------------ATAA-------------------------GCATGCGAATGCGAATACGAAtgcgaatatatatat-----------------------aaa------------------------------------------------cat-------------------- s droKik2.KB459527 281412 99 - 1234237 ACATTTCATATCGGATTTCAACCAAATTT-GGCTGCCTTT--TGCGGTTCG--------------------------------AGAggttaa-----------------agtt-------------------------ttat--------------------------atatatgtatgtgttatGCACGAGTATA-AAA------------------------------------------------CAT-------------------- s droTak2.KB461535 146508 83 - 669855 ACATTTCATATCGGATTGCAGCCAAATTT-GGCATCC-TTTGTGTGGCACG--------------------------------CGGGgttaa-----------------acat-------------------------atac--------------------------atactc-----------------CAACA-AAA------------------------------------------------CAT-------------------- s droRho2.KB449310 41029 95 - 65043 ACATTTCATATCGGATTGCAGCCAAATTT-GGCATCCTTT--TGTGGCACG--------------------------------CGGggttaa-----------------atat-------------------------acatatacagatatacacacat--------atgtat-----------------------aaa------------------------------------------------CAT-------------------- s droFic2.KB457177 85885 88 + 995874 ACATTTCATATCGGGTTGCAGCCAAATTT-GGCATCC-TT--TGTGGCACG--------------------------------CGGGGTTAA-----------ATGCacagat-------------------------atac--------------------------atatac-----------------gAGTACCAA------------------------------------------------CAT-------------------- s droPse3.chr3 1354739 75 - 19787792 ATATCTCATATCGGATTTCAGCCAAATTTGGGTGTTC-TT--TGTagttcg-----------------------------------gatcgg-----------------atct-------------------------gaATT-------------------------ATACTC-----------------------GTG------------------------------------------------CAT-------------------- s droPer1.super_34 543598 75 - 916997 ATATCTCATATCGGATTTCAGCCAAATTTGGGTGTTC-TT--TGTAGTTCG-----------------------------------GATCGG-----------------ATCT-------------------------GAATT-------------------------ATACTC-----------------------GTG------------------------------------------------CAT-------------------- s droMir2.chr3 1395852 75 - 20862834 ATATCTCATATCGGATTTCAGCCAAATTTGGGTGTTC-TT--TGTAGTTCG-----------------------------------GATCAG-----------------ATCT-------------------------GAATT-------------------------ATACTC-----------------------GTG------------------------------------------------CAT-------------------- s droVir3.scaffold_12875 7358729 67 + 20611582 ---------------TTGCA----------AGTAGCC-----AAAAAATAA--------------------------------CAAAACAAA-----------------AAAA-------------------------AAAA--------------------------AAAACT-----------------------AAA------------------------------------------------GTCGTCTGCTTTATATAT---AT s droMoj3.scaffold_6496 26153819 112 + 26866924 ---------------TTGCA----------AGTGTaa-----aaaaaaaaa--------------------------------acaaacaaa-----------------gcaa-------------------------aaaa--------------------------ggaatc-----------------------aaatcgaaaaacaaaaacaaaaataactaaaatgaccgaaaaaaaagaaCTATTGTCTGGCTTAAAT------T s droAlb1.JH854640 315744 75 + 406291 ---------------TTGCa----------agtagcc-----aaaaaaaaa--------------------------------cattgcagaA------------ATTCGAAT-------------------------AGCG--------------------------AAAACG-----------------------CAA------------------------------------------------TTCGTTTAccatttttgtttctc s droGri2.scaffold_15245 908684 110 + 18325388 ---------------TTGCA----------AGTAGCC-----AAAAAAAAAACAACAAAAAAACAACACACACAAGAAACAATAAAAGCAAACTTTGGCTTATATATCTATAT-------------------------ATAT--------------------------GTATAA-----------------------AGA------------------------------------------------TATATCTGCTTT---------TT a score=1130046.000000 s dm6.chr2R 24362946 183 + 25286936 --------CG------ATTC-----GGC-GGGCTTATC---------GGCCTGGGAATTGTGGCA------------------------------------------ATGGCA---GCG--------GCGAAGGCTCATTGTTCTGGCCGT--GTGTTG-CCAGCG----------TTTGCAG---------CGGCTTCGCCG--------TTGTGCAA-CGAC-TTTAAAAAGCTGTTAACATGCGTTGTCATCGCTGCCATATGTTGCACGACAG------------G------CGACTCCT-G-------GTCGCCACCA s droSim1.chr2R 18701307 183 + 19596830 --------CG------ATTC-----GGC-GGGCTTATC---------GGCCTGGGAATTGTGGCA------------------------------------------ATGGCA---GCG--------GCGAAGGCTCATTGTTCTGGCCGT--GTGTTG-CCAGCG----------TTTGCAG---------CGGCTCCGGCG--------TTGTGCAA-CGAC-TTTAAAAAGCTGTTAACATGCGTTGTCATCGCTGCCATATGTTGCACGACAG------------G------CGACTCCT-G-------GTCGCCACCA s droSec1.super_23 121081 183 + 989336 --------CG------ATTC-----GTC-GGGCTTATC---------GGCCTGGGAATTGTGGCA------------------------------------------ATGGCA---GCG--------GCGAAGGCTCATTGTTCTGGCCGT--GTGTTG-CCAGCG----------CTTGCAG---------CGGCTCCGGCG--------TTGTGCAA-CGAC-TTTAAAAAGCTGTTAACATGCGTTGTCATCGCTGCCATATGTTGCACGACAG------------G------CGACTCCT-G-------GTCGCCACCA s droYak3.chr2R 20210551 183 + 21139217 --------CG------ATTC-----GGC-GGACTTATC---------GGCCTGGGAATTGTGGCA------------------------------------------ATGGCA---GCG--------GCGAAGGCTCATTGTTCTGGCCGT--GTGTTG-CCAGCA----------CTGCCAG---------CGTTTGCAGCG--------TTGTGCAA-CGAC-TTTAAAAAGCTGTTAACATGCGTTGTCATCGCTGCCATATGTTGCACGACAG------------G------CGACTCCT-G-------GTCGCCACCA s droEre2.scaffold_4845 21608393 197 + 22589142 --------CGG-CAACATTC-----GGC-GGACTTATC---------GGCCTGGGAATTGTGGCA------------------------------------------ATGGAA---GCG--------GCGATGGCTCATTGTTCTGGCCGT--GTGTTG-CCAGCG----------TTTCCAGTGGTTCCATTGGTTCCAGCG--------TTGTGCAA-CGAC-TTTAAAAAGCTGTTAACATGCGTTGTCATCGCTGCCATATGTTGCACGACAG------------G------CGACTCCT-G-------GTCGCCACCA s droBia2.KB462602 801456 145 + 3129309 --------CG------ATTC-----GCT-GGGCTTATC---------GGCCTGGGAATTGTG-------------------------------------------------------------------------TTATTGTTCTTGCC----GTTTCG-CCGGC---------------CAG-----------------ATG--------TGTTGCAA-CGAC-TTTAAAAAGCTGTTAACATGCGTTGTCATCGCTGCCATATGTTGCACGACAG------------C------CGACTCCT-G-------GTCGCCA--- s droSuz1.KI419649 12046560 146 - 14502029 --------CG------ATTC-----GTT-GGGCTTATC---------GGCCTGGGAATTGTG-------------------------------------------------------------------------TTATTGTTCTTGCC----GTTTTGCCCGGC---------------CAG-----------------ATG--------TGTTGCAA-CGAC-TTTAAAAAGCTGTTAACATGCGTTGTCATCGCTGCCATATGTTGCACGACAG------------C------CGACTCCT-G-------GTCGCca--- s droBip2.KB464407 1964093 146 + 2915140 --------CG------ATTC---------AGGCTTATC---------GGCCTGGGAattgtgtta------------------------------------------ttg-------------------------ttattgttcttgtatttggtgttg---------------------ttg-----------------tcg--------ttgtgcAA-CGAC-TTTAAAAAGCTGTTAACATGCGTTGTCATCGCTGCCATATGTTGCACGACag----------cag------caac--------------ttgcaacta s droEug2.KB465067 605434 166 + 1515531 --------CG------ATTC-----GGT-GGGCTTATC---------GGCCTGGGAATTGTGGCa------------------------------------------aaggca---acggcaaca--gcaacggctTATTGTTCTTGCT----GTGCCG-C-------------------CAG------------------CG--------TTGTGCAA-CGAC-TTTAAAAAGCTGTTAACATGCGTTGTCATCGCTGCCATATGTTGCACGACAG------------C------CGACTCCT-G-------gtcgcca--- s droEle2.KB458573 527119 168 - 5320397 --------cg------ATTCGGCTGGGC-TGGCTTATC---------GGCCTGGGAATTGTGGCA------------------------------------------AAAGGC---GC-----------------TTATTGTtcttgctgt--ttgctg-tttgc-------------tgccG-----------------CCG--------TTGTGCAA-CGAC-TTTAAAAAGCTGTTAACATGCGTTGTCATCGCTGCCATATGTTGCACGACAG------------C------CGACTCCT-G-------gtcgccaccg s droKik2.KB459527 281511 135 - 1234237 --------TG------ATTC-----GGCGGGGCTTATC---------GGCCTGGGAATTGTG-------------------------------------------------------------------------GCATTGTTCT--------GCGCCT-G-------------------CCG------------------CG--------TTGTGCAA-CGAC-TTTAAAAAGCTGTTAACATGCGTTGTCATCGCTGCCATATGTTGCAcgacag------------c------ag-----c-g-------gcaaccAGCA s droTak2.KB461535 146591 144 - 669855 --------CG------ATTC-----GGT-GGGCTTATC---------GGCCTGGGAATTGTG-------------------------------------------------------------------------TTATTGTTCTTGCT----GCATGG-C-------------------CAG-----------------ATG--------TGTTGCAA-CGAC-TTTAAAAAGCTGTTAACATGCGTTGTCATCGCTGCCATATGTTGCACGACAG------------C------CGACTCCT-G-------GTCGCCACCA s droRho2.KB449310 41124 165 - 65043 --------CG------ATTC-----GGCTGGGCTTATC---------GGCATGGGAATTGTGGCA------------------------------------------AAAGGC---GC-----------------TTATTGTTCTTG------CTGTTG---------------------CCG-----------------CCG--------TTGTGCAA-CGAC-TTTAAAAAGCTGTTAACATGCGTTGTCATCGCTGCCATATGTTGCACGACAGCCGCCGCCACCGG------CGACTCCT-G-------GTCGCCACCG s droFic2.KB457177 85973 152 + 995874 --------CG------ATTC------GC-GGGCTTATC---------GGCCTGGGAATTGTGG-A------------------------------------------ACGGGC---GC-----------------TTATTGTTCTCGCC----GTGTTG---------------------CCG-----------------GCG--------TTGTGCAA-CGAC-TCTAAAAAGCTGTTAACATGCGTTGTCATCGCTGCCATATGTTGCACGACGG------------C------CGACTCCT-G-------GTCGCCACCG s droPse3.chr3 1354814 159 - 19787792 --------CGGATCACATCC-----AGT---GCTTATC---------GGCCTGGGAATTGtggca-----------------------------------------cacagcc---acagacacaagacag----ttattgttt------------------------------------ttg-----------------ttg--------ttgtgcaa-TGAC-TTTAAAAAGCTGTTAACATGCGTTGTCATCGCTGCCATATGTTGCACgacaa------------c------gagcagc----------agcagcagca s droPer1.super_34 543673 153 - 916997 --------CGGATCACATCC-----AGT---GCTTATC---------GGCCTGGGAATTGTGGCA-----------------------------------------CACAGCC---ACAGACACAAGACAG----TTATTGTTT------------------------------------TTG-----------------TTG--------TTGTGCAA-TGAC-TTTAAAAAGCTGTTAACATGCGTTGTCATCGCTGCCATATGTTGCacgacaa------------c------g----------------agcagcagca s droMir2.chr3 1395927 165 - 20862834 --------CGGATCACATCC-----AGT---GCTTATC---------GGCCTGGGAATTgtggca-----------------------------------------cacagcc---acagacacaagacag----ttattgtttttgttgttgttgttg-ttg-----------------ttg-----------------ttg--------ttgtgcaa-tGAC-TTTAAAAAGCTGTTAACATGCGTTGTCATCGCTGCCATATGTTGCACgacaa------------c------g----------------------agca s droWil2.CH963894 1317238 203 + 2843958 --------cg------cTTC-----CGA-TGGCTTATC---------TGCCTGGGAATTGTGGCA-----------------------------------------CACAGCccgagtg----------------ttttttttttgggttt--ttgttg-ttggtggtgtcttttttttcttg-----------------ttgattGTTGCTTGTGCAA-TGCCTTTTAAAAAGCTGTTAACATGCGTTGTCATCGCTGCCATATGTTGCacgacaa------------cggcaaacgacaaca-gcaacgacgacgacgacg s droVir3.scaffold_12875 7358796 176 + 20611582 TTTTTTGGTG------CTTC-----CGA-TGGCTTATCTGGCACTTGGGCCTGGGAATTGTGGCA------------------------------------------AAGCGA---GAA--------GCGTGTG-TGGCtgctgttgctg---ttgctg---------------------ttg-----------------ttg--------ttgtGCAATTGCC-TTTAAAAAGCTGTTAACATGCGTTGTCATCGCTGCCATATGTTGCAcgacac------------g------acgcgacg-c-------gacgc----- s droMoj3.scaffold_6496 26153931 213 + 26866924 TATTTTGGCG------CTTC-----CGA-TGGCTTATCTGTCTATTAGGCCTGGGAATCGTGGCAAGCGAGG--------GGCGAGAGCCGAGTGGCGAGAGACGAGAGACGA---GAA--------ACGTGAG-TTGCCGTTATTACCAACTGTATTG---------------------TTG-----------------CAG--------TTGTGCAATTGCC-TTTAAAAAGCTATTAACATGCGTTGTCATCGCTGCCATATGTTGCACGACGC------------A------TCGCGGCG-C-------GGCGA----- s droAlb1.JH854640 315819 219 + 406291 ttctttGGCG------CTTC-----CGA-TGGCTTATCTGCCACATGGGCCTGGGAATTGTGGCAAGCGAGGCTAACTGAAGcgtgtgctgttgctgttgaggtggttgtcgat--gtc--------gctgctg-ttgttgttgttgctg---ctgctg---------------------ttc-----------------ttg--------ttgtgcaATTGCC-TTTAAAAAGCTGTTAACATGCGTTGTCATCGCTGCCATATGTTGcacgacgc------------g------acgcgacg-c-------gactc----- s droGri2.scaffold_15245 908794 159 + 18325388 TATTTTGGCG------CTTC-----CGA-TGGCTTATCTGCCACTTGGGCCTGGGAATTGTGGCA------------------------------------------AAGCGA---GAA--------GCAGC---------------------GTG-TG---------------------TTG-----------------TTG--------TTGTGCAATTGCC-TTTAAAAAGCTGTTAACATGCGTTGTCATCGCTGCCATATGTTGCACGACGC------------G------ACGCGCAGTC-------GACAG----- a score=-314891.000000 s dm6.chr2R 24363129 84 + 25286936 GCAGCCGTA-CTCCAT----------------------------------CCACCGCCACCGT------------------------------------CATT-------GATCG---------------------GCGATCG-------CTTTT-GGGGC----------------------------------AG--------------C-----------TGAGCCAC------CGGC--GA------------------C--GGCG----------ACT---------------------------TGTCA s droSim1.chr2R 18701490 102 + 19596830 GCAGCCGTA-CTCCATCCACATCC------------ACCG----------CCACCGCCACCGT-----------------------------CATCG-CCATT-------GATCG---------------------GCGATCG-------CTTTT-GGGGC----------------------------------AG--------------C-----------TGAGCCAC------CGGC--GA------------------C--GGCG----------ACT---------------------------TGTCA s droSec1.super_23 121264 96 + 989336 GCAGCCGTA-CTCCATCCACAT----------------------------CCACCGCCACCGT-----------------------------CATCG-CCATT-------GATCG---------------------GCGATCG-------CTTTT-GGGGC----------------------------------AG--------------C-----------TGAGCCAC------CGGC--GA------------------C--GGCG----------ACT---------------------------TGTCA s droYak3.chr2R 20210734 126 + 21139217 GCAGCCGTA-ctccatccacatccatatccacatctaccg----------ccaccgccaccgccaag------------------------CCACCG-TCATTGATCGGCGATCG---------------------GCGATCG-------CTTTT-GGGGC----------------------------------AG--------------C-----------TGAGCCAC------CGGC--GA------------------C--GGCG----------ACT---------------------------TGTCA s droEre2.scaffold_4845 21608590 101 + 22589142 GCAGCCGTA-CTCCAT----------------------------------CCACCGCCACCGCCAAG------------------------CCACCG-TCATT-------GATCG---------------------GCGATCG-------CTTTT-GGGGC----------------------------------AG--------------C-----------TGAGCCACCGACGACGGC--GA------------------C--GGCG----------ACT---------------------------TGTCA s droBia2.KB462602 801601 77 + 3129309 ------------CCAT-----------------------------------------CACCAT----------------------------CCGCCG-CCATC-------GATCG---------------------GCGATCG-------CTTTTCGGGGC----------------------------------AG--------------C-----------AAAGCCAc------cggc--ga---------------cggc--ggcg----------acT---------------------------TGTCA s droSuz1.KI419649 12046706 87 - 14502029 ------------ccatccacat----------------------------ccacatccaccat----------------------------CCGCCG-CCATC-------GATCG---------------------GCGATCG-------CTTTTCGGGGC----------------------------------AG--------------C-----------AAAGCCAC------CGGC--GA------------------C--GGCG----------ACT---------------------------TGTCA s droBip2.KB464407 1964239 130 + 2915140 gCAACCAAC-AACAAGCCA-------------------------------GCAGCGACACCGACAAACA-------------GACGACTCCTGGTCG-CCATT-------GATCGACCGGGCCGCACCGCTGTGCTGTGATCG-------CTTTT-GGGTC----------------------------------TG---------------------------GGTCTGC------TGGG--GT------------------CTGGGGG----------TCT---------------------------TGTCA s droEug2.KB465067 605600 99 + 1515531 --------------------------------------------------ccaccaccaccatcagcT-----------------------CCACCG-CCATC-------GATCG---------------------GCGATCG-------CTTTT-GGGGC----------------------------------AG--------------C-----------AGCACCAC------CGGC--GACGACGACGGAGATGGCGAC--GGCG----------ACT---------------------------TGTCA s droEle2.KB458573 527287 89 - 5320397 --------------------------------------------------ccaccgccatcgc-----------------------------catcg-ccatt-------gaTCG---------------------TCGATCG-------CTTTT-GGGGC----------------------------------AGGCACAACAGCAGCAC-----------AGCACCAC------CGAC--GA------------------C--GGCG----------ACT---------------------------TGTCA s droKik2.KB459527 281647 96 - 1234237 ACAACCGGC-GACAACCAACAA----------------------------ccaccgacgacgacgacga------------cgacgactcctGGTCG-CCATT-------GATCG---------------------GTGATCG-------CTTTC-GGGGC------------------------------------------------------------------------------------------------------T--GGCG----------ACT---------------------------TGTCA s droTak2.KB461535 146736 89 - 669855 ACA-----------------------------------------------CCATC--CACCAT----------------------------CCGCCG-CCATC-------GATCG---------------------GCGATCG-------CTTTTCGGGGC----------------------------------AG--------------CA----------AAAGCCAC------CGGC--GA------------------C--GGCGATGTCGACTTACT---------------------------TGTCA s droRho2.KB449310 41291 70 - 65043 ATAG----------------------------------------------CCATTGCCATCGA----------------------------TCGGCGATCCGC-------GATCC---------------------CCGATCG-------CTTTT-GGGGC----------------------------------AG--------------C-------------------------CAG-----------------------C--AGCA----------ACT---------------------------TGTCA s droFic2.KB457177 86125 85 + 995874 --------------------------------------------------ACATTGCCATCGC------------------------------ACCG-CCATC-------GATCG---------------------GCGATCG-------CTTTT-ggggc----------------------------------ag--------------caggcagcaggcagcaccAC------CGGC--GA------------------C--GGCG----------ACT---------------------------TGTCA s droPse3.chr3 1354973 149 - 19787792 gcagcagcagcggcagcaacaacca-------------------------ccaccGACACCgccgacgacaacaacgacggCGACGACTCCTGGTCG-CCATT-------GATCG---------------------GTGATCG-------CTTTT-Ggggc--------------------ctggctggctggctgg--------------c-----------tggctggc------tggctggc------------------t--ggcg------gctTGCT---------------------------TGTCA s droPer1.super_34 543826 149 - 916997 gcagcagcagcggcagcaacaacca-------------------------ccaccgacaccgccgacgacaacaacgacggcgacgacTCCTGGTCG-CCATT-------GATCG---------------------GTGATCG-------CTTTT-GGGGC--------------------ctggctggctggctgg--------------c-----------tggctggc------tggctggc------------------t--ggcg------gctTGCT---------------------------TGTCA s droMir2.chr3 1396092 169 - 20862834 gcagcagcagcggcagcaacaacca-------------------------ccaccGACACCgccgacgacaacaacgacggcgacgactCCTGGTCG-CCATT-------GATCG---------------------GTGATCG-------CTTTT-Ggggcctggctggctggctggctggctggctggctggctgg--------------c-----------tggctggc------tggctggc------------------t--ggcg------acTTGCT---------------------------TGTCA s droWil2.CH963894 1317441 106 + 2843958 acgacttcG-----------------------------------------ATTTCGACTCCTG------------------------------GTCG-CCATTG------GGTcg---------------------acaattg-------ttgtt-gttgt----------------------------------tg--------------t-----------tgg-----------cggc--GG------------------T--GGTT----------GCTGCTGTGAATTGACTTGGTTTGACTTTGTGTCA s droVir3.scaffold_12875 7358972 67 + 20611582 ------------------------------------gccg------cgactcgaAGTCAACT---------------------TCGACGCGAATTCGACTCCT-------GGTCG---------------------CCATTGGAGAGACACAATT-GCC------------------------------------------------------------------------------------------------------------------------------------------------------------ s droMoj3.scaffold_6496 26154144 50 + 26866924 ------------------------------------GC-----------TCCGAAGTGAGC--------------------------------TTCGACTCCT-------GGTCG---------------------CCAATCG-GAGAGACAATT-GCT------------------------------------------------------------------------------------------------------------------------------------------------------------ s droAlb1.JH854640 316038 74 + 406291 ------------------------------------GCAGTCGAGTCGACCCAAAGTCTTCTC-----GATGTTGAGGCGAAGTCAAACCGAGTTCGACTCCT-------GATT------------------------------------CAATT-GTC------------------------------------------------------------------------------------------------------------------------------------------------------------ a score=3292047.000000 s dm6.chr2R 24363213 186 + 25286936 ACCACCTGGCACAACTGCACCACTTTTGTGGCGGTTGCATCAACGGGCTGAACTTCAAACCGGCGGCAGGCGTTGGTTTCCCTCGAAATCTACGCGAAAGTGGAAACGCCAGCGATTTGCGTAGCCCGCAGCGATAGTTATAGCTTCCTCAGCTCACATGTGCCGTCCCTTATTTGGAAGCTTG-----TG s droSim1.chr2R 18701592 186 + 19596830 ACCACCTGGCACAACTGCACCACTTTTGTGGCGGTTGCATCAACGGGCTGAACTTCAAACCGGCGGCAGGCGTTGGTTTCCCGCGAAATCTACGCGAAAGTGGAAACGCCAGCGATTTGCGTAGCCCGCAGCGATAGTTATAGCTTCCTCAGCTCACATGTGCCGTCCCTTATTTGGAAGCTTG-----TG s droSec1.super_23 121360 186 + 989336 ACCACCTGGCACAACTGCACCACTTTTGTGGCGGTTGCATCAACGCGCTGAACTTCAAACCGGCGGCAGGCGTTGGTTTCCCTCGAAATCTACGCGAAAGTGGAAACGCCAGCGATTTGCGTAGCCCGCAGCGATAGTTATAGCTTCCTCAGCTCACATGTGCCGTCCCTTATTTGGAAGCTTG-----TG s droYak3.chr2R 20210860 191 + 21139217 ACCACCTGGCACAACTGCACCACTTTTGTGGCGGTTGCATCAACGGGCTGAACTTCAAACCGGCGGCAGGCGTTGGTTTCCCTCGAAATCTACGCGAAAGTGGAAACGCCAGCGATTTGCGTAGCCCGCAGCGATAGTTATAGCTTCCTCAGCTCACATGTGCCGTCCCTTATTTGGAAGCTTGTGTGCTG s droEre2.scaffold_4845 21608691 186 + 22589142 ACCACCTGGCACAACTGCACCACTTTTGTGGCGGTTGCATCAACGGGCTGAACTTCAAACCGGCGGCAGGCGTTGGTTTCCCTCGAAATCTACGCGAAAGTGGAAACGCCAGCGATTTGCGTAGCCCGCAGCGATAGTTATAGCTTCCTCAGCTCACATGTGCCGTCCCTTATTTGGAAGCTTG-----TG s droBia2.KB462602 801678 185 + 3129309 ACCACCTGGCACAACTGCACCACTTCTGTGACGC-TGCATCAACGGGCTGAACTTCAGACCGACGGCAGGCGTTGGTTTCCCTCGAAATCTATGCGAAAGTGGAAACGCCACCGATTTGCGTAGCCTGCAGCGATAGTTATAGCTTCCTCAGCTCACATGTGCCGTCCCTTATTTGGAAGCTTG-----TG s droSuz1.KI419649 12046793 186 - 14502029 ACCACCTGGCACAACTGCACCACTTTTGTGACGCTTGCATCAACGGGCTGAACTTCAAATCGACGGCAGGCGTTGGTTTCCCTCGAAATCTATGCGAAAGTGGAAACGCCACCGATTTGCGTAGCCTGCAGCGATAGTTATAGCTTCCTCAGCTCACATGTGCCGTCCCTTATTTGGAAGCTTG-----TG s droBip2.KB464407 1964371 186 + 2915140 GCCACCTGGCACAACTGAACCAATTTTGTGACGGTTGCATCCACCCGCTGAACTCCAGACTGACGGCAGGCGTTGGTTTCCATCGAAATCTATGCGAAAGTGGAAACGCCACAGATTTGCGTAGCCTGCAGCGATAGTTATAGCTTCCTCAGCTCACATGTGCCGTCCCTTATTTGGAAGCTTG-----TG s droEug2.KB465067 605699 186 + 1515531 ACCACCTGGCACAACTGCACCACTTTTGTGACGGTTGCATCAACGGGCTGAACTTCAAATCGACGGCAGGCGTTGGTTTCCCTCGAAATCTATGCGAAAGTGGAAACGCCAGCGATTTGCGTAGCCTGCAGCGATAGTTATAGCTTCCTCAGCTCACATGTGCCGTCCCTTATTTGGAAGCTTG-----TG s droEle2.KB458573 527376 185 - 5320397 -CCACCTGGCACAACTGAACCACTTTAGTGACGGTTGCATCAACGGGCTGAACTTCTGATTGGCGGCATGCGTTGGTTTCCCTCGAAATCTATGCGAAAGTGGAAACGCCAACGATTTGCGTAGCCTGCAGCGATAGTTATAGCTTCCTCAGCTCACATGTGCCGTCCCTTATTTGGAAGCTTG-----TG s droKik2.KB459527 281743 185 - 1234237 -CCACCTGGCACAACTGAACCATTTTCAAGGCGGTTGCATCAACGCGCTGGACTCCCGCTTGGCGGCATGCGTTGGTTTACCCCGAAATCTATGCGAAAGTGGAAACGCCAGCGATTTGCGTGGCCCGCAGCGATAGTTATAGCTTCCTCAGCTCACATGTGCCGTCCCTTATTTGGAAGCTTG-----TG s droTak2.KB461535 146825 186 - 669855 ACCACCTGGCACAACTGCACCACTTTTGTGACGCTTGCATCAACGGGCTGAACTTCAAATCGACGGCAGGCGTTGGTTTCCCTCGAAATCTATGCGAAAGTGGAAACGCCAGCGATTTGCGTAGCCTGCAGCGATAGTTATAGCTTCCTCAGCTCACATGTGCCGTCCCTTATTTGGAAGCTTG-----TG s droRho2.KB449310 41361 185 - 65043 -CCACCTGGCACAACTGCACCACTTTTGTGACGGTTGCATCAACGGGCTGAACTTCAGATTGGCGGCATGCGTTGGTTTCCCTCGAAATCTATGCGAAAGTGGAAACGCCAGCGATTTGCGTAGCCTGCAGCGATAGTTATAGCTTCCTCAGCTCACATGTGCCGTCCCTTATTTGGAAGCTTG-----TG s droFic2.KB457177 86245 186 + 995874 ACCACCTGGCACAACTGCACCACTTTTGTGACGCTTGCATCAACGGGCTGAACTTCAGATTGGCGGCAGGCGTTGGTTTCCCTCGAAATCTACGCGAAAGTGGAAACGCCAGCGATTTGCGTAGCCCGCAGCGATAGTTATAGCTTCCTCAGCTCACATGTGCCGTCCCTTATTTGGAAGCTTG-----TG s droPse3.chr3 1355122 185 - 19787792 -CCACCTGGCACAACTGAACCAATTTTGTGGCAGTTGCATCAATGCGCTGAACTTCAGATTGGCGGCATGCGttgatttccatggaaatctATGCGAAAGTGGAAACGCCAGCGATTTGCGTGGCCCGCAGCGATAGTTATAGCTTCCTCAGTTCACATGTGCCGTCCCTTATTTGGAAGCttg-----tg s droPer1.super_34 543975 185 - 916997 -CCACCTGGCACAACTGAACCAATTTTGTGGCAGTTGCATCAATGCGCTGAACTTCAGATTGGCGGCATGCGTTGATTTCCATGGAAATCTATGCGAAAGTGGAAACGCCAGCGATTTGCGTGGCCCGCAGCGATAGTTATAGCTTCCTCAGTTCACATGTGCCGTCCCTTATTTGGAAGCTTG-----tg s droMir2.chr3 1396261 185 - 20862834 -CCACCTGGCACAACTGAACCAAttttgtggcagttgcatCAATGCGCTGAACTTCAGATTGGCGGCATGCGTtgatttccatggaaatctATGCGAAAGTGGAAACGCCAGCGATTTGCGTGGCCCGCAGCGATAGTTATAGCTTCCTCAGTTCACATGTGCCGTCCCTTATTTGGAAGCttg-----tg s droWil2.CH963894 1317547 182 + 2843958 ACCACCTGGCACAACTGAACCAATTTTGTGATGGTTGCATCAACTCGCTGAACTTGAGTTTGTCAGCATACGTTGATTTCCATTGAAATCTATGCGAAAGTGGAAACGCCAGTGATTTGCGTAGCATACAGCAATAGTTATAGCTTCCTCAGTTCACATGTGCCGTCCCTTATTTGGAAGCT--------- s droVir3.scaffold_12875 7359039 186 + 20611582 GCCACCTGGCACAACTGAACCCATTTTGCGCTGCTTGGATCAATCCGCGAGGCTGCAGTTTGTCAGCATGCGTTGATTTCCATTGAAATCTATGCGAAAGTGCAAAGCCCACAGATTTGCGTAGCTCACAGCGCTAGTTATAGCTTCCTCAGTTCACATGTGCCGTCCCTTATTTGGAAGCTTG-----TG s droMoj3.scaffold_6496 26154194 186 + 26866924 GCCACCTGGCAGAATCGAACTCATTTTGCGACGCTTGGATCAACGCGCGGGGCTGCAGTTTGTCAGCATGCGCTGATTTACATTGAAATCTATGCGAAAGTGCAAAGCCCACAGATTTGCGTAGCTCGCAGCGCTAGTTATAGCTTCCTCAGTTCACATGTGCCGTCCCTTATTTGGAAGCTTG-----TG s droAlb1.JH854640 316112 186 + 406291 GCCACCTGGCACAACTGACCCCATTTTCTGACGCTTGGATCAACGCGTGAAGCTGCAGTTTGTCATCATGCGTTTATTTACATTGAAATCTATGCGAAAGTGCAAAGCCCACAGATTTGCGTAGCTCTCAACGCTAGTTATAGCTTCCTCAGTTCACATGTGCCGTCCCTTATTTGGAAGCTTG-----TG s droGri2.scaffold_15245 909044 186 + 18325388 GCCACCTGGCGCAACTGAACCCATTTTGCTTGGCTTCAATCAACTTGCGAGGCTGCAGTTTGTCAGCATGCGTTGATTTCCATTGAAATCTATGCGAAAGTGCAAAGCCCACAGATTTGCGTAGCTCACAGCACTAGTTATAGCTTCCTCAACTCACATGTGCCGTCCCTTATTTGGAAGCTTG-----TG a score=16670.000000 s dm6.chr2R 24363399 1 + 25286936 T s droSim1.chr2R 18701778 1 + 19596830 T s droSec1.super_23 121546 1 + 989336 T s droYak3.chr2R 20211051 1 + 21139217 T s droEre2.scaffold_4845 21608877 1 + 22589142 T s droBia2.KB462602 801863 1 + 3129309 T s droSuz1.KI419649 12046979 1 - 14502029 T s droBip2.KB464407 1964557 1 + 2915140 T s droEug2.KB465067 605885 1 + 1515531 T s droEle2.KB458573 527561 1 - 5320397 T s droKik2.KB459527 281928 1 - 1234237 T s droTak2.KB461535 147011 1 - 669855 T s droRho2.KB449310 41546 1 - 65043 T s droFic2.KB457177 86431 1 + 995874 T s droPse3.chr3 1355307 1 - 19787792 t s droMir2.chr3 1396446 1 - 20862834 t s droWil2.CH963894 1317729 1 + 2843958 T s droVir3.scaffold_12875 7359225 1 + 20611582 T s droMoj3.scaffold_6496 26154380 1 + 26866924 T s droAlb1.JH854640 316298 1 + 406291 C s droGri2.scaffold_15245 909230 1 + 18325388 T a score=79028.000000 s dm6.chr2R 24363400 8 + 25286936 GCGAAGCG s droSim1.chr2R 18701779 8 + 19596830 GCGAAGCG s droSec1.super_23 121547 8 + 989336 GCGAAGCG s droYak3.chr2R 20211052 8 + 21139217 GCGAAGCG s droEre2.scaffold_4845 21608878 8 + 22589142 GCGAAGCG s droBia2.KB462602 801864 8 + 3129309 GCGAAGCG s droSuz1.KI419649 12046980 8 - 14502029 GCGAAGCG s droBip2.KB464407 1964558 7 + 2915140 GCG-AGCG s droEug2.KB465067 605886 8 + 1515531 GCGAAGCG s droEle2.KB458573 527562 8 - 5320397 GCGAAGCG s droKik2.KB459527 281929 8 - 1234237 GCGAAGCG s droTak2.KB461535 147012 8 - 669855 GCGAAGCG s droRho2.KB449310 41547 8 - 65043 GTGAAGCG s droFic2.KB457177 86432 8 + 995874 GCGAAGCG s droWil2.CH963894 1317730 8 + 2843958 GCAAAGCg s droVir3.scaffold_12875 7359226 6 + 20611582 --GGTGCG s droMoj3.scaffold_6496 26154381 6 + 26866924 --GCTGCG s droAlb1.JH854640 316299 6 + 406291 --GCAccg s droGri2.scaffold_15245 909231 6 + 18325388 --GGTGCG a score=10500.000000 s dm6.chr2R 24363408 1 + 25286936 C s droSim1.chr2R 18701787 1 + 19596830 C s droSec1.super_23 121555 1 + 989336 C s droYak3.chr2R 20211060 1 + 21139217 C s droEre2.scaffold_4845 21608886 1 + 22589142 C s droBia2.KB462602 801872 1 + 3129309 C s droSuz1.KI419649 12046988 1 - 14502029 C s droBip2.KB464407 1964565 1 + 2915140 C s droEug2.KB465067 605894 1 + 1515531 C s droEle2.KB458573 527570 1 - 5320397 c s droKik2.KB459527 281937 1 - 1234237 c s droTak2.KB461535 147020 1 - 669855 C s droRho2.KB449310 41555 1 - 65043 c s droFic2.KB457177 86440 1 + 995874 C s droWil2.CH963894 1317738 1 + 2843958 c a score=78552.000000 s dm6.chr2R 24363409 16 + 25286936 ------AACAATTA------TATGTACG s droSim1.chr2R 18701788 16 + 19596830 ------AACAATTA------TATGTACG s droSec1.super_23 121556 16 + 989336 ------AACAATTA------TATGTACG s droYak3.chr2R 20211061 22 + 21139217 ------AACAATTATACTCGTATGTGCG s droEre2.scaffold_4845 21608887 16 + 22589142 ------AACAATTA------TATGTGCG s droBia2.KB462602 801873 16 + 3129309 ------aacaatta------tatatatg s droSuz1.KI419649 12046989 16 - 14502029 ------Aacaatta------tatatatg s droBip2.KB464407 1964566 16 + 2915140 ------AACAATTG------TATATACG s droEug2.KB465067 605895 16 + 1515531 ------aacaatta------tatatatg s droEle2.KB458573 527571 16 - 5320397 ------aacaatta------tatatata s droKik2.KB459527 281938 16 - 1234237 ------aacaatta------tatatata s droTak2.KB461535 147021 16 - 669855 ------AAcaatta------tatatatg s droRho2.KB449310 41556 16 - 65043 ------aacaatta------tatatata s droFic2.KB457177 86441 16 + 995874 ------AAAAATTA------TATGCTCG s droAlb1.JH854640 316307 12 + 406291 --aaaaaataaata-------------- s droGri2.scaffold_15245 909237 14 + 18325388 Caaaaaaaaaaaaa-------------- a score=26374.000000 s dm6.chr2R 24363425 12 + 25286936 GCGCGGCCTGAG s droSim1.chr2R 18701804 12 + 19596830 GCGCGGCCTGAG s droSec1.super_23 121572 12 + 989336 GCGCGGCCTGAG s droYak3.chr2R 20211083 12 + 21139217 ACGCGGCCTGAG s droEre2.scaffold_4845 21608903 12 + 22589142 GCGCGGCCTGAG s droBia2.KB462602 801890 12 + 3129309 acgcGGGCTGAG s droSuz1.KI419649 12047006 12 - 14502029 acgcGGGCTGAG s droBip2.KB464407 1964589 12 + 2915140 GTGTGTCTGTGT s droEug2.KB465067 605912 12 + 1515531 acgcgGGCTGAG s droEle2.KB458573 527596 12 - 5320397 atgcgaaCTGAG s droTak2.KB461535 147038 12 - 669855 aagcGGGCTGAG s droRho2.KB449310 41575 12 - 65043 gtgcgAGCTGAG s droFic2.KB457177 86458 12 + 995874 ATGCGAACTGAG s droMoj3.scaffold_6496 26154387 7 + 26866924 -CAAAAGC---- s droAlb1.JH854640 316319 10 + 406291 ataaaaacag-- s droGri2.scaffold_15245 909251 10 + 18325388 acaaaaacaa-- a score=10714.000000 s dm6.chr2R 24363437 3 + 25286936 CGG s droSim1.chr2R 18701816 3 + 19596830 CGG s droSec1.super_23 121584 3 + 989336 CGG s droYak3.chr2R 20211095 3 + 21139217 CAG s droEre2.scaffold_4845 21608915 3 + 22589142 CAG s droBia2.KB462602 801902 3 + 3129309 CAG s droSuz1.KI419649 12047018 3 - 14502029 CAG s droBip2.KB464407 1964601 3 + 2915140 CAG s droEug2.KB465067 605924 3 + 1515531 CAG s droEle2.KB458573 527608 3 - 5320397 CAA s droTak2.KB461535 147050 3 - 669855 CAG s droRho2.KB449310 41587 3 - 65043 CAA s droFic2.KB457177 86470 2 + 995874 CA- s droPse3.chr3 1355334 2 - 19787792 -tg s droAlb1.JH854640 316329 3 + 406291 cga s droGri2.scaffold_15245 909261 3 + 18325388 caa a score=1464.000000 s dm6.chr2R 24363440 2 + 25286936 AC s droSim1.chr2R 18701819 2 + 19596830 AC s droSec1.super_23 121587 2 + 989336 AC s droYak3.chr2R 20211098 2 + 21139217 AC s droEre2.scaffold_4845 21608918 2 + 22589142 AC s droBia2.KB462602 801905 2 + 3129309 AC s droSuz1.KI419649 12047021 2 - 14502029 AC s droBip2.KB464407 1964605 2 + 2915140 AC s droEug2.KB465067 605927 2 + 1515531 AC s droEle2.KB458573 527611 2 - 5320397 AC s droKik2.KB459527 281978 2 - 1234237 AC s droTak2.KB461535 147053 2 - 669855 AC s droRho2.KB449310 41590 2 - 65043 AC s droFic2.KB457177 86472 2 + 995874 AC s droPse3.chr3 1355338 1 - 19787792 g- s droAlb1.JH854640 316332 1 + 406291 a- s droGri2.scaffold_15245 909264 1 + 18325388 a- a score=71473.000000 s dm6.chr2R 24363442 21 + 25286936 --------TCACACA-----GGCGAGCGAGCGCG s droSim1.chr2R 18701821 21 + 19596830 --------TCACACA-----GGCGAGCGAGCGCG s droSec1.super_23 121589 21 + 989336 --------TCACACA-----GGCGAGCGAGCGCG s droYak3.chr2R 20211100 21 + 21139217 --------TCACACA-----GGCGAGCGAGCGCG s droEre2.scaffold_4845 21608920 21 + 22589142 --------TCACACA-----GGCGAGCGAGCGCG s droBia2.KB462602 801907 21 + 3129309 --------TCACACA-----GGCGAGTGCGCGCG s droSuz1.KI419649 12047023 21 - 14502029 --------TCACACA-----GGCGAGTGAGCGCG s droBip2.KB464407 1964607 26 + 2915140 --------TCACACAActctggaaaaaaaatgag s droEug2.KB465067 605929 21 + 1515531 --------TCACACA-----GGCGACTGAGCGCG s droEle2.KB458573 527613 21 - 5320397 --------TCACACA-----GGCGAGTGGCTGTG s droKik2.KB459527 281980 21 - 1234237 --------GCACACA-----GCTGAAcgccagag s droTak2.KB461535 147055 21 - 669855 --------TCACACA-----GGCGAGTGAGCGCG s droRho2.KB449310 41592 21 - 65043 --------TCACACA-----GGCGAGTGACTGAG s droFic2.KB457177 86474 21 + 995874 --------TCACACA-----GGCGAGTGGTTGGG s droPse3.chr3 1355339 21 - 19787792 --------ttgtgta-----tgCGATTCAACGCA s droPer1.super_34 544186 21 - 916997 --------ttgtGTA-----TGCGATTCAACGCA s droMir2.chr3 1396478 21 - 20862834 --------ttgtgta-----tgCGATTCAACGCA s droMoj3.scaffold_6496 26154394 8 + 26866924 -----------caac-----gaca---------- s droAlb1.JH854640 316333 19 + 406291 aaactgaataacaaa-----acca---------- s droGri2.scaffold_15245 909265 19 + 18325388 aaaaaaTATTGAAAA-----AATA---------- a score=210430.000000 s dm6.chr2R 24363463 24 + 25286936 AAAAA-AACCAGCACAACCACATCA s droSim1.chr2R 18701842 24 + 19596830 AAAAA-AACCAGCACAACCACATCA s droSec1.super_23 121610 24 + 989336 AAAAA-AACCAGCACAACCACATCA s droYak3.chr2R 20211121 24 + 21139217 aaaaa-aaCCAGCACAACCACATcg s droEre2.scaffold_4845 21608941 23 + 22589142 -AAAA-AACCAGCACAGCAACATCG s droBia2.KB462602 801928 23 + 3129309 -AAAA-AACCAGCACAACAACATCa s droSuz1.KI419649 12047044 24 - 14502029 aaaaa-aaCCAGCACAACAACATCa s droBip2.KB464407 1964633 23 + 2915140 -aaaa-aaccAGCACAACAAcgtca s droEug2.KB465067 605950 23 + 1515531 -AAAA-AACCAGCACAACAACATCa s droEle2.KB458573 527634 24 - 5320397 aaaaa-aaccagcacaacaacaaca s droKik2.KB459527 282006 24 - 1234237 aaaaa-aaccagcacaacaacatca s droTak2.KB461535 147076 24 - 669855 aaaaa-aaCCAGCACAACAACATCG s droRho2.KB449310 41613 24 - 65043 aaaaa-aaCCAGCACAACAACATCa s droFic2.KB457177 86495 24 + 995874 aaaaa-aaCCAGCACAACAACATCA s droPse3.chr3 1355360 24 - 19787792 GCAAT-TACACGTACACTCATATAT s droPer1.super_34 544207 24 - 916997 GCAAT-TACACGTACACTCATATAT s droMir2.chr3 1396499 24 - 20862834 GCAAC-TACACGTACACTCATATAT s droVir3.scaffold_12875 7359281 24 + 20611582 aacaa-aaccagcacaacaacaacc s droMoj3.scaffold_6496 26154407 25 + 26866924 aacaacaactactactactacaaca s droAlb1.JH854640 316359 25 + 406291 aacaacagcagcagcgtcggcggcg s droGri2.scaffold_15245 909289 23 + 18325388 AACAA-AACCAGCACAAC-ACAGCC a score=59146.000000 s dm6.chr2R 24363487 15 + 25286936 GTGCACTTA--AAAAAA s droSim1.chr2R 18701866 15 + 19596830 GTGCACTGG--AAAAAA s droSec1.super_23 121634 14 + 989336 GTGCACTGG---AAAAA s droYak3.chr2R 20211145 15 + 21139217 ctgcactgc--gagaaa s droEre2.scaffold_4845 21608964 15 + 22589142 GTGCACTGG--AAAAAA s droBia2.KB462602 801951 15 + 3129309 gtgcactcg--gaaaaa s droSuz1.KI419649 12047068 15 - 14502029 gtgcactcg--aaaaaa s droEug2.KB465067 605973 15 + 1515531 gtgcactgg--gagaaa s droEle2.KB458573 527658 15 - 5320397 gtacactca--aaaaaa s droKik2.KB459527 282030 15 - 1234237 ataaactga--gaaaaa s droTak2.KB461535 147100 15 - 669855 GTGCACTCG--AAAAAA s droRho2.KB449310 41637 15 - 65043 gtgcactca--aaaaaa s droFic2.KB457177 86519 15 + 995874 GTACACTCG--GAGAAA s droPse3.chr3 1355389 15 - 19787792 gtatatatg--tataaa s droPer1.super_34 544236 15 - 916997 GTATATATG--TATAAA s droMir2.chr3 1396528 15 - 20862834 gtatatatg--tataaa s droVir3.scaffold_12875 7359305 7 + 20611582 --------a--caacaa s droMoj3.scaffold_6496 26154432 7 + 26866924 --------a--caacaa s droAlb1.JH854640 316384 7 + 406291 --------a--cagcag s droGri2.scaffold_15245 909312 9 + 18325388 --------AGCCAACAA a score=-73005.000000 s dm6.chr2R 24363502 5 + 25286936 ----AAATT s droSim1.chr2R 18701881 5 + 19596830 ----AAGTG s droSec1.super_23 121648 5 + 989336 ----AAGTG s droYak3.chr2R 20211162 5 + 21139217 ----cGGCT s droEre2.scaffold_4845 21608979 5 + 22589142 ----CGAGT s droBia2.KB462602 801966 3 + 3129309 ------att s droSuz1.KI419649 12047083 3 - 14502029 ------atg s droEug2.KB465067 605988 5 + 1515531 ----agggg s droEle2.KB458573 527673 5 - 5320397 ----aggct s droKik2.KB459527 282045 5 - 1234237 ----ataaa s droTak2.KB461535 147115 5 - 669855 ----GATAT s droRho2.KB449310 41652 5 - 65043 ----atcat s droPse3.chr3 1355408 2 - 19787792 ----aa--- s droPer1.super_34 544256 2 - 916997 ----AA--- s droMir2.chr3 1396549 2 - 20862834 ----aa--- s droVir3.scaffold_12875 7359312 4 + 20611582 cagc----- s droMoj3.scaffold_6496 26154439 4 + 26866924 caac----- s droAlb1.JH854640 316391 4 + 406291 cagc----- s droGri2.scaffold_15245 909321 2 + 18325388 CA------- a score=-13208.000000 s dm6.chr2R 24363507 12 + 25286936 TGATTCATCTTA s droSim1.chr2R 18701886 12 + 19596830 GGATTCAACTTC s droSec1.super_23 121653 12 + 989336 GGATTCAGCTTA s droYak3.chr2R 20211167 12 + 21139217 GGATTCGGGTGC s droEre2.scaffold_4845 21608984 11 + 22589142 -GATTCCGCTGG s droBia2.KB462602 801969 12 + 3129309 GACTGCATTTCA s droSuz1.KI419649 12047086 12 - 14502029 GTCTgcaattta s droEle2.KB458573 527678 12 - 5320397 acttttttttaa s droKik2.KB459527 282050 12 - 1234237 taataattttta s droTak2.KB461535 147120 12 - 669855 Gactaatatttt s droRho2.KB449310 41657 12 - 65043 agtcTAAATGCA s droGri2.scaffold_15245 909323 4 + 18325388 -------GCTC- a score=-8574.000000 s dm6.chr2R 24363519 6 + 25286936 -GAAATT s droSim1.chr2R 18701898 6 + 19596830 -GAAATT s droSec1.super_23 121665 6 + 989336 -GAAATT s droYak3.chr2R 20211179 6 + 21139217 -GAAATG s droEre2.scaffold_4845 21608995 6 + 22589142 -GGAACT s droSuz1.KI419649 12047112 6 - 14502029 -ggGAAA s droEug2.KB465067 605993 6 + 1515531 -gaaatt s droEle2.KB458573 527690 6 - 5320397 -gaaatt s droTak2.KB461535 147132 6 - 669855 -gaaatt s droRho2.KB449310 41669 6 - 65043 -GAAATT s droPse3.chr3 1355411 5 - 19787792 -aaaac- s droPer1.super_34 544259 5 - 916997 -AAAAC- s droMir2.chr3 1396552 5 - 20862834 -aaaac- s droVir3.scaffold_12875 7359316 6 + 20611582 agcgtc- s droAlb1.JH854640 316403 6 + 406291 cgagtc- s droGri2.scaffold_15245 909327 6 + 18325388 AGCGTC- a score=-19858.000000 s dm6.chr2R 24363525 6 + 25286936 --GGCCAT s droSim1.chr2R 18701904 6 + 19596830 --AGCCAA s droSec1.super_23 121671 6 + 989336 --AGCCAA s droYak3.chr2R 20211185 6 + 21139217 --CGCCAT s droEre2.scaffold_4845 21609001 6 + 22589142 --GGCCAT s droSuz1.KI419649 12047118 6 - 14502029 --GGGGAA s droEug2.KB465067 605999 6 + 1515531 --caccaa s droEle2.KB458573 527696 5 - 5320397 --cgGCA- s droRho2.KB449310 41675 6 - 65043 --CACCAT s droPse3.chr3 1355416 6 - 19787792 --gagcac s droPer1.super_34 544264 6 - 916997 --GAGCAC s droMir2.chr3 1396557 6 - 20862834 --gagcac s droVir3.scaffold_12875 7359322 6 + 20611582 ggcggc-- s droAlb1.JH854640 316409 5 + 406291 -acaac-- s droGri2.scaffold_15245 909333 6 + 18325388 GGCGGC-- a score=-13673.000000 s dm6.chr2R 24363531 21 + 25286936 GCTGCAGACCTGGCC-TCTGGC s droSim1.chr2R 18701910 21 + 19596830 GTTACAGACCTCGCC-TCTGGC s droSec1.super_23 121677 21 + 989336 GTTACAGACTTCGCC-TCTGGC s droYak3.chr2R 20211191 6 + 21139217 GCTCCA---------------- s droEre2.scaffold_4845 21609007 21 + 22589142 GCCCCACTCTTCGCT-TCTGGG s droSuz1.KI419649 12047124 21 - 14502029 GTTGTGATCCAGTTC-CCAGTC s droEug2.KB465067 606005 21 + 1515531 gcttttgttttcatt-tctaaG s droEle2.KB458573 527701 16 - 5320397 -----AAGCTTTGTT-TGTAGC s droVir3.scaffold_12875 7359329 13 + 20611582 gcagcag---------ccaagc s droAlb1.JH854640 316415 21 + 406291 gcagcagatacaATA-CTGAGC s droGri2.scaffold_15245 909340 22 + 18325388 GCGGCAGCAGCAGCAGTCAAGC a score=-22949.000000 s dm6.chr2R 24363552 6 + 25286936 TCTTCA--- s droSim1.chr2R 18701931 6 + 19596830 TCTTCA--- s droSec1.super_23 121698 6 + 989336 TCTTCA--- s droYak3.chr2R 20211197 5 + 21139217 -GAACA--- s droEre2.scaffold_4845 21609028 6 + 22589142 CGTCCA--- s droEug2.KB465067 606043 5 + 1515531 -TTTTA--- s droEle2.KB458573 527717 6 - 5320397 TCCTAA--- s droPse3.chr3 1355426 2 - 19787792 ----ca--- s droPer1.super_34 544277 5 - 916997 -caaca--- s droMir2.chr3 1396564 2 - 20862834 ----ca--- s droVir3.scaffold_12875 7359342 6 + 20611582 ---cgagtc s droAlb1.JH854640 316436 6 + 406291 ---TTAccc s droGri2.scaffold_15245 909362 6 + 18325388 ---CGAGTC a score=-39067.000000 s dm6.chr2R 24363558 13 + 25286936 TTAGTACGCCAAG--------- s droSim1.chr2R 18701937 13 + 19596830 TTCGTCCGCAAAG--------- s droSec1.super_23 121704 13 + 989336 TTAGAACGCCAAG--------- s droYak3.chr2R 20211202 13 + 21139217 TCAATAGCCAAAA--------- s droEre2.scaffold_4845 21609034 13 + 22589142 ACGATACTCAAAG--------- s droEug2.KB465067 606048 13 + 1515531 GTAACAACTTTAG--------- s droPse3.chr3 1355428 5 - 19787792 gcagc----------------- s droPer1.super_34 544282 5 - 916997 gcagc----------------- s droMir2.chr3 1396566 5 - 20862834 gcagc----------------- s droVir3.scaffold_12875 7359348 12 + 20611582 -----acacaacaaca-----a s droAlb1.JH854640 316442 17 + 406291 -----acagagcgagagagaga s droGri2.scaffold_15245 909368 15 + 18325388 -----ACACAACAACG--CCGA a score=-168046.000000 s dm6.chr2R 24363571 42 + 25286936 TAA------ATGGCAAGGCATTTAA----------ACAG--------------------C-TGAGAAT-------------------AAGAATATCTC s droSim1.chr2R 18701950 37 + 19596830 TAA--------------------------------ACAG--------------------C-TGAGAATGGGATTC-------GAT-CAGGAATATCTC s droSec1.super_23 121717 42 + 989336 TAA------ATGGCAAGGCATTTAG----------ACAG--------------------C-TGAGAAT-------------------AGGAATATCTC s droYak3.chr2R 20211215 43 + 21139217 TAA------ATGATAA---------------------CG--------------------TAGGAGAAGGAGATTT-------GAT-TAGGGAGGCTTT s droEre2.scaffold_4845 21609047 47 + 22589142 TAA------ATGGCAG-GCGTTCGC----------ACAG--------------------CAAGAGAAAGGGATTC-------GAT-TAGGAA------ s droSuz1.KI419649 12047727 41 - 14502029 TAA------ATGGTTTGGCATTTGCA----ACTGTACaa--------------------cttttgaat-------------------aat-------- s droEug2.KB465067 606070 73 + 1515531 TAATGTTTTATAGCTACCACTTTACGT---AAGAGATGG--------------------T-AAAGAGATGGTTCCCTAGGGTGGT-AAAATAAATCTT s droPse3.chr3 1355433 25 - 19787792 -------------------------------agcagcag--------------------cagctgaaa--------------gctgaaag-------- s droPer1.super_34 544287 24 - 916997 -------------------------------agcagcag--------------------cagcTGAAA--------------GCT-AAAG-------- s droMir2.chr3 1396571 24 - 20862834 -------------------------------aacagcag--------------------cagctgaaa--------------gcT-AAAG-------- s droVir3.scaffold_12875 7359360 31 + 20611582 --------------------------caTgcagcagcag--------------------cagcagcagcagcTTGAA--------------------- s droAlb1.JH854640 316459 51 + 406291 --------------------------gagagagcaaaagaaagagaNCAAGCCGagtcacaacagcagcagatacaA--------------------- s droGri2.scaffold_15245 909383 24 + 18325388 --------------------------GAGAGAGCGAGAG--------------------GGAGAGAGGGG---------------------------- a score=-5700.000000 s dm6.chr2R 24363613 12 + 25286936 ATTACTATAT--------------------AG s droSim1.chr2R 18702001 12 + 19596830 ATTACTATAT--------------------AG s droSec1.super_23 121759 12 + 989336 ATTATCATAT--------------------AG s droYak3.chr2R 20211258 32 + 21139217 ATTATAAGATGATATTACTACGCGTGACTCAC s droEre2.scaffold_4845 21609094 7 + 22589142 --CATAA-----------------------AT s droEug2.KB465067 606143 12 + 1515531 CTTACTTAGC--------------------AA s droEle2.KB458573 528251 12 - 5320397 ATCTTTACAA--------------------GT a score=-20.000000 s dm6.chr2R 24363625 1 + 25286936 T s droSim1.chr2R 18702013 1 + 19596830 T s droSec1.super_23 121771 1 + 989336 T s droYak3.chr2R 20211290 1 + 21139217 A s droEre2.scaffold_4845 21609101 1 + 22589142 T s droEug2.KB465067 606155 1 + 1515531 A s droEle2.KB458573 528263 1 - 5320397 T s droKik2.KB459527 282678 1 - 1234237 T a score=-1030.000000 s dm6.chr2R 24363626 1 + 25286936 A s droSim1.chr2R 18702014 1 + 19596830 A s droSec1.super_23 121772 1 + 989336 A s droYak3.chr2R 20211291 1 + 21139217 C s droEre2.scaffold_4845 21609102 1 + 22589142 C s droEug2.KB465067 606156 1 + 1515531 C s droEle2.KB458573 528264 1 - 5320397 G s droKik2.KB459527 282679 1 - 1234237 A s droRho2.KB449310 42377 1 - 65043 a a score=2997.000000 s dm6.chr2R 24363627 1 + 25286936 T s droSim1.chr2R 18702015 1 + 19596830 T s droSec1.super_23 121773 1 + 989336 T s droYak3.chr2R 20211292 1 + 21139217 T s droEre2.scaffold_4845 21609103 1 + 22589142 T s droEug2.KB465067 606157 1 + 1515531 T s droEle2.KB458573 528265 1 - 5320397 T s droKik2.KB459527 282680 1 - 1234237 T s droTak2.KB461535 147567 1 - 669855 t s droRho2.KB449310 42378 1 - 65043 c a score=2888.000000 s dm6.chr2R 24363628 11 + 25286936 TTTCTCCGAGT s droSim1.chr2R 18702016 11 + 19596830 TTTCTTTGTGT s droSec1.super_23 121774 11 + 989336 TTTCTTCGAGT s droYak3.chr2R 20211293 11 + 21139217 TTTCGCGCAGT s droEre2.scaffold_4845 21609104 11 + 22589142 TTTCGCCCAGT s droBia2.KB462602 802587 11 + 3129309 TTTTTTCCACT s droSuz1.KI419649 12047768 11 - 14502029 tttttgcaaGT s droEug2.KB465067 606178 11 + 1515531 TTTTCAGCAGT s droEle2.KB458573 528266 11 - 5320397 TTTTCGCGAGT s droKik2.KB459527 282681 11 - 1234237 TTTCTTTCCGT s droTak2.KB461535 147568 11 - 669855 tttttcccagt s droRho2.KB449310 42379 11 - 65043 tttttacgAGT s droFic2.KB457177 86807 11 + 995874 TTTTTGCAAGT s droPse3.chr3 1355458 2 - 19787792 ---------cc s droPer1.super_34 544311 2 - 916997 ---------CC s droMir2.chr3 1396595 2 - 20862834 ---------CC s droVir3.scaffold_12875 7359391 4 + 20611582 ---C----GGC s droAlb1.JH854640 316510 8 + 406291 ---CACTGAGC a score=-23502.000000 s dm6.chr2R 24363639 47 + 25286936 -----GTA--GCGTC-----GGCGGC--CGAA--AGCCGCG-TC---G-----CGGGTTCAGACTA----------------------------------------AAG-CGT s droSim1.chr2R 18702027 47 + 19596830 -----GTA--GCGTC-----GGCGGC--CGAA--AGCCGCG-TC---G-----CGGGTTCAGACTG----------------------------------------AAG-CGA s droSec1.super_23 121785 47 + 989336 -----GTA--GCGTC-----GGCGGC--CGAA--AGCCGCG-TC---G-----CGGGCTCAGACTG----------------------------------------AAG-CGA s droYak3.chr2R 20211304 28 + 21139217 -----GTA--GCGTC-----GGCGGC---------------------------CGAGTTCA---------------------------------------------GTG-CGA s droEre2.scaffold_4845 21609115 74 + 22589142 -----GTA--GCGTC-----GGCGTC---------------------G-----CGAGTTCATGCTAAAgcgagtgcgagtgcgagtgcgagtgAGAGGGTGGGAGGGCG-CGG s droBia2.KB462602 802598 48 + 3129309 -----GCA--GCGTC-----GGTGGC--CGAA--AGCCGTG-CC---T-----CGAGTTCAGGTTA----------------------------------------AAGCCGA s droSuz1.KI419649 12047779 48 - 14502029 -----GCA--GCGTC-----GGTGGC--CGAA--AGCCGTG-TC---T-----CGAGTTCAGGTTA----------------------------------------AAGCCGA s droEug2.KB465067 606189 48 + 1515531 -----GTA--GCGTC-----GGTGGC--CGAA--AGCCGAG-GC---T-----CGAGTTGAGGTTA----------------------------------------AAGCCGA s droEle2.KB458573 528277 47 - 5320397 -----GCAGCGCGTC-----GGTGGC--CAAA--AGCCGAG-T----------CGAGTTCA-GTTA----------------------------------------AAGCCGA s droKik2.KB459527 282692 49 - 1234237 -----GCA--GCGTC-----GGTGGC--CAAA--AGGCGAGCTT---T-----TGAGTTGATTTCA----------------------------------------AAGCCGA s droTak2.KB461535 147579 48 - 669855 -----ATA--GCGTC-----GGTGGC--CGAA--AGCCGAG-TC---T-----CGAGTTCAGGTTA----------------------------------------AAGCCGA s droRho2.KB449310 42390 49 - 65043 -----GTA--GCGTC-----GGTGGC--CAAA--AGGCGAG-TC--GT-----CGAGTTCAGGTTA----------------------------------------AAGCCGA s droFic2.KB457177 86818 46 + 995874 -----GTA--GCGTC-----GGTGGC--CGAA--AGCTGAG------T-----CGCGTTCAGGTTA----------------------------------------AAGCCGA s droPse3.chr3 1355460 52 - 19787792 -----aGA--GCGTC-----GGTGGCGGCCAG--GCCCGAG-ACATAG-----AGAGC-CAAGCCA----------------------------------------GGCCCGA s droPer1.super_34 544313 52 - 916997 -----TAA--GCGTC-----GGTGGCGGCCAG--GCCCGAG-ACATAG-----AGAGC-CAAGCCA----------------------------------------GGCCCGA s droMir2.chr3 1396597 57 - 20862834 -----TAA--GCGTC-----GGTGGCGGCCAG--ACCCGAg-acacagagagcagagc-caagcCA----------------------------------------GGCCCGA s droVir3.scaffold_12875 7359396 36 + 20611582 -----GCG--GGGCC-----AGCGGC--AGCG--GGACAGA-AA---C-----TGAGCCGA---------------------------------------------------- s droMoj3.scaffold_6496 26154544 36 + 26866924 -----GCG--GGGGC-----AGCCGC--GCGG--AGGCATA-GA---C-----CGAGCCGA---------------------------------------------------- s droAlb1.JH854640 316552 38 + 406291 -----aga--gagcg-----agcgag--cgagtcgagtata-ta---g-----cgagccga---------------------------------------------------- s droGri2.scaffold_15245 909407 46 + 18325388 GTAAGACG--GCGGCAATGAAGCCGA--GCCG--AGGCATA-AA---C-----TGAGCCGA---------------------------------------------------- a score=60135.000000 s dm6.chr2R 24363686 17 + 25286936 GTGCAGCGGAAAGGAGA s droSim1.chr2R 18702074 17 + 19596830 GTGCAGCGGAAAGGAGA s droSec1.super_23 121832 17 + 989336 GTGCAGCGGAATGGAGA s droYak3.chr2R 20211332 17 + 21139217 GTGCAGCGGAAAGGAGC s droEre2.scaffold_4845 21609189 17 + 22589142 GTGCAGCGGAAAGGAGC s droBia2.KB462602 802646 16 + 3129309 GTGCAGCGG-AAGGAGA s droSuz1.KI419649 12047827 17 - 14502029 GTGCAGCGGAAAGGAGA s droBip2.KB464407 1964873 17 + 2915140 GTGTGGCCGAGTGCAGG s droEug2.KB465067 606237 11 + 1515531 GTGCAGCGGAG------ s droEle2.KB458573 528324 11 - 5320397 GTGCAGCGAGA------ s droKik2.KB459527 282741 17 - 1234237 GTGCAGCGGAGAAGtct s droTak2.KB461535 147627 17 - 669855 GTGCAGCGGAAAGGAGA s droRho2.KB449310 42439 12 - 65043 GTGCAGCGGAGA----- s droFic2.KB457177 86864 12 + 995874 GTGCAGCGGAGA----- s droPse3.chr3 1355512 7 - 19787792 GTGCAAC---------- s droPer1.super_34 544365 7 - 916997 GTGCAAC---------- s droMir2.chr3 1396654 7 - 20862834 GTGCAAC---------- s droVir3.scaffold_12875 7359432 7 + 20611582 GTGCAAC---------- s droMoj3.scaffold_6496 26154580 7 + 26866924 GTGCAGC---------- s droAlb1.JH854640 316590 7 + 406291 gTGCAAT---------- s droGri2.scaffold_15245 909453 7 + 18325388 GTGCAAC---------- a score=44374.000000 s dm6.chr2R 24363703 4 + 25286936 AGTC s droSim1.chr2R 18702091 4 + 19596830 AGTC s droSec1.super_23 121849 4 + 989336 AGTC s droYak3.chr2R 20211349 4 + 21139217 AGTC s droEre2.scaffold_4845 21609206 4 + 22589142 AGTC s droBia2.KB462602 802662 4 + 3129309 AGTC s droSuz1.KI419649 12047844 4 - 14502029 AGTC s droAna3.scaffold_13266 5714939 4 - 19884421 AGTC s droBip2.KB464407 1964892 4 + 2915140 AGTC s droEug2.KB465067 606248 4 + 1515531 AGTC s droEle2.KB458573 528335 4 - 5320397 AGTC s droKik2.KB459527 282779 4 - 1234237 tgcc s droTak2.KB461535 147644 4 - 669855 AGTC s droRho2.KB449310 42451 4 - 65043 AGTC s droFic2.KB457177 86876 4 + 995874 AGTC s droPse3.chr3 1355519 3 - 19787792 -ATC s droPer1.super_34 544372 3 - 916997 -ATC s droMir2.chr3 1396661 3 - 20862834 -ATC s droVir3.scaffold_12875 7359439 3 + 20611582 -GTG s droMoj3.scaffold_6496 26154587 3 + 26866924 -GTG s droAlb1.JH854640 316597 3 + 406291 -GTG s droGri2.scaffold_15245 909460 3 + 18325388 -GTG a score=1409342.000000 s dm6.chr2R 24363707 80 + 25286936 GTCGCCACATTGGCTGACTTATGACGAAAATAATTGCTGGCTATTGCTATCGCTAACTGGCGATCGCG------------T------CAGCGTTATCG s droSim1.chr2R 18702095 80 + 19596830 GTCGCCACATTGGCTGACTTATGACGAAAATAATTGCTGGCTATTGCTATCGCTAACTGGCGATCGCG------------T------CAGCGTTATCG s droSec1.super_23 121853 80 + 989336 GTCGCCACATTTGCTGACTTATGACGAAAATAATTGCTGGCTATTGCTATCGCTAACTGGCGATCGCG------------T------CAGCGTTATCG s droYak3.chr2R 20211353 83 + 21139217 GTCGCCACATTGGCTGACTTATGACGAAAATAATTGCTGGCTATTGCTATCGCCAACTGGCGATCGCGTCA---------T------CATCGCTATCG s droEre2.scaffold_4845 21609210 80 + 22589142 GTCGCCACATTGGCTGACTTATGACGAAAATAATTGCTGGCTATTGCTATCGCTAACTGGCGATCGCG------------T------CAGCGCTATCG s droBia2.KB462602 802666 86 + 3129309 GTCGCCACATTGGCTGACTTATGACGAAAGTAATTGCTGGCTATTGCTATCGCTAACTGGCGATcgcgtca------tcgt------catcgttaTCG s droSuz1.KI419649 12047848 86 - 14502029 GTCGCCACATTGGCTGACTTATGACGAAAATAATTGCTGGCTATTGCTATCTCTAACTGGCGATcgcgtca------tcgt------catcgttaTCG s droAna3.scaffold_13266 5714943 86 - 19884421 GTCGCCACATTGGCTGACTTATGACGAAAATAATTGCTGGCTATTGCTATCTCTAACTGGCGATCGCGTCA------TCGT------CATCGTTATCG s droBip2.KB464407 1964896 86 + 2915140 GTCGCCACATTGGCTGACTTATGACGAAAATAATTGCTGGCTATTGCTATCTTTAACTGGCGATcgcgtca------tcgt------catcgttaTCG s droEug2.KB465067 606252 86 + 1515531 GTCGCCACATTGGCTGACTTATGACGAAAATAATTGCTGGCTATTGCTATCTTTAACTGGCGATcgcgtca------tcgt------catcgttaTCG s droEle2.KB458573 528339 86 - 5320397 GTCGCCACATTGGCTGACTTATGACGAAAATAATTGCTGGCTATTGCTATCTTTAACTGGCGATcgcgtca------tcgt------catcgttaTCG s droKik2.KB459527 282783 86 - 1234237 gccgccgcattGGCTGACTTATGACGAAAATAATTGCTGGCTATTGCTATCTCTAACTGGCGATcgcgtca------tcgt------catcgttatCG s droTak2.KB461535 147648 86 - 669855 GTCGCCACATTGGCTGACTTATGACGAAAATAATTGCTGGCTATTGCTATCTCTAACTGGCGATcgcgtca------tcgt------catcgttaTCG s droRho2.KB449310 42455 86 - 65043 GTCGCCACATTGGCTGACTTATGACGAAAATAATTGCTGGCTATTGCTATCTCGAACTGGCGATcgcgtca------tcgt------catcgttaTCG s droFic2.KB457177 86880 86 + 995874 GTCGCCACATTGGCTGACTTATGACGAAAATAATTGCTGGCTATTGCTATCTCTAACGGGCGATcgcgtca------tcgt------catcgttaTCG s droPse3.chr3 1355522 87 - 19787792 GTCGCCACATTGGCTGACTTATGACGAAAATAATTGCTGTCG-----TATCTCTAGCGGGCGATcgcgtcatcgtcatcgc------catcgttaTCG s droPer1.super_34 544375 87 - 916997 GTCGCCACATTGGCTGACTTATGACGAAAATAATTGCTGTCG-----TATCTCTAGCGGGCGATCGCGTCATCGTCATCGC------CATCGTTATCG s droMir2.chr3 1396664 87 - 20862834 GTCGCCACATTGGCTGACTTATGACGAAAATAATTGCTGTCG-----TATCTCTGGCGGGCGATcgcgtcatcgtcatcgc------catcgttaTCG s droWil2.CH963894 1317878 78 + 2843958 gTCGCCACATTGGCTGACTTATGACGAAAATAATTGCGGG-----GCTATCTGTGACTGGCGATCGCGTCA---------T------CATATGTTTTG s droVir3.scaffold_12875 7359442 78 + 20611582 GTCGCCACATTGGCTGACTTATGACGAAAATAATTGC-GGCTATCGC-------GACTGGCGATCGCGTCA------TCGTCATCGACATCG------ s droMoj3.scaffold_6496 26154590 72 + 26866924 GTCGCCACATTGGCTGACTTATGACGAAAATAATTGC-GGCTATCGC-------GGCTGGCGATCGCGTCA------TCGC------CATCG------ s droAlb1.JH854640 316600 72 + 406291 GTCGCCACATTGGCTGACTTATGACGAAAATAATTGC-GGCTATCGC-------GACTGGCGATCGCGTCA------TCGC------CGTCG------ s droGri2.scaffold_15245 909463 72 + 18325388 GTCGCCACATTGGCTGACTTATGACGAAAATAATTGC-GGCTATCGC-------GACTGGCGATCGCGTCA------TCGT------CATCG------ a score=11095.000000 s dm6.chr2R 24363787 1 + 25286936 A s droSim1.chr2R 18702175 1 + 19596830 A s droSec1.super_23 121933 1 + 989336 A s droYak3.chr2R 20211436 1 + 21139217 A s droEre2.scaffold_4845 21609290 1 + 22589142 A s droBia2.KB462602 802752 1 + 3129309 A s droSuz1.KI419649 12047934 1 - 14502029 A s droAna3.scaffold_13266 5715029 1 - 19884421 A s droBip2.KB464407 1964982 1 + 2915140 A s droEug2.KB465067 606338 1 + 1515531 A s droEle2.KB458573 528425 1 - 5320397 A s droKik2.KB459527 282869 1 - 1234237 A s droTak2.KB461535 147734 1 - 669855 A s droRho2.KB449310 42541 1 - 65043 A s droFic2.KB457177 86966 1 + 995874 A s droPse3.chr3 1355609 1 - 19787792 G s droPer1.super_34 544462 1 - 916997 G s droMir2.chr3 1396751 1 - 20862834 G s droAlb1.JH854640 317308 1 + 406291 A s droGri2.scaffold_15245 909535 1 + 18325388 A a score=139236.000000 s dm6.chr2R 24363788 16 + 25286936 TGAT--TCG-TAGAAAGCC s droSim1.chr2R 18702176 16 + 19596830 TGAT--TCG-TAGAAAGCC s droSec1.super_23 121934 16 + 989336 TGAT--TCG-TAGAAAGCC s droYak3.chr2R 20211437 16 + 21139217 TTAT--TCG-CAGAAAGCC s droEre2.scaffold_4845 21609291 16 + 22589142 TTAG--TCG-TAGAAAGCC s droBia2.KB462602 802753 16 + 3129309 TTAT--TCG-TAGAAAGCC s droSuz1.KI419649 12047935 16 - 14502029 TTAT--TCG-TAGAAAGCC s droAna3.scaffold_13266 5715030 16 - 19884421 TTAT--TTG-TATAAAGCT s droBip2.KB464407 1964983 16 + 2915140 TTAT--TTG-TATAAAGCT s droEug2.KB465067 606339 16 + 1515531 TTAT--TCG-TAGAAAGCC s droEle2.KB458573 528426 16 - 5320397 TTAT--TCG-TAGAAAGCC s droKik2.KB459527 282870 16 - 1234237 TTAT--TCG-CAGAAAGCC s droTak2.KB461535 147735 16 - 669855 TTAT--TCG-TAGAAAGCC s droRho2.KB449310 42542 16 - 65043 TTAT--TCG-TAGAAAGCC s droFic2.KB457177 86967 16 + 995874 TTAT--TCG-CAGAAAGCC s droPse3.chr3 1355610 17 - 19787792 TTGC--CCGCTAGAAGGCT s droPer1.super_34 544463 17 - 916997 TTGC--CCGCTGGAAGGCT s droMir2.chr3 1396752 17 - 20862834 TTGC--CCGCTAGAAGGCT s droWil2.CH963894 1317956 10 + 2843958 --------G-TAGAAAGCT s droVir3.scaffold_12875 7359520 12 + 20611582 ------ACA-TCGTCAGCA s droMoj3.scaffold_6496 26154662 12 + 26866924 ------ACA-TAGTcagcc s droAlb1.JH854640 317309 16 + 406291 TAATTTGCA-TAGAGAG-- a score=37807.000000 s dm6.chr2R 24363804 13 + 25286936 CATCGCAG-----TTA-------------------G---------C s droSim1.chr2R 18702192 13 + 19596830 CATCGCAG-----TTA-------------------G---------C s droSec1.super_23 121950 13 + 989336 CATCGCAG-----TTA-------------------G---------C s droYak3.chr2R 20211453 13 + 21139217 CATCGCAG-----TTA-------------------G---------C s droEre2.scaffold_4845 21609307 13 + 22589142 CATCGCAG-----TTA-------------------G---------C s droBia2.KB462602 802769 13 + 3129309 CATCGCAG-----TTC-------------------G---------C s droSuz1.KI419649 12047951 13 - 14502029 CATCGCAG-----TTA-------------------G---------C s droAna3.scaffold_13266 5715046 29 - 19884421 CATCGCAG-----TTGTCCCGACAGGCCG---ACTG---------C s droBip2.KB464407 1964999 32 + 2915140 CATCGCAA-----ATGTCCCGACAGACTGACTACTG---------T s droEug2.KB465067 606355 13 + 1515531 CATCGCAG-----TTA-------------------G---------C s droEle2.KB458573 528442 13 - 5320397 CATCGCAG-----TTA-------------------G---------C s droKik2.KB459527 282886 13 - 1234237 CATCGCAG-----TTT-------------------G---------C s droTak2.KB461535 147751 13 - 669855 CATCGCAG-----TTA-------------------G---------C s droRho2.KB449310 42558 13 - 65043 CATCGCAG-----TTA-------------------G---------C s droFic2.KB457177 86983 13 + 995874 CATCGCAG-----TTA-------------------G---------C s droPse3.chr3 1355627 11 - 19787792 CATCGCAG-----TTG------------------------------ s droPer1.super_34 544480 11 - 916997 CATCGCAG-----TTG------------------------------ s droMir2.chr3 1396769 11 - 20862834 CATCGCAG-----TTG------------------------------ s droWil2.CH963894 1317966 22 + 2843958 CAGCTCAC-----TGG-------------------GTGCCTGGTCC s droVir3.scaffold_12875 7359551 8 + 20611582 CATCGAAG-------------------------------------- s droAlb1.JH854640 317325 13 + 406291 TCTCGCAGTTGTG--------------------------------- a score=22582.000000 s dm6.chr2R 24363817 2 + 25286936 CC s droSim1.chr2R 18702205 2 + 19596830 CC s droSec1.super_23 121963 2 + 989336 CC s droYak3.chr2R 20211466 2 + 21139217 CC s droEre2.scaffold_4845 21609320 2 + 22589142 CC s droBia2.KB462602 802782 2 + 3129309 CC s droSuz1.KI419649 12047964 2 - 14502029 CC s droAna3.scaffold_13266 5715075 2 - 19884421 CT s droBip2.KB464407 1965031 2 + 2915140 CT s droEug2.KB465067 606368 2 + 1515531 CC s droEle2.KB458573 528455 2 - 5320397 CC s droKik2.KB459527 282899 2 - 1234237 CC s droTak2.KB461535 147764 2 - 669855 CC s droRho2.KB449310 42571 2 - 65043 CC s droFic2.KB457177 86996 2 + 995874 CC s droWil2.CH963894 1317988 2 + 2843958 CT s droVir3.scaffold_12875 7359559 2 + 20611582 CT s droMoj3.scaffold_6496 26154962 2 + 26866924 CT s droAlb1.JH854640 317350 2 + 406291 TC a score=104443.000000 s dm6.chr2R 24363819 13 + 25286936 GTTTTCATTAG-----------CC s droSim1.chr2R 18702207 13 + 19596830 GTTTTCATTAG-----------CC s droSec1.super_23 121965 13 + 989336 GTTTTCATTAG-----------CC s droYak3.chr2R 20211468 13 + 21139217 GTTTTCATTAG-----------CC s droEre2.scaffold_4845 21609322 13 + 22589142 GTTTCCATTGG-----------CC s droBia2.KB462602 802784 13 + 3129309 GTTTTCATTAG-----------CC s droSuz1.KI419649 12047966 13 - 14502029 GTTTTCATTAG-----------CC s droAna3.scaffold_13266 5715077 22 - 19884421 GCCTGC--CAGCCTGCCAACCTCC s droBip2.KB464407 1965033 24 + 2915140 GCCTGCCTCAGCCAGCAAACCTCC s droEug2.KB465067 606370 13 + 1515531 GTTTTCATTAG-----------CC s droEle2.KB458573 528457 13 - 5320397 GTTTTCATTAG-----------GC s droKik2.KB459527 282901 13 - 1234237 GTTTTCATTAG-----------CC s droTak2.KB461535 147766 13 - 669855 GTTTTCATTAG-----------CC s droRho2.KB449310 42573 13 - 65043 GTTTTCATTAG-----------CC s droFic2.KB457177 86998 13 + 995874 GTTTTCATTAG-----------AC s droPse3.chr3 1355638 3 - 19787792 ----------G-----------TC s droPer1.super_34 544491 3 - 916997 ----------G-----------TC s droMir2.chr3 1396780 3 - 20862834 ----------G-----------TC s droWil2.CH963894 1317990 13 + 2843958 GTTTTCATTAG-----------CC s droVir3.scaffold_12875 7359561 13 + 20611582 GTTGTCGTCGT-----------CC s droMoj3.scaffold_6496 26154964 13 + 26866924 GCTTTGCTTGG-----------CC s droAlb1.JH854640 317352 13 + 406291 GGTTTCCTTAG-----------TC s droGri2.scaffold_15245 910499 13 + 18325388 GCTTCCTTTGG-----------CC a score=2923681.000000 s dm6.chr2R 24363832 413 + 25286936 CGTTGCACGCGG--------CGTATGAGTAATCAATAATAATTTGACCGCCGTCCC----C-----------------ACTGC---------------------------------------GACTTTTC--------TTC------------------------------GTCGC---TTCCCGCGATGTC----------A---TCGTGTG---TGTGTGT---GGT--CC--------------------------CAAATCGATTGCCATAATAATTTCGCGCAGAT---------------------------ATAGCAC-----------------------GG-------------------------------------------CAAA------TGCA-G---G----------------------------------CAGAACCACTT------CGACT-GCGACAATCATCGTACTCGTACAGTATTGTAATTTACTTAATT----------TCGAATCGTTCTGAATACGCAAA-TTTTGC-A----TT---TGCA-AAGCGGG----------AAAAAAGT-------GCAGGAAAACATTGTCCGTG-CATTAGTTACA-----------T------GT---CT-----------------AT--AGTC---------------GCGCTTGT--TTTCGC-------------------------------------------------TTAC-----------------TTGCTGT-------TATGAAAGGCGACTGCGCGGC---------GTCTGTTTC-GCCTGCTTTTTGGTT--G-----TTTTTCA--------GCTTTTC----TGCTGCGTTTGATATGCAAATT s droSim1.chr2R 18702220 417 + 19596830 CGTTGCACGCGG--------CGTATGAGTAATCAATAATAATTTGACCGCCGTTCCCCCGC-----------------CCCGC---------------------------------------GACTCTTC--------TTC------------------------------GCCGC---CTCCCGCGATGTC----------A---GCGTGTG---TGTGTGT---GGT--CC--------------------------CAAATCGATTGCCATAATAATTTCGCGCAGAT---------------------------ATAGCGC-----------------------TG-------------------------------------------CAAA------TGCA-G---G----------------------------------CAGAACCACTT------CGAAT-GCGACAATCATCGTGCTCGTACCGTATTGTAATTTACTTAATT----------TCGAATCGTTCTGAATACGCAAA-TTTCGC-A----TT---TGCA-AAGCGGG----------AAAAAAGT-------GCAGGAAAACATTGTCCGTG-CATTAGTTACA-----------T------GT---CT-----------------AT--AGTC---------------GCGCTTGT--TTTCGC-------------------------------------------------TTAC-----------------TTGCTGT-------TATGAAAGGCGACTGCGCGGC---------GTCTGTTTC-GCCTGCTTTTTGGTT--G-----TTTTTCA--------GCTTTTC----AGCTGCGTTTGATATGCAAATT s droSec1.super_23 121978 417 + 989336 CGTTGCACGCGG--------CGTATGAGTAATCAATAATAATTTGACCGCCGTCCCCCCGC-----------------CCCGC---------------------------------------GACTCTTC--------TTC------------------------------GCCGC---CTCCCGCGATGTC----------A---GCGTGTG---TGTGTGT---GGT--CC--------------------------CAAATCGATTGCCATAATAATTTCGCGCAGAT---------------------------ATAGCGC-----------------------GG-------------------------------------------CAAA------TGCA-G---G----------------------------------CAGAACCACTT------CGAAT-GCGACAATCATCGTGCTCGTACCGTATTGTAATTTACTTAATT----------TCGAATCGTTCTGAATACGCAAA-TTTCGC-A----TT---TGCA-AAGCGGG----------AAAAAAGT-------GCAGGAAAACATTGTCCGTG-CATTAGTTACA-----------T------GT---CT-----------------AT--AGTC---------------GCGCTTGT--TTTCGC-------------------------------------------------TTAC-----------------TTGCTGT-------TATGAAAGGCGACTGCGCGGC---------GTCTGTTTC-GCCTGCTTTTTGGTT--G-----TTTTTCA--------GCTTTTC----AGCTGCGTTTGATATGCAAATT s droYak3.chr2R 20211481 435 + 21139217 CGTTacacgctg--------cgtatgagtaatcaataataatttgacCGTCGTTC-----C-----------------ATTCC---------------------------------------tagttttcccattttttcc------------------------------gattt---tccctCC---GTC----------A---GCGAG-----TGTGTGT---GGT-CCC--------------------------CAAATCGATTGCCATAATAATTTCGCGCAGATATAG---------CAA-----------ATAGCAC-----------------------GG-------------------------------------------CAAA------TGCA-G---G----------------------------------CACAACCACTT------CGCCG-GCGACAATCAACGTACT------GAAttgtaatttacttaatt----------tcGAATCGTTCTGAATACgcaaa-ttttgc-at---tt---tgcc-aagcggggg--aa-aaaaaaaaagt-------gggaGAAAACATTGTCCGTG-CATTAGTTACA-----------T------GT---CT-----------------ATAGAGTC---------------GCGCTTGT--TTTCGC-------------------------------------------------TTAC-----------------TTGCTGT-------TATGAAAGGCGACTGCGCGGC---------GTctgtttt-gcctgctttttggtt--g-----ttttgcagctctgctgcttttc----tgctgcgtttgATATGCAAATT s droEre2.scaffold_4845 21609335 415 + 22589142 CGTTGCACGCGG--------CGTATGAGTAATCAATAATAATTTGACCGCCGTTC-----C-----------------ATGGC---------------------------------------GATGCTCC--------TCC------------------------------GCTGC---TCGCCGCGATGTC----------A---ACGTGGA--CCGCGTGT---GGT--CC--------------------------CAAATCGATTGCCATAATAATTTCGCGCAGAT---------------------------TTAGCAC-----------------------GG-------------------------------------------CAAA------TGCA-G---G----------------------------------CACAACCACTT------CGACT-GCGACAATCGGCGTGCC------GTATTGTAATTTACTTAATT----------TCGAATCGTTCTGAATACGCAAA-TTTTGC-AT---TT---TGCC-AGGCGGG----------AAAAAAGT-------GGAGGAAAACATTGTCCGTG-CATTAGTTACA-----------T------GT---CT-----------------AT--AGTC---------------GCGCTTGT--TTTCGC-------------------------------------------------TTAC-----------------TTGCTGT-------TATGAAAGGCGACTGCGCGGC---------GTCTGTTTC-GCCTGC-TTTTGGTT--G-----TTTTTCAGCTTTTCTGCTTTTC----TGCTGCGTTTGATATGCAAATT s droBia2.KB462602 802797 442 + 3129309 CGTTACAtgcgg--------cgtatgagtaatcaataataattttaccGCCAGTTT----T-----------------ATTGC---------------------------------------TATTTTTC--------TTA------------------------------GTCCC--CTTTTCCCGATGTCTctggacgtgg---atgtgga---tgtgtgt---GGT-CCC--------------------------CAAATCGATTGCCATAATAATTTCACGCAAATATAGCATATAGCACAT-----------ATAGCAC-----------------------AG-------------------------------------------CGaa------tgca-g---c----------------------------------aacaacaactt------tgCCT-GCGACAATCATCGTACA------ATATTgtaatttacttaatt----------tcgTATCGTTCAGAATACGTAAA-TTTTGC-A------------A-AAGCGAG---------aaaaaaaGT-------GGAAGAAAACATTGTCTATG-CATTAGTTACA-----------T------Gt---ct-----------------gt--agtt---------------gtagttgt--tattgc-----tttagtttttg---------------------------------ttgc---------tcttgcttttgttgt-------tatgAAAGGCGACTGCGCGGC---------GTCTGTTTT-GCCTgctttttggtt-----------------------gtttttc----tGCTGCGtttgatatgcaaatt s droSuz1.KI419649 12047979 454 - 14502029 CGTTACAtgcgg--------cgtatgagtaatcaataataattttatcgccagttt----t-----------------attac---------------------------------------tatttttc--------tTC------------------------------GTCGC--TTTTTCCCGATGTC---------------TGTGGA---TGTGTGT---GGTCCCC--------------------------CAAATCGATTGCCATAATAATTTCACGCAAATATAGCATATAGCACAT-----------ATAGCAC-----------------------AG-------------------------------------------CAaa------tgca-gcaac----------------------------------aacaacaactt------cgACT-ACGACAATCATCGTACA------ATATTgtaatttacttaatt----------tcgTATCGTTCAGAATACGCAAA-TTTTGcaa------------a-aagcgag--------aaaaaaaagt-------ggaagaaAACATTGTCTATG-CATTAGTTACA-----------T------GT---ct-----------------gt--agtt---------------gtagttgt--tattgc-----tttagttgttg---------------tatgtgccttagttgttattgt---------ttttgctgttgttgt-------tatgaAAGGCGACTGCGCGGC---------GTctgtttt-gcctgctttttggtt-----------------------gtttttc----tgctgcgtttgatatgcaaatt s droAna3.scaffold_13266 5715099 442 - 19884421 CGTTACACGCGG--------CGTATGAGTAATCAATAATAATTTTATCGACAATTT----T-----------------ATTAC---------------------------------------TATTTTTC--------TTC------------TTCTTTTGCCATAT----GCCTC---CCTCTACCGCCTC----------C---------------TGTGT---GGT--CC--------------------------AAAATCGATTGCCATAATAATTTCGCACAAAT---------------------------ATAGCac-----------------------aa------------------------caacaa----------caacaaa------agca-a---c----------------------------------aacTTGCAACT---------AT-CCGACAATCATCGCACA------ATATTGTAATTTACTTAATT----------TCGTATCGTTCAGAATACGCAAATTTTTGC-AAAA-AA---AACA-AAATGGG-------AAAAAAAAAGT-------GGAAGAAAACATTGTCCATG-CATTAGTTACA-----------T------GT---CC-----------------CC--AGAC---------------gttgttat--tgttgc-----tatagttcttg---------------------------------ttgt---------agttgctgttgttgt-------tATGGAAGGCGACTGCGCGGCGGCGGCGGTGTCTGTTTT-GCTTGCTTTTTGGTT-----------------------GTATT-------GCTGCGTTTGATATGCAAATT s droBip2.KB464407 1965057 476 + 2915140 CGTtacacgcgg--------cgtatgagtaatcaataataattttatcgacaattt----t-----------------attac---------------------------------------aatttttc--------ttc-------gttttttctTCTGCCATTT---GGCCTC---CCTCTACCACCTC----------CTTTTAGCGTT---TGTGTGT---GGT--CC--------------------------AAAATCGATTGGCATAATAATTTCGCACAAAT---------------------------ATAGCCC-----------------------ag-----------------------ccaccag----------caacaac------tgcACA---C----------------------------------CACAAGCATCT---------AT-CCGACAATCATCGCACA------ATATTGTAATTTACTTAATT----------TCGTATCGTTCAGAATACGCAAA--TTTGC-AAaatac---agca-aaaaaaa-------aaaaaatgggg-------ggaAGAAAACATTGTCCATG-CATTAGTTACA-----------T------GT---CC-----------------CC--Agacgttgttgttgttcaggttgttat--tgttgc-----tatagttcttg---------------------------------ttgt---------agttgttgttgttgt-------tatgaaAGGCGACTgcgcggcggcggcggtgtcTGTTTT-GCTTGCTTTTTGGTT-----------------------GTATT-------GCTGCGTTTGATATGCAAATT s droEug2.KB465067 606383 405 + 1515531 CGTTACAtgcgg--------cgtatgagtaatcaataataattttaccGCCAGTTT----T-----------------ATGAC---------------------------------------TATTTTCC--------TTC------------------------------GCCGC--TTTTCCGCGACAAC----------T---GCG-------TGTGTGT---GGT--CC--------------------------CAAATCGATTGCCATAATAATTTCACGCAAAT---------------------------ATAGCCC-----------------------AG-------------------------------------------CAAA------cgcg-g---c----------------------------------aacaacaactccGACTACGACT-GCGACAATCATCGTACA------ATATTGTAATTTACTTAATT----------TCGTATCGTTCAGAATACGCAAA-TTTTGc-a------------a-aagcgag--------aaaaaaaagt-------ggaagaaAACATTGTCCATG-CATTAGTTACA-----------T------GT---CT-----------------Gt--ggtt---------------gtagttgtagttttac-------------------------------------------------ttgt------------tgttgttgttgt-------tatgaaAGGCGACTGCGCGGC---------GGttgtttt--ccagctttttggtt-----------------------gtttttc----tgctgcgtttgatatgcaaatt s droEle2.KB458573 528470 443 - 5320397 CGTTACAtgcgg--------cgtatgagtaatcaataataattttatcgccagttt----t-----------------attac---------------------------------------tatttttc--------ttc------------------------------gtagcttttttttgcaacgtc----------t---gcg-------tgtgtgt---ggt--cC--------------------------CAAATCGATTGCCATAATAATTTCACGCAAAT---------------------------ATAGCAC-----------------------AG-------------------------------------------CAAA------TACA-G---C---------------------------------AAACAACAACTT------CGACT-ACGACAATCATCGTACA------ATATtgtaatttacttaatt----------tcgTATCGTTCAGAATACGCAAA-TTTTGc-a------------a-aagcgag---------aaaaaaagT-------GGAAGAAAACATTGTCCATG-CATTAGCTTCA-----------T------GT---CC------------------C--AGAC---------------GTAgttgt--ttttgc-----tatagttgttacggttgttgttgttgtatgtgctttagttg---ttgc---------tattgttgttgttgt-------tatgaAAGGCGACTGCGCGGC---------GTctgtttt-gcctgctttttggtt-----------------------gtttttc----tgctgcgtttgatatgcaaatt s droKik2.KB459527 282914 462 - 1234237 CGTTACAtgcgg--------cgtatgagtaatcaataataattttatcgccaattt----t-----------------attac---------------------------------------tatttttc--------ttctacgatttttttttttcttgacttGCTCGAGCCTC---TTTTCCC-----C----------T---GAGAGTAGTTTGTGTGT---GGT--CC--------------------------CAAATCGATTGCCATAATAATTTCACGCAAAT---------------------------ATAGCAC-----------------------AG----------------------------------------------------------A---C-------------------------------------------------------T-GCGACAATCGTCGTaca-----aatattgtaatttacttaatt----------tcgTATCGTTCAGAATACGCAAA-TTTTGC-G----CT------A-Aagcgag-------aaaataaaaattgttgggGGGAAAAAACATTGTCCATGCCATTAGCTACagacattgttgtt------gt---tg-----------------tt--cgtt---------------ctcgttgt--tattgtttgtttttagttgttg---------------------------------ctgt---------agttgtagttgttgt-------caTGAAAGGCGACTGCGCGGCGTC------GTCTGtttttacttgcttttcgggttgt-----tttttct--------ttttttt----agctgcgtttgatatgcaaatt s droTak2.KB461535 147779 462 - 669855 CGTTACAtgcgg--------cgtatgagtaatcaataataattttatcgCCAGTTT----T-----------------ATTCC---------------------------------------TATTTTTC--------TTC------------------------------ATTGC---TTTTT------------------T---CTGTGGA---TGTGTGT---GGTCCCC--------------------------CAAATCGATTGCCATAATAATTTCACGCAAATATAGCGTATAGCGCATATACATATAGCACAGCAC-----------------------AG-------------------------------------------Caaa------tgca-gcaac----------------------------------aacaacaactt------tgAGT-ACGACAATCATCGTACA------ATATtgtaatttacttaatt----------tcgTATCGTTCAGAATACgcaaa-ttttgc-a----a-------a-aagcgag--------aaaaaaaaGT-----GGGGGAGAAAACATTGTCCATG-CATTAGTTACA-----------T------Gt---ct-----------------gt--agtt---------------gtagttgt--tattgc-----tttagttgttgctattggtattgctattc---------------ttgt---------tgtagttgttgttgt-------tatgaAAGGCGACTGCGCGGC---------GTCTgtttt-gcccgctttttggtt-----------------------gtttttct--ttgctgcgtttgatatgcaaatt s droRho2.KB449310 42586 430 - 65043 CGTTACAtgcgg--------cgtatgagtaatcaataataattttatcgccaattt----t-----------------attac---------------------------------------tatttttc--------ttC------------------------------GTAGC--TTTTTCGCGACGAC----------A----TCTGCG---TGTGTGT---GGT--CC--------------------------CAAATCGATTGCCATAATAATTTCACGCAAAT---------------------------ATAGCAC-----------------------AG-------------------------------------------CAaa------taca-g---c----------------------------------aacaacaactt------tgaCT-ACGACAATCATCGTACA------ATATtgtaatttacttaatt----------tcGTATCGTTCAGAATACGCAAA-Ttttgc-a------------a-aagcaaaagcaac-aaaaaaaaagt-------ggaagaAAACATTGTCCATG-CATTAGCTTCA-----------T------GT---CC------------------C--AGTC---------------gcagttgt--ttttgt-----tgttatagttg---------------------------------ttgcctgtgctttagttgttgttgttgt-------tatgaaAGGCGACTGCGCGGC---------GTCTGTTTT-CCATgctttttggtt-----------------------gtttttc----tGCTGCGtttgatatgcaaatt s droFic2.KB457177 87011 442 + 995874 CGTTACAtgcgg--------cgtatgagtaatcaataataattttatcgCCAGCTT----T-----------------ATTAC----------------------------------------AGTTTTC--------CCC------------------------------GTCGC--TTTTTCGCGACGTC----------T---GCA-------TGTGTGT---GGT--CC--------------------------CAAATCGATTGCAATAATAATTTCACGCAAAT---------------------------ATAGCAC-----------------------AG-------------------------------------------CAAA------TACA-G---C----------------------------------GACAACAGCTC------CGGCT-ACGACAATCATCGTACA------ATATTGTAATTTACTTAATT----------TCGTATCGTTCAGAATACGCAAA-TTTTGc-a------------a-aagcgag---------aaaaaaagT-------GGAAGAAAACATTGTCCATG-CATTAGGTACA-----------T------GT---CC------------CAGTCCC--ATTC---------------GTAgttgt--ttttgc-----tatagttgttcttgttgttgttgctgttg---------------ttgtcagtgctttagatattgttgttgt-------tttaaaagGCGACTGCGCGGC---------GTCTGTTTT-CCTTgctttttggtt-----------------------gtttttc----aACTGCGtttgatatgcaaatt s droPse3.chr3 1355641 550 - 19787792 TGTTACACGCGAGTCGGACTCGTATGAGtaatcaataataattttatcgATCATTT----T-----------------ATTGCTTCTACATA----Cgtactg------ctctctctctctctatccttc--------TGC------------------------------GCCGC---TCATCGTTTTTCC----------T---GTG-------TTTGGGT---GGT--CC--------------------------AAAATCGATTGCCATAATAATTTCACGCAAAT---------------------------Atagcac-----------------------ag----------------------------------------acacaca------caca-g---ccatgcATATagacccccccaccccacccccactgcACGGTAACAT------CCACT-GCGGCAACCGTCGTACA------ATATTGTAATTTACTTAATTTCGTACCGTATCGTATCGTTCAGAATACGCAAA-TTTGTT-A----AGGaaaaaa-aGGCGag---tgc-aaacaaaaatt-------ggAAGAAAACATTGTCCATG-CATTAGCTAca-----------tgtcccagt---ccca------gtcccagtcgt--agtc---------------gtagttgt--tcttgt-----tgttgccgttgcaagtg---------------------------ttgt---------tgtggttgttgctgt-------tatgaAAGGCGACTGCGCGGcggc------gtttgtttt-gttggtgctttgctt--gctttattttgca--------gcttttttcattgctacatttgatatgcaaatt s droPer1.super_34 544494 538 - 916997 CGTTACACGCGAGTCGTACTCGTATGAGTAATCAATAATAATTTTATCGATCATTT----T-----------------ATTGCTTCTACATA----CGTACTC------CTCTCTCTCTCTCTATCCTTC--------TGC------------------------------GCCGC---TCATCGTTTTTCC----------T---GTG-------GTTGGGT---GGT--CC--------------------------AAAATCGATTGCCATAATAATTTCACGCAAAT---------------------------ATAGCAC-----------------------AG----------------------------------------ACACACA------CACA-G---CCATACATATAGACC------CCCCACCCCCACTGCACGGTAACAT------CCACT-GCGGCAATCGTCGTACA------ATATTGTAATTTACTTAATTTCGTACCGTATCGTATCGTTCAGAATACGCAAA-TTTGTT-A----AGGAAAAAA-AGGCGAG---TGC-AAACAAAAATT-------GGAAGAAAACATTGTCCATG-CATTAGCTACA-----------T------GT---CCCA------GTCCCAGTCGT--AGTC---------------GTAgttgt--tcttgt-----tgttgccgttgcaagtg---------------------------ttgt---------tgtggttgttgctgt-------tATGAAAGGCGACTGCGCGGCGGC------GTTTGTTTT-GTTGGTGCTTTGCTT--GCTTTATTTTGCA--------GTTTTTTTCATTGCTACATTTGATATGCAAATT s droMir2.chr3 1396783 544 - 20862834 CGTTAGACGCGAGTCGTACTCGTATGAGtaatcaataataattttatcgATCATTT----T-----------------ATTGCTTCTACATA----Cgtactcct----ctctctctctctctatccttc--------TGC------------------------------GTCGC---TCATCGTTTTTCC----------T---GTG-------GTTGGGT---GGT--CC--------------------------AAAATCGATTGCCATAATAATTTCACGCAAAT---------------------------Atagcac-----------------------ag----------------------------------------acacaca------caca-g---ccatacatatagacccc----ccccacccccactccacGGTAACAT------CCACT-GCGGCAATCGTCGTACA------ATATTGTAATTTACTTAATTTCGTACCGTATCGTATCGTTCAGAATACGCAAA-TTTGTT-A----AGGAAAAAAGAGgcgag---tgcaaaaaaaaaatt-------ggaagAAAACATTGTCCATG-CATTAGCTACa-----------t------gt---ctca------gtcccagtcgt--agtc---------------gtagttgt--tctttt-----tgttgctgttgcaagtg---------------------------ttgt---------tgtggttgttgctgt-------tatgaAAGGCGACTGCGCGGCggc------gtttgtttt-gttggtgctttgctt--gctttattttgca--------gtttttttcaTTGCTAcatttgatatgcaaatt s droWil2.CH963894 1318031 355 + 2843958 cgtcgtATGCGG--------CGTATGAGtaatcaataataattttatcgCCAGTTT----T-----------------CTAGCTTCAGCTCAAAGCTGAACTGCTGCAGCTC----------TAGCTTTA--------GCT------------------------------GCAAC---TT-----AAAGTC----------T---GTGTGGT---CGTCGGT---CGA--TCGCTGCTATaaagcatttaattttcatcaaATCGATTGCCATAATAATTTCACGCAAAT---------------------------ATAGCAC-----------------------AG----------------------------------------------------------A---C----------------------------------GACAAACACAA-----------------------------------CGATTGTAATTTAGTTAATT--------CGCCAGAGAGCTCAGAATacgcaga--------a------------a-a----------------aaaaaagt-------gaagaaaaacATTGTCTATG-CATT------------------T------GG---CT------------------T--ACAT---------------GCGGTTGT--TGTTGC----------------------------------------------------------------------------------------------GACTGCGCGGC---------GTCGGTTTG--------------TT----------------------------------GGCCACGTTTGATATGCAAATT s droVir3.scaffold_12875 7359856 442 + 20611582 CGTTATACGCGG--------CGTATGAGTAATCAATAATAATTTTATCGCCCGTTT----T-----------------CTAGT---------------------------------------CAGCCTGT--------GTG------------------------------GTCGA---CGCATTTAATTTT----------C---AT--------AATGTTTTAAGAC--GC--------------------------ACAATCGATTGCCATAATAATTTCACGCAAAT---------------------------ATAGCAC-----------------------AAAACGTCGCAAAATGGGGGTTACTGCTGCGGCCAGGGGGTAAATCGAA------TGCG-G---GTGCTGGGGCAAGGGGG------------------GAACACACAAG------CGGATCCCAACGACAATTTCAC-------ATATTGTAATTTAGTTAATT-----------CGCATCGTTCGGCGTACGCAAA-TTCGCC-A------------A------------------------------------------CATTGTCTATG-CATTAGCTACA-----------t------gt---cgtagttgttgttgttgttgt--tgtt---------------gtttgtgt--tgttgt-----tactcttgttg------------------------------------------------ttgttgctgttgttgtAACGTATCGAAGGCGACTGTGCGGC---------GTCTGTTGT---------------T----------------------------------GACTGCGTTTGATATGCAAATT s droMoj3.scaffold_6496 26154978 438 + 26866924 TTTCATACGCGG--------CGTATGAGTAATCAATAATAATTTTATCGCCCGTTT----T-----------------CCAGT---------------------------------------CGGCTTGT--------GTG------------------------------GTCGG---CGCATTTAATTTT----------C---AT--------AATGTAGCAAGAC--GC--------------------------ACAATCGATTGCCATAATAATTTCACGCATCT---------------------------CCAG--------------------------GGGAGGT------GTGGGTGTGGGTGTGAGGAGTGAGGAGTGAGGAGTGGGGACTTGGG-G---GTGTTGTTGTCAGAG------------------------ACACAAG------CGGAT-CCAGCGACAATTTCAC-------ATATTGTAATTTAGTTAATT-----------CGCATCGTTCGGCGTACGCGAA-TTCGCC-A------------A------------------------------------------CATTGTCTATG-CATTAGCGACA-----------t------gt---cgtagttgttgtttgtgttac--tgtt---------------gttattgt--tgttgt-----tcttgttgttg---------------------------------ttgt---------tcttgttgttgttgttgtGTCGCATTAAAGGCGACTGTGCGGC---------GTCTGTTGT---------------T----------------------------------GACTACGTTTGATATGCAAATT s droAlb1.JH854640 317365 428 + 406291 -GTtatacgctg--------cgtatgagcaatcaataataattttatcgCCCGTTT----T-----------------CTAGT---------------------------------------CAGCTTGT--------GTG------------------------------GTCGg---cgcatttaaattt----------c---at--------aatgttTTAAGAC--GC--------------------------ACAATCGATTGCCATAATAATTTCACGCAAAT---------------------------ATAGCACGAATT--------GGAACAGAGAGGAGTGCTAAAAGACGTGTGTGGGGGAGGCAA-----GAGCAGACCGAG------AGCG-A---G--------------------------------------ACACACG------CGGCT-CCAACGACAATTTCAC-------TTAttgtaatttagttaatt-----------CGCATCGTTCGGCGTACGCGAA-TTCACT-A------------A------------------------------------------CATTGTCTATG-CATTAGCGACA-----------t------gttggagttgttgctgttgtacttgt--tgct---------------ttaactgt--tgtggt-----tgctgttgttg------------------------------------------------ttgtggttgttgt-----cgtatcgaaggcgacgttgcggc---------gtctgttgt---------------t----------------------------------gACTGCGtttgatatgcaaatt s droGri2.scaffold_15245 910514 502 + 18325388 CGTTGTACGCTG--------CGTATGAGTAATCAATAATAATTTTATCGCCCGTTT----TTCTTTTTTGTTTTTTTGCTAGA---------------------------------------CAGCATGT--------GTG------------------------------GTCGG---CGCATTTAATTTT----------C---ATA-------AATGTTTTAAGAC--GC--------------------------ACAATCGATTGCCATAATAATTTCACGCAAAT---------------------------ATAGCACAAATCGTCCGACGGGTAGGGGAGGGGGTGTAGGAGGTTAGGCAGTGCTCAAGTGA--AGAGGGGAAAACGGG------TAGG-G---GTGAAGGGGGTGGGGAGT-----------------TGGCAGACAAG------CGGAT-TCAACGACAATTTCAC-------ATATTGTAATTTAGTTAATT-----------CGCATCGTTCGTCGTACGCAAA-TTCGCC-A------------A------------------------------------------CATTGTCTATG-CATTAGCTACA-----------T------GT---CGCAAAtgttgttgttgttgt--tgtt---------------gttattgt--tgttgt-----tactgttcttgttgttgctgttgctg------------------ttgt---------tgttgctgttgttgttgttTGGTATCGAAGGCGACTGTGCGGC---------GTCTGTTGT---------------T----------------------------------GACTGCGTTTGATATGCAAATT a score=80429.000000 s dm6.chr2R 24364245 8 + 25286936 GTGTGCTT s droSim1.chr2R 18702637 8 + 19596830 GTGTGCTT s droSec1.super_23 122395 8 + 989336 GTGTGCTT s droYak3.chr2R 20211916 8 + 21139217 GTGTGCTT s droEre2.scaffold_4845 21609750 8 + 22589142 GTGTGCTT s droBia2.KB462602 803239 8 + 3129309 ttgtGCTC s droSuz1.KI419649 12048433 8 - 14502029 ttgtgctt s droAna3.scaffold_13266 5715541 7 - 19884421 -AGTGCTT s droBip2.KB464407 1965533 7 + 2915140 -TGtgctt s droEug2.KB465067 606788 8 + 1515531 tcgTGCTT s droEle2.KB458573 528913 8 - 5320397 ttgtgctt s droKik2.KB459527 283376 8 - 1234237 ttgtGCTT s droTak2.KB461535 148241 8 - 669855 ttgtgctt s droRho2.KB449310 43016 8 - 65043 ttgtGCTT s droFic2.KB457177 87453 8 + 995874 ttgtgCTT s droPse3.chr3 1356191 7 - 19787792 -tgtgcaT s droPer1.super_34 545032 7 - 916997 -TGTGCAT s droMir2.chr3 1397327 7 - 20862834 -tgtgcaT s droWil2.CH963894 1318386 2 + 2843958 TT------ s droMoj3.scaffold_6496 26155416 7 + 26866924 -TCTGTTT s droGri2.scaffold_15245 911016 8 + 18325388 TTCTGTTT a score=67617.000000 s dm6.chr2R 24364253 6 + 25286936 TTACAA s droSim1.chr2R 18702645 6 + 19596830 TTACAA s droSec1.super_23 122403 6 + 989336 TTACAA s droYak3.chr2R 20211924 6 + 21139217 TTACAA s droEre2.scaffold_4845 21609758 6 + 22589142 TTACAA s droBia2.KB462602 803247 6 + 3129309 TTAGAA s droSuz1.KI419649 12048441 6 - 14502029 ttAGAA s droAna3.scaffold_13266 5715548 6 - 19884421 TTAGAA s droBip2.KB464407 1965540 6 + 2915140 tttgaa s droEug2.KB465067 606796 6 + 1515531 TTAGAA s droEle2.KB458573 528921 6 - 5320397 ttAGAA s droKik2.KB459527 283384 6 - 1234237 TTAGAA s droTak2.KB461535 148249 6 - 669855 ttAGAA s droRho2.KB449310 43024 6 - 65043 TTAGAA s droFic2.KB457177 87461 6 + 995874 TTAGAA s droPse3.chr3 1356198 6 - 19787792 TTAGAA s droPer1.super_34 545039 6 - 916997 TTAGAA s droMir2.chr3 1397334 6 - 20862834 TTAGAA s droMoj3.scaffold_6496 26155423 6 + 26866924 GCACaa a score=121482.000000 s dm6.chr2R 24364259 104 + 25286936 AGAGTCGCAGAATTAT--------CGTATCTGTCGACGgtc---gttgttgttgttg----ttgctgctgtcgctgttgtGGGAGCTTCG-------------------------------------------------------------AAGCGGGAGTTCCA---T-------------------------ATGGTAATTCC------------A------TA s droSim1.chr2R 18702651 107 + 19596830 AGAGTCGCAGAATTAT--------CGTATCTGTCGGCGgtcgttgttgttgttgttg----ctgctgctgtcgttgttgtGGGAGCTTCG-------------------------------------------------------------AAGCGGGAGTTCCA---T-------------------------ATGGTAATTCC------------A------TA s droSec1.super_23 122409 107 + 989336 AGAGTCGCAGAATTAT--------CGTATCTGTCGACGGTCGACgttgttgttgctg----ctgctgctgtcgttgttgtGGGAGCTTCG-------------------------------------------------------------AAGCGGGAGTTCCA---T-------------------------ATGGAAATTCC------------A------TA s droYak3.chr2R 20211930 95 + 21139217 AGAGACGCAGAATTAT--------CGTATCTGTCGAcgact---g---------ttg----ttgttgttgatgttgttttGGGAGCTTTG-------------------------------------------------------------AATCGGGGGTTCCA---T-------------------------ATGGTAATGCC------------A------CA s droEre2.scaffold_4845 21609764 104 + 22589142 GGAGACGCAGAATTAT--------CGTATCTGTCGACGgtc---gtcgttgtttttg----ttgttgttgttgttgttgtGGGAGCTTTG-------------------------------------------------------------AATCGGGGGTTCCA---T-------------------------ATGGTAATTGC------------A------CA s droBia2.KB462602 803253 178 + 3129309 AGAGACACAGAATTAT--------CGTATCTGTCG---------GT--------TTG----ccg--attgttgttgttgtaggaGCAACGAATCAGGGGTTGCGTATGGTAATTTCGCATGTATGTCTACCCGACTAGGAAAAGCCCAGGAAATCGTGTATTCAG---TGTTCCTAATTGTACTATTCAGCAAAACAgtattgtt------------ttt--tgta s droSuz1.KI419649 12048447 92 - 14502029 AGAGACACAGAATTAT--------CGTATCTGTCG---------GT--------TTG----gcg--attgttgttgttgtgggaGCTACG-------------------------------------------------------------AATCAGGGGTTGCG---T-------------------------ATGGTAATTTC------------ATA--TGTA s droAna3.scaffold_13266 5715554 76 - 19884421 AGAGAAACAGAATTGT--------CGTATCTGTTG---------GTGG------------------CTTGTTTTTGTTGCTGCCACCACT-------------------------------------------------------------GGGAGAGAAATACG-----------------------------AGGGT-------------------------AA s droBip2.KB464407 1965546 77 + 2915140 aaagaaacagaatTGT--------CGTATCTGGCG---------Gata------------------cttgtttttgttgctgggaCTACT-------------------------------------------------------------ACAAGAGAGATGTA---C-------------------------GGGGT-------------------------GA s droEug2.KB465067 606802 84 + 1515531 AGAGACACAGAATTAT--------CGTATCTGTCG---------g---------------------ctggctgttgttgtggGAGCTACG-------------------------------------------------------------AATCAGGGGTTGCA---T-------------------------ATGCTAATTTTCC---------GA------TA s droEle2.KB458573 528927 89 - 5320397 AGAGACACAGAATTAT--------CGTATCTGTCG----------------------------------GCAGTTGTTGTGGGAGCTAGG-------------------------------------------------------------AATCAGGGGTTGCA---T-------------------------ATGgaaatttttcttatatatgta------tg s droKik2.KB459527 283390 97 - 1234237 AGAGACACAGAATTAT--------CGTATCTG------------ACtctagttgttg----ttgttgttgctgatgttgtGGGAGCTATA-------------------------------------------------------------GAGCAGGGGCAACA---T-------------------------ATGGAAATTAG------------ATG----TA s droTak2.KB461535 148255 94 - 669855 AGAGACACAGAATTAT--------CGTATCTGTCG---------GT--------TTGgcgattgttgttgtttttgttgtgggAGCTACG-------------------------------------------------------------AATCAGGGGTTGCA---T-------------------------ATggtaatttt------------a------ta s droRho2.KB449310 43030 79 - 65043 AGAGACACAGAATTAT--------CGTATCTGTCG----------------------------------GCAGTTGTTGTGGGAGCTACG-------------------------------------------------------------AGGCAGGGGTTGCA---T-------------------------Atggaaattat------------ata----ta s droFic2.KB457177 87467 83 + 995874 AGAGACACAGAATTAT--------CGTATCTGTCG----------------------------------GCAGTTGTTGTAGGAGGAACG-------------------------------------------------------------AAGTAGGGGTTGCA---T-------------------------GTGGAAACTTt------------acgtgtgta s droPse3.chr3 1356204 52 - 19787792 AGAGACGCAGAATTAT--------CGTATCTG-----------------------------------------------------------------------------------------------------------------------AGGGGGAAATTATA---C-------------------------GCGTGTGTGCT-------------------CG s droPer1.super_34 545045 52 - 916997 AGAGACACAGAATTAT--------CGTATCTG-----------------------------------------------------------------------------------------------------------------------AGGGGGGAATTATA---C-------------------------GCGTGTGTGCT-------------------CG s droMir2.chr3 1397340 47 - 20862834 AGAGACACAGAATTAT--------CGTATCTG-----------------------------------------------------------------------------------------------------------------------AGGGGGAAATTaaa---c-------------------------gcgtgtgt------------------------ s droWil2.CH963894 1318388 117 + 2843958 -----CACAGAATTTTGTGGTTAgcttgttttttctctctctctctctctcttttttctcGTATTATTTGTCTGTACTTTTTATGCTGTT-------------------------------------------------------------ATTGTGTTGTTACAGCGC-------------------------atggaaattat------------a------ta a score=135968.000000 s dm6.chr2R 24364363 47 + 25286936 TATCCAGTCGA--------GCAG-GCACAGCTCAGAGAATTGG--ATAT-TAAGTGGCT- s droSim1.chr2R 18702758 46 + 19596830 CATCCACTCGA--------GCAG-GCACAGCTCAGGGAATTGG--ATAT-TTAGTGGC-- s droSec1.super_23 122516 46 + 989336 TATCCACTCGA--------GCAG-GCACAGCTCAGGGAATTGG--ATAT-TTAGTGGC-- s droYak3.chr2R 20212025 46 + 21139217 CATCTACTCGA--------GCGG-GCTAAGCCCAGAAAATCGG--ATAT-TTGGTGGT-- s droEre2.scaffold_4845 21609868 45 + 22589142 CATCTAC-CGA--------GCGG-GCAAAGCCCAGAAAATCGG--ATAT-TTAGTGGC-- s droBia2.KB462602 803431 43 + 3129309 tctGTTCT-----------TTAT-GAActgttgaaaaaatatt--gtct-TTCAAATT-- s droSuz1.KI419649 12048539 46 - 14502029 TATCTACCCGA--------CTAG-GAAAAGCCCAGGAAATCGT--ATAT-TTAGAGTG-- s droAna3.scaffold_13266 5715630 41 - 19884421 AACCCATTAAA--------ATAATATAGAGAGCAGGGGTTAGA--GGTG-GT-------- s droBip2.KB464407 1965623 47 + 2915140 Aacccattaaa--------ataatatagagAACAAGGGAGAGA--GTCG-TTAGTCTC-- s droEug2.KB465067 606886 46 + 1515531 TATATGCTCGA--------CTAG-GAAAAGCCCaggaaattgt--ttat-ttagtgGC-- s droEle2.KB458573 529016 46 - 5320397 tatgggCTAGA--------CTAG-GAAAAGCCCAGgaaattgt--atat-ttactGGG-- s droKik2.KB459527 283487 54 - 1234237 TATGCATTCGAggacaaacacaa-aaaaagcctaggaaattgt--atat-ttagtgGT-- s droTak2.KB461535 148349 46 - 669855 tatctgcCCGA--------CTAG-GAAAAGCCCAGGAAATTGA--ATGT-TTAGTGGG-- s droRho2.KB449310 43109 46 - 65043 tatgtactagA--------CTAG-GAAAAGCCCAGGAAATTGT--ATAT-TAAGTGGG-- s droFic2.KB457177 87550 47 + 995874 tgtgtgctcGA--------CTAG-GAAAAGCCCAGgaaattgt--gtgtgtttgcggg-- s droPse3.chr3 1356256 46 - 19787792 CGTGTGCTCGT--------AGAG-GAAAAGCCCAGAAAACTGC--ATAT-TTAGTGGG-- s droPer1.super_34 545097 46 - 916997 CGTGTGCTCGT--------AGAG-GAAAAGCCCAGAAAACTGC--ATAT-TTAGTGGG-- s droMir2.chr3 1397387 45 - 20862834 -gtgtgctcgt--------agAG-GAAAAGCCCAGAAAACTGA--ATAT-TTAGTGGG-- s droWil2.CH963894 1318505 28 + 2843958 tac----------------gcaa-----------gaaaattgt--attt-ttattgtg-- s droAlb1.JH854640 318970 48 + 406291 TAGTCAGTATT--------GCAA-GT-CAGCTAAGATGAATGTTAGTAT-GAAGTGCA-T a score=-42369.000000 s dm6.chr2R 24364410 8 + 25286936 TTAAAG-----TT s droSim1.chr2R 18702804 8 + 19596830 TTGAAG-----TT s droSec1.super_23 122562 8 + 989336 ATGAAG-----TT s droYak3.chr2R 20212071 8 + 21139217 CTAAAC-----tt s droEre2.scaffold_4845 21609913 8 + 22589142 CCAAAC-----TC s droBia2.KB462602 803474 8 + 3129309 TACAAT-----TA s droSuz1.KI419649 12048585 13 - 14502029 CCTAATTGTACTA s droAna3.scaffold_13266 5715671 8 - 19884421 CAAAAA-----AA s droBip2.KB464407 1965670 8 + 2915140 CCAAAA-----AC s droEle2.KB458573 529063 6 - 5320397 --TAAG-----TT s droKik2.KB459527 283542 8 - 1234237 AATAAT-----TG s droTak2.KB461535 148396 7 - 669855 -CTAAT-----TG s droRho2.KB449310 43155 8 - 65043 TTAAAT-----TG s droFic2.KB457177 87614 7 + 995874 TCAAAG-----T- s droPse3.chr3 1356304 7 - 19787792 AATAAT-----T- s droPer1.super_34 545145 7 - 916997 AATAAT-----T- s droMir2.chr3 1397434 7 - 20862834 AATAAT-----T- s droWil2.CH963894 1318534 7 + 2843958 -AACAT-----TG s droAlb1.JH854640 319018 6 + 406291 TTCGGC------- a score=-33539.000000 s dm6.chr2R 24364418 4 + 25286936 CACA-- s droSim1.chr2R 18702812 4 + 19596830 CACA-- s droSec1.super_23 122570 4 + 989336 CACA-- s droYak3.chr2R 20212079 4 + 21139217 caca-- s droEre2.scaffold_4845 21609921 4 + 22589142 CACA-- s droBia2.KB462602 803482 4 + 3129309 TTCA-- s droSuz1.KI419649 12048598 4 - 14502029 CTCA-- s droAna3.scaffold_13266 5715679 3 - 19884421 CGC--- s droBip2.KB464407 1965678 3 + 2915140 AGC--- s droKik2.KB459527 283550 4 - 1234237 CACA-- s droTak2.KB461535 148406 2 - 669855 CA---- s droRho2.KB449310 43163 4 - 65043 TACT-- s droFic2.KB457177 87623 2 + 995874 TA---- s droPse3.chr3 1356312 3 - 19787792 AAC--- s droPer1.super_34 545153 3 - 916997 AAC--- s droMir2.chr3 1397442 3 - 20862834 AAC--- s droWil2.CH963894 1318544 2 + 2843958 ca---- s droAlb1.JH854640 319024 4 + 406291 --CAAT a score=-7504.000000 s dm6.chr2R 24364422 2 + 25286936 TT s droSim1.chr2R 18702816 2 + 19596830 TT s droSec1.super_23 122574 2 + 989336 TT s droYak3.chr2R 20212083 2 + 21139217 tt s droEre2.scaffold_4845 21609925 2 + 22589142 TT s droBia2.KB462602 803486 2 + 3129309 GT s droSuz1.KI419649 12048602 2 - 14502029 GA s droAna3.scaffold_13266 5715682 2 - 19884421 TC s droBip2.KB464407 1965681 2 + 2915140 TC s droKik2.KB459527 283973 2 - 1234237 tt s droTak2.KB461535 148408 2 - 669855 TT s droRho2.KB449310 43167 2 - 65043 TC s droFic2.KB457177 87626 1 + 995874 T- s droPse3.chr3 1356315 1 - 19787792 -T s droPer1.super_34 545156 1 - 916997 -T s droMir2.chr3 1397445 1 - 20862834 -T s droWil2.CH963894 1318547 1 + 2843958 t- s droAlb1.JH854640 319028 2 + 406291 TT a score=10983.000000 s dm6.chr2R 24364424 2 + 25286936 TA s droSim1.chr2R 18702818 2 + 19596830 TA s droSec1.super_23 122576 2 + 989336 TA s droYak3.chr2R 20212085 2 + 21139217 ta s droEre2.scaffold_4845 21609927 2 + 22589142 TA s droBia2.KB462602 803488 2 + 3129309 AA s droSuz1.KI419649 12048604 2 - 14502029 AA s droAna3.scaffold_13266 5715684 2 - 19884421 TA s droBip2.KB464407 1965683 2 + 2915140 TA s droEle2.KB458573 529622 2 - 5320397 TA s droTak2.KB461535 148410 2 - 669855 CA s droRho2.KB449310 43169 2 - 65043 TC s droFic2.KB457177 87627 2 + 995874 TA s droPse3.chr3 1356317 2 - 19787792 CA s droPer1.super_34 545158 2 - 916997 CA s droMir2.chr3 1397447 2 - 20862834 CA s droWil2.CH963894 1318551 2 + 2843958 ta s droAlb1.JH854640 319030 2 + 406291 CA a score=-120493.000000 s dm6.chr2R 24364426 5 + 25286936 A---------GT-----------------------AT--- s droSim1.chr2R 18702820 5 + 19596830 A---------GT-----------------------AT--- s droSec1.super_23 122578 5 + 989336 A---------GT-----------------------AT--- s droYak3.chr2R 20212087 8 + 21139217 a---------at--------------------ttaat--- s droEre2.scaffold_4845 21609929 8 + 22589142 A---------GT--------------------TTAAT--- s droBia2.KB462602 803490 5 + 3129309 A---------CG-----------------------At--- s droSuz1.KI419649 12048606 14 - 14502029 AACTATATTgct-----------------------at--- s droAna3.scaffold_13266 5715686 11 - 19884421 G---------TTTTCCAACA-------------------- s droBip2.KB464407 1965685 3 + 2915140 A---------TT---------------------------- s droEle2.KB458573 529624 22 - 5320397 A---------GTGTTAAAGAAATTG------TTTGAT--- s droKik2.KB459527 283975 5 - 1234237 --------------------------------tttat--- s droRho2.KB449310 43171 5 - 65043 --------------------------------AGGAT--- s droFic2.KB457177 87629 3 + 995874 ----------------------------------GGT--- s droPse3.chr3 1356319 17 - 19787792 --------------------AAATGGTTCCCTGGGAT--- s droPer1.super_34 545160 17 - 916997 --------------------AAATGGTTCCCTGGGAT--- s droMir2.chr3 1397449 17 - 20862834 --------------------AAATGGTTCCCTGGGAT--- s droWil2.CH963894 1318553 5 + 2843958 --------------------------------tacat--- s droAlb1.JH854640 319032 5 + 406291 -----------------------------------ACTCA a score=-9230.000000 s dm6.chr2R 24364431 14 + 25286936 TTATAAAA------TTGATC s droSim1.chr2R 18702825 14 + 19596830 TTATAAAA------TTGATC s droSec1.super_23 122583 14 + 989336 TTATAAAA------TTGATC s droYak3.chr2R 20212097 14 + 21139217 ctataaAG------TCGATA s droEre2.scaffold_4845 21609937 6 + 22589142 --------------GCGATA s droBia2.KB462602 803497 20 + 3129309 ttttCAGACTTTTCTCAATC s droSuz1.KI419649 12048622 14 - 14502029 ttgtaaaa------ttaaac s droEle2.KB458573 529648 7 - 5320397 TTTCAAA------------- s droKik2.KB459527 283982 12 - 1234237 ttgcaaAA------ACGA-- s droRho2.KB449310 43593 14 - 65043 TTGTGCAA------ATGatc s droFic2.KB457177 87633 14 + 995874 TTGAAAAG------AAGACC s droPse3.chr3 1356342 14 - 19787792 ATATGGGG------GAAATC s droPer1.super_34 545183 14 - 916997 ATATGGGG------GAAATC s droMir2.chr3 1397472 14 - 20862834 ATATGGGG------GAAATC s droWil2.CH963894 1318558 14 + 2843958 atagaaaa------ataatt s droAlb1.JH854640 319037 12 + 406291 TTCCAAAA------ACAA-- a score=-36645.000000 s dm6.chr2R 24364445 11 + 25286936 AAAC--------TTTACTT---- s droSim1.chr2R 18702839 6 + 19596830 A-------------CACTT---- s droSec1.super_23 122597 6 + 989336 A-------------CACTT---- s droYak3.chr2R 20212111 6 + 21139217 G-------------CACCT---- s droEre2.scaffold_4845 21609943 6 + 22589142 A-------------CACTT---- s droBia2.KB462602 803517 11 + 3129309 AACT--------GTCActt---- s droSuz1.KI419649 12048636 11 - 14502029 atcT--------GTTGATT---- s droRho2.KB449310 43607 19 - 65043 gatttaaataaatgcattt---- s droFic2.KB457177 87647 9 + 995874 TAAA----------TGCTC---- s droPse3.chr3 1356356 11 - 19787792 GAAT--------TGCAATT---- s droPer1.super_34 545197 11 - 916997 GAAT--------TGCAATT---- s droMir2.chr3 1397486 11 - 20862834 GAAT--------TGCAATT---- s droWil2.CH963894 1318572 11 + 2843958 gaaC--------TCTGCCT---- s droGri2.scaffold_15245 911904 11 + 18325388 ------------AAAAACTATGC a score=-29158.000000 s dm6.chr2R 24364456 4 + 25286936 --CA-TC s droSim1.chr2R 18702845 4 + 19596830 --CA-TC s droSec1.super_23 122603 4 + 989336 --CA-TC s droYak3.chr2R 20212117 4 + 21139217 --TT-TT s droEre2.scaffold_4845 21609949 5 + 22589142 --TTCTT s droBia2.KB462602 803528 4 + 3129309 --aa-tc s droSuz1.KI419649 12048647 4 - 14502029 --TT-TC s droRho2.KB449310 43626 4 - 65043 --ta-tt s droFic2.KB457177 87656 2 + 995874 --TC--- s droPse3.chr3 1356367 4 - 19787792 --CA-AA s droPer1.super_34 545208 4 - 916997 --CA-AA s droMir2.chr3 1397497 4 - 20862834 --CA-AA s droAlb1.JH854640 319049 3 + 406291 -ATG--- s droGri2.scaffold_15245 911915 4 + 18325388 AATG--- a score=-110155.000000 s dm6.chr2R 24364460 16 + 25286936 CT--------------AGCCGATAAATACA s droSim1.chr2R 18702849 16 + 19596830 CT--------------AGTCGATAAATACA s droSec1.super_23 122607 16 + 989336 CT--------------AGCCGATAAATACA s droYak3.chr2R 20212121 25 + 21139217 CTGTGAAAT-----GAGGAGGATATCTACT s droEre2.scaffold_4845 21609954 25 + 22589142 CTGTGAAGG-----GCGGAGGAAAACTACT s droBia2.KB462602 803532 13 + 3129309 -----------------ataaataaatacc s droAna3.scaffold_13266 5715697 9 - 19884421 CT--------------GGTCCAT------- s droBip2.KB464407 1965688 8 + 2915140 -T--------------GGGCCAT------- s droEle2.KB458573 529655 28 - 5320397 --CTGATAgcttaaacaaatcaaaaaaaca s droKik2.KB459527 283994 9 - 1234237 ---------------------ATAAATTCA s droRho2.KB449310 43630 15 - 65043 ---------------ctaccaaaaactatt s droFic2.KB457177 87658 16 + 995874 ------------CTAGCGGCTCGAACTG-- s droPse3.chr3 1356371 16 - 19787792 --------------GCCATTGGAAAATGTC s droPer1.super_34 545212 16 - 916997 --------------GCCATTGGAAAATGTC s droMir2.chr3 1397501 16 - 20862834 --------------GCCATTGGAAAATGTC s droAlb1.JH854640 319052 14 + 406291 ----------GTTTAC--CATATAAA---- s droGri2.scaffold_15245 911919 16 + 18325388 ----------CTCAGCAGCAAATAAA---- a score=-47013.000000 s dm6.chr2R 24364476 4 + 25286936 ---ACA-T s droSim1.chr2R 18702865 4 + 19596830 ---ACA-G s droSec1.super_23 122623 4 + 989336 ---ACA-A s droYak3.chr2R 20212146 5 + 21139217 ---GCCTT s droEre2.scaffold_4845 21609979 4 + 22589142 ---TTC-T s droEle2.KB458573 529683 4 - 5320397 ---act-t s droKik2.KB459527 284005 2 - 1234237 ---AT--- s droRho2.KB449310 43650 2 - 65043 ---at--- s droFic2.KB457177 87676 2 + 995874 ---GC--- s droPse3.chr3 1356394 2 - 19787792 ---AT--- s droPer1.super_34 545235 2 - 916997 ---AT--- s droMir2.chr3 1397524 2 - 20862834 ---AT--- s droAlb1.JH854640 319066 4 + 406291 TACA---- s droGri2.scaffold_15245 911935 4 + 18325388 CGGT---- a score=-27070.000000 s dm6.chr2R 24364480 7 + 25286936 -TTGGAAG s droSim1.chr2R 18702870 7 + 19596830 -TGGAAGG s droSec1.super_23 122627 7 + 989336 -TGGAAAG s droYak3.chr2R 20212151 7 + 21139217 -CCTAATA s droEre2.scaffold_4845 21609983 7 + 22589142 -CCTAATA s droBia2.KB462602 803545 7 + 3129309 -taatATG s droSuz1.KI419649 12049034 7 - 14502029 -TGATAAG s droRho2.KB449310 43652 6 - 65043 --aaaatg s droFic2.KB457177 87679 6 + 995874 -TTAAAG- s droPse3.chr3 1356397 6 - 19787792 -CTGAAC- s droPer1.super_34 545238 6 - 916997 -CTGAAC- s droMir2.chr3 1397527 6 - 20862834 -CTGAAC- s droAlb1.JH854640 319070 7 + 406291 ATGGAAG- s droGri2.scaffold_15245 911939 7 + 18325388 TTGATCG- a score=-43076.000000 s dm6.chr2R 24364487 8 + 25286936 CTTC-------------------------------TCTA------ s droSim1.chr2R 18702877 8 + 19596830 CATT-------------------------------GATG------ s droSec1.super_23 122634 8 + 989336 CATT-------------------------------GATG------ s droEre2.scaffold_4845 21609990 7 + 22589142 CAAC-------------------------------TCT------- s droBia2.KB462602 803552 39 + 3129309 GTTTACATTTCATTGGAAAGTGGTTGATCAAGAAATCAG------ s droSuz1.KI419649 12049041 8 - 14502029 CTTT-------------------------------TCTG------ s droEug2.KB465067 607217 4 + 1515531 -----------------------------------TTTG------ s droPse3.chr3 1356403 3 - 19787792 ------------------------------------CCG------ s droPer1.super_34 545244 3 - 916997 ------------------------------------CCG------ s droMir2.chr3 1397533 3 - 20862834 ------------------------------------CCG------ s droAlb1.JH854640 319077 8 + 406291 -------------------------------------CGCTATCA s droGri2.scaffold_15245 911946 8 + 18325388 -------------------------------------CGTTCTCA a score=-98840.000000 s dm6.chr2R 24364495 2 + 25286936 G---------------------A s droSim1.chr2R 18702885 3 + 19596830 G--------------T------A s droSec1.super_23 122642 3 + 989336 G--------------T------A s droEre2.scaffold_4845 21609997 2 + 22589142 ---------------T------A s droBia2.KB462602 803591 3 + 3129309 A--------------G------A s droSuz1.KI419649 12049049 3 - 14502029 A--------------T------A s droEug2.KB465067 607221 9 + 1515531 G-----ACCT---TTT------a s droEle2.KB458573 529687 1 - 5320397 ----------------------a s droTak2.KB461535 148702 10 - 669855 -------CTTATCTGG------A s droRho2.KB449310 43659 6 - 65043 -----------cttTG------G s droFic2.KB457177 87685 3 + 995874 --------------TT------A s droPse3.chr3 1356406 17 - 19787792 AGGGTAGGCTTGGAAT------A s droPer1.super_34 545247 17 - 916997 AGGGTAGGCTTGGAAT------A s droMir2.chr3 1397536 23 - 20862834 AGGGTAGGCTTggaatgcataca s droVir3.scaffold_12875 7361468 2 + 20611582 -------GC-------------- s droAlb1.JH854640 319096 2 + 406291 -------GC-------------- s droGri2.scaffold_15245 911965 2 + 18325388 -------GC-------------- a score=-779810.000000 s dm6.chr2R 24364497 69 + 25286936 TTTACTTAAC---------------GTTTT---CCA--------GACTT-------TTG-------------------------------------CTTCCTGCTGCAGGGAACAC-----TTTTAGG-GGAAA---CCTGCGAGTG---C--------------------------- s droSim1.chr2R 18702888 74 + 19596830 CAAACCGACA---------------AGCTC---CCA--------GACTT-------TTGC------------AAA--------------------GCTTCCTGCTGCAGGGAACAG-----TTTAAAG-GGAAA---CCTGCGAGTG---C--------------------------- s droSec1.super_23 122645 74 + 989336 CAAACCGACA---------------AGCTT---CCA--------GACTT-------TTGC------------AAA--------------------ACTTCCTGCTGCAGGGAACAG-----TTTAAAG-GGAAA---CCTGCGAGTG---C--------------------------- s droYak3.chr2R 20212158 68 + 21139217 ---------------------------CTT---CTC--TGCTTTGATTT-------TAGC------------CAA--------------------ACTTCCCGCTGCAGGGAATGC-----TTTTTGG-GGAAA---CCAGCGTGtg---c--------------------------- s droEre2.scaffold_4845 21609999 77 + 22589142 GAAGCTGACA---------------AGCTT---CTC--TGGATTGACTT-------AA---------------CG--------------------TCCTTCCGCTGCTGGGAACAC-----TTTTCGG-GGAAA---CCTGCGTGTG---C--------------------------- s droBia2.KB462602 803594 94 + 3129309 AACATGTTCTTAAAA-------tagttgtt---tta--------aaattaatggagTTGC------------AGT------------------TAGCTTTCTTCTAGACGTGTTAT-ACAAGATTGTT-TATAG---TAGATGTTTT------------------------------- s droSuz1.KI419649 12049052 77 - 14502029 AATATATTCC---------------ACTTT---CTC--------CACTT-------TTGC------------AAT---------------------CTTTCTGCTGCAAGGAATAT--CTTTTTTGGC-TAAAA---CCTATGATTT--GC--------------------------- s droAna3.scaffold_13266 5715706 37 - 19884421 -----------------------------------------------------------------------------------------------CCCTGATTCTTGAAGACCGAT--AACTT--------------TTTACTTGTA---C--------------------------- s droBip2.KB464407 1965696 26 + 2915140 -----------------------------------------------------------------------------------------------CTTTTCGGCTTAA-------------CT--------------CCTAAGGGTA---C--------------------------- s droEug2.KB465067 607230 71 + 1515531 catatttccc---------------atttt---ctc--------caCTC-------CTTC------------GAA-----------------------TCCTGC-GAAGCAATCGT-----TTTTCGGCTGAAA---TCTGCTAGTt---c--------------------------- s droEle2.KB458573 529688 93 - 5320397 GAAAAGTGTA---------------GTTTTAGCCca--------aactt-------ttga------------tttattgattatt--ttcttatcCTTACCCTCTGCAA-----AT-----CATCCAG-GAAAATCTCTTTTGGGCG---C--------------------------- s droKik2.KB459527 284007 74 - 1234237 --------------------------CTCT---CCA-TTAGACCTACCT-------GTCC------------GAT---------------------CTTTTGGCAAAACGcaaggttttctttttcgg-cAAAA---TCTGTTCACG---c--------------------------- s droTak2.KB461535 148712 83 - 669855 TATACCGAAC---------------ATTTT---CCT-CTTATCCTATTT-------GAAT------------AAT---------------------CTTCCTGCTGAAAGGCAAAT--CATTTTTGGG-TGTAA---CCTACGATGG---C--------------------------- s droRho2.KB449310 43665 91 - 65043 TAAGAGTAGT---------------TTTTA---CTA--------AGGTT-------TGGC------------ATA------TACTGATAACTTCCACTTCCTTCTCCTTTGCAAAT-----CTTCCTG-GAAAATCTCTTTTGGGcg---c--------------------------- s droFic2.KB457177 87688 82 + 995874 AGCATCTCCTTTGAATTACTTTTGGGTTTC---CTA--------AGTTT-------TTTC------------CAA---------------------TTTACCTCGgca------aa-----tattcat-aaaaa---atcaTGTTGG---C--------------------------- s droPse3.chr3 1356423 90 - 19787792 TATATGAATCTGAACTTCACAGAATGTTTT---CTGACATGAATATCCT-------TTGTCGTCAA------ACT--------------------CCTGCCTGCCGC--------------TTTTCTC---------CTTTTGACTg--gc--------------------------- s droPer1.super_34 545264 90 - 916997 TATATGAATCTGAACTTCACAGAAAGTTTT---CTGACATGAATATCCT-------TTGTCGTCAA------ACT--------------------CCTGCCTGCCGC--------------TTTTCTC---------CTTTTGACTG--GC--------------------------- s droMir2.chr3 1397559 90 - 20862834 tatatgaatctGAACTTCACAGAAAGTTGT---CCGACATGAATATCCT-------TTAT------CGTCAAACT--------------------CCTGCCTGCCGC--------------TTTTCTC---------CTTTTGACTg--gc--------------------------- s droWil2.CH963894 1320654 55 + 2843958 -------------------------------------------tttgtt-------ttac------------gtt--------------------tttccttgttgttgttattgt-----tgttgtg---------acTGTCAAAGATAC--------------------------- s droVir3.scaffold_12875 7361470 57 + 20611582 -----------------------------------------------------------------------------------------------TTCATTTGTCGCA-------------TTTCATT-TG--G---CCATTTGCAG---CTGATTGACTGCGAACAACTGCAA---- s droAlb1.JH854640 319098 63 + 406291 -----------------------------------------------------------------------------------------------TTCATTTGTCGCA-------------TTTTTGC-TGAAG---CCATTTGCTG---CTGATTGACTACGAACAACTGCAGCTGT s droGri2.scaffold_15245 911967 58 + 18325388 -----------------------------------------------------------------------------------------------TTCATTTGTCGCA-------------TTTCATT-TG--G---CCATTTGCAG---CTGATTGACTGTGAACAACTGCGGC--- a score=459190.000000 s dm6.chr2R 24364566 26 + 25286936 CACAC--GGCGTATGCGCAATATTTGC----G s droSim1.chr2R 18702962 26 + 19596830 CACAC--GGCGTATGCGCAATATTTGC----G s droSec1.super_23 122719 26 + 989336 CACAC--GGCGTATGCGCAATATTTGC----G s droYak3.chr2R 20212226 26 + 21139217 cacac--ggcgtatgcgcaatatcTGC----G s droEre2.scaffold_4845 21610076 26 + 22589142 CACAC--GGCGAATGCGCAACATTTGC----G s droBia2.KB462602 803688 23 + 3129309 ---TC--GTGgaataagaaatattcaa----a s droSuz1.KI419649 12049129 26 - 14502029 CAccc--ggcgtatgcgcaatattttc----g s droAna3.scaffold_13266 5715743 26 - 19884421 CACAC--GGCGTATGCGCAATATTTGC----G s droBip2.KB464407 1965722 26 + 2915140 AAccc--ggcgtatacgcaatatttgC----G s droEug2.KB465067 607301 26 + 1515531 cacac--ggcgtatgcgcaacatTTGC----G s droEle2.KB458573 529781 26 - 5320397 CAccc--ggcgtatgcgcaatatttGC----G s droKik2.KB459527 284081 28 - 1234237 cacacggggcgtatgcgcaatatttgC----G s droTak2.KB461535 148795 26 - 669855 CAccc--ggcgtatgcgcaatatttgC----G s droRho2.KB449310 43756 26 - 65043 cacgc--ggcgtatgcgcaatatttGC----G s droFic2.KB457177 87775 26 + 995874 cacgg--ggcgtatgcgcaatatttgC----G s droPse3.chr3 1356513 26 - 19787792 cacat--ggcgtatgcgcaatatttgC----G s droPer1.super_34 545354 26 - 916997 CACAT--GGCGTATGCGCAATATTTGC----G s droMir2.chr3 1397649 26 - 20862834 cacat--ggcgtatgcgcaatatttgC----G s droWil2.CH963894 1320709 30 + 2843958 AACGc--ggcgtatgcgcaatatTTGCCACTG s droVir3.scaffold_12875 7361527 26 + 20611582 CACAC--GGCGTATGCGCAATATTTGC----A s droMoj3.scaffold_6496 26156495 26 + 26866924 CACAT--GGCGTATTCGCGATATTTGC----A s droAlb1.JH854640 319166 25 + 406291 cacac--ggcgtatgcgcaatatttgc----- s droGri2.scaffold_15245 912025 25 + 18325388 CACAT--GGCGTATGCGCAATATTTGC----- a score=-30151.000000 s dm6.chr2R 24364592 27 + 25286936 TAAG-AT-CTTTG-G-AAATC------AGC--AA-----------------------GCAGC s droSim1.chr2R 18702988 27 + 19596830 TAAG-AT-CTTTG-G-AAATC------AGC--AA-----------------------GCAGC s droSec1.super_23 122745 27 + 989336 TAAG-AT-CTTTG-G-AAATC------AGC--AA-----------------------GCAGC s droYak3.chr2R 20212252 27 + 21139217 TAAG-AT-CTTCT-G-AAATC------AGC--AA-----------------------GCAGC s droEre2.scaffold_4845 21610102 27 + 22589142 TAAG-AT-CTTTG-G-AAATC------AGC--AA-----------------------GCAGC s droBia2.KB462602 803711 51 + 3129309 tagt-GTGTTTTG-G-GAATA------CGt--tgacttaaataaaaaatattaaattgtggG s droSuz1.KI419649 12049155 29 - 14502029 taat-at-cttta-a-aaatc------agC--TGAC---------------------GTGGG s droAna3.scaffold_13266 5715769 27 - 19884421 TAAG-AT-CTGGG-G-AAATC------AGC--TT-----------------------CCAAC s droBip2.KB464407 1965748 27 + 2915140 TAAG-AT-CTGGA-G-AAATC------AGC--TT-----------------------CCAGC s droEug2.KB465067 607327 26 + 1515531 TAAG-AT-CTCGG-A-AAATC------AGC--CG-----------------------GCAG- s droEle2.KB458573 529807 26 - 5320397 TAAG-AT-CTTTG-A-AAATC------GGC--TG-----------------------GCAG- s droKik2.KB459527 284109 25 - 1234237 TAAG-AT-CTGAG-GTAAATC------AG----------------------------GCAGC s droTak2.KB461535 148821 27 - 669855 TAAG-AT-CTTTG-G-AAATC------AGC--TG-----------------------GCAGT s droRho2.KB449310 43782 27 - 65043 TAAG-AT-CTTTG-G-AAATC------GGC--TG-----------------------ACTGT s droFic2.KB457177 87801 27 + 995874 TAAG-AT-CTTTG-G-AAATC------ATC--TG-----------------------GCAGT s droPse3.chr3 1356539 30 - 19787792 TAAG-AT-CTCAGAG-AAATC------AGCGGTG-----------------------CCAGT s droPer1.super_34 545380 30 - 916997 TAAG-AT-CTCAGAG-AAATC------AGCGGTG-----------------------CCAGT s droMir2.chr3 1397675 30 - 20862834 TAAG-AT-CTCAGAG-AAATC------AGCGGTG-----------------------CCAGT s droWil2.CH963894 1320739 20 + 2843958 TAGGCAC-CTTTG-G-------------GC--tg-----------------------g--gc s droVir3.scaffold_12875 7361553 12 + 20611582 ---------------------------agcattg-----------------------gcaga s droAlb1.JH854640 319191 19 + 406291 ------------------AACACTG--CGCAGGG-----------------------GCAAA s droGri2.scaffold_15245 912050 22 + 18325388 -----------------aagcatcagcagcatca-----------------------gcagc a score=-344950.000000 s dm6.chr2R 24364619 41 + 25286936 TCGGA----TCgg-----------------------ctttggt----ttgggt-----------ttttggtttgggtt---ttggt s droSim1.chr2R 18703015 23 + 19596830 TCGGAC---TCGG-----------------------C----------------------------------TTTGGTT---TTGGT s droSec1.super_23 122772 41 + 989336 TCGGAC---TCGG-----------------------CTTTGGT----TTGGG------------CTTGGGTTTTGGTT---TTGGT s droYak3.chr2R 20212279 60 + 21139217 TCGAAC---TCGGACTCAGCTtagtttttg-----attttgat----tttggt-----------tgtggttttgggtt---ttggg s droEre2.scaffold_4845 21610129 35 + 22589142 TCGGAC---TCGG-----------------------CTTTGGT----TTTGG------------------CTTGGGCT---TTGGT s droBia2.KB462602 803762 34 + 3129309 GCGAACTGTTCGG------------------------TT---T----TTCGA------------------ATTTGGTT---TTCGT s droSuz1.KI419649 12049184 35 - 14502029 GCAAACGGTTCgg-----------------------ttt---t----ttcgg------------------ttttggtt---ttggc s droAna3.scaffold_13266 5715796 36 - 19884421 TT-------CCAG-----------------------CCTAGCCT---TTGAGG-----------CATACAGTTTG------CTGAG s droBip2.KB464407 1965775 11 + 2915140 TT-------CCAG----------------------------------TTGAG---------------------------------- s droEug2.KB465067 607353 24 + 1515531 ---------TGGG----------------------------------GCAAA----------------cagtttggtt---ttggg s droEle2.KB458573 529833 38 - 5320397 ---------TGGG----------------GCAAACACTTTGGC----TTgac-------------------ttggcttggcttggt s droKik2.KB459527 284134 6 - 1234237 ------------G--------------------------------------------------------------------TTCGT s droTak2.KB461535 148851 42 - 669855 GCAAACGGTTcgg-----------------------tttt--t----ttgggt-----------tttaggTTTTGGC----TTGGC s droRho2.KB449310 43812 19 - 65043 GCAAACGGTTTGG-----------------------------T--------------------------------------TTGTC s droFic2.KB457177 87828 7 + 995874 ---------TCGG-----------------------------C--------------------------------------TT--- s droPse3.chr3 1356569 6 - 19787792 ------------G--------------------------------------------------------------------GTGGC s droPer1.super_34 545410 6 - 916997 ------------G--------------------------------------------------------------------GTGGC s droMir2.chr3 1397705 6 - 20862834 ------------G--------------------------------------------------------------------GTGGC s droWil2.CH963894 1320759 6 + 2843958 ------------g--------------------------------------------------------------------atggc s droVir3.scaffold_12875 7361567 40 + 20611582 -------------------------------------------gcagcccagcagcagcagcggcggcggcggcggca---gaggc s droAlb1.JH854640 319212 40 + 406291 -------------------------------------------CTGGTCCAGCCTAAGCGTTAGCGTCGGCTTCAACT---tcggc a score=1480766.000000 s dm6.chr2R 24364660 133 + 25286936 t--tggC----------TGCCACTTACG-----CGACAACGCCTTGACATGCCCACACGTCC-----GGC------------------------GACAACAACA----------------------------------C------CCAACAACTTTGCAACATGCCACAGCA--TTTTGGAATG------------------------------------------------------------------------TTT----TGCCGCTGTTGC---------------------------------------------------------------------------------------------------GG----------------CGTGTGAGAAT-----------------TCACGA----GTG- s droSim1.chr2R 18703038 133 + 19596830 T--TGGC----------TGCCACTTACG-----CGACAACGCCTTGACATGCCCACACGTCC-----GGC------------------------GACAACAACA----------------------------------C------CCAACAAGTTTGCAACATGCCACAGCA--TTTTGGAATG------------------------------------------------------------------------TTT----TGCCGCTGTTGC---------------------------------------------------------------------------------------------------GG----------------CGTGTGAGAAT-----------------TCACGA----GTG- s droSec1.super_23 122813 133 + 989336 T--TGGC----------TGCCACTTACG-----CGACAACGCCTTGACATGCCCACACGTCC-----GGC------------------------GACAACAACA----------------------------------C------CCAACAAGCATGCAACATGCCACAGCA--TTTTGGAATG------------------------------------------------------------------------TTT----TGCCGCTGTTGC---------------------------------------------------------------------------------------------------GG----------------CGTGTGAGAAT-----------------TCACGA----GTG- s droYak3.chr2R 20212339 133 + 21139217 t--tggC----------TGCCACTTACG-----CGACAACGCCTTGACATGCCCACACGTCC-----GGC------------------------GAGGACAACA----------------------------------C------CCAACAACTTTGCAACATGCCACAGCA--TTTTGGAATG------------------------------------------------------------------------TTG----TGCCGCTGTTGC---------------------------------------------------------------------------------------------------GG----------------CGTGTGAGAAT-----------------TCACGA----GTG- s droEre2.scaffold_4845 21610164 133 + 22589142 T--TGGC----------TGCCACTTACG-----CGACAACGCCTTGACATGCCCACACGTCC-----GGC------------------------GACAACAACA----------------------------------C------CCAACAACTTTGCAACATGCCACAGCA--TTTTGGAATG------------------------------------------------------------------------CTT----GGCCGCTGTTGC---------------------------------------------------------------------------------------------------GG----------------CGTGTGAGAAT-----------------TCACGA----GTG- s droBia2.KB462602 803796 141 + 3129309 T--TGGC----------TGCCACTTACGCCTTGCGACAACGCCTTGACATGCCCACACGTCC-----GGC------------------------GACAACAACA----------------------------------C------CCAACAACTTTGCAACATGCCACAAGAC-TTTTGGAATT------------------------------------------------------------------------TCT----CGATGCTGTAGC---------------------------------------------------------------------------------------------------GG----------------CGTGTGAGAAT-----------------CCACAA--GTGTG- s droSuz1.KI419649 12049219 139 - 14502029 t--tggC----------TGCCACTTACGCCTTACGACAACGCCTTGACATGCCCACACGTCC-----GGC------------------------GACAACAACA----------------------------------C------CCAACAACTTTGCAACATGCCACAAGAC-TTTTGGAATT------------------------------------------------------------------------TCT----CGATGCTGTTGC---------------------------------------------------------------------------------------------------GG----------------CGTGTGAGAAT-----------------TCACAA----GTG- s droAna3.scaffold_13266 5715832 131 - 19884421 T--TTGC----------TGCCACTTACG-----CGACAACGCCTTGACATGCCCACACGTTC-----GAC------------------------GACAACAACA----------------------------------C------CCAACAACTTTGCAACATGCCACAACAC-TTTTGGAATT------------------------------------------------------------------------TTT----CACCGCTGTTGT---------------------------------------------------------------------------------------------------GG----------------CGTGTGAGAAT----------------CTTACA--------- s droBip2.KB464407 1965786 132 + 2915140 -----AC----------TGCCACTTACG-----CGACAACGCCTTGACATGCCCACACGTTC-----GAC------------------------GACAACAACA----------------------------------C------CCAACAACTTTGCAACATGCCACAAcac-ttttggaatt------------------------------------------------------------------------ttt----cgtcGCTGTTGT---------------------------------------------------------------------------------------------------GG----------------CGTGTGAGAAT----------------tttacat----gtg- s droEug2.KB465067 607377 134 + 1515531 t--tgGC----------TGCCACTTACG-----CGACAACGCCTTGACATGCCCACACGTCC-----GGC------------------------GACAACAACA----------------------------------C------CCAACAACTTTGCAACATGCCACAACGC-TTTTGGAATT------------------------------------------------------------------------TTT----CGCCGCTGTTGC---------------------------------------------------------------------------------------------------GG----------------CGTGTGAGAAT-----------------TCACAA----GTG- s droEle2.KB458573 529871 134 - 5320397 t--TGGC----------TGCCACTTACG-----CGACAACGCCTTGACATGCCCACACGTCC-----GGC------------------------GACAACAACA----------------------------------C------CCAACAACTTTGCAACATGCCACCAAAC-TTTTGGAATT------------------------------------------------------------------------TTT----CGTCGCTGTTGC---------------------------------------------------------------------------------------------------GG----------------CGTGTGAGAAT-----------------Tcacaa----gtg- s droKik2.KB459527 284140 135 - 1234237 T--CGAC----------TGCCACTTACG-----CGACAACGCCTTGACATGCCCACACGTCC-----GGC------------------------GACAACAACA----------------------------------C------CCAACAACTTTGCAACATGCCACAACAC-TTTTGGAATT------------------------------------------------------------------------TTT----CGCTGCTGTTGC---------------------------------------------------------------------------------------------------GG----------------CGTGTGAGAAT----------------TCCACAG----GTG- s droTak2.KB461535 148893 139 - 669855 T--CGGC----------TGCCACTTACGCCTTACGACAACGCCTTGACATGCCCACACGTCC-----GGC------------------------GACAACAACA----------------------------------C------CCAACAACTTTGCAACATGCCACAAGAC-TTTTGGAATT------------------------------------------------------------------------TCT----CGATGCTGTTGC---------------------------------------------------------------------------------------------------GG----------------CGTGTGAGAAT-----------------TCACAA----ctg- s droRho2.KB449310 43831 134 - 65043 T--TGGC----------TGCCACTTACG-----CGACAACGCCTTGACATGCCCACACGTCC-----GGC------------------------GACAACAACA----------------------------------C------CCAACAACTTTGCAACATGCCACCAAAC-TTTTGGAATT------------------------------------------------------------------------TTT----CGCCGCTGTTGC---------------------------------------------------------------------------------------------------GT----------------CGTGTGAGAAT-----------------TCAcaa----gtg- s droFic2.KB457177 87835 138 + 995874 T--TCGC----------CGCCACTTACG-----CGACAACGCCTTGACATGCCCACACGTCC-----GGC------------------------GACAACAACA----------------------------------G------CCAACAACTTTGCAACATGCCACCAAAC-TTTTGGAATT------------------------------------------------------------------------TTT----CGCCGATGTTGC---------------------------------------------------------------------------------------------------GG----------------CGTGTGAGAAT-----------------TCACAaccgtgtg- s droPse3.chr3 1356575 146 - 19787792 TACCGCC----------TGCCACTT-CG-----CGACAACGCCTTGACATGCCCACACGTCC-----AGT------------------------GACAACAACA----------------------------------C------CCAACAACTCTGCAACatgccacaaaac-ttttggTATT------------------------------------------------------------------------TCT-----GCTACTGTCGC---------------------------------------------------------------------------------------------------TGCTTGCCGCAGCGCTCCCGTGTGAGAAT-----------------GCCCC--------- s droPer1.super_34 545416 146 - 916997 TACCGCC----------TGCCACTT-CG-----CGACAACGCCTTGACATGCCCACACGTCC-----AGT------------------------GACAACAACA----------------------------------C------CCAACAACTCTGCAACATGCCACAAAAC-TTTTGGTATT------------------------------------------------------------------------TCT-----GCTACTGTCGC---------------------------------------------------------------------------------------------------TGCTTGCCGCAGCGCTCCCGTGTGAGAAT-----------------GCCCC--------- s droMir2.chr3 1397711 146 - 20862834 TACCGGC----------TGCCACTT-TG-----CGACAACGCCTTGACATGCCCACACGTCC-----AGT------------------------GACAACAACA----------------------------------C------CCAACAACTCTGCAacatgccacaaaac-ttttggTATT------------------------------------------------------------------------TCT-----GCTACTGTCGC---------------------------------------------------------------------------------------------------TGCTTGCCGCAGCGCTCCCGTGTGAGAAT-----------------GCCCC--------- s droWil2.CH963894 1320765 218 + 2843958 g--------------------------a-----tggcgatgccTTGACATGCCCACACGTCCAGcatggc------------------------aacaaaaacaaca------------------------------cc------cCAACAACTTTGCAACATGCCACAAAAC-ttttggaatttatgttgcgccttctcttgttttgtattttgttatttgttttttctgtttttttttttttcttgttttcttcttt----ttcttttatatc---------------------------------------------------------------------------------------------------gG----------------CGTGTGAgaatttcttttgaaatgcAATTTACGC----GTG- s droVir3.scaffold_12875 7361615 211 + 20611582 ---tgac----------tgcCACTTACG-----CGAC---GCCTTGACATGCCCACACgt-------agc------------------------aacaacaacaacatcagcagcagcagcagcggcagcaacaacACC------CCAACAACTTTGCAACATGCCACGAAACTTTTTGGAATT------------------------------------------------------------------------TATGTTGCGCCGCTGTTGT-------------------CTTTTTTT--CTCTTCGTT----------------------------TGTTTTTCAATTTTTT------CGCTCCCGAGCGG----------------CGTGTGAGAAT-----------------TTCTT-----TTGA s droMoj3.scaffold_6496 26156577 205 + 26866924 --CTGAG----------TGCCACTTACG-----CGAC---GCCTTGACATGCCCACACGT-------AGC------------------------AACAACAACAGCAGCAG-----------------------------------CAACAACTTTGCAACATGCCACGAAACTTTTTGGAATT------------------------------------------------------------------------TATGCTGCGCCGCTTTTTTTTATACATTTGCTTCTCAATTTTTTCT--CTCTTTGTCTCCA-----------------------GTGCTTTTCATCTCTTT--------TTAATGGGCGG----------------CGTGTGAGAAT-----------------TTCTT-----TTGA s droAlb1.JH854640 319259 216 + 406291 --tcgacATCGGCGACTTGCCACTTTCG-----CGAC---GCCTTGACATGCCCACACGT-------agca-----------------------aacaacacaggcagcagcagcaacaactgcagcaacagcaacctcaaacaacgaacaactttgcaacaTGCCACGAAACTTTTTGGAATT------------------------------------------------------------------------TATGTAGCAGCGCGTTATT------------Tgaccaattttattt---------------------------------------tattttt-----------------ttaacggGCGG----------------CGTGTGagaat-----------------ttctt-----ttga s droGri2.scaffold_15245 912127 288 + 18325388 --ctgac----------tgccacttacg-----cgac---gccttgacatgcccacacgt-------agcaacaacaacagcaacaacaacagcaacaacaacagcaacagctgcagcagcagcagcagcaacaacaCC------CCAACAACTTTGCAACATGCCACGAAACTTTTTGGAATT------------------------------------------------------------------------TATGTTGCGCCGCTTTTTT---CCCCTTTTTTTTTGTACTTTTTCTTGCTGTTTGTTTTTGCGCTCTCTCGAttttttttttttgtttttttcgtttttttgtttttGTTGAACGGGCGG----------------CGTGTGAGAAT-----------------TTCTT-----TTGA a score=-162939.000000 s dm6.chr2R 24364793 10 + 25286936 ---------------------GATGTCCC---------------------TC s droSim1.chr2R 18703171 10 + 19596830 ---------------------GATGTCCC---------------------TC s droSec1.super_23 122946 10 + 989336 ---------------------GATGTCCC---------------------TC s droYak3.chr2R 20212472 8 + 21139217 -----------------------TGTCCC---------------------GC s droEre2.scaffold_4845 21610297 8 + 22589142 -----------------------TGCCCC---------------------TC s droBia2.KB462602 803937 12 + 3129309 ---------------------TGTGCTCC-------------------TGTC s droSuz1.KI419649 12049358 12 - 14502029 ---------------------TGTGCTCC-------------------TGTC s droAna3.scaffold_13266 5715963 2 - 19884421 --------------------------------------------------TG s droBip2.KB464407 1965918 6 + 2915140 ---------------------tgtg-------------------------tg s droEug2.KB465067 607511 16 + 1515531 ---------------------TGTGTCCGAGAG---------------TGTC s droEle2.KB458573 530005 23 - 5320397 ---------------------tgtgtgtgtgtgt--gtttg------ctgtC s droKik2.KB459527 284281 25 - 1234237 ---------------------TGGGTCCAAGACCAGGTCCA------GGTTC s droTak2.KB461535 149032 26 - 669855 ---------------------tgtgtgtttctgtgtgtCCTC-----CTGTC s droRho2.KB449310 43965 31 - 65043 ---------------------tgtgtatgtgtgtgtgtgcctgtttGTTGAC s droFic2.KB457177 87973 13 + 995874 ---------------------tgtgtctg------------------ttggC s droVir3.scaffold_12875 7361826 25 + 20611582 AATGCAGC---GTGTGCAACGCGTGTTT------------------------ s droMoj3.scaffold_6496 26156782 25 + 26866924 AATGCAGC---GAATGCAACGCGTGCTT------------------------ s droAlb1.JH854640 319475 23 + 406291 aatgcAGC-----ATGCAACCCGTGTTT------------------------ s droGri2.scaffold_15245 912415 28 + 18325388 AATGCAGCAGCGTGTGCAACGCGTGTTT------------------------ a score=-83891.000000 s dm6.chr2R 24364803 35 + 25286936 AGTGGATGC---------GGGGGA---------AACC------------CTTAATAAGGGAG-CCC---------------------------------------------------- s droSim1.chr2R 18703181 34 + 19596830 CGTGGATGC----------GGGGA---------AACC------------CTTAATAAGGGAG-CCC---------------------------------------------------- s droSec1.super_23 122956 35 + 989336 CGTGGATGC---------GGGGGA---------AACC------------CTTAATAAGGGAG-CCC---------------------------------------------------- s droYak3.chr2R 20212480 35 + 21139217 CGTCGGTGT---------GGGGGC---------AACC------------CTTAATAAGGGAG-CCC---------------------------------------------------- s droEre2.scaffold_4845 21610305 35 + 22589142 CGTGGATGT---------GGGGGA---------AGCC------------CTTAATAAGGGAG-CCC---------------------------------------------------- s droBia2.KB462602 803949 35 + 3129309 CGCGAGTGT---------GGGGAA---------GACC------------TTTAATAAGGGAT-CCG---------------------------------------------------- s droSuz1.KI419649 12049370 37 - 14502029 CGCGAGTGTA--------AGGGAA---------AACC------------TTTAATAAGGGATACCG---------------------------------------------------- s droAna3.scaffold_13266 5715965 35 - 19884421 TGTGTGTGT---------GTTTAA---------AAAC------------TTTAATAAGGGAG-CCT---------------------------------------------------- s droBip2.KB464407 1965924 35 + 2915140 tgtgtgtgt---------gtttaa---------aaac------------tttaataaggGAG-CTT---------------------------------------------------- s droEug2.KB465067 607527 36 + 1515531 CGTGAGTGCG--------GAGGAA---------AACC------------TTTAATAAGGGAG-CCC---------------------------------------------------- s droEle2.KB458573 530028 36 - 5320397 CGCGAATGTA--------AAGGAA---------AGCC------------TTTAATAAGGGAG-CCC---------------------------------------------------- s droKik2.KB459527 284306 46 - 1234237 AGTTCCAGT----------AGAGA---------AgccttccttcttttttttaataagggAG-CCA---------------------------------------------------- s droTak2.KB461535 149058 39 - 669855 CGCGAGTGTATAT-----GGGAAA---------AACC------------TTTAATAAGGGAG-Ccc---------------------------------------------------- s droRho2.KB449310 43996 36 - 65043 CGCGAGTGTA--------AAGGAA---------AACC------------TTTAATAAGGGAG-TCC---------------------------------------------------- s droFic2.KB457177 87986 36 + 995874 CGCGAGTGTA--------AAGGAA---------AGCC------------TTTAATAAGGGAG-CCG---------------------------------------------------- s droPse3.chr3 1356843 29 - 19787792 -----------actggaAGATGGG---------GAGC------------ATTGA----GGAG-CCA---------------------------------------------------- s droPer1.super_34 545724 29 - 916997 -----------ACTGGAAGATGGG---------GAGC------------ATTGA----GGAG-CCA---------------------------------------------------- s droMir2.chr3 1397975 28 - 20862834 -----------actggaaGATGGG---------GAGC------------ATTGA----GG-G-CCA---------------------------------------------------- s droVir3.scaffold_12875 7361851 56 + 20611582 -----------------AGAGACA-GCATCG--AACC------------TTTAATAA----g-ctgct-gctgctg-ctgctg-----------------------ctgcCCAGCGTT s droMoj3.scaffold_6496 26156807 79 + 26866924 -----------------AGAGACA-GCATCG--GACC------------TTTAATAA----G-CTGCT-CCTGCTA-CTCCTGCTCGGCTTGGCTTGGCCTGGCCCCTGCCCAGCGCT s droAlb1.JH854640 319498 58 + 406291 -----------------AGAGACA-GCATTG--AACC------------CTTAATAA----G-CTGCTGGCTACTGACTTCTG----------------------GCTGCCCagtg-t s droGri2.scaffold_15245 912446 36 + 18325388 -----------------AGAGACAGGCATCGAAAACC------------TTTAATAA----G-CCACC------------------------------------------------TT a score=1791904.000000 s dm6.chr2R 24364838 90 + 25286936 AAATTTATAATGTGGCACGCAATTAATTCACTG---C------CA-----AA---------G---CTGCCAAGCG------------AAGGCGCAAAAATTATCA-CACCATTCAAATGACGCTCACGA s droSim1.chr2R 18703215 90 + 19596830 AAATTTATAATGTGGCACGCAATTAATTCACTG---C------CA-----AA---------G---CTGCCAAGCG------------AAGGCGCAAAAATTATCA-CACCATTCAAATGACGCTCACGA s droSec1.super_23 122991 90 + 989336 AAATTTATAATGTGGCACGCAATTAATTCACTG---C------CA-----AA---------G---CTGCCAAGCG------------AAGGCGCAAAAATTATCA-CACCATTCAAATGACGCTCACGA s droYak3.chr2R 20212515 96 + 21139217 AAATTTATAATGTGGCACGCAATTAATTCACTG---CCACAGGCA-----AA---------G---CTGCCAAACG------------AAGGCGCAAAAATTATCA-CACCATTCAAATGACGCTCAcga s droEre2.scaffold_4845 21610340 90 + 22589142 AAATTTATAATGTGGCACGCAATTAATTCACTG---C------CA-----AA---------G---CTGCCAAGCG------------AAGGCGCAAAAATTATCA-CACCATTCAAATGACGCTCACGA s droBia2.KB462602 803984 89 + 3129309 AAATTTATAATGTGGCACGCAATTAATTCACTG---C------CA-----AA---------G---CTGCCAGGCG------------AAGGCGCAAAAATTATCA-CACCATTCAAATGACGCTCACG- s droSuz1.KI419649 12049407 90 - 14502029 AAATTTATAATGTGGCACGCAATTAATTCACTG---C------CA-----AA---------G---CTGCCAAGCG------------AAGGCGCAAAAATTATCA-CACCATTCAAATGACGCTCACGA s droAna3.scaffold_13266 5716001 93 - 19884421 AAATTTATAATGTGGCACGCAATTAATTCACTGCCAC------CA-----AA---------G---CTGCCACCAG------------AAGGCGCAAAAATTATCA-CACCATTCAAATGACGCTCACGA s droBip2.KB464407 1965960 90 + 2915140 AAATTTATAATGTGGCACGCAATTAATTCACTG---C------CA-----AA---------G---CTGCCACAAG------------AAGGCGCAAAAATTATCA-CACCATTCAAATGACGCTCACGA s droEug2.KB465067 607563 90 + 1515531 AAATTTATAATGTGGCACGCAATTAATTCACTG---C------CA-----AA---------G---CTGCCAAGCG------------AAGGCGCAAAAATTATCA-CACCATTCAAATGACGCTCACGA s droEle2.KB458573 530065 90 - 5320397 AAATTTATAATGTGGCACGCAATTAATTCACTG---C------CA-----AA---------G---CTGCCAAACG------------AAGGCGCAAAAATTATCA-CACCATTCAAAGGACGCTCACGa s droKik2.KB459527 284352 95 - 1234237 AAATTTATAATGTGGCACGCAATTAATTCACTG---C------CACAGAGCA---------G---CTGCCAAGCG------------AAGGCGCAAAAATTATCA-CACCATTCAAATGACGCTCACGA s droTak2.KB461535 149098 93 - 669855 aaatttataatgtgGCACGCAATTAATTCACTG---C------CA-----AA------GCTG---CTGCCAAACG------------AAGGCGCAAAAATTATCA-CACCATTCAAATGACGCTCACGA s droRho2.KB449310 44033 90 - 65043 AAATTTATAATGTGGCACGCAATTAATTCACTG---C------CA-----AA---------G---CTGCCAACCA------------AAGGCGCAAAAATTATCA-CACCATTCAAATGACGCTCACGA s droFic2.KB457177 88023 90 + 995874 AAATTTATAATGTGGCACGCAATTAATTCACTG---C------CA-----CA---------G---CTGCCACACG------------AAGGCGCAACAATTATCA-CACCATTCAAATGACGCTCACga s droPse3.chr3 1356873 90 - 19787792 AAATGTATAATGTGGCACGCAATTAATTCACTG---C------CA-----AA---------G---CTGCCAAACG------------GAGGCGCAAAAATTATCA-CACCATTCAAATGACGCTCACGA s droPer1.super_34 545754 90 - 916997 AAATTTATAATGTGGCACGCAATTAATTCACTG---C------CA-----AA---------G---CTGCCAAACG------------GAGGCGCAAAAATTATCA-CACCATTCAAATGACGCTCAcga s droMir2.chr3 1398004 90 - 20862834 AAATTTATAATGTGGCACGCAATTAATTCACTG---C------CA-----AA---------G---CTGCCAAACG------------GAGGCGCAAAAATTATCA-CACCATTCAAATGACGCTCACGA s droWil2.CH963894 1321045 99 + 2843958 AAATTGATAATGTGGCACGCAATTAATTCACTG---G------CA-----AACAACTGGCAA---CTGACTGGCG------------AAGGCGCAAAAATTATCA-CACCATTCAAATGACGCTCACGA s droVir3.scaffold_12875 7361907 102 + 20611582 AAATTTATAATGTGGCACGCAATTAATTCACTG---C------CA-----AA---------G---CTGCCAAGCAGACGGCAGCCAAAAGGCGCAAAAATTATCA-CACCATTCAAATGACGCTCACGA s droMoj3.scaffold_6496 26156886 98 + 26866924 CAATTTATAATGTTGTGCGCAATTACTTCACTG---C------CA-----AA---------G---CTGCCAAACAGCTG---GCCAAAAGGCG-AAAAATTATCA-CACCATTCAAATGACGCTCACGA s droAlb1.JH854640 319556 99 + 406291 atatttataatgtggCACGCAATTAATTCACTG---C------CA-----CA---------GCAACTGCCACATGC------AACAGAAGGCGCAAAAATTATCA-CACCATTCAAATGACGCTCACGA s droGri2.scaffold_15245 912482 88 + 18325388 AAATTTATAATGTGGCACGCAATTAATTCACTG---C------CA-----AA---------G---CTGCCACGGGCTTG--------------CAAAAATTATCGCCACCATTCAAATGACGCTCAAA- a score=-25813.000000 s dm6.chr2R 24364928 8 + 25286936 AT----GT-T----TTT s droSim1.chr2R 18703305 8 + 19596830 AT----GT-T----TTT s droSec1.super_23 123081 8 + 989336 AT----GT-T----TTT s droYak3.chr2R 20212611 8 + 21139217 at----gt-t----ttt s droEre2.scaffold_4845 21610430 8 + 22589142 AT----GT-T----TTT s droBia2.KB462602 804073 7 + 3129309 AT----GT-T----TT- s droSuz1.KI419649 12049497 7 - 14502029 AT----GT-T----TT- s droAna3.scaffold_13266 5716094 8 - 19884421 AT----TT-T----TGT s droBip2.KB464407 1966050 8 + 2915140 AT----TT-T----GTT s droEug2.KB465067 607653 9 + 1515531 AT----GTGT----TTt s droEle2.KB458573 530155 8 - 5320397 at----gt-t----ttt s droKik2.KB459527 284447 12 - 1234237 AT----GT-TACCCTTT s droTak2.KB461535 149191 6 - 669855 AT----GT-T----T-- s droRho2.KB449310 44123 8 - 65043 AT----gt-g----ttt s droFic2.KB457177 88113 8 + 995874 at----gt-g----ttt s droPse3.chr3 1356963 10 - 19787792 ATtcgggc-t----t-- s droPer1.super_34 545844 10 - 916997 attcgggc-t----t-- s droMir2.chr3 1398094 10 - 20862834 ATTttggt-t----t-- s droWil2.CH963894 1321144 2 + 2843958 TG--------------- s droVir3.scaffold_12875 7362019 8 + 20611582 AT----GT-T----TGT s droMoj3.scaffold_6496 26156995 8 + 26866924 AT----GT-T----TCc s droGri2.scaffold_15245 912570 7 + 18325388 AT----GT-T----TT- a score=-130878.000000 s dm6.chr2R 24364936 16 + 25286936 CGAGCCGGACT---------------------TGCGG------- s droSim1.chr2R 18703313 24 + 19596830 CGAGCCGGACTT-------------GCGGAGCTGCGG------- s droSec1.super_23 123089 16 + 989336 CGAGCCGGACT---------------------TGCGG------- s droYak3.chr2R 20212619 18 + 21139217 t--------gtt-----------ttttcgagTGGCGA------- s droEre2.scaffold_4845 21610438 32 + 22589142 CGAGCCGCAGTT-----GCGGAGCTGCCGAGCGGCAG------- s droAna3.scaffold_13266 5716102 28 - 19884421 AGTTTCGGGATT---------GGAATTGGGTTTGGGG------- s droBip2.KB464407 1966058 12 + 2915140 TGT-------------------------AGTTTGGGG------- s droEug2.KB465067 607662 8 + 1515531 cgagct-----------------------------gg------- s droEle2.KB458573 530163 35 - 5320397 cgtttttcgtttt--tttctttttgcccaTGTTGCGG------- s droKik2.KB459527 284459 9 - 1234237 TGGG----------------------------TGGGG------- s droFic2.KB457177 88121 25 + 995874 ------------tgtttttcgttttttcttttggtgg------- s droPse3.chr3 1356973 15 - 19787792 ----------------------gggcttgggcttggg------- s droPer1.super_34 545854 15 - 916997 ----------------------gggcttgggcttggg------- s droMir2.chr3 1398104 15 - 20862834 ----------------------gggcttgggcttggg------- s droWil2.CH963894 1321146 8 + 2843958 -----------------------------CGATGCAA------- s droVir3.scaffold_12875 7362027 7 + 20611582 ----------------------------------CGAATCG--- s droMoj3.scaffold_6496 26157003 10 + 26866924 ----------------------------------cgacttgtcg a score=-237140.000000 s dm6.chr2R 24364952 88 + 25286936 AGCTGG-----TGGGATTGGCTGGCCACC---------------AGCGA-------CTT------GCAACATGCAAC------------------AA-----------CTG---------GTGGCA------------------------------------------AGCAA-AG----TCGACACATTTTGTTT-GTT--------------CCGA-----ACC s droSim1.chr2R 18703337 88 + 19596830 AGCTGG-----TGGGATTGGCTGGCCACC---------------AGCGA-------CTT------GCCACATGCAAC------------------AA-----------CTG---------GTGGCA------------------------------------------AGCAA-AG----TCGACACATTTTGTTT-GTT--------------CCGA-----ACC s droSec1.super_23 123105 88 + 989336 AGCTGG-----TGGGATTGGCTGGCCACC---------------AGCGA-------CTT------GCCACATGCAAC------------------AA-----------CTG---------GTGGCA------------------------------------------AGCAA-AG----TCGACACATTTTGTTT-GTT--------------CCGA-----ACC s droYak3.chr2R 20212637 92 + 21139217 ATGTTG-----CGAGATTGGCTGGCCACCG-----------GCGAGCGA-------ctt------gcaacatgcaac------------------aa-----------CTG---------GTGGCA------------------------------------------AGCAA-AG----TCgacacattttgttt-gtt--------------ccgA-----ACC s droEre2.scaffold_4845 21610470 88 + 22589142 AACTGG-----TGGGATTGGCTGGCCACC---------------AGCGA-------CTT------GCAGCATGCAAC------------------AA-----------CTG---------GTGGCA------------------------------------------AGCAA-AG----TCGACACATTTTGTTT-GTT--------------CCGA-----ACC s droBia2.KB462602 804080 87 + 3129309 ---------------------TGGGCACC---------------GACAA-------CTT------GCCACATGCAACTCAAGAGCCGAACAACTGAA-----------CCC---------CTGGCA---------------------------------------------AA-AG----CCGacacattttgttt-gtt--------------cCGA-----ACC s droSuz1.KI419649 12049504 86 - 14502029 ---------------------TGGCCACC---------------GGCAA-------CTT------GCCACATGCAAC----AAACTGAACAACTGAA-----------CTG---------GTGGCA------------------------------------------ACCAA-AG----CCGACACATTTTGTTT-GTT--------------CCGA-----ACC s droAna3.scaffold_13266 5716130 91 - 19884421 AAAGGA---ATAGGGATGGGATGGT-------------------------------ATG------GCCACTGGTGGC------------------AAGTTAG-----TCGG---------CTAACT------------------------------------------GGCAG-AGCATCTCGACACATTTTGTTT-GTT--------------CCGA-----ACC s droBip2.KB464407 1966070 105 + 2915140 AAAGGA---ATAGGGATGGAATGGCCACC---------------GGCCAACGGTCACCG------GCGACTGGTGGC------------------AACTTG-------CTG---------GTAACT------------------------------------------GGCAG-AGACTCTCGACACATTTTGTTT-GTT--------------CCGA-----ACC s droEug2.KB465067 607670 88 + 1515531 agctgg-----agggATTGGCCGGCCACC---------------AGCGA-------CTT------GCAACATGCGGC------------------AA-----------CAA---------CTGGCA------------------------------------------ACCAA-AG----TCGACACATTTTGTTT-GTT--------------CCGA-----ACC s droEle2.KB458573 530198 82 - 5320397 T----------AAGGATTGAATGGCCACCGTG-------CAACGTGCAA-------CTT------GCAACATGCAAC------------------AA-----------CTG---------CT----------------------------------------------------AG----TCgacacattttgttt-gtt--------------ccGA-----ACC s droKik2.KB459527 284468 97 - 1234237 GGAGGG---CCTTGGATTGAATGGCCACCAGGA----GCCAACAGCCAA-------CTT------GCAACATGC---------------------AA-----------CTG---------GCA------------------------------------------------AG-AG----TCGACACATTTTGTTT-GTG--------------CCAAACCGTACC s droTak2.KB461535 149197 97 - 669855 ---------------------TGGCCACC---------------GGCAA-------CTT------GCCACATGCAAC------------------AAGCAAGAAGCTCAGG---------CTGGCA------------------------------------------ACCAA-AG----CCGacacattttgttt-gtttgttcctAACCGAACCGA-----AGC s droRho2.KB449310 44923 86 - 65043 agCGGG-----AAGGATTGAATGGCCACC--------AGCAACGTGCAA-------CTT------GCAACATGCAAC------------------AA-----------CTG---------CT----------------------------------------------------AG----TCgacacattttgttt-gtt--------------ccGA-----ACC s droFic2.KB457177 88149 106 + 995874 ATCGGA-----AAGGATTGAATGGCCACCGGCGGGCTGGCCgccagcaa-------ctt------gcaacatgcaac------------------at-----------gca---------acagcaac----------------------------------------agcagcag----tcgacacattttgttt-gtt--------------ccGA-----ACC s droPse3.chr3 1356988 76 - 19787792 ---------tttgggtttgggtggCAA-----------------GACCA-------GCT------AGAGGAGTCGTC------------------AC-----------CCG---------ACagtt--------------------------------------------ccg-at----ccgatccgatccgttt-------------------cgt-----tcc s droPer1.super_34 545871 80 - 916997 ---tggt--tttgggtttgggtGGCAA-----------------GACCA-------GCT------AGAGGAGTCGTC------------------AC-----------CCG---------ACAGTT--------------------------------------------CCG-AT----CCGATGCGATCCGTTT-------------------CGT-----TCC s droMir2.chr3 1398121 85 - 20862834 ---tggc--ttTGAGTTTGGGTGGCAA-----------------GACCA-------GCT------AGAGGAGTCGTC------------------AC-----------CCG---------ACAGtt--------------------------------------------ccg-at----ccgatgcgatccgtttcgtt--------------ccgt-----tcc s droWil2.CH963894 1321154 97 + 2843958 ------TGCGATGAGACTGTGTGTTTATC---------------TTCTC-------CTTTTGGCGGCGGCATTTAAC------------------AA-----------GCT---------CTGGTC------------------------------------------GGCTG--G----TCGGCA-GGCTTGCTG-GCT--------GGCTAGTCGG-----ATC s droVir3.scaffold_12875 7362034 42 + 20611582 --------------------------------------------AGcca-------gtt------gcccagttgccc------------------gg-----------ttg---------ccaattgcccagttgTC----------------------------------------------------------------------------------------- s droMoj3.scaffold_6496 26157013 86 + 26866924 ----------------------------------------acttgtcca-------att------gtccgactgtcc------------------ga-----------ctgtccgatggtccgattgtccaattgtccgacCGCCTAGTTGCCGCCCCGTTTGCTATG---------------------------------------------------------- s droGri2.scaffold_15245 912577 18 + 18325388 --------------------------------------------------------GTC------GCCCAGTTGT--------------------GT-----------TTG------------------------------------------------------------------------------------------------------------------- a score=4178404.000000 s dm6.chr2R 24365040 672 + 25286936 GTTCTCTTTGGCGGCAA-ACATTTAACAAGCATCGC-------CTGTCC-GC---------------------------TGG-CCG-----------------AG-GATGCCACCTAGAAAGC-TCACGCTAGGCGTCCAATTGGCTG--------------GA-------------------------GTTGCCGCCGATCATGGTCATGCCACATGGTGCCCACCGTCCA-----Ttgccttg-c----gcccaatgactggtgactagtgcctagtgccgaa---tgccACC-AA---------GTGG--ACAATG-CCCG---------GGTC------------------TTCG--GCC------GGTGGTCCTTTGTCTC---------------GGGAGC-----------------GC--TC---CTTGCC----------------GCCTGTCAGTGCTAATTTG-------------TTGCT-------GCTCGTGCAG-----------------------------------------------------TGCCACT------AAAAATATAGC-----CATAAATGCTGATGGGCAGGGAGGAT--------------GGAGGA------------GCTGCTCCG----CTGGTCGAGG----GAGGAGAAATCTGCATGTCCTTAATGCCGGCAACGTGCGAGTTTTACAAATTACGA---AATG---------------------------AG-------CA--------------------TCCA-----------------------------------------GGCAGTC----GCG--------------------G-TCCACT--------CTTTTTCCCACGTCTCATTAAAATTGCAGTTTAAATT-CAAGA------------------------------------TG--CTG--------------------------------------------------------CC----------TCTG----TTCTTTTA----CTTTCTATC--------ATCGTCATCGAGTCACCGAGTCAACGAGGCAGC-----------------------------------------GGTGCAGAGATGC------GA-CCAAGACGACGTC-CCATCGTCATTATTGTCAACTC--TCAACGA-GTTGCCTTGCCAATCG--TCTGT-----CGT--------------CTGTC------------------CCGGCTATCTT-------------TCTGCCTGC---------------------------------------CGTTT---CTAGATTGAT-GTCTCTGCAGTCGG s droSim1.chr2R 18703425 665 + 19596830 GTTCTCTTTGGCGGCAA-ACATTTAACAAGCATCGC-------CTGTCC-GC---------------------------TGG-CCG-----------------AG-GATGCCACCTAGAAAGC-TCACGCTAGGCGTCCAATTGGCTG--------------GA-------------------------GTTGCCGCCGATCATGGTCATGCCACATGGTGCCCGCCGTCCA-----CTGCCTTG-C----GCCCAATGACTGGTGACTAGTGCCTAGTGCCCAA---TGCCACC-AA---------GTGG--ACAATG-CCCG---------GGTC------------------TTCG--GCC------GGTGGTCCTTTGTCTC---------------GGGAGC-----------------GC--TC---CTTGCC----------------GCCTGTCAGTGCTAATTTG-------------TTGCT-------GCTCGTGCAG-----------------------------------------------------TGCCACT------AAAAATATAGC-----CATAAATGCTGATGGGCAGGGAGGAT--------------GGAGGA------------GCTGCTCCG----CTGGTCGAGG------GGAGAAATCTGCATGTCCTTAATGCCGGCAACGTGCGAGTTTTACAAATTACAA---AATA---------------------------AG-------CA--------------------TCCA-----------------------------------------GGCAGTC----GCG--------------------G-TCCACT--------CTTTTTCCCACGTCTCATTAAAATTGCAGTTTAAATT-CAAGA------------------------------------TG--CTG--------------------------------------------------------CC----------TCTG----TTCTTTTA----CTTTCTATC--------ATCGTCATCGAGTCACCGAGTAAACGAGGCAGC-----------------------------------------GGTGCAGAGATGC------GA-CCAAGACGACGTC-CCATCGTCATTATTGTCAACTC--TCAACGA-G-----TTGCCAATCG--TCTGT-----CGT--------------CTGTC------------------CCGGCTATCTT-------------TCTGCCTGC---------------------------------------CGTTT---CTAGATTGAT-GTCTCTGCAGTCGG s droSec1.super_23 123193 665 + 989336 GTTCTCTTTGGCGGCAA-ACATTTAACAAGCATCGC-------CTGTCC-GC---------------------------TGG-CCG-----------------AG-GATGCCACCTAGAAAGC-TCACGCTAGGCGTCCAATTGGCTG--------------GA-------------------------GTTGCCGCCGATCATGGTCATGCCACATGGTGCCCACCGTCCA-----CTGCCTTG-C----GCCCAATGACTGGTGACTAGTGCCTAGTTCCCAA---TGCCACC-AA---------GTGG--ACAATG-CCCG---------GGTC------------------TTCG--GCC------GGTGGTCCTTTGTCTC---------------GGGAGC-----------------TC--TC---CTTGCC----------------GCCTGTCAGTGCTAATTTG-------------TTGCT-------GCTCGTGCAG-----------------------------------------------------TGTCACT------AAAAATATAGC-----CATAAATGCTGATGGGCAGGGAGGAT--------------GGAGGA------------GCTGCTCCG----CTGGTCGAGG------GGAGAAATCTGCATGTCCTTAATGCCGGCAACGTGCGAGTTTTACAAATTACGA---AATG---------------------------AG-------CA--------------------TCCA-----------------------------------------GGCAGTC----GCG--------------------G-TCCACT--------CTTTTTCCCACGTCTCATTAAAATTGCAGTTTAAATT-CAAGA------------------------------------TG--CTG--------------------------------------------------------CC----------TCTG----TTCTTTTA----CTTTCTATC--------ATCGTCATCGAGTCACCGAGTCAACGAGGCAGC-----------------------------------------GGTGCAGAGATGC------GA-CCAAGACGACGTC-CCATCGTCATTATTGTCAACTC--TCAACGA-G-----TTGCCAATCG--TCTGT-----CGT--------------CTGTC------------------CCGGCTATCTT-------------TCTGCCTGC---------------------------------------CGTTT---CTAGATTGAT-GTCTCTGCAGTCGG s droYak3.chr2R 20212729 724 + 21139217 GTTCTCTTTGGCGGCAA-ACATTTAACAAGCATCGC-------CTGTCC-GC---------------------------TGG-CCG-----------------AG-GATGCCACCTAGAAAGC-TCACGCTAGGCGTCCAATTGGCTG--------------CA-------------------------GTTGCCGCCGATCATGGTCATGCCACATGGTGCCCACCGTCCA-----CTGCCTTG-C----GCCCAATGACTGGTGACTAGTGGCTGG----------TGCCACC-AA---------GTGG--ACAATG-CCCG---------GGTC------------------TTCG--GCC------GGTGGTCCTTTGTCTT---------------GGAAGC-----------------GC--TC---CTTGCC------------GCCTGCCTGTCAGTGCTAATTTG-------------TTGCT-------GCTCGTGCAG-----------------------------------------------------TGCCACT------AAAAATATAGC-----CATAAATGCTGATCGCCAGGGA------------------GGAGGC-------------------------------------------AGAAATCTGCATGTCCTTAATGCCGGCAACGTGCGAGTTTTACAAATTACGA---AATG---------------------------AG-------CA--------------------GTCGA--GCAGTT----GAGCATTCGAGCAGCC------------AGGAGTC----GCA--------------------G-TCCACTCGTTTCCACTTTTTCCCACGTCTCATTAAAATTGCAGTTTAAATT-CAAGA------------------------------------TG--CTG--------------------------------------------------------CC----------TCTG----TTCTTTTA----CTTTCTATC--------ATCGTCATCGAGTCATCCAGTCACCGAGTTACCCAGCTACCGAGGCAGCGGTGCAGGGATGTAAAGATGCAGGAGATGCAGAGATGC------GAGCCAAGACGACGTC-CCATCGTCATTATTGTCAACTC--TCAACGA-G-----TTGCCAATCG--TCTGT-----CGTCCGTCTGCTGTCCCCTGTC------------------CCGGCTATCTT-------------TCTGCCTGC---------------------------------------CGTTT---CTAGATTGAT-GTCTCTGCAGTCGG s droEre2.scaffold_4845 21610558 662 + 22589142 GTTCTCTTTGGCGGCAA-ACATTTAACAAGCATCGC-------CTGTCC-GC---------------------------TGG-CCG-----------------AG-GATGCCACCTAGAAAGC-TCACGCTAGGCGTCCAATTGGCTG--------------GA-------------------------GTTGCCGCCGATCATGGTCATGCCACATGGTGCCCGCCGTCCA-----CTGACTGG------------TGACTAGTGCCTGCTGCCTGG----------TGCCACC-AA---------GTGG--ACAATG-CACG---------GGTC------------------TTCG--GCC------GGTGGTCCTTTGTCTC---------------GGGAGC-----------------GC--TC---CTTGCC----------------GCCTGTCAGTGCTAATTTG-------------TTGCT-------GCTCGTGCAG-----------------------------------------------------TGCCACT------AAAAATATAGC-----CATAAATGCTGATCGGCAGGGA------------------GGAGGA------------GCAGCTCCG----CCGCTCGGG-------GGAGAAATCTGCATGTCCTTAATGCCGGCAACGTGCGAGTTTTACAAATTACGA---AATG---------------------------AG-------CC------------------------------------------------TGGAT------------GGCAGTC----GCA--------------------G-TCCACT--------CTTTTTCCCACGTCTCATTAAAATTGCAGTTTAAATT-CAAGA------------------------------------TG--CTG--------------------------------------------------------CC----------TCTG----TTCTTTTA----CTTTCTATC--------ATCgtcatcgagtcaccgagtcaccgagtcacc-----------------------------------------gagGCAGAGATGC------GAGCCAAGACGACGTC-CCATCGTCATTATTGTCAACTC--TCAACGA-G-----TTGCCAATCG--TCTGC-----CGTCTGTCCTTTGTCTTCTGTC------------------CCGGCTATCTT-------------TCTGCCTGC---------------------------------------CGTTT---CTAGATTGAT-GTCTCTGCAGTCGG s droBia2.KB462602 804167 622 + 3129309 GTTCTCTTTGGCGGCAA-ACATTTAACAACCATCGG-------CTGTCC-GC---------------------------TGCACCG-----------------AG-GATGCCACCTAGAAAGC-TCACGCTAGGCGTCCAATTGGCTG--------------GA-------------------------GCTGCCGCCGATCATGGTCATGCCACATGG------------------CCACATGG-T----GCCTACTGCCTAGTGGCTAGTGTCCAGTGTCCAG---TGCCACC-AA---------GTGG--ACAATG-CCCA---------GGCT------------------CTCG--GCCCGTGGTGGTGGTCCTTTGTCTC---------------GGGAGC-----------------GC--TC---CTTGCC----------------GCCTGTCAGTGCTAATTTG-------------TTGCT-------GCTCGTGCAG-------CC----GCGAAGGGGGCACTCGA-------------CTCCCTTGCAGGCCACT------AAAAATATAGC-----CATAAATGCTGATCAATATGGTGG----------------GACAGG------------ACAG-------------------------GGAGAAATCTGCATGTCCTTAATGCCGGCAACGTGCGAGTTTTACAAATTACGA---AATG---------------------------AG-------CA--------------------GCCC-----------------------------------------GGCAT-----------------------------G-TCCGCT--------CTTTTTCCCACGTCTCATTAAAATTGCAGTTAAAATG-CAAGA------------------------------------TG--CTG--------------------------------------------------------CC----------TCTG----TTCTTTTA----CTTTCTATC--------ATCGC---------------------------------------------------------------------GA------------------A-CGAAGACGACGTC-CCATCGTCATTATTGTCAACTC--TCAACGA-G-----TTGCCAATCG--ACTGT----------------------CTGT-------------------CCGGCTATCTT-------------TCTGCCTGC---------------------------------------CGTTT---CTAGATTGAT-GTCTCTGcagtcag s droSuz1.KI419649 12049590 624 - 14502029 GTTCTCTTTGGCGGCAA-ACATTTAACAAGCATCGG-------CTGTCC-GC---------------------------TGGACCG-----------------AG-GATGCCACCTAGAAAGC-TCACGCTAGGCGTCCAATTGGCTG--------------GA-------------------------GTTGCCGCCGATCATGGTCATGCCACATGG------------------CCAAATGG-----------CCACATGGTGCCTAGTGCCTGGTGTCCAG---TGCCACC-AA---------GTGG--ACAATG-CCCA---------GGCT------------------TTTG--GCCTGTGGTGGTGGTCCTTTGTCTC---------------GGGAGC-----------------AC--TC---CTTGCC----------------GCCTGTCAGTGCTAATTTG-------------TTGCT-------GCTCGTGCAG-------CC----GAGAAGGGGGAACTCGAACGAGATCC----CCCTCTGCCATTCCACT------AAAAATATAGC-----CATAAATGCTGATCAATATGGTGG----------------GACAGG------------ACAG-------------------------AGAGAAATCTGCATGTCCTTAATGCCGGCAACGTGCGAGTTTTACAAATTACGA---AATG---------------------------AG-------CA--------------------GACC-----------------------------------------GGCAT-----------------------------C-TCCACT--------CTTTTTCCCACGTCTCATTAAAATTGCAGTTAAAATG-CAAGA------------------------------------TG--CTG--------------------------------------------------------CC----------TCTG----TTCTTTTA----CTTTCTATC--------ATCGG---------------------------------------------------------------------GA------------------A-CGAAGACGACGTC-CCATCGTCATTATTGTCAACTC--TCAACGA-G-----TTGCCAATCG--ACTGT----------------------CTGT-------------------CCGGCTATCTT-------------TCTGCCTGC---------------------------------------CGTTT---CTAGATTGAT-GTCTCTGCAGTCA- s droAna3.scaffold_13266 5716221 725 - 19884421 GTTCTCTTTGGCGGCAA-ACATTTAACAAGCTCAGC-------CTGTCC-GC---------------------------TGGGCCG-----------------AG-GATGCCACCTAGAAAGC-TCACGCTAGGCGTCCAATTGGCTA--------------GA-------------------------ATCGCCGCCGATCATGGTCATGCCACGTTG------------------CCACATGG-C--C-GGCCA-----------------CATGG----------TGCCACCAAA---------GCGGACACAATG-GCCA-CACCGGACAGTGGG--CAAGCCATGCCATGCCAA--GCC------GGTGGTCTTTTGTCTCT-------------CGGAAGCGAGAGA-----TCCCGAGC--TC---CTTGGC---------CCTGTTAGCCTGTCAGTGCTAATTTG-------------TTACT-------GCTCGTGCAG------------------------GCTC-------------------------TGCCACT------AAAAATATAGC-----CATAAATGCTGATCAATAAAACGCGGTGGCCGGCGGAAGAGAAGGG------------A----------------------------GGAGAAATCTGCATGTCCTTAATGCCGGCAACGTGCGAGTTTTACAAATTACGA-GCAACG---------------------------AGCTCTGGTCA---------------------CCGA--AAGGATGGGAGGACAGCCTCCACTCTGGCTCTGACTCTGGCCGTG----GCA--------------------G-ACGG----------CTTTTTCCCACGTCTCATTAAAATTGCAGTTAAAATG-CAAGAGCAG------------------------------GCCA--CTG---------CCACTACCAT-------------------------------------CCAAAGATCGTTTCTG----TTCTTTTA----CTTTCTATC--------ATCGTCATCGAGTCAGC---------------------------------------------------------GAGGC--AGACGC------GAACGAAGACGACATC-CCATCGTCATTATTGTCAACTC--TCAACGA-G-----TTGCCAATCG--T--------------------------CTGTC------------------CCGGCTATCTT-------------TCTGCCTGC---------------------------------------CGTTT---CTAGATTGAT-GTCTCTGcagtcag s droBip2.KB464407 1966175 688 + 2915140 GTTCTCTTTGGCGGCAA-ACATTTAACAAGCTCGGC-------CTGTCC-GC---------------------------TGGGCCG-----------------AG-GATGCCACCTAGAAAGC-TCACGCTAGGCGTCCAATTGGCTA--------------GA-------------------------ATCGCCGCCGATCATGGTCATGCGACATTG------------------CCACATGG-C--CGGGCCA-----------------CATGG----------TGCCACCAAA---------GCGG--ACAATG-GCCA-------GTAGTG-----------CGGCAGGCCAG--GCC------GGTGGTCTTTTGTCTCT-------------TGGAAGCGAGATCTCGCTTCCCGAGC--TCCCTCCTGTA---------TCTGGTTGCCTGTCAGTGCTAATTTG-------------TTACT-------GCTCGTGCTG------------------------GCTC-------------------------TGCCACT------AAAAATATAGC-----CATAAATGCTGATCAATAAAACGCGCTACC----------GAAGGG------------A-----------------------------GAGAAATCTGCATGTCCTTAATGCCGGCAACGTGCGAGTTTTACAAATTACGA-GCAACG---------------------------AG--CTGGCAA--------------------GCCCG--AAGGAT-GGAGGACAGCCAGAAGGAT-GCCCTG-----GGCCGTG----GCA--------------------G-ACGA----------CTTTTTCCCACGTCTCATTAAAATTGCAGTTAAAATG-CAAGAGCAG------------------------------GCCA--CTG--------------------------------------------------------CCAGAGATCGTTTCTG----TTCTTTTA----CTTTCTATC--------ATCGTCATCGAGTCAGC---------------------------------------------------------GATGC--AGACGC------GAACGAAGACGACATC-CCATCGTCATTATTGTCAACTC--TCAACGA-G-----TTGCCAATCG--T--------------------------CTGTC------------------CCGGCTATCTT-------------TCTGCCTGC---------------------------------------CGTTT---CTAGATTGAT-GTCTCTGCAGTCAG s droEug2.KB465067 607758 714 + 1515531 GTTCTCTTTGGCGGCAA-ACATTTAACAAGCATCGC-------CTGTCC-GT---------------------------TGGGCCG-----------------AG-GATGCCACCTAGAAAGC-TCACGCTAGGCGTCCAATTGGCTG--------------GA-------------------------GTTGCCGCCGATCATGGTCATGCCACATGG----------CCAAATGGCCACATGG-t----gcctactgcctactgcctactgcctag----------tgccACC-AA---------GTGG--ACAATG-CTCA---------GGC-------------------TTTG--GCC------GGTGGTCCTTTGTCTC---------------GGGAGC-----------------GT--TC---CTTGCC----------------GCCTGTCAGTGCTAATTTG-------------TTGCT-------GCTCGTGCAG-------CC---AGTGTAGGCCCCTTTTCCACTTCCCCC--TGTCCCTTCCTCGAACACT------AAAAATATAGC-----CATAAATGCTGATCAATATGGAGG----------------GACtgg------------acaaggaca----aggacagGG-------AGAGAAATCTGCATGTCCTTAATGCTGGCAACGTGCGAGTTTTACAAATTACCA---AATG---------------------------AG-------CA--------------------GGAggctgtggcagtggcagtggcggtggcggt------------ggcagtT----GCAGTACAAAC----TCGCATGTG-TCCACT--------CTTTTTCCCACGTCTCATTAAAATTGCAGTTAAAATG-CAAGA------------------------------------TG--CTG--------------------------------------------------------CC----------TCCG----TTCTTTTA----CTTTCTATC--------ATCGTCATCGAGTCAGC---------------------------------------------------------GAGCCAGAGACGC------GAACGAAGACGACGTC-CCATCGTCATTATTGTCAACTC--TCAACGA-G-----TTGCCAATCG--T--------------------------CTGTC------------------CCGGCTATCTT-------------TCTGCCTGC---------------------------------------CGTTT---CTAGATTGAT-GTCTCTgcagtcag s droEle2.KB458573 530280 676 - 5320397 GTTCTCTTTGGCGGCAA-ACATTTAACAAGCATCGG-------CTGTCC-GT---------------------------TGGGCCG-----------------AG-GATGCCACCTAGAAAGC-TCACGCTAGGCGTCCAATTGGCTA--------------GA-------------------------GTTGCCGCCGATCATGGTCATGCCACATGG----------CCAATGG-CCACATGG-TGCCTGCCTGCTGCCTGGTTCTTGGTGCCTGGTGCCAG----TGCCACC-AA---------GTGG--ACAATG-GTTA---------AGCCAC----------------ACTG--GCC------GGTGGTCCTTTGTCTC---------------GGAAGT-----------------GC--TC---CTTGCATTGCCTTGCCTTTGCCGCCTGTCAGTGCTAATTTG-------------TTGCT-------GCTCGTGCAG-----------------------CGGTCGC-----------------------TTCCACT------AAAAATATAGC-----CATAAATGTTGATCAATAAGAC------------------GGAGGG------------ACTGACTGG----T---------------AGAGAAATCTGCATGTCCTTAATGCCGGCAACGTGCGAGTTTTACAAATTACGA---AATG---------------------------AG------------------------------CCA-----------------------------------------GGCAGAC----GAACTGGATGCGA--CAACGTATG-TCCACT--------CTTTTTCCCACGTCTCATTAAAATTGCAGTTAAAATG-CAAGA------------------------------------TG--CTG--------------------------------------------------------CC----------TCTG----TTCTTTTA----CTTTCTATC--------ATCGTCATCGAGTCAGCCAGGCAGC-------------------------------------------------GAGGCAGAGATGC------GAACGAAGACGACGTC-CCATCGTCATTATTGTCAACTC--TCAACGA-G-----TTGCCAATCG--T--------------------------CTGTC------------------CCGGCTATCTT-------------TCTGCCTGC---------------------------------------CGTTT---CTAGATTGAT-GTCTCTGCAGTCAG s droKik2.KB459527 284565 682 - 1234237 GTTCTCTTTGGCGGCAA-ACATTTAACAAGCATCGA-------CTGTCC-GT---------------------------TGGGCCA-----------------AG-GATGCCACCTAGAAAGC-TCACGCTAGGCGTCCAATTGGCTA--------------GA----------------------------GCCGCCGATCATGGTCATGCCACATGG------------------CCACATTGGC----GGCCA-----------------CATGG----------TGCCACC-AA---------CTGG--ACAATG-GTCA-------CTGATC------------------GCTG--GCC------GGTGGTCCTTTGTCTCTCTC---------CCGGCAGC------------CCCATCC--TC---TTCTCC-------------TCTGCCTGTCAGTGCTAATTTG-------------TTGCT-------GCTCGTGCAG-------GCTGCAGCCCAAAGGCAGCAG-------------------------TAGTACT------AAAAATATAGC-----CATAAATGTTGATCGGCCAGGCAG----------------GACAAC------------AAGTTCCAA----CCGATGAGGGAG--GGAGAGAAATCTGCATGTCCTTAATGCCGGCAACGTGCGAGTTTTACAAATTACGA---AACG---------------------------AG-------CA-------------------------------------AAACGGCAAGGAAACT------------GGCATTCGGTGGCATTCGTCGTGG-TACATATATG-TCGACT--------CTTTTTCCCACGTCTCATTAAAATTGCAGTTAAAATG-CAAGA------------------------------------TGCTCTG--------------------------------------------------------CC----------TTCG----TTCTTTTA----CTTTCTATC--------ATCGTCATCGAGTCAGC---------------------------------------------------------GAGCC--AGACGC------GAACGAAGACGACGTC-CCATCGTCATTATTGTCAACTC--CCAACGA-G-----TTGCCAATCG--T---------CGT--------------CTGTC------------------CCGGCTATCTT-------------TCTGCCTGC---------------------------------------CGTTT---CTAGATTGAT-GTCTCTGCAGTCag s droTak2.KB461535 149294 630 - 669855 GTTCTCTTTGGCGGCAA-ACATTTAACAAGCATCGG-------CTGTCC-GC---------------------------TGGACCG-----------------AG-GATGCCACCTAGAAAGC-TCACGCTAGGCGTCCAATTGGCTG--------------GA-------------------------GTTGCCGCCGATCATGGTCATGCCACATGG------------------CCGAATGG-C--C-ACATGGTGCCTGGAGTCGATGGCGTAG----------TGCCACC-GA---------GTGG--ACAATG--------------------------------------------C------GGTGGTCCTTTGTCTC---------------GGCAGC-----------------GC--TC---CTTGCC----------------GCCTGTCAGTGCTAATTTG-------------TTGCT-------GCTCGTGCGG--------------TAAAGAGAGGGCGGGGAGGGGTTTCCCCCACCCTTTTTAGTCCACT------AAAAATATAGC-----CATAAATGCTGATCAATATGGAGGAACTG-----------GACAGG------------ACAGGACAG--------------------AGAGAAATCTGCATGTCCTTAATGCCAGCAACGTGCGAGTTTTACAAATTACGA---AATG---------------------------AG-------CA--------------------GCGC-----------------------------------------GGCGAAG----GCAT-------------------C-TCCACT--------CTTTTTCCCACGTCTCATTAAAATTGCAGTTAAAATG-CAAGA------------------------------------TG--CTG--------------------------------------------------------CC----------TCTG----TTCTTTTA----CTTTCTATC--------ATCGC---------------------------------------------------------------------GA------------------A-CGAAGACGACGTC-CCATCGTCATTATTGTCAACTC--TCAACGA-G-----TTGCCaatcg--tctgtctgtccgt--------------ctgt-------------------ccggcTATCTT-------------TCTGCCTGC---------------------------------------CGTTT---CTAGATTGAT-GTCTCTGCAGTCAG s droRho2.KB449310 45009 616 - 65043 GTTCTCTTTGGCGGCAA-ACATTTAACAAGCATCGG-------CTGTCC-GT---------------------------TGGGCCG-----------------AG-GATGCCACCTAGAAAGC-TCACGCTAGGCGTCCAATTGGCTG--------------GA-------------------------GTTGCCGCCGATCATGGTCATGCCACATGG---------------------------T----GCCCG--------TGGCTAGTGGCTAG----------TGCCACC-GA---------GTGG--ACAATG------------------------------------------GCC------GGTGGTCCTTTGTCTC---------------GGAAGT-----------------GC--TC---CTTGCC-TCGACTTGCCTCGCCGCCTGTCAGTGCTAATTTG-------------TTGCT-------GCTCGTGCAG-----------------------CGGCC-------------------------TTCCACT------AAAAATATAGC-----CATAAATGTTGATCAATAAGGC------------------GGTGGG------------ACAGGGAC---------------------AGCGAAATCTGCATGTCCTTAATGCCGGCAACGTGCGAGTTTTACAAATTACGACGAAATG---------------------------AG-------CA--------------------AGGC----------------------TCAAGAC------------GGAATAT----GTATGTGC---------------G-TCCACT--------CTTTTTCCCACGTCTCATTAAAATTGCAGTTAAAATG-CGAGA------------------------------------TG--CTG--------------------------------------------------------CC----------TCTG----TTCTTTTA----CTTTCTATC--------ATCGTCATCGAGCCAGC---------------------------------------------------------GATGCAGAGACGC------GAACGAAGACGACGTC-CCATCGTCATTATTGTCAACTC--TCAACGA-G-----TTGCCAATCG--T--------------------------CTGTC------------------CCGGCTATCTT-------------TCTGCCTGC---------------------------------------CGTTT---CTAGATTGAT-GTCTCTGcagtcag s droFic2.KB457177 88255 596 + 995874 GTTCTCTTTGGCGGCAA-ACATTTAACAAGCTGCTG-------CTGTCC-GC---------------------------TGGGCCG-----------------AG-GATGCCACCTAGAAAGC-TCACGCTAGGCGTCCAATTGGCTG--------------GA-------------------------GTTGCCGCCGATCATGGTCATGCCACATGG------------------CCGAGTGG-C-----------------TTATGGCCGCATGGTGCCCAAAGTCACCAGC-GA---------GTGG--ACAATG-CCCG---------GGCC------------------TTCG--GCC------GGTGGTCCTTTGTCTC---------------GGCAGC-----------------GC--TC---CTCGCC----------------GCCTGTCAGTgctaatttg-------------ttgct-------gctcgTGCAG------------------CTCGCAGCTCGG-----------------------CTCCACT------AAAAATATAGC-----CATAAATGCTGATCAATAAGGAGG----------------GACGAC------------AGAG-------------------------AGCGAAATCTGCATGTCCTTAATGCCGGCAACGTGCGAGTTTTACAAATTACGA---GCCG---------------------------AA-------CT-----------------------------------------------------------------GGCAGAC----GG---------------------G-TCCACT--------CTTTTTCCCACGTCTCATTAAAATCGCAGTTAAAATG-CAAGA------------------------------------TG--CTG--------------------------------------------------------CC----------TCCG----TTCTTTTA----CTTTCTATC--------ATCGTCATCGAGTCAGC---------------------------------------------------------GAGCCAGA---------------------GACGTC-CCATCGTCATTATTGTCAACTC--GCAACGA-G-----TTGCCAATCG--T--------------------------CTGTC------------------CCGGCTATCTT-------------TCTGCCTGC---------------------------------------CGTTT---CTAGATTGAT-GTCTCTGCAGTCAG s droPse3.chr3 1357064 735 - 19787792 gttctcTTTGGCGGCAA-ACATTTAACAAGCAGCGG-------CTGTCCGGC---------------------------TGCACTG-----------------AG-GATGCCACCTAGAAAGC-TCACGCTAGGCGTCCAATTGGCTA--------------GA----------------------------GCCGACGATCATGGTCATGCCACATGG---------------------------------------------------------------------TGCCACC-GC---------ATGG--ACAATG-GGCC---------GGCCGAATCGAACCGAGG----CCGG--ACC------GGTGGtcctttgtctctctctcgctctctccggcctc-----------tcC---GC--CC---CTTCTC------CACTGTGGAGGCCTGTCAGTGCTAATTTG-------------TTGCTACTCGTGGCTCGCGCAG-------ACTGCGGC--------------------------------------TACCACT------AAAAATATAGC-----CATAAATGTTGATCAATAAGGA------------------gagggcatgggt------atgggtatgggtatgggtaagggtGCTGTAGGGAAATCTGCATGTCCTTAATGCTGGCAACGTGCGAGctttacaaattacaa---aacg---------------------------AG-------CA--------------------GCC------------------------------------------AGGAGCC----GCATTCGtggtacatatat----a-tcgagT--------ATTTTTCCCACgtctcattaaaattgcagtTAAAATG-CAGAAGCAGGCC-------------AGAGATCG-TCTTCGCCG--TTG--------------------------------------------------------CTCTTGGCCG--TTGG----TTCTTTTA----CTTTCTATC--------ATCGTCATCGATTTTgc---------------------------------------------------------gacgc--agacgc------agacggagACGTC--C-TCAGCGTCATTATTGTCAACTC--TCAACGA-G-----TTGCCAATCG--T--------------------------CTGTC------------------CCAACTATctt-------------tctgcctgcctgcctgctggctgcctggctgcctgcttgcctgcctgccgtct---CTAGATTGAT-GTCTCTGcagtcag s droPer1.super_34 545951 735 - 916997 GTTCTCTTTGGCGGCAA-ACATTTAACAAGCAGCGG-------CTGTCCGGC---------------------------TGCACTG-----------------AG-GATGCCACCTAGAAAGC-TCACGCTAGGCGTCCAATTGGCTA--------------GA----------------------------GCCGACGATCATGGTCATGCCACATGG---------------------------------------------------------------------TGCCACC-GC---------ATGG--ACAATG-GGCC---------GGCCGAATCGAACCGAGG----CCGG--ACC------GGTGGTCCTTTGTCTCTCTCTCGCTCTCTCCGGCCTC-----------TCC---GC--CC---CTTCTC------CACTGTGGAGGCCTGTCAGTGCTAATTTG-------------TTGCTACTCGTGGCTCGCGCAG-------ACTGCGGC--------------------------------------TACCACT------AAAAATATAGC-----CATAAATGTTGATCAATAAGGA------------------GAGGGC------------ATGGGTATGGGTATGGGTAAGGGTGCTGTAGGGAAATCTGCATGTCCTTAATGCTGGCAACGTGCGAGTTTTACAAATTACAA---AACG---------------------------AG-------CA--------------------GCC------------------------------------------AGGAGCC----GCATTCGTGGTACATATAT----A-TCGAGT--------ATTTTTCCCACGTCTCATTAAAATTGCAGTTAAAATG-CAGAAGCAGGCC-------------AGAGATCG-TCTTCGCCG--TTG--------------------------------------------------------CTCTTGGCCG--TTGG----TTCTTTTA----CTTTCTATC--------ATCGTCATCGATTTTGC---------------------------------------------------------GACGC--AGACGCAGACGGAGACGGAGACGTC--C-TCAGCGTCATTATTGTCAACTC--TCAACGA-G-----TTGCCAATCG--T--------------------------CTGTC------------------CCAACTATCTT-------------TctgcctgcctgcctgctggctgcctggctgcctgcttgcctgcctgccGTCT---CTAGATTGAT-GTCTCTGcagtcag s droMir2.chr3 1398206 710 - 20862834 gttctctTTGGCGGCAA-ACATTTAACAAGCAGCGG-------CTGTCCGGC---------------------------TGCGCTG-----------------AG-GATGCCACCTAGAAAGC-TCACGCTAGGCGTCCAATTGGCTA--------------GA----------------------------GCCGACGATCATGGTCATGCCACATGG---------------------------------------------------------------------TGCCACC-GC---------ATGG--ACAATG-GGCC---------GGCCGAGTCGAACCGAGG----CCGG--ACC------GGTGgtcctttgtctctctctctctctctccggccTC-----------TGC---CC--CC---CTTCTC------CACTGTGGAGGCCTGTCAGTGCTAATTTG-------------TTGCTACTCGTGGCTCGCGCAG-------ACTGCGGC--------------------------------------TACCACT------AAAAATATAGC-----CATAAATGTTGATCAATAAGGA------------------gagggc------------atgggtatgggtatgggtaagGGTGCTGTAGGGAAATCTGCATGTCCTTAATGCTGGCAACGTGCGAgttttacaaattacaa---aacg---------------------------aG-------CA--------------------GCC------------------------------------------AGGAGCC----GCATTCgtggtacatatat----a-tcgagT--------ATTTTTCCCACGtctcattaaaattgcagtTAAAATG-CAGAAGCAGGCC-------------AGAGATCG-TCTTCGCCG--TTG--------------------------------------------------------CTCTTGGCCG--TTGG----TTCTTTTA----CTTTCTATC--------ATCGTCATCGATTCGgc---------------------------------------------------------gacgc--agacgc------agacggagacgTC--C-TCAGCGTCATTATTGTCAACTC--TCAACGA-G-----TTGCCAATCG--T--------------------------CTGTC------------------CCAACTAtctt-------------tctgcctgc-------------------ctgcctgcttgcctgcctgccgtct---CTAGATTGAT-GTCTCTGcagtcag s droWil2.CH963894 1321251 662 + 2843958 GATGGCTATAGTGGTGG---------------CGGC-------CTGTCT-CC----AAA--------------------TGCATCG-----------------AGAGATGCCACCTAGAAAGC-GCACGCTAGGTGTCCAATTGGCTACCAAGAAGAGAACCGC-------------------------ATCGCAATCG-TTGTTGTCATTGAATGCGG------------------ACA-ATGG-T----GGTCCCTTTGTCAAGTCTATGGACTTGGCC-------TGTCAGC-gctaatttgttgttg--ctactg-gCTG-------------------------------CCAA--TTC------GATTCGATTCCGTTTC----------------GATGC-----------------GG--TT---CGTTTC----------------GATT--------CGAGTTG-------------TTACT-------GCAAGTTCTC------------------------------------------------------------------AAAAATATAGC-----CATAAATGTTTA----------------------------CGCCGA------------TCA--------------------------ATAAAAATCTGCATGTCCTTAATGCTGGCAACGTGCCAGGTTTACAAATTACAA--CAATGTCCGATGTCTGATGTCCAATGTCGGCCAG-------CA-----------------------------------------------------------------GATTGCT----GCTTATGCGAATCGG--------A-ACGAGT--------ATTTTTCCCACGTCTCATTAAAATTGCAGTTTAAATG-CGAAG--AGATCGATGAAACGATGGATGGATCGATcactgctt--ctg--------------------------------------------------------ct----------tctgctgcttcttTTA----CTTTCTATC--------C-------------------------------------------------------------------------GAAGACCAAAAGC------AAACAGCAACGTCGT------CGTCATTATTGTCAACTC--TCAACGA-C-----TTGCCAatcg--tctgt----------------------ctgtctgtctgtatgtctttcagtctgtagtctg-------------tctgCCTGC---------------------------------------CGT-T---CTAGATTGAT-GTCTCTTCAGTCAG s droVir3.scaffold_12875 7362076 694 + 20611582 ----GCTTTGGCGGCAAAACATTTAACAAGCTCAG--------CTGCCC-AG-CAGCTG-TCCAAGTTAGCCAGTTAGCCGTGCCA----------CAGATGCGG-CATGCCACCTAGCAAGC-GCACGCTAGGCGTCCAATTGGCTG--------------CC--------CAAGCTTCAGC------TTCAGCTTCAAC-------------CGCAG------------------CCACAGCT-C--------------------------CAAGT----------GGG-----GA---------GTGG--ACAATG-GCCACCATT---TGACC------------------GCTG--GCC------GGTGGTCCTTTGTCAG------------------CGA-----------------GC--GC---GCTGTC-----------------------AACGCTAATTTG-------------TGGCC-------AGTAGCCGAG-----------CTCTCTCTCTCCCTCCCTCTCGGTATCTCATCCCACTCGCTGTCCGTCT---CTCAAAAATATAGC-----CATTAATGTTTAGCACATG--C------------------AGTTGA------------TCA--------------------------ATAAAAATCTGCATG-------------CAACGTGCGAGTTTTACAAATTACTT---GCGT---------------------------CA-------TA-----------------------C-----------------------------------------GGCATTT----AAGTAC-----------------ATTCGAGT--------A-TTTTCCCACGTCTCATTAAAATTGCAGTTAAAATT-C----------------------------------------TG--CTAAAAAAGGCCCAGAGTCAGGCCGGGACGAA---ACCGAGGCCTTAGCCACAGCTCCATCTCCAGCTCATGCTG----TTCTTTTA----CTTTCTATCGATGCAT-TGCATCGTCCAACC---------------------------------------------------------------------------------CGCCAAGCCTCATCGTCATCGTCATTATTGTCAACTC--TCAACCA-G-----TTGCCAATCg--t--------------------------ctgt-------------------ccaattgtctctccctgttgtctgtctgtctga---------------------------------------ctgtctgactatctttcA-GCTCCTGCCTGCCG s droMoj3.scaffold_6496 26157099 690 + 26866924 --TTGCTTTGGCGGCAAAACATTTAACAAGCTCAGCCGCTCAACCGCCC-AG-CAGTTG-TCGCCG-CAGCCGCTG---CGAGGCA----------CAGATGCCG-CATGCCACCTAGAAAGCTGGACGCTAGGCGTCCAATTGGCTG--------------GC--------CAAACAGCAGCAGCTATCTCCGCTTCCCCACTCCCCACCCCACGCTG----------CCCACTGCCCACTGCT-C----------------------------AGG----------GGA-----GG---------GGCA--ACAAGGCGGCAGCAGTGGCTGACC------------------GCTG--GCT------GGTGGTCCTTTGTCAC------------------CGG-----------------GCGAGT---GCTGTC-----------------------AACGCTAATTTGTGGGGATGGCGGCTGGAC-------GGTGGCCGCG------------------GCTGCCGCCTTTT----------------------TCCAGCT------AAAAATATAGC-----CATAAATGTTCAGCACTTGCAC------------------AGTGGC------------TCA--------------------------AT-AAAATCTGCATT-------------CAACGTGCGAGCTTTACAAATTACCT---GTGC---------------------------TG-------CA----GTGCCTCGCTG-----GCCG-----------------------------------------AGCATTT----AACTGC-----------------G-TCGAGT--------A-TTTTCCCACGTCTCATTTAAATTGTAGTTAAAAAT-T----------------------------------------TG--ATG---------CTGGGCCTGCTGGGGCTGAAAAGACCCAGGCCGCGTCTGTGGCAGTATC----------GCTG----CTCCCTTA----CTTTATGTCGATCCAC-TGCATCGTCCAA------------------------------------------------------------------------------------------CATCGTCCCCATCGTCATTATTGTCAACTC--TCAACCA-G-----TTGCCAATCG--T--------------------------CTGT-------------------CCCATTGTCCCtctccgtc-----tctgtctct---------------------------------------gtctccgtctctgtctct-gtctctg------- s droAlb1.JH854640 319748 693 + 406291 gttgtctTTGGCGGCAAAACATTTAAGAAGCTCAG--------CTGTCC-AGTTAGCCGAGCCAAGCTGGCTAACT---TGGCCAA----------CAGATGCGG-CATGCCACCTAGAAAGC-GCACGCTAGGCGTCCAATTGGCTG--------------CCT-------TCAACTGCAGC------TTCAGCGACAAT-------------TTCAG------------------CAACAATC-T--------------------------CAAAG---ACAA---GGG-----GA---------GGGG--ACAATG------------CCGATC------------------GTTG--GCT------GGTGGTCCTTTGTCAA------------------AGC-----------------GC--AC---GCTGTC-----------------------GAGGCTAATTTG-------------TGACC-------agcagtagaagaagaagcatgTGGACTGTCAGCAGCTTGTT----------------------TGCAACAAGGCGAAGAAATATAGTCATAACATAAATGTTTAGCACTTG--C------------------AGTTGCGCTCGCTTTTGGCCA--------------------------ATAAAAATCTGCATGTTTTTAATGCCATCAACGTGCGAGTTTTACAAATTagaa---gcta---------------------------ca-------aaaaaaatgcctCATTGCAGGCGAAG-----------------------------------------AGCAGAT----GAT----------------------TCAAGT--------A-TTTTCCCACGTCTCATTAAAGCTGCAGCTTAAATG-C----------------------------------------TG--CCA---------AGGAGCCTTGTTG----------------------------------TC----------TCCG----TTCTTTTA----CTTTCTATCACAGCACATTCAGCatgcagcaaga---------------------------------------------------------gcaacagca--gc------agcatcgaacGTCCTCATCATCATTAACATCATCAA--C--TCATCGA-G-----TTGCCAATCGTCT--------------------------CTGA-------------------AGAACTGTCTCATTCTTTC---AGTCTCTCTGT---------------------------------------CGCTTCGATTGGGTGGCT-GTCCGTCTC----- s droGri2.scaffold_15245 912595 688 + 18325388 -----CTTTGGCGGCAAAACATTTAACAAGCTCAGCG------CTGTCC-AG----TTA-GCGACGTTGGCTAGCC---CGCGCTAGCCATGACACCAGATGCGG-CATGCCACCTAGAAAGC-GCACGCTAGGCGTCCAATTGGCTG--------------ACCAAGCGTACCAACAATGGCCGGTGGTCCTTTGTCAGTGCGAGTCAGCTG-CGCTG------------------TCAACGCT-A----------------------------ATT----------TGT-----GG---------CCAC--AAAATG-TTTTGCAGTAgctg-ct------------------gctgctgct------gctg--ccactgctat------------------tgc-----------------aa--ct---gctgct-----------------------gcaactgctgct-------------gcaac-------tgctgctgct------------------gctgctgctgttg----------------------GCCAGTC----ACAAAAATATAGC-----CATAAATGTTTAGCGCTTT--T------------------------------------TCA--------------------------ATAAAAATCTGCATG-------------CAACGTGCGAGTTGTACAAATTACGA---ATCG---------------------------CA-------TA---AGTACTTGG--------AAAA-----------------------------------------AGCATTTCGAGAAC----------------------GCGGCT--------A-TTTTCCCACGTCTCATTAAAATTGCAGTTAAAGTTGC----------------------------------------TG--CTG---------CTGCTGCTGCCGATGTTGCAACCAGCAAAGGAG--------------GC----------AACA----ACAAATTGAAGCCTCAACTCTGATGCTG-TTCCTCTTTTACTTTCT---------------------------------------------------------ATCGCCGCATTGC------ATCGTCT--CAGCGTCCTCATCGTCATTATTGTCAACTCAGTCAACCAGG-----TTGCCAATCg--t--------------------------ctgt-------------------ccagctgtctc--tctgtc-----tctgtccgt---------------------------------------ctgtctggctatctTTGAGGCTTCTGCCTGCCG a score=58002.000000 s dm6.chr2R 24365712 7 + 25286936 GCAGACA s droSim1.chr2R 18704090 7 + 19596830 GCAGACA s droSec1.super_23 123858 7 + 989336 GCAGACA s droYak3.chr2R 20213453 7 + 21139217 GCagaca s droEre2.scaffold_4845 21611220 7 + 22589142 GCAGCCA s droBia2.KB462602 804789 7 + 3129309 acagtcg s droAna3.scaffold_13266 5716946 7 - 19884421 acattca s droBip2.KB464407 1966863 7 + 2915140 acattca s droEug2.KB465067 608472 7 + 1515531 acagtca s droEle2.KB458573 530956 7 - 5320397 ACAATCA s droKik2.KB459527 285247 3 - 1234237 aca---- s droTak2.KB461535 149924 7 - 669855 ACAGTCA s droRho2.KB449310 45625 7 - 65043 acagtca s droFic2.KB457177 88851 7 + 995874 Acagtcg s droPse3.chr3 1357799 7 - 19787792 acagtca s droPer1.super_34 546686 7 - 916997 acagtca s droMir2.chr3 1398916 7 - 20862834 acagcca s droWil2.CH963894 1321913 6 + 2843958 -CAGACA s droMoj3.scaffold_6496 26157789 7 + 26866924 GCTATCT s droAlb1.JH854640 320441 7 + 406291 TCAGTCT s droGri2.scaffold_15245 913309 7 + 18325388 gcagtca a score=46727.000000 s dm6.chr2R 24365719 30 + 25286936 GTCAGTC-AGTCGG----T--CCACGAGTCCATCTGT----- s droSim1.chr2R 18704097 30 + 19596830 GTCAGTC-AGTCGG----T--CCACGAGTCCATCTGT----- s droSec1.super_23 123865 30 + 989336 GTCAGTC-AGTCGG----T--CCACGAGTCCATCTGT----- s droYak3.chr2R 20213460 25 + 21139217 gtcagtc-agtcgg----t--cCACGAGTCCA---------- s droEre2.scaffold_4845 21611227 25 + 22589142 GTCAGTC-AGTCGG----T--CCACGAGTCCA---------- s droBia2.KB462602 804796 25 + 3129309 gacagtc-agacag----t--cggacagtcag---------- s droSuz1.KI419649 12050214 9 - 14502029 -----------------------GACAGTCAG---------- s droAna3.scaffold_13266 5716953 21 - 19884421 gtcagtc-agtcag----t--ct----gtccc---------- s droBip2.KB464407 1966870 13 + 2915140 gtcagtc-agtcag---------------------------- s droEug2.KB465067 608479 25 + 1515531 gtcagtc-cggccg----t--ccagcagtcca---------- s droEle2.KB458573 530963 25 - 5320397 GAcagtc-agtcgg----t--ccatcagtcca---------- s droKik2.KB459527 285250 25 - 1234237 gtcagtc-agtcag----t--ccaTCGGTCCG---------- s droTak2.KB461535 149931 25 - 669855 GTCAGTC-CATCAG----T--CCGGCAGTCTG---------- s droRho2.KB449310 45632 25 - 65043 gtcggtc-catcag----t--ccaccagtcca---------- s droFic2.KB457177 88858 25 + 995874 gtcggtc-caccgg----t--ccatcggtccc---------- s droPse3.chr3 1357806 29 - 19787792 gtcagtc-agtccgtcagt--ccttcagtcca---------- s droPer1.super_34 546693 29 - 916997 gtcagtc-agtccgtcagt--ccttcagtcca---------- s droMir2.chr3 1398923 21 - 20862834 gtcagtc-agtccg----------tcagtcca---------- s droMoj3.scaffold_6496 26157796 24 + 26866924 TTCAGCT---TCTG----C--CTGACGTTCTA-----G---- s droAlb1.JH854640 320448 30 + 406291 Ttc-gctctgtctg----t--ctgacaaTCTA-----TCTGT s droGri2.scaffold_15245 913316 24 + 18325388 gccagcc-agtcag----cagccagcagc------------- a score=-101840.000000 s dm6.chr2R 24365749 72 + 25286936 CCTGAGTCCATCTGTCCATCTGTC----CGGCCGTC-----------------CGACAGTCC----------CG------------CGGAATTATGCGAG----------GCGGAGGTGATCGCT--- s droSim1.chr2R 18704127 71 + 19596830 CCTGCGTCCATCTGTCCA-CAGTC----CGGCCGTC-----------------CGAAAGTCC----------CG------------CGGAATTATGCGAG----------GCGGAGGTGGTCGGA--- s droSec1.super_23 123895 71 + 989336 CCTGCGTCCATCTGTCCA-CAGTC----CGGCCGTC-----------------CGAAAGTCC----------CG------------TGGAATTATGCGAG----------GCGGAGGTggccgga--- s droYak3.chr2R 20213485 62 + 21139217 --CGAGTCCAT--------GGGTC----CATCTGTC-----------------CATGTGTCC----------CG------------CGGAATTATGCGAG----------GCGGTGGTGATCggg--- s droEre2.scaffold_4845 21611252 68 + 22589142 --TGGGTCCATCTGTCCC-GAGTC----CGCCCGTC-----------------CGAAAGTCC----------CG------------CGGAATTATGCGAG----------GTGGTGGTGATC-GG--- s droBia2.KB462602 804821 56 + 3129309 --tcagtccatcagtcCCGCCGTC----TG---GTC-----------------CAAAAGTCC----------CG------------C-GAATTacaggag----------gcgga------------- s droSuz1.KI419649 12050223 63 - 14502029 --TCAGTCCATCAGTCCCGCCGTC----TG---GTC-----------------CAAAAGTCC----------CG------------C-GAATTATaggag----------gcggaggtgatc------ s droAna3.scaffold_13266 5716974 39 - 19884421 --tcagtcCGTTGGTCCA--------------------------------------------------------------------CTGATTTCAAGGAG----------GCGGTGGTC--------- s droBip2.KB464407 1966883 39 + 2915140 --tcggtccgtctgtccg--------------------------------------------------------------------ctgATTTCAGGGAG----------GCGGTGGTC--------- s droEug2.KB465067 608504 54 + 1515531 --gcagtccatcagtcca-------------------------------------agagtcc----------CG------------CGGAATAACAGGAG----------GCGGAGGTGATCGAA--- s droEle2.KB458573 530988 77 - 5320397 --tcagtccaccagtccgccggtc----caaaagtc-----------------ccccagtccatcccagAATCG------------CAGATTCACAGGAG----------GCGGAGGCGATC------ s droKik2.KB459527 285275 63 - 1234237 --TTGGACCATCAATTTC---------------GTC-----------------CGT---CCC----------CG------------CAGAATCAGAGAAGAGGAATCATCGGGGAGGAGATC------ s droTak2.KB461535 149956 43 - 669855 ---------------------------------GTC-----------------CAAAAGTCC----------CG------------CGGAATTATAGGAG----------GCGGAGGTGATCGGA--- s droRho2.KB449310 45657 66 - 65043 --tcggtccatcagt----cagtc----cgccggtc-----------------caaaagtcc----------CG------------CAGAATCGCggggg----------gcggagggggcgggg--- s droFic2.KB457177 88883 82 + 995874 --tcagtccatcagtccagcagtc----catcagtc-----------------cagcagtcc----------cgcagtccatccaACAGAATTTTAAGAG----------GCGAATGCGATCGAG--- s droPse3.chr3 1357835 73 - 19787792 --tcagtccatctgcacagcagccgca-ccgcagcca----------------cagcaacca----------cG------------CCAAAGGA-GGAAG----------GTGGCAAGAGCCAGA--- s droPer1.super_34 546722 73 - 916997 --tcagtccatcTGCACAGCAGCCGCA-CCGCAGCCA----------------CAACAACCT----------CG------------CCAAAGGA-GGAAG----------GTGGCAAGAGCCAGA--- s droMir2.chr3 1398944 74 - 20862834 --tcagtccatctccacagcagccgcagccgcagcca----------------cagcaaccT----------CG------------CCAAAGGA-GGAAG----------GTGGCAAGAGCCAGA--- s droMoj3.scaffold_6496 26157820 59 + 26866924 ------------------------------------ATTGATGTCTGCGAGTCCAGCAGCCA-----------G------------CAGCCAGAAGTCAG----------AAGTCAGCTGCCAGCATC s droGri2.scaffold_15245 913340 20 + 18325388 -----------------------------------------------------cagcagcca-----------g------------ca------------------------------tgccaTCA-- a score=-43161.000000 s dm6.chr2R 24365821 25 + 25286936 GAAGGGGCTGGAGATGAAGTTGGAG s droSim1.chr2R 18704198 25 + 19596830 GGAGGGGCTGCAGATGGAGTTGGAG s droSec1.super_23 123966 25 + 989336 ggaggggctggagatggagctggag s droYak3.chr2R 20213547 25 + 21139217 ggagggaatggagctggagctggag s droEre2.scaffold_4845 21611320 25 + 22589142 GGAGCGGCTGGAGCTGGAGGTGGAG s droBia2.KB462602 804877 24 + 3129309 ggagcaggggCGACAGGAGCAGAA- s droSuz1.KI419649 12050286 25 - 14502029 ggaggaggtggagatggagcaggag s droTak2.KB461535 149999 22 - 669855 GGagaagcaggaggaggagcag--- s droRho2.KB449310 45723 5 - 65043 CGATC-------------------- s droFic2.KB457177 88965 21 + 995874 GGAGGAGCACGAGGAGGAGAC---- s droPse3.chr3 1357908 1 - 19787792 A------------------------ s droPer1.super_34 546795 1 - 916997 A------------------------ s droMir2.chr3 1399018 1 - 20862834 A------------------------ s droWil2.CH963894 1321942 12 + 2843958 ------------GGAGGACCAGGA- s droMoj3.scaffold_6496 26157879 19 + 26866924 AAAGATGCTGAGATTCGAG------ s droGri2.scaffold_15245 913360 19 + 18325388 ACAGATTCTGAGATTCTGA------ a score=325411.000000 s dm6.chr2R 24365846 44 + 25286936 CT---------GG-GGGAGTG--GGC-------AGAGGA-------------C----GG-----CTTGGCACAGTTTGCGCAC--TT s droSim1.chr2R 18704223 50 + 19596830 CTGGAGCA---GG-GGGAGTG--GGC-------AGAGGC-------------C----GG-----CTTGGCACAGTTTGCGCAC--TT s droSec1.super_23 123991 50 + 989336 ctggagca---gg-gggagtg--ggc-------agaggc-------------c----gg-----CTTGGCACAGTTTGCGCAC--TT s droYak3.chr2R 20213572 50 + 21139217 gtggaggt---gg-gggagtg--ggC-------AGAGGC-------------C----AG-----CTTGGCACAGTTTGCGCAC--TT s droEre2.scaffold_4845 21611345 49 + 22589142 GTGGAGCT----G-GGCAGTG--GGC-------AGAGGC-------------C----AG-----CTTGGCACAGTTTGCGCAC--TT s droBia2.KB462602 804901 42 + 3129309 -----------GG-AGGAGTG--GGC-------AGAGGC-------------C----AG-----CTTGGCACAGTTTGCGCAC--TT s droSuz1.KI419649 12050311 51 - 14502029 --ggaccatccgg-aggagTG--GGC-------AGAGGC-------------C----AG-----CTTGGCACAGTTTGCGCAC--TT s droAna3.scaffold_13266 5717013 48 - 19884421 -----------GCAAGGAGTG--GAATCA----AGAGGC-------------C----AA-----CTTGGCACAGCTTGGCGCACTTT s droBip2.KB464407 1966922 49 + 2915140 -----------GC-AGGAGTGCCGATAAA----AGAGGC-------------C----AA-----CTTGGCACAGTTTGTGGactttt s droEug2.KB465067 608558 42 + 1515531 -----------GG-AGGAGTG--GGC-------AGAAGC-------------C----AG-----CTTGGCACAGTTTGCGCAC--TT s droEle2.KB458573 531065 42 - 5320397 -----------GG-AGGAGTG--GGC-------AGAATT-------------T----AG-----CTTGGCACAGTTTGCGCAC--TT s droKik2.KB459527 285338 46 - 1234237 -----------AG-AGGAGTG--GGC-------AGAAGC-------------CAGAGAG-----CTTGGCACAGTTTGCGCAC--TT s droTak2.KB461535 150021 42 - 669855 -----------tg-GGCAGTG--GGC-------AGAGGC-------------C----AG-----CTTGGCACAGTTTGCGCAC--TT s droRho2.KB449310 45728 49 - 65043 -----------GG-AGGAGTG--GGCAGAAGGCAGAAGC-------------C----AG-----CTTGGCACAGTTTGCGCAC--TT s droFic2.KB457177 88986 42 + 995874 -----------GG-AGGAGTG--GGC-------AGAAGC-------------C----AA-----CTTGGCACAGTTTGCGCAC--TT s droPse3.chr3 1357909 49 - 19787792 -----------GC-AAAGGCA--GACCC-----AGAGTC-------------C----AGGAGAAGTTGGCACAGTTTGCGCAC--TT s droPer1.super_34 546796 49 - 916997 -----------GC-AAAGGCA--GACCC-----AGAGCC-------------C----AGGAGAAGTTGGCACAGTTTGCGCAC--TT s droMir2.chr3 1399019 49 - 20862834 -----------GC-AAAGGCA--GACCC-----AGAGCC-------------C----AGGAGAAGTTGGCACAGTTTGCGCAC--TT s droWil2.CH963894 1321954 48 + 2843958 -----------AA-AGGAGTA--GTACCATCA-GGAGCA-------------G----AG-----CTTGGCACAGTTTGCGCAC--tt s droVir3.scaffold_12875 7362812 38 + 20611582 --------------------------------------CTGAGAGATTCGAGC----TG-----CTTGGCACAGTTTGCGCAC--TT s droMoj3.scaffold_6496 26157898 24 + 26866924 ----------------------------------------------------C----TG-----CTTGGCACAGTTTGCGCAC--TT s droGri2.scaffold_15245 913381 24 + 18325388 ----------------------------------------------------C----AG-----CTTGGCACAGTTTGCGCAC--TT a score=118757.000000 s dm6.chr2R 24365890 9 + 25286936 CGGCATCT-C s droSim1.chr2R 18704273 9 + 19596830 CGGCATCT-C s droSec1.super_23 124041 9 + 989336 CGGCATCT-C s droYak3.chr2R 20213622 10 + 21139217 CGGCATCTCC s droEre2.scaffold_4845 21611394 10 + 22589142 CGGCATCTCC s droBia2.KB462602 804943 9 + 3129309 CGGCATTT-C s droSuz1.KI419649 12050362 9 - 14502029 CGGCATTT-C s droAna3.scaffold_13266 5717061 9 - 19884421 TTGTATTT-C s droBip2.KB464407 1966971 9 + 2915140 tagtattt-t s droEug2.KB465067 608600 9 + 1515531 CGGCATTT-C s droEle2.KB458573 531107 9 - 5320397 TGGCATTT-C s droKik2.KB459527 285384 9 - 1234237 TGGCATTT-C s droTak2.KB461535 150063 9 - 669855 CGGCATTT-C s droRho2.KB449310 45777 9 - 65043 CGGCATTT-C s droFic2.KB457177 89028 9 + 995874 CGGCATTT-C s droPse3.chr3 1357958 9 - 19787792 TGGCATTT-C s droPer1.super_34 546845 9 - 916997 TGGCATTT-C s droMir2.chr3 1399068 9 - 20862834 TGGCATTT-C s droVir3.scaffold_12875 7362850 9 + 20611582 TGGCATCT-C s droMoj3.scaffold_6496 26157922 9 + 26866924 TGGCATCC-T s droGri2.scaffold_15245 913405 9 + 18325388 TGGCAtct-c a score=28424.000000 s dm6.chr2R 24365899 7 + 25286936 AC-TGCCC-- s droSim1.chr2R 18704282 7 + 19596830 AC-TGCCC-- s droSec1.super_23 124050 7 + 989336 AG-TGCCC-- s droYak3.chr2R 20213632 7 + 21139217 AC-TGCCC-- s droEre2.scaffold_4845 21611404 7 + 22589142 AC-TGCCC-- s droBia2.KB462602 804952 7 + 3129309 AT-TGCCC-- s droSuz1.KI419649 12050371 7 - 14502029 AT-TGCCC-- s droAna3.scaffold_13266 5717070 7 - 19884421 AG-TTTCC-- s droBip2.KB464407 1966980 7 + 2915140 at-tttcc-- s droEug2.KB465067 608609 7 + 1515531 AT-TGCCC-- s droEle2.KB458573 531116 7 - 5320397 AT-TGCCC-- s droKik2.KB459527 285393 7 - 1234237 AT-TTTTC-- s droTak2.KB461535 150072 7 - 669855 AT-TGCCC-- s droRho2.KB449310 45786 7 - 65043 AT-TGCCC-- s droFic2.KB457177 89037 7 + 995874 AT-TGCCC-- s droPse3.chr3 1357967 8 - 19787792 ATCTGTCC-- s droPer1.super_34 546854 8 - 916997 ATCTGTCC-- s droMir2.chr3 1399077 8 - 20862834 ATCTGTCC-- s droVir3.scaffold_12875 7362859 7 + 20611582 ---TTTTTTT s droMoj3.scaffold_6496 26157931 7 + 26866924 ---TTTTGGT a score=19425.000000 s dm6.chr2R 24365906 2 + 25286936 CT s droSim1.chr2R 18704289 2 + 19596830 CT s droSec1.super_23 124057 2 + 989336 CT s droYak3.chr2R 20213639 2 + 21139217 CT s droEre2.scaffold_4845 21611411 2 + 22589142 CT s droBia2.KB462602 804959 2 + 3129309 CT s droSuz1.KI419649 12050378 2 - 14502029 CT s droBip2.KB464407 1966987 2 + 2915140 ct s droEug2.KB465067 608616 2 + 1515531 CG s droEle2.KB458573 531123 2 - 5320397 CT s droKik2.KB459527 285401 2 - 1234237 CT s droTak2.KB461535 150079 2 - 669855 CT s droRho2.KB449310 45793 2 - 65043 CT s droFic2.KB457177 89044 2 + 995874 CT s droPse3.chr3 1357975 2 - 19787792 CC s droPer1.super_34 546862 2 - 916997 CC s droMir2.chr3 1399085 2 - 20862834 CC s droVir3.scaffold_12875 7362866 2 + 20611582 CT s droMoj3.scaffold_6496 26157938 2 + 26866924 GT a score=34293.000000 s dm6.chr2R 24365908 20 + 25286936 GGCCGAGATGGAA------------------T----------TTTCGG s droSim1.chr2R 18704291 20 + 19596830 GGCCGAGATGGAA------------------T----------TTTCGG s droSec1.super_23 124059 20 + 989336 GGCCGAGATGGAA------------------T----------TTTGGG s droYak3.chr2R 20213641 20 + 21139217 CGTCGAGATGGAA------------------T----------TTTGGG s droEre2.scaffold_4845 21611413 19 + 22589142 CGCCGAGATGGAA------------------T----------TTC-GG s droBia2.KB462602 804961 20 + 3129309 GCTCGAGATGGAA------------------T----------TTTTGG s droSuz1.KI419649 12050380 20 - 14502029 GCTCGAGATGGAA------------------T----------TTTTGG s droEug2.KB465067 608618 20 + 1515531 GCTCGAGATGGAA------------------T----------TTTCGG s droEle2.KB458573 531125 20 - 5320397 GGAAGCGATGGAA------------------T----------TTTTGG s droKik2.KB459527 285403 29 - 1234237 ---------GGAACCGcagttacttttttttt----------ttttgg s droTak2.KB461535 150081 21 - 669855 GCTCGAGATGGAA-----------------TT----------TTTCGG s droRho2.KB449310 45795 20 - 65043 GCAAACGATGGAA------------------T----------TTTCGG s droFic2.KB457177 89046 20 + 995874 GCTGCAGATGGAA------------------T----------TTTCGG s droPse3.chr3 1357977 12 - 19787792 --------GGGAC------------------C----------TCTCCT s droPer1.super_34 546864 12 - 916997 --------GGGAC------------------C----------TCTCCT s droMir2.chr3 1399087 12 - 20862834 --------GGGAC------------------C----------TCTCCT s droVir3.scaffold_12875 7362868 17 + 20611582 -------------------------------TTGCACGAAACTTTTGG s droMoj3.scaffold_6496 26157940 6 + 26866924 -------------------------------T----------TTTTG- a score=131788.000000 s dm6.chr2R 24365928 39 + 25286936 GAGGAG-----A------TTGCCCCAACTTC-----GAG-----ATAAGGCACACA--ATTT------------ s droSim1.chr2R 18704311 39 + 19596830 GAGGAG-----A------TTGCCCCAACTTC-----GAG-----ATAAGGCACACA--ATTT------------ s droSec1.super_23 124079 39 + 989336 GAGGAG-----A------TTGCCCCAACTTT-----GAG-----ATAAGGCACACC--ATTT------------ s droYak3.chr2R 20213661 39 + 21139217 GCGGAG-----A------TTGCCCCAACTTC-----GAG-----ATAAGGCACACA--GTTT------------ s droEre2.scaffold_4845 21611432 39 + 22589142 GCGGAG-----A------TTGCCCCAACTTC-----GAG-----ATAAGGCACACA--GTTT------------ s droBia2.KB462602 804981 39 + 3129309 GAGGAG-----A------TTGCCCGTGCTTC-----AAG-----ATAAGAGactga--attt------------ s droSuz1.KI419649 12050400 39 - 14502029 GAGGAG-----A------TTGCCCGTACTTC-----CAG-----ATAAGAGAcaga--attt------------ s droEug2.KB465067 608638 38 + 1515531 GAGGAG-----A------TTGCTCCTACTCC-----GAG-----ATAAGG-accaa--attt------------ s droEle2.KB458573 531145 44 - 5320397 GAGGAG-----A------TTGCTCCTACTCCAACATAAG-----ATAGGGaactaa--attt------------ s droKik2.KB459527 285432 50 - 1234237 gaggggTGGACT------CTGTTTGTATTCC-----CAAGAGTCATAGGGAACACA-GATTC------------ s droTak2.KB461535 150102 39 - 669855 GAGGAG-----A------TTGCCCGTACTTC-----AAG-----ATAAGAGactga--attt------------ s droRho2.KB449310 45815 44 - 65043 GAGGAG-----A------TTGGTCTTACTCCAGCATAAG-----ATAAGGAATAAA--Attg------------ s droFic2.KB457177 89066 44 + 995874 GAGGAG-----A------TTGCTCGTATTCCAACATGAG-----ATAAGGGAcgaa--atat------------ s droPse3.chr3 1357989 45 - 19787792 GCAGAG-----GCCACTCTTGGTCCTACTTC-----AAA-----ATTCGATAACGA--ATCT------------ s droPer1.super_34 546876 45 - 916997 GCAGAG-----GCCACTCTTGGTCCTACTTC-----AAA-----ATTCGATAACGA--ATCT------------ s droMir2.chr3 1399099 45 - 20862834 GCAGAG-----GCCACTCTTGGTCCTACTTC-----AAA-----ATTCGATAACGA--ATCT------------ s droMoj3.scaffold_6496 26157946 50 + 26866924 ---gaa-----c------ccattgaaagtgg-----gaa-----atcagggtataatggttttgtgaaaagtat a score=155583.000000 s dm6.chr2R 24365967 57 + 25286936 TCA------------------TTTGGGAGCTGAAGAA--TTTCGGGCAC-------------TATATG--------TGATATGCGTCGAAAATGT----------ATT s droSim1.chr2R 18704350 57 + 19596830 TCA------------------TTTGGGAGCTGAAGAA--TTTCGGGTAC-------------TATATG--------TGATATGCGTCGAAAATGT----------ATT s droSec1.super_23 124118 57 + 989336 TCA------------------TTTGGGAGCTGAAGAA--TTTCGGGTAC-------------TATATG--------TGATATGCGTCGAAAATGT----------ATT s droYak3.chr2R 20213700 57 + 21139217 TCA------------------TTTGCGAGCTGAAGAA--TTTTGGGTAC-------------TATATG--------TGATATGCGtcgaaaatgt----------att s droEre2.scaffold_4845 21611471 57 + 22589142 TCA------------------TTTGAGAGCTGAAGAA--TTTTGGGTTC-------------TATATG--------TGATATGCGTCGAAAATGT----------ATT s droBia2.KB462602 805020 64 + 3129309 tcat-----------------tttaaaagccaAGGAA--TTTCGGGGAC--GTATAG-----TATAAG--------TGATATGCgtcgaaaatgt----------att s droSuz1.KI419649 12050439 64 - 14502029 tcat-----------------tttaaaagccaAGGAA--TTTCGGGGAC--GTATAG-----TATATG--------TGATATGCgtcgaaaatgt----------att s droEug2.KB465067 608676 69 + 1515531 tcat-----------------tttgaaagcCAAAGAA--TTTCGGAGAC--GGATAGCTGACTTCATG--------TGATATGCctcgaaaatgt----------att s droEle2.KB458573 531189 75 - 5320397 tcat-----------------tttcgaaGCTTAAGAA--TTTTGGACATACAGATAGTTGACTTCATGCTTTGCACTGCTGTgcttt----atgt----------att s droKik2.KB459527 285482 94 - 1234237 TTATGCTAGTGAGTACAAAGCTTAGGGATCTAGGGAA--GCTTGGTAAC----AAAGTTAAGAGCCTT--------TAAgctgttttacaaatattcaaCGGGAGCCT s droTak2.KB461535 150141 71 - 669855 tcat-----------------tttaaaagccAAGGAATTTTTTGGGGAC--AGATAGCTGGGTATATG--------TGATATGCgtcgaaaatgt----------att s droRho2.KB449310 45859 73 - 65043 tcat-----------------tttaaaaagtaaagaa--tTTTGGGTGC--GGATAGTTGACTTTATGTGCTACACTAATATGCTTCga----gc----------att s droFic2.KB457177 89110 61 + 995874 tcat-----------------ttttaggGCTGAAGAA--TTTTGGGCAC--GGGCAG-----TAC-----------TGATATGCCccgaaaatgt----------att s droMoj3.scaffold_6496 26157996 58 + 26866924 ttat-----------------caggcagaacgaatca--ttgcagacag-------------tatgtt--------tgtcgcatgacgtatatat----------att a score=-25645.000000 s dm6.chr2R 24366024 30 + 25286936 TATTAAACG------TATTT-TGACGC---ATGGCCTAA------------A s droSim1.chr2R 18704407 30 + 19596830 TATTAATAG------TATTT-TGACGC---ACGGCCCAA------------A s droSec1.super_23 124175 29 + 989336 TATTAAAAG------TATTT-TGACGC---ACGGCCCGG------------- s droYak3.chr2R 20213757 30 + 21139217 tattaaacG------TATGT-TTTCGC---ATGGACTGA------------A s droEre2.scaffold_4845 21611528 9 + 22589142 TATTAAACG------------------------------------------- s droBia2.KB462602 805084 20 + 3129309 tattaaaaa------tgttt-caacgC------------------------- s droSuz1.KI419649 12050503 20 - 14502029 tattaaaca------tgTTT-CAACGC------------------------- s droEug2.KB465067 608745 37 + 1515531 tattaaacGTTGAAATACTT-TGCTGG---TTGAAATAA-----------CA s droEle2.KB458573 531264 38 - 5320397 tattaaaca----------a-taaagc---tTGGGCCCAACTTCTCATTCAA s droKik2.KB459527 285576 32 - 1234237 TTTTAAAAG------TGTCTACAGTAC---TCCTACCAA-----------CC s droTak2.KB461535 150212 32 - 669855 tattaaaca------tgTCC-CAACGCTTTTTTAACTGC------------- s droRho2.KB449310 45932 29 - 65043 tattaaaaa------tgttt-caaagc---TTGGCCAAA------------- s droFic2.KB457177 89171 17 + 995874 tattattca------caGCT-TGA---------------------------- a score=-32230.000000 s dm6.chr2R 24366054 22 + 25286936 -GTATGTTTTACTTTGC------AAATAC s droSim1.chr2R 18704437 22 + 19596830 -GTCTGTTTTACTTTGC------AAATAA s droYak3.chr2R 20213787 22 + 21139217 -AGCCTGCTTACGTTTC------ACATAC s droEre2.scaffold_4845 21611537 28 + 22589142 -AGCCTGCTTACGCTACAGATGTACAGAC s droBia2.KB462602 805104 24 + 3129309 -----TTTTTTAGTTACCCAAAAATATGC s droSuz1.KI419649 12050523 23 - 14502029 ------TTTTTAGTTACCCCAAAATATTC s droEug2.KB465067 608782 28 + 1515531 -CATTAAGTTACGTTTTTAGTTGATATTT s droEle2.KB458573 531302 28 - 5320397 -GTACTTCTTTAGTTACGaccacaaaaat s droKik2.KB459527 285608 28 - 1234237 -TACCTACCTACCCTCCTACTTCGAAGAG s droTak2.KB461535 150244 22 - 669855 -GAAATTTATTAGTTAT------GAACTT s droFic2.KB457177 89188 29 + 995874 TCTGAATCTCCAATTTTTAGTGACTTTAC a score=-22719.000000 s dm6.chr2R 24366076 14 + 25286936 ---AAGGAAGA-------AAATAA s droSim1.chr2R 18704459 14 + 19596830 ---AAGGAAGA-------AAATAA s droYak3.chr2R 20213809 13 + 21139217 ---GAGGATG--------AAATGA s droEre2.scaffold_4845 21611565 13 + 22589142 ---GAAGTTG--------AAATTA s droBia2.KB462602 805128 14 + 3129309 ---TAGCATAA-------ACACAA s droSuz1.KI419649 12050546 14 - 14502029 ---TAgcacaa-------aaacaa s droEug2.KB465067 608810 14 + 1515531 ---TAACACAA-------GGaaca s droEle2.KB458573 531330 21 - 5320397 ---taaaaacattactCCCAATGG s droKik2.KB459527 285636 13 - 1234237 ---CAAAACT--------CAAGGA s droTak2.KB461535 150266 13 - 669855 ---GAAAAAG--------AACCAA s droFic2.KB457177 89217 3 + 995874 ---CAG------------------ s droPer1.super_34 547341 17 - 916997 AAGAAGAAAAA-------TAAATA a score=-30955.000000 s dm6.chr2R 24366090 24 + 25286936 TGACATTCGAAA-----GTACCCGAA------ACT-- s droSim1.chr2R 18704473 24 + 19596830 AGGCATTCGAAA-----ACACACAAA------ACT-- s droYak3.chr2R 20213822 24 + 21139217 TGCCATTCTTAA-----GCACAAAAA------ACT-- s droEre2.scaffold_4845 21611578 24 + 22589142 TGGCATTTTAAA-----GCACTCAGA------AAT-- s droBia2.KB462602 805142 23 + 3129309 AATGGCATGAAA-----GGAGCCTTA-------TT-- s droSuz1.KI419649 12050560 30 - 14502029 catttattGAAA-----GGAaccatataatatttt-- s droEug2.KB465067 608824 24 + 1515531 tatttaaaagaa-----agaaatcgA------TTT-- s droEle2.KB458573 531351 24 - 5320397 TGGCCTCTAAAT-----acttcataa------att-- s droKik2.KB459527 285649 29 - 1234237 TATTTTCTTAAGAATTTGTCTAAATA------ATC-- s droTak2.KB461535 150279 24 - 669855 AGGGATATTTTA-----GCACCAGCA------ATT-- s droPer1.super_34 547358 24 - 916997 TATCTCTCGATA-----TTATACAAA------ACT-- s droGri2.scaffold_15245 914180 26 + 18325388 TGATTTTCAAAA-----TTTAATGTA------ATACT a score=2329.000000 s dm6.chr2R 24366114 1 + 25286936 C s droSim1.chr2R 18704497 1 + 19596830 C s droYak3.chr2R 20213846 1 + 21139217 C s droEre2.scaffold_4845 21611602 1 + 22589142 C s droBia2.KB462602 805165 1 + 3129309 T s droSuz1.KI419649 12050590 1 - 14502029 c s droEug2.KB465067 608848 1 + 1515531 C s droEle2.KB458573 531375 1 - 5320397 t s droKik2.KB459527 285678 1 - 1234237 C s droPer1.super_34 547382 1 - 916997 T s droGri2.scaffold_15245 914206 1 + 18325388 C a score=-1478.000000 s dm6.chr2R 24366115 3 + 25286936 AAA s droSim1.chr2R 18704498 3 + 19596830 ACA s droYak3.chr2R 20213847 3 + 21139217 TCA s droEre2.scaffold_4845 21611603 3 + 22589142 ACA s droBia2.KB462602 805166 3 + 3129309 ATG s droSuz1.KI419649 12050591 3 - 14502029 att s droEug2.KB465067 608849 3 + 1515531 ATA s droEle2.KB458573 531376 3 - 5320397 tta s droKik2.KB459527 285679 3 - 1234237 AGT s droGri2.scaffold_15245 914207 3 + 18325388 AGA a score=-4544.000000 s dm6.chr2R 24366118 9 + 25286936 AAAGAAACA- s droSim1.chr2R 18704501 9 + 19596830 AAAGAATCT- s droYak3.chr2R 20213850 9 + 21139217 AAAGGAACG- s droEre2.scaffold_4845 21611606 9 + 22589142 AAAGTATCT- s droBia2.KB462602 805169 9 + 3129309 AAAGATCGA- s droSuz1.KI419649 12050594 9 - 14502029 gaaaatgtA- s droEug2.KB465067 608852 9 + 1515531 CAAAGTAGG- s droEle2.KB458573 531379 9 - 5320397 aaaacttga- s droKik2.KB459527 285682 9 - 1234237 gatgtaata- s droWil2.CH963894 1323209 9 + 2843958 AAGGAATTA- s droGri2.scaffold_15245 914212 9 + 18325388 -AATGATCAA a score=-15727.000000 s dm6.chr2R 24366127 4 + 25286936 -TTAG s droSim1.chr2R 18704510 4 + 19596830 -TTAG s droYak3.chr2R 20213859 4 + 21139217 -TCCT s droEre2.scaffold_4845 21611615 4 + 22589142 -TTGA s droBia2.KB462602 805178 4 + 3129309 -TTTG s droSuz1.KI419649 12050603 1 - 14502029 -T--- s droEug2.KB465067 608861 4 + 1515531 -TTCC s droEle2.KB458573 531388 4 - 5320397 -tCCT s droKik2.KB459527 285691 4 - 1234237 -tatt s droRho2.KB449310 46371 4 - 65043 -taaa s droFic2.KB457177 89220 4 + 995874 -TTAG s droWil2.CH963894 1323218 1 + 2843958 ----G s droGri2.scaffold_15245 914221 4 + 18325388 TTTA- a score=295.000000 s dm6.chr2R 24366131 1 + 25286936 A s droSim1.chr2R 18704514 1 + 19596830 A s droKik2.KB459527 285695 1 - 1234237 t s droPer1.super_34 547400 1 - 916997 A s droWil2.CH963894 1323222 1 + 2843958 A s droGri2.scaffold_15245 914225 1 + 18325388 A a score=-61052.000000 s dm6.chr2R 24366132 22 + 25286936 --TACATTATTTCAGGCCTATCTT s droSim1.chr2R 18704515 22 + 19596830 --TAAATTATTTCTGGCCCATCTT s droBia2.KB462602 805182 16 + 3129309 --------ATACCATACGTTCTTG s droSuz1.KI419649 12050604 16 - 14502029 --------ACTGCAAGAGTGTTTA s droEug2.KB465067 608865 20 + 1515531 ----CCATAGCCCATGTTCGCGTT s droEle2.KB458573 531392 12 - 5320397 ---------TGCCTGGATCAA--- s droKik2.KB459527 285696 22 - 1234237 --aataatacctAATATTTACCTC s droTak2.KB461535 150316 19 - 669855 --TATGTAGTTCTAGTTGTAT--- s droRho2.KB449310 46375 22 - 65043 --aaaagttttccatttaaatcag s droFic2.KB457177 89227 18 + 995874 --TACTGATTGTCACATCCC---- s droPer1.super_34 547401 18 - 916997 --TACAATTTCTGAAAACTT---- s droWil2.CH963894 1323223 22 + 2843958 --TGCTAGAATTAGAGACTACTTT s droGri2.scaffold_15245 914226 24 + 18325388 TAATCAGATTTTCAAGACTGCTCT a score=-33034.000000 s dm6.chr2R 24366154 10 + 25286936 CTTTT-------CCAAA-- s droSim1.chr2R 18704537 10 + 19596830 CCTTT-------CCAAA-- s droSec1.super_23 124204 6 + 989336 ----T-------CCTAA-- s droYak3.chr2R 20213863 6 + 21139217 ----T-------TTCAA-- s droEre2.scaffold_4845 21611619 13 + 22589142 ----TAAATTGGTTGAG-- s droBia2.KB462602 805198 10 + 3129309 CCGCC-------CCAAC-- s droSuz1.KI419649 12050620 10 - 14502029 Ccatt-------taaaa-- s droAna3.scaffold_13266 5717077 7 - 19884421 ---CT-------TCAAC-- s droEug2.KB465067 608885 10 + 1515531 CATTT-------TCAGG-- s droEle2.KB458573 531404 7 - 5320397 ---TT-------TTAgc-- s droKik2.KB459527 285722 10 - 1234237 TAATT-------TAGAa-- s droTak2.KB461535 150335 8 - 669855 --GTT-------GCAAA-- s droRho2.KB449310 46397 8 - 65043 --ctt-------ataaa-- s droFic2.KB457177 89245 7 + 995874 CCATT-------CC----- s droPer1.super_34 547419 10 - 916997 TCTAT-------GTAAA-- s droWil2.CH963894 1323246 9 + 2843958 TAATC-------ttga--- s droGri2.scaffold_15245 914250 10 + 18325388 --GTT-------TTGAAAA a score=-18669.000000 s dm6.chr2R 24366164 10 + 25286936 -------TTCTTAGTAT s droSim1.chr2R 18704547 10 + 19596830 -------TGCTTAGTAT s droSec1.super_23 124210 10 + 989336 -------TGCTTAGTAT s droYak3.chr2R 20213869 10 + 21139217 -------TGCTAAGTAA s droEre2.scaffold_4845 21611632 10 + 22589142 -------TGCTGAGTAA s droBia2.KB462602 805209 10 + 3129309 -------TTTTAAGAGT s droSuz1.KI419649 12051118 10 - 14502029 -------tttttgttgc s droAna3.scaffold_13266 5717087 10 - 19884421 -------CTCTTGGGGT s droEug2.KB465067 608895 9 + 1515531 --------ACTTAAACG s droEle2.KB458573 531414 10 - 5320397 -------aaataagaaa s droKik2.KB459527 285739 10 - 1234237 -------attttacaat s droTak2.KB461535 150344 10 - 669855 -------TCCTTCGGAA s droRho2.KB449310 46407 10 - 65043 -------ttcttatttg s droPer1.super_34 547430 9 - 916997 -------CTTTGGGTA- s droWil2.CH963894 1323255 8 + 2843958 ---------ttaagaat s droGri2.scaffold_15245 914260 17 + 18325388 TCAGATCTGTTTAATAC a score=930.000000 s dm6.chr2R 24366174 2 + 25286936 TT s droSim1.chr2R 18704557 2 + 19596830 TT s droSec1.super_23 124220 2 + 989336 TT s droYak3.chr2R 20213879 2 + 21139217 TT s droEre2.scaffold_4845 21611642 2 + 22589142 TT s droSuz1.KI419649 12051128 2 - 14502029 tt s droAna3.scaffold_13266 5717097 2 - 19884421 TT s droEug2.KB465067 608906 1 + 1515531 T- s droEle2.KB458573 531424 2 - 5320397 tt s droKik2.KB459527 285749 1 - 1234237 -t s droRho2.KB449310 46417 2 - 65043 TT s droPer1.super_34 547440 1 - 916997 C- s droWil2.CH963894 1323265 2 + 2843958 tt s droGri2.scaffold_15245 914277 2 + 18325388 TT a score=-746387.000000 s dm6.chr2R 24366176 62 + 25286936 ATCAAA-------------------------ACTGTGTT---CT-----A-------------TGAT------------------------------------------AGATCA------------------AGTTTC------T---------------------AAATAAATGAAGTGAAA------------------------ACTCT--------G-------------------------------------------GAACA s droSim1.chr2R 18704559 79 + 19596830 ATCAAA-------------------------ACTGTGTT---CT-----ATTCGTACGTAAATTAGT------------------------------------------AAATTACAAT--------------AGTTAC------T---------------------AAATAGATGAAATTGAA------------------------ACTCT--------G-------------------------------------------GCACA s droSec1.super_23 124222 79 + 989336 ATCAAA-------------------------ACTGTGTT---CT-----ATTCGTACTTAAATTAGT------------------------------------------AAATTACAAT--------------AGTTAC------T---------------------AAATAAATGAAATGAAA------------------------ACTCT--------G-------------------------------------------TCACA s droYak3.chr2R 20213881 120 + 21139217 ATTACA-------------------------ACAGTGTT---CT-----ATTCAAAAGTAAACCAAT-----TTCTCGCATTT-----------------------CAAAGCTTACAGT----------TC--GCTATC-------------------------------TAAATGA-------------------------------ACTTC----ATATG----TCTAATGTATCT-----ACCTATTC--TAATCGAAGAACATGCA s droEre2.scaffold_4845 21611644 157 + 22589142 ATT-----------------------------CAGTGTT---CTAATCAA-----ACGTTACCCCATTTCAGTACTTTCATTT--------------------G--CGATAAATAAAGT----------GC--AATTTCTGCAAAT---------------------AAATAAATGAAATGTAA------ATT---------------ACTTCCCCAGTATGATATTCACATGTACTTCATAGATCTAATCTATAATCTTGGATCATACA s droBia2.KB462602 805585 83 + 3129309 ATCATA------------------------------ATT---GT-----ATATTATTGGGTAATATT-----TCCTTCCTAT---------------------------AGACAACTAT--------------AGCTGC----------------------------ACATTTAGGGATTAAAT------------------------ACATT--------A-------------------------------------------TTGCT s droSuz1.KI419649 12051131 87 - 14502029 ATCATATGGCGTTGAAAGGATATCCTTTAAAactacatt---tt-----atataaaaatgaaatatt-----ttcttcc---------------------------------------G--------------AGCTGT----------------------------ACAT--------------------------------------CCCT--------T-------------------------------------------TTGCT s droAna3.scaffold_13266 5717100 49 - 19884421 -------------------------------------------------------------------------------------------------------GGCTAAAATTTACTA---------------AACTAT----------------------------AGTCATAGAAAGTCTAA------------------------ACTCT--TAATAA------------------------------------------------- s droEug2.KB465067 608907 67 + 1515531 GTAAAA-------------------------ACTGTTTTGGGCT-----GCTAGAATATCCTGCTTT------------------------------------------ATAGCAAAG---------------AAATGT----------------------------GAATAAAATGAGTTA---------------------------------------------------------------------------------------- s droEle2.KB458573 531426 60 - 5320397 ------------------------------------------------------aacaaaaaggGAT-----AGCTAAGATTTC-------------------AGAACCAAGgcaaaa---------------aattac-----------------------------tttatagGCTATCA---------------------------------------------------------------------------------------- s droKik2.KB459527 285751 68 - 1234237 -----------------------------------------------------------------------------------ct-------TATGAC----AAGCTGAAAGccaatag--------------atatat------ttt---------------ttgagagtctataaattatac------att--------ttctctgACT----------------------------------------------------------- s droTak2.KB461535 150361 58 - 669855 ----------------------------------------------------------------------ACAAATACTTTTTTCAA-----TGTGCC----AGAATCGAAGGTATTAT--------------ATCtac----------------------------atttctaaaata------------------------------------------------------------------------------------------- s droRho2.KB449310 46419 55 - 65043 ---------------------------------------------------------------------------------------------------------------------------------ACTTGGTTGC------C---------------------TTATATTTGAGGTCTAatataatattctttaatatttttaaact----------------------------------------------------------- s droFic2.KB457177 89252 42 + 995874 ---------------------------------------------------------------------------------------------------------TGAgggaacaaaat--------------aaatat------ttg-----------cta-ttGATTTTTTGTGAGA------------------------------------------------------------------------------------------- s droPer1.super_34 547441 68 - 916997 -------------------------------------------------------------------ATTAGTATTGGGTTTTCAGAAACGCTCTAGT----TTGGTTCAAGCTAT-----------------AGCTAT----------------------------GTATGTTTTCTGCATAA-------------------------------------------------------------------------------------- s droWil2.CH963894 1323267 50 + 2843958 -------------------------------------------------------------------------------------------tattgaCCTCATCAATAGAAACTATAAATAGAAAGTAGGC--AGTTAG----------------------------AAAC--------------------------------------------------------------------------------------------------- s droGri2.scaffold_15245 914279 51 + 18325388 ---------------------------------------------------------------------------------------------------------TCCATAGCCACAAA--------------GACTGA------TCAGATTTTCAAGACTGCTCTGATTTTCACA---------------------------------------------------------------------------------------------- a score=-12968.000000 s dm6.chr2R 24366238 6 + 25286936 --AAAA------------------GG s droSim1.chr2R 18704638 6 + 19596830 --AAAA------------------TG s droSec1.super_23 124301 6 + 989336 --AAAA------------------TG s droYak3.chr2R 20214001 24 + 21139217 --AAAAGGACTTAAAATGTCCTTCTG s droEre2.scaffold_4845 21611801 24 + 22589142 --AAAAGGACCTCAAGTGTCCTGCTG s droBia2.KB462602 805668 14 + 3129309 --TGAG----------TGATTTCTTG s droSuz1.KI419649 12051218 14 - 14502029 --TAAG----------TGtttttttG s droPer1.super_34 547511 4 - 916997 --CAAC-------------------- s droGri2.scaffold_15245 914330 6 + 18325388 ACAAAG-------------------- a score=-632281.000000 s dm6.chr2R 24366244 52 + 25286936 TAAACTA------------------TCTCTT----GGAT-----ATATATCTATTCTGA-----------------------------AATCTATTCTAAT-------------------------------------GTTTTTG s droSim1.chr2R 18704644 24 + 19596830 TAAACTA------------------------------------------------------------------------------------CCAATCTGAT-------------------------------------GTAGCTC s droSec1.super_23 124307 19 + 989336 TAAACTA-----------------------------------------------------------------------------------------CTAAT-------------------------------------GTAACTC s droYak3.chr2R 20214025 70 + 21139217 CAGACTGTTTCCTA-----------TCTGTCTTAAGCAA-----ATGCAATCACTGGTTC----------------------------CAACCGATTTATTTAAA-------------------------------CAGTTTTTG s droEre2.scaffold_4845 21611825 62 + 22589142 CAGACTG------------------TCTGTCCTAAGCAA-----ATGCAATTACTTGAT-----------------------------AAACCGATTTATTTGTA-------------------------------CAGTTTTTG s droBia2.KB462602 805682 31 + 3129309 TGTTCTC----------------------------------------------ATCAGt-------------------------------ttttttCTGGT-------------------------------------GATGTTC s droSuz1.KI419649 12051232 32 - 14502029 TGAGCCC----------------------------------------------ATCAAT------------------------------AATTTGTCTGGT-------------------------------------AATGTTC s droAna3.scaffold_13266 5717149 34 - 19884421 -------------------------TTAAACCACAATAA-----CTCCCTAC-------------------------------------ATCCCTTCT--------------------------------------------TTA s droBip2.KB464407 1967097 93 + 2915140 -------------AAGA-GGAAGTCTCTATCTTtagtat-----atacatacttt---------------------------------agtcttttttatattcaaaacaTTATAACTCGAGAAAACTCTATAGATCTGTACTTA s droEug2.KB465067 608974 49 + 1515531 --------------------------------AAAAAGT-----TCTCGATTGCTTGATCGC----------------------TCATCAATTTGTCTGGC-------------------------------------AAAGTTC s droEle2.KB458573 531486 55 - 5320397 ---------------------------CATTATTAAAAT-----GCCTAACGAATAGATAgtgtttg--ttaaa----------tatttagtttttctg---------------------------------------------- s droKik2.KB459527 285819 64 - 1234237 ----------------------------------AATCG-----ATGacattatttaatactttttga-gTATATT------CCTcttcaattaatttcccaaGA---------------------------------AATAT-- s droTak2.KB461535 150419 50 - 669855 ------------------tacaaatattaaccAAATCAC-----ACATATCTACTCATATGG--------------------------ATGTTTACCTG---------------------------------------------- s droRho2.KB449310 46474 66 - 65043 --------------------------------tcctgat-----ataaaaactttttgttgtaTTGAT-TTCTTGT----GAGCTCATCAATTATTATACT-------------------------------------ACTAATG s droFic2.KB457177 89294 30 + 995874 --------------------ATAATGTGATCTGTGGGGA-----AAAAAGCCACC------------------------------------------------------------------------------------------ s droPse3.chr3 1358654 65 - 19787792 ---------------------TAAATTATATTGCAGAGG-----ATACCTATAATTGGTTATTTGTAACCTATTAC----TAATGTTTAAAGGAG-------------------------------------------------- s droPer1.super_34 547515 65 - 916997 ---------------------TAAATTATATTGCAGAGG-----ATACCTATAATTGGTTATTTGTAACCTATTAC----TAATGTTTAAAGTAG-------------------------------------------------- s droMir2.chr3 1399710 65 - 20862834 ---------------------TAAATTATATTGCAGAGG-----ATACCTATAATTGGTTATTTGTAACCTATTAC----TAATGTTTAAAGTTG-------------------------------------------------- s droWil2.CH963894 1323317 43 + 2843958 --------------TTATTAGCCAATTAGTTAATCGAAATCTCTATAAATCTCCTTG---------------------------------------------------------------------------------------- s droGri2.scaffold_15245 914336 51 + 18325388 -----------------------------------------------CATTTTAATCATAATTTCTCAACTAGATCATTATTACACCCAAAGTTCTGT----------------------------------------------- a score=-230072.000000 s dm6.chr2R 24366296 19 + 25286936 ----------TCAGTTGATA-ACTT------C----------TAT--G s droSim1.chr2R 18704668 20 + 19596830 ----------ATATCCTATAGATAT------C----------TAT--C s droSec1.super_23 124326 20 + 989336 ----------ATATCTCATAGAAAT------C----------TAT--C s droYak3.chr2R 20214095 16 + 21139217 ----------TGAGCTGATG-ACTG------C---------------C s droEre2.scaffold_4845 21611887 21 + 22589142 ----------TGAGCTGATG-ACTC------C----------AATCAC s droBia2.KB462602 805713 24 + 3129309 ----------TCAAGCTAAA-GTTCACTAG-C----------TTC--T s droSuz1.KI419649 12051264 25 - 14502029 ----------TCAAGTAAAA-GTTCACTTGAC----------TTC--T s droAna3.scaffold_13266 5717183 15 - 19884421 ----------AAAAGCCAAA-GTTC----------------------T s droBip2.KB464407 1967190 15 + 2915140 ----------AAAAGTCATA-GTTC----------------------T s droEug2.KB465067 609023 23 + 1515531 ----------TGGG--AAAA-GTACACTTGAG----------TTC--T s droKik2.KB459527 285883 29 - 1234237 ----------TCTGGGAATA-ACCC------CGCTCTCAAAGCAC--T s droTak2.KB461535 150469 12 - 669855 -----------------ACA-ATCC------C----------Taa--c s droRho2.KB449310 46541 19 - 65043 ----------GCTGGGAAAA-ACTA------C----------TCT--C s droFic2.KB457177 89324 7 + 995874 -------------------A-ACTT------C----------T----- s droPse3.chr3 1358728 10 - 19787792 ----------TCCTCTAGTA---------------------------- s droPer1.super_34 547589 10 - 916997 ----------TCCTCTAGTA---------------------------- s droMir2.chr3 1399784 10 - 20862834 ----------TCCTCTAGTA---------------------------- s droWil2.CH963894 1323367 10 + 2843958 ----------ACCTGTAATA---------------------------- s droGri2.scaffold_15245 914387 19 + 18325388 TGAATCAATGCGTTCTAAT----------------------------- a score=-35273.000000 s dm6.chr2R 24366315 21 + 25286936 -------------TATTGTATTTCACAAGAATGA--------- s droSim1.chr2R 18704688 19 + 19596830 -------------TAT--TCTTTCATAAGAAAGA--------- s droSec1.super_23 124346 19 + 989336 -------------TAT--TCTTTCATAAGAAAGA--------- s droYak3.chr2R 20214111 19 + 21139217 -------------AAG--TATTTCAACAGAAAGA--------- s droEre2.scaffold_4845 21611908 19 + 22589142 -------------GAG--TATTTCATTAGAAAGA--------- s droBia2.KB462602 805737 19 + 3129309 -------------TCG--AGATTCCCAAGAACGA--------- s droSuz1.KI419649 12051289 19 - 14502029 -------------TGG--TTATTCCCAAGAATAA--------- s droAna3.scaffold_13266 5717198 16 - 19884421 -------------TGG--TATTTCACAAGTA------------ s droBip2.KB464407 1967205 16 + 2915140 -------------TGG--TATCTCACAAGTA------------ s droEug2.KB465067 609046 19 + 1515531 -------------CGG--CAATTCTTAGGGATGA--------- s droKik2.KB459527 285912 19 - 1234237 -------------ATT--TACTTCTAAACTATCA--------- s droTak2.KB461535 150689 19 - 669855 -------------TGA--TAATTCCTGAGAACGA--------- s droRho2.KB449310 46574 12 - 65043 -------------TTG--AAATTCTTA---------------- s droFic2.KB457177 89331 19 + 995874 -------------TCT--TATTTCCCAAGAATTA--------- s droPse3.chr3 1358741 19 - 19787792 -------------CTG--AGTGCCCTACGTATCT--------- s droPer1.super_34 547602 19 - 916997 -------------CTG--AGTGCCCTACGCATCT--------- s droMir2.chr3 1399798 19 - 20862834 -------------CCG--AGTGCCCTACGTATCT--------- s droWil2.CH963894 1323378 19 + 2843958 -------------CCT--GACTTCCTAGGGGATA--------- s droGri2.scaffold_15245 914406 41 + 18325388 TTTTAGAAACCACTAA--GACTTTACAACTGCCACAAGTCTAA a score=-41733.000000 s dm6.chr2R 24366336 26 + 25286936 AGTTCTC---ATCCGAT--------------------------CCGCA-------AGTT-----CG--T s droSim1.chr2R 18704707 26 + 19596830 AGTTCTC---GTCCGAT--------------------------CCGCA-------AGTT-----CG--T s droSec1.super_23 124365 26 + 989336 AGTTATC---GTCCGAT--------------------------CCGCA-------AGTT-----CG--T s droYak3.chr2R 20214130 26 + 21139217 ACTTCTC---ATTCGAT--------------------------CCGCA-------AGTT-----CG--T s droEre2.scaffold_4845 21611927 26 + 22589142 ACTTCTC---ATCCGAT--------------------------CCGCA-------AGTT-----CG--T s droBia2.KB462602 805756 26 + 3129309 AGTACTC---CTCCGTT--------------------------CCTAG-------GGTT-----CG--A s droSuz1.KI419649 12051308 26 - 14502029 AGTACTC---CTCCGTT--------------------------TCTAA-------GGTT-----CG--T s droAna3.scaffold_13266 5717214 24 - 19884421 ---CCTCA--AAACGAC--------------------------TCTAA-------AGAT-----CG--T s droBip2.KB464407 1967221 23 + 2915140 ---CCTC---AGACGAC--------------------------TCTAA-------AGAT-----CG--T s droEug2.KB465067 609065 17 + 1515531 AGTACTC---CTCC------------------------------------------GCT-----CG--A s droEle2.KB458573 531925 26 - 5320397 AGTACTC---CGTCGCT--------------------------TCTAA-------GGTT-----CG--C s droKik2.KB459527 285931 26 - 1234237 AGTACTC---CCTCGGC--------------------------TCTAA-------GGTT-----CG--T s droTak2.KB461535 150708 26 - 669855 AGTACTC---CTCCGTT--------------------------GCTAA-------GGTT-----CG--T s droRho2.KB449310 46586 31 - 65043 AGCACTC---CTTCGTT--------------------------TCTAA-------GGTTCTCGGCG--T s droFic2.KB457177 89350 29 + 995874 AGTACTCGATCATCGAC--------------------------TCTAA-------GGTC-----CG--C s droPse3.chr3 1358760 19 - 19787792 TGGGCTT---GTTC------------------------------------------GTT-----CGACT s droPer1.super_34 547621 19 - 916997 TGGGCTC---GTTC------------------------------------------GTT-----CGACT s droMir2.chr3 1399817 19 - 20862834 TGGGCTC---GTTC------------------------------------------GTT-----CGACT s droWil2.CH963894 1323398 52 + 2843958 AGTTCTG---TTTCGTTGAACTATTTAAACACAAGTTAGGGTATCTAA-------AATT-----CC--A s droGri2.scaffold_15245 914447 24 + 18325388 -----TC---GTAATAT--------------------------CCGAAGTAATTGAGT----------- a score=235146.000000 s dm6.chr2R 24366362 16 + 25286936 TGTAATTGTGCAATTC s droSim1.chr2R 18704733 16 + 19596830 TGTAATTGTGCAATTC s droSec1.super_23 124391 16 + 989336 TGTAATTGTTCAATTC s droYak3.chr2R 20214156 16 + 21139217 TGTAATTGTGCAAttc s droEre2.scaffold_4845 21611953 16 + 22589142 CGCAGTTGTGCAATTC s droBia2.KB462602 805782 16 + 3129309 TGTAATTGTGCAATTC s droSuz1.KI419649 12051334 16 - 14502029 TGTAATTGTGCAATtc s droAna3.scaffold_13266 5717238 16 - 19884421 AGTAATTGTGCAATTC s droBip2.KB464407 1967244 16 + 2915140 AGTAATTGTGCAATtc s droEug2.KB465067 609082 16 + 1515531 TGTAATTGTGCAAttc s droEle2.KB458573 531951 16 - 5320397 TGTAATTGTGCaattc s droKik2.KB459527 285957 16 - 1234237 TGTAATTGTGCAATTC s droTak2.KB461535 150734 16 - 669855 TGTAATTGTGCAATTC s droRho2.KB449310 46617 16 - 65043 TGTAATTGTGCAAttc s droFic2.KB457177 89379 16 + 995874 TGTAATTGTGCAATTC s droPse3.chr3 1358779 16 - 19787792 TGCAATTGTGTAATTC s droPer1.super_34 547640 16 - 916997 TGCAATTGTGTAATTC s droMir2.chr3 1399836 16 - 20862834 TGTAATTGTGTAATTC s droWil2.CH963894 1323450 16 + 2843958 CGTTGTTATATagttt s droMoj3.scaffold_6496 26159452 16 + 26866924 tgcgattctgcgattc s droGri2.scaffold_15245 914471 16 + 18325388 TGAGATCGTTTAGTTT a score=4476954.000000 s dm6.chr2R 24366378 578 + 25286936 TTCTGT--------TTGATTTGGCCGCTTAGTTGCG--ACGT-AC-TTTTAGCTGT----------GCTGCCCACGATGTGG-------------A----------TAATTGTTTAGCTGTTATTGTTGTTATTGGACGTTAATATACATTTGATTCTGGTT-----A-------------------------------------------TACATAT--------AAAAAGA--------------GAAAAACGTG---------------------GAGTGTG--T-GTGCGCCTTAATT---------AAAAC-----------------------TGCGG-CC--GCTG-----CTCGTAGGAGTTAATTAGACTGCGGAGGTGT---ACGG-GCCcagttttc-----------------------------------a---g------------ctttcagttttcagttcgcagctcccagtctcagatct--GC---------------------CGATCC---GGC--G---ATC--GTTCGCTTTCAAGTCAAGCCCCAGCTATTAGTCGCTCAATATTACGCG-TTT-------GGCGG---------AC-AACATTGTTCT-TAC---------TTT----TTGC------------------GC-------------------------------------------------------------------------------------TCCCCGTGTT--CT--GTGATCTTGACTT----ATCgacg--g--tata-gga------tgga---------------tg---------gga-----tggggatggggatg-------ggggctgg-----cgaatgggggatggtatagggg----ata--c-----ggg---ctgCTGCTGTTCACACGCTGCTCATCAACAATTGCTGTCACGAATTTTCCACTCGGCGCTTTTTGCGCGCGCTACTTGTTTGTATTTTAAAATTTATTTATTTGTGCAGCCTCCACA s droSim1.chr2R 18704749 601 + 19596830 TTCTGT--------TTGATTTGGCCGCTTAGTTGCG--ACGT-AC-TTTTAGCTGT----------GCTGCCCACGATGTGG-------------A----------TAATTGTTTAGCTGTTATTGTTGTTATGGGTCGTTAATATACATTTGATTCTGGTT-----ATA---------------------------------------TGTACATAT--------AGAAAGA--------------GCAAAACGTG---------------------GAGTGTG--T-GTGCGCCTTAATT---------AAAAC-----------------------TGCGG-CC--GCTG-----CTCGTAGGAGTTAATTAGACTGCGGAGGTGT---ACGG-GCCCAGTTTTC-----------------------------------A---G------------CTTTCAGTTTTCAGTTTGCAGCTCCCAGTCTCAGATCC--GCC-----GATCCGG--------CGATCC---GGC--G---ATC--GTTCGCTTTCAAGTCAAGCCCCAGCTATTAGTCGCTCAATATTACGCG-TTT-------GGCGG---------AC-AACATTGTTCT-TAC---------TTT----TTGC------------------GC-------------------------------------------------------------------------------------TGCCCGTGTT--CT--GTGATCTTGACTT----ATCGACG--G--TATA-GGA------TGGA---------------TG---------GGATGGGTTGGGGATGGGGATACCCAAT-GGGGCTGG-----CGAATGGGGGATGGTACAGGAG----ACA--C-----GGG---CTGCTGCTGTTCACACGCTGCTCATCAACAATTGCTGTCACGAATTTTCCACTCGGCGCTTTTTGCGCGCGCTACTTGTTTGtattttaaaatttatttatttGTGCAGCCTCCACA s droSec1.super_23 124407 617 + 989336 TTCTGT--------TTGATTTGGCCGCTTAGTTGCG--ACGT-AC-TTTTAGCTGT----------GCTGCCCACGATGTGG-------------A----------TAATTGTTTAGCTGCTATTGTTGTTATTGGACGTTAATATACATTTGATTCTGGTT-----ATA---------------------------------------TGTACATAT--------AGAAAGA--------------GCAAAACGTG---------------------GAGTGTG--T-GTGCGCCTTAATT---------AAAAC-----------------------TGCGG-CC--GCTG-----CTCGTAGGAGTTAATTAGACTGCGGAGGTGT---ACGG-GCCCAGTTTTC-----------------------------------A---G------------CTTTCAGTTTTCAGTTTGCAGCTCCCAGTCTCAGATCC--CCC-----GATCCGG--------CGATCC---GGC--G---ATC--GTTCGCTTTCAAGTCAAGCCCCAGCTATTAGTCGCTCAATATTACGCG-TTT-------GGCGG---------AC-AACATTGTTCT-TAC---------TTT----TTGC------------------GC-------------------------------------------------------------------------------------TCCCCGTGTT--CT--GTGATCTTGACTT----ATCGACG--G--Tata-gga------tggatgggatgggatgggttg---------ggatgggttggggatgggGATACCCAATGGGGGCTGG-----CGAATGGGGGATGGTATAGGGG----ACA--C-----GGG---CTGCTGCTGTTCACACGCTGCTCATCAACAATTGCTGTCACGAATTTTCCACTCGGCGCTTTTTGCGCGCGCTACTTGTTTGtattttaaaatttatttatttGTGCAGCCTCCACA s droYak3.chr2R 20214172 633 + 21139217 ttttgt--------ttgatttggcCGCTTAGTTGCG--ACGT-ACTTTTTTACTCT----------GCTGCCCACGATGTGG-------------A----------TAATTGTTtagctgttattgttgttattggaCGTTAATATACATTTGATTCTTgtt-----ata------------------------------------ct-cgtacatat-------------ga--------------G-AAAAGAtg---------------------gagtgtg--t-gtgcgccttAATT---------AAAAC-----------------------TGTGC-CC--GCTG-----CTCGTAGGAGTTAATTAGACTGCGGAGGTGT---ACGG-GCCcagttttcagtttgtagtttgtagtttgtagttttcagttttca---g------------tttttagtttttagctTGCAGCTTTCAGTCTCAGATCC--GCC-----GATCTGGAGATCCAGCGATTC---AGC--G---ATC--GTTCGCTTTCAAGTCAAGCCCCAGCTATTAGTCGCTCAATATTACGCG-TTT-------GGCGG---------AC-AACATTGTTCT-TGC---------TTT----TTGC------------------GC-------------------------------------------------------------------------------------TCCCCGAGTT--CT--GTGATCTTGACTT----ATCGACG--G--Tatg-gga------tgga---------tcgggttg---------ggatggtatcgagttggggatg-------ggg-------------aatggggatggtatagggg----aCA--C-----GGG---CTGCTGCTGTTCACACGCTGCTCATCAACAATTGCTGTCACGAATTTTCCACTCGGCGCTTTTTGCGCGCGCTActtgtttgtattttaaaatttatttatttgtgcagCCTCCACA s droEre2.scaffold_4845 21611969 592 + 22589142 TTTTGT--------TTGATTTGGCCGCTTAGCTGCG--ACGT-AC-TTTTAGTTGT----------GCTGCCCACGATGTGG-------------A----------TAATTGTTTAGCTGTTATTGTTGTTATTGGACGTTAATATACATTTGATTCTTGTT-----ACA------------------------------------CT-CGTACATGTGTAT----AAGAAGT--------------G-GAAACGTG---------------------GAGTGTG--T-GTGCGCCTTAATT---------AAAAC-----------------------CGTGG-CC--GCTG-----CTCGTAGGAGTTAATTAGACTGCGGAGGTGT---ACGG-GCCCAGTTTTC---------------------------------------------------------AGTGTTCAGTTTGCAGCTTTCAGTCTCAGATAC--GCC-----GATCCGGCGATCCGACGATCC---AGC--G---ATC--GTTCGCTTTCAAGTCAAGCCCCAGCTATTAGTCGCTCAATATTACGCG-TTT-------GGCGG---------AC-AACATTGTTCT-TGC---------TTT----TTGC------------------GC-------------------------------------------------------------------------------------TCTCCGTGTT--CT--GTGATCTTGACTT----ATCGACG--G--TATG-GGA------TGGA---------------TG---------GGATGGTATCgggttggggttg-------ggg--------------ttggggatggTATAGGGG----ACA--C-----GGG---CTGCTGCTGTTCACACGCTGCTCATCAACAATTGCTGTCACGAATTTTCCACTCGGCGCTTTTTGCGCGCGCTACTTGTTTGtattttaaaatttatttatttGTGCAGCCTCCACA s droBia2.KB462602 805798 533 + 3129309 -TTTGT--------TTGATTTGGCCGCTTGGCTGCG--GCGT-AC-TTT--GGCTTT--------AGCTGCCCACGATCTGG-------------T----------TGATTGTTtagctgttattgttgttactGGACGCTAATATACATTTGATTCTTGTT-----ATAT-----------------------A-----------CT-TGCGCACAT--------AAT--A-----------------AAAGTATC---------------------GAGCGTG--T-GTGCGCCTTAATT---------AAAAC-----------------------CGTGGCCC--GCTG-----CTCGTAGGAGTTAATTAGACTGCGGAGGTGT---ACGG-GCCCAGTTTCC-----------------------------------A---G------------CGTTCAGTCTTTGGTTTTCAGC-----------------------------------------CGATCC----GC--T---GTC--GTTCGCTTTCAAGTCAAGCTCCGGCTATTAGTCGCTCAATATTACGCG-TTT-------GCCCG---------AC-AAcattgtttt-tac---------ttt----ttgc------------------gc-------------------------------------------------------------------------------------TCTCCGTGTT--CT--GGGATCTTGAGTT----ATCGACG--A--TATG-GGA------CGGA---------------T---------------------------------------GGA----------------TGCGATGGCAT-GGGG----GCA--c----gggg---ctgctgctgttcaCACGCTGCTCATCAACAATTGCTGTCACGAATTTTCCACTCGGCGCTTTTTGCGCGCGCTacttgtttgtattttaaaatttatttatttgtgcagCCTCCACA s droSuz1.KI419649 12051350 521 - 14502029 ttttgt--------ttgatttggCCGCTTAGCTGCG--GCGT-AC-TTTTAGCTTTT--------AGCTGCCCACGACCTGG-------------T----------TGATTGTTtagttgttattgttgttat----------tatacATTTGATTCTTGTT-----ATAT-----------------------A-----------CT-TGTAcacat--------aataaa-----------------aaagtatC---------------------GAGCATG--T-GTGCgccttaatt--------aaaaac-----------------------tgaGGCCC--GCTG-----CTCGTAGGAGTTAATTAGACTGCGGAGGTGT---ACGG-Gcccagttttc-----------------------------------a---g------------ttttcagtctTTAGTTTTCAAC-----------------------------------------CGATCC----GC--T---GTC--GTTCGCTTTCAAGTCAAGCCCCAGCTATTAGTCGCTCAATATTACGCG-TTT-------GCCCG---------AC-aacattgtttt-tat---------tct----ttgt------------------GC-------------------------------------------------------------------------------------TCTCCGTGTT--CT--GGGATCTTGAGTT----ATCGACG--A--TATG-GGA------TG-------------------------------------------------------------------------------GATGGTATAGGGG----GCA--C----GGGG---CTGCTGCTGTTCACACGCTGCTCATCAACAATTGCTGTCACGAATTTTCCACTCGGCGCTTTTTGCGCGCGCTActtgtttgtattttaaaatttatttatttgtgcagCCTCCACA s droAna3.scaffold_13266 5717254 530 - 19884421 TTTTGT--------TTGATTTGGCCGC-------------------CTTTGGCTTTC--------AGCTGCCCACGATTGGG-----CCG----CT----------TGATTGTTTAGCTATTATTGTTGCTATTGGGCTTTAATATACATCTGATTCTTGTT-----ATAT-----------------------A-------GTATCTCCCAATATAT--------AAATAA-----------------AAAGTAAT------------------TCCGTGTGTG--T-GTTTGTATTAATT--------AAAAAC-----------------------CGTGG-CC-TGCTG-----CTCGTAGGAGTTAATTAGACTGCGGAGGTGT---ACGG-CCCCAGTTTCA-----------------------------------A---G---------------------------TCGAAGC------GATCGGATCC--GTT-----G--------------TTGTCG---TTC--C---GTC--GTTCGCTTTCAAGTCAAGCCCCAGCTATTAGTCGCTCAATATTACGCGTTTT-------GCCGG---------AC-AACATTTTTTT-TTT---------TTT----TTTC------------------A---------------------------------------------------------------------------------------------ATT--CT--GTGATCTTGAGTTCTTGATCGAGA--G--CAAT-GG----------------------------------------------GGGAAGGAGTATG----------------------------GACCGTGGCTGGA----------------TGG---GGGCTGGTGTTCACACGCTGCTCATCAACAATTGCTGTCACGAATTTTCCACTCGGCGCTTTTTGCGCGCGCTACTTGTTTGtattttaaaatttatttatttGTGCAGCCTCCGCA s droBip2.KB464407 1967260 568 + 2915140 ttttgt--------ttgatttggcCGC-------------------CTTTGGCTTTT--------AGCTGCCCACGATTGGG----CCCG----CT----------TGATTGTTTAGCTGTTATTGTTGCTATTGGGCTTTAATATACATTTGATTCTTGTT-----ATAT-----------------------A-------GTATCt-acaatatat--------aaataa-----------------aaagtattccGCG---TGCTTGTCTGcctgtgtgtg--c-ttgtgtatTAATT--------AAAAGC-----------------------CGTGG-CCGTGCTG-----CTCGTAGGAGTTAATTAGACTGCGGAGGTGT---ACGG-CCCCAGTTTCG-----------------------------------A---G---------------------------TCGAAGC------GATCGGAtcc--gtt-----g--------------tcgt----------t---gtc--gttcgCTTTCAAGTCAAGCCCCAGCTATTAGTCGCTCAATATTACGCGTTTT-------GCCGG---------Ac-aacattgtttt-tat---------ttt-------------------------------------------------------------------------------------------------------------------------tt--ct--gtgatCTTGAGTTCTTGATCGAGA--G--CATT-GGC------GGGG--------------------------GAATGGTATGGCAAGGAGTATGgtt----gagctgct-----gctgctgcggctgctacTGGA----------------TGG---GGGCTGGTGTTCACACGCTGCTCATCAACAATTGCTGTCACGAATTTTCCACTCGGCGCTTTTTGCGCGCGCTActtgtttgtattttaaaatttatttatttgtgcaGCCTCCGCA s droEug2.KB465067 609098 562 + 1515531 ttttgt--------ttgatttggcCGCTGAGCTGCG--CCGC-A--GTTTAGCTTTT--AACTTCAGCTGCCCACGAGCTGG-------------T----------AGATTGTTtagctgttattgttgttatggGACGTTAATATACATTTGATTCTTGTT-----ATAT-----------------------------------CT-CATATAGAT--------ATACAGATGT----GTATAATGAAAAGTATC---------------------GAGTGTG--T-GCGCgccttaatt--------aaaaac-----------------------tgtgGCCC--GCTG-----CTCGTAGGAGTTAATTAGACTGCGGAGGTGT---ACGG-GCCCAGTTTTC-----------------------------------A---G------------CGTTCAGCATTCAGTTTACAGC-----------GGTCC--GAC-----GATCCGG--------CGATCC----GT--C---GTC--GTTCGCTTTCAAGTCAAGCCCCAGCTATTAGTCGCTCAATATTACGCG-TTT-------GGCCG---------AC-aacattgtttt-tat---------ttt----ttgt------------------gc-------------------------------------------------------------------------------------tc-CCGTGTT--CT--GTGATCTTGAGTT----ATCGACG--G--CATG-GGA------TGGA-------------------------------------------------------------------------------TGCTGTAGGGG----ACA--C----gggg---ctgctgctgttcaCACGCTGCTCATCAACAATTGCTGTCACGAATTTTCCACTCGGCGCTTTTTGCGCGCGCTActtgtttgtattttaaaatttatttatttgtgcaGCCTCCACA s droEle2.KB458573 531967 548 - 5320397 ttttgt--------ttgatttggcCGCTTAGTTGCG--CTGT-AC-TTT----TTT---------AGCTGCCCACGATCTGG-------------T----------TGATTGTTtagctgttattgttgttatgggactttaatatacatttgattcttgtt-----atat-----------------------atatatatatagct-gatatatat--------atgatgA----------------AAAGTATC---------------------GAGTGTG--T-GCGCgccttaatt--------aaaaac-----------------------tgtgGCCC--GCTG-----CTCGTAGGAGTTAATTAGACTGCGGAGGTGT---ACGG-GCCCAGTTTTG-----------------------------------AAACG------------CCGTCGATCTGTCGTCCGTCGT-----------------------------------------CCGTCG----AC--C---GTC--GTTCGCTTTCAAGTCAAGCCCCAGCTATTAGTCGCTCAATATTACGCG-TTT-------GCCCG---------AC-Aacattgtgtt-tgt---------ttt----ttgt------------------gc-------------------------------------------------------------------------------------tcTCCGTGTT--CT--GTGATCTTGAGTT----ATCGAT-----------GGA------TGGC---------------CG---------AGATGGGTTGG------------------------------------------TAACATGGGGG----ACA--C----GGGA---CTGCTGCTGTTCACACGCTGCTCATCAACAATTGCTGTCACGAATTTTCCACTCGGCGCTTTTTGCGCGCGCTActtgtttgtattttaaaatttatttatttgtgcagCCTCCACA s droKik2.KB459527 285973 527 - 1234237 TTTTGT--------TTGATTTGGCCGCTTAGCTGCG--TTGTGAC-TTTTAGCTTTC--------AGCTGCCCACGACCTGC-------------T----------TGATTGTTtagctgttattgttgttattggactttaatatacatttgattcttgtt-----ata---------------------------------------tatatatac--------aataaat----------------aatactgA---------------------GAGCGAG--T-GTGTgccttaattaaaaagaaaaaaac-----------------------cgtGGCCC--GCTG-----CTCGTAGGAGTTAATTAGACTGCGGAGGTGT---ACGG-ACCCAGTTCCG-----------------------------------A---G-------------------------------AGC-----------GATCC--GTC-----GATC-----------CGGCGC----GT--C---GTC--GTTCGCTTTCAAGTCAAGCCCCGGCTATTAGTCGCTCAATATTACGCG-TTT-------GCCCG---------Ac-aacattgtttt-tat---------ttt----ttcctccaGCTCTGCTCAGCCAGC-------------------------------------------------------------------------------------TCCCCGTGTT--CT--GTGATCTTGAGTT----ATCGACG--G--GATC-gg--------------------------------------------------------------------------------------------------------------------ggg---ctgctgctgttcaCACGCTGCTCATCAACAATTGCTGTCACGAATTTTCCACTCGGCGCTTTTTGCGCGCGCTacttgtttgtattttaaaatttatttatttgtgcagcctccaca s droTak2.KB461535 150750 531 - 669855 TTTTGT--------TTGATTTGGCCGCTGAACTGCG--GCGT-A--CTTAAGCTTTT--------AGCTGCCCACGATCTGG-------------T----------TGATTGTTCagctgttattgttgttattggcCGTTAATAtacatttgatttttgtt-----atat-----------------------a-----------ct-tgtacacat--------aataaaa--------------c-aaagtatc---------------------gagtgtg--t-gtgcgccttaatt--------aaaaac-----------------------tgtgGCCC--GCTG-----CTCGTAGGAGTTAATTAGACTGCGGAGGTGT---ACGG-GCCcagtttta-----------------------------------a---g--------------------------ttttcaac--------------------C-----GATT-----------CGATCC----GT--T---GTC--GTTCGCTTTCAAGTCAAGCCCCGGCTATTAGTCGCTCAATATTACGCG-TTT-------GCCCG---------AC-aacattgtttt-tat---------ttttatttttt------------------gc-------------------------------------------------------------------------------------tctcTGTGTT--CT--GTGATCTTGAGTT----ATCGACG--G--TATG-GGA------TGGA---------------TG---------GGATGGCATGG---------------------------------------GGATGGTATAGGG----------------GG---------GCTGTTCACACGCTGCTCATCAACAATTGCTGTCACGAATTTTCCACTCGGCGCTTTTTGCGCGCGCTActtgtttgtattttaaaatttatttatttgtgcaGCCTCCGCA s droRho2.KB449310 46633 511 - 65043 ttttgt--------ttgatttggcCGCCTAGTTGCG--CTGT-AC-TTTTAA-------------AGCTGCCCACGATCTGT-------------T----------TGATTGTTtagctgttattgttgttattggacgttaatatacatttgattcttgtt-----atat-----------------------a-----------ta-tatatatat--------gtgtaat--------------GAAAATCAtc---------------------gagtgtg--t-gtgcgccttaatt--------aaaaac-----------------------tgtGGCCC--GCTG-----CTCGTAGGAGTTAATTAGACTGCGGAGGTGT---ACGG-GCCCAGTTTCG-----------------------------------A---A------------------------------CTGC-----------------------------------------CGATCCGTCGTC--C---GTC--GTTCGCTTTCAAGTCAAGCCCCAGCTATTAGTCGCTCAATATTACGCG-TTT-------GCCCG---------AC-Aacattgcttt-tat---------ttt-----tgt------------------gc-------------------------------------------------------------------------------------tcCCCGTGTT--CT--GTGATCTTGAGTT----ATCGatg--g---atg-gga------tggg---------------------------------------------------------------------------atggtaACACAGGG----------------GGA---CTGCTGCTGTTCACACGCTGCTCATCAACAATTGCTGTCACGAATTTTCCACTCGGCGCTTTTTGCGCGCGCTActtgtttgtattttaaaatttatttatttgtgcaGCCTCCACA s droFic2.KB457177 89395 489 + 995874 -TTTGT--------TTGATTTGGCCGCTAG--TGCG--CTGT-AC-TTTTT--------------AGCTGCCCACGATCCGG-------------C----------TGATTGTTTAGCTGTTATTGCTGCTATTGGACGTTAATATACATTTGATTCTtgtt-----ata---------------------------------------------tat--------aaagtaa----------------aaagtggc---------------------gagtgtg--t-gtgcgcctTAATT--------AAAAGC-----------------------CGTGGCCC--GCTG-----CTCGTAGGAGTTAATTAGACTGCGGAGGTGT---ACGG-GCCCAGTTTCC-----------------------------------A---G---------------------------------------------------------------------------CGATCC----GTCGC---GTT--GTTCGCTTTCAAGTCAAGCCCCGGCTATTAGTCGCTCAATATTACGCG-TTT-------GGCCG---------AC-AACATTGTTTT-TAC---------TTC----T---------------------GC-------------------------------------------------------------------------------------CCGCCGTGTT--CT--GTGATCTTGAGTT----ATCGACG--GACCGAT-GGG------TGGG--------------------------------------------------------------------------------GGCGAGGGGG----CTG--C----GGGG---CAGCTGCTGTTCACACGCTGCTCATCAACAATTGCTGTCACGAATTTTCCACTCGGCGCTTTTTGCGCGCGCTacttgtttgtattttaaaatttatttatttgtgcag--TCCGCA s droPse3.chr3 1358795 606 - 19787792 --TTGT--------TTGATTTGACCGCTTGGCGTCT--ctgt-ag-gaggaggaggaggaggaggagctgcccaCGATGTGG-GGAATCG-----T----------TgattgttttgctgttgttgcggctaTTGGGCTTTAATATACATTTGATTCTTGTC-----ATA------------------------------------ct-ggtatatatgtac----atatatatatatgtatatatataagatCTGT---------------------GAGAGTG--TGGTGCGCCTTAATT--------AAAAGC-----------------------TGAGGCCC--GCTG-----CTCGTAGGAGTTAATTAGACTGCGGAGGTGTACCACGG-CCCCAG----------------------------------------A---G--------------------------AGTGGAGC----GATCTCCGATCCaagcc-----gatc-----------cgatcc----gg--c---GTCGTGTTCGCTTTCAAGTCAAGCCCCAGCTATTAGTCGCTCAATATTACGCG-TTT-------GCCCG---------AC-Aacattgtttt-gtattttttctgttt----tttc------------------tg-------------------------------------------------------------------------------------tttttttgtt--ctgaGAGATCTTGAGTTCtggatggatg--g--tgga-cgg------cgga---------------tg-------gtggatgggtggggga-----------------------------------gtggtggcagcgggg----aca--------agg---ctgctgctgttcacACGCTGCTCATCAACAATTGCTGTCACGAATTTTCCACTCGGCGCTTTTTGCGCGCGCTActtgtttgtattttaaaatttatttatttgtgcagCATCcaca s droPer1.super_34 547656 598 - 916997 --TTGT--------TTGATTTGACCGCATGGTGTCT--CTGT-----aggaggaggaggaggaggagCTGCCCACGATGTGG-GGAATCG-----T----------TGATTGTTTTGCTGTTGTTGCGGCTATTGGGCTTTAATATACATTTGATTCTTGTC-----ATA------------------------------------GT-TGtatatatgtacatatatatatatatatgtatatatataAGATCTGT---------------------GAGAGTG--TGGTGCGCCTTAATT--------AAAAGC-----------------------TGAGGCCC--GCTG-----CTCGTAGGAGTTAATTAGACTGCGGAGGTGTACCACGG-CCCCAG----------------------------------------A---G--------------------------AGTGGAGC----GATCTCCGATCCAAGCC-----GATC-----------CGATCC----GG--C---GTCGTGTTCGCTTTCAAGTCAAGCCCCAGCTATTAGTCGCTCAATATTACGCG-TTT-------GCCCG---------AC-AACATTGTTTT-GTA---------TTT----TTTC------------------TG-------------------------------------------------------------------------------------TTTTTTTGTT--CTGAGAGATCTTGAGTTCTGGATGGATG--G--TGGA-CGG------CGGA---------------TG-------GTGGATGGGTGGGGGA-----------------------------------GTGGTGGCAGCGGGG----ACA--------AGG---CTGCTGCTGTTCACACGCTGCTCATCAACAATTGCTGTCACGAATTTTCCACTCGGCGCTTTTTGCGCGCGCTACTTGTTTGtattttaaaatttatttatttGTGCAGCATCCACA s droMir2.chr3 1399852 599 - 20862834 --TTGT--------TTGATTTGACCGCTTCGCGTCT--atgt-ag-gaggaggaggaggaggaaaagctGCCCACGATGTGG-GGAATCG-----T----------TGATTGTTTTGCTGTTATTGCGGCTATTGGGCTTTAGTATACATTTGATTCTTGTC-----ATa------------------------------------ct-tgtatatac--------atatatatata---atacatataagaTCTAT---------------------GAGAGTG--TGGTGCGCCTTAATT--------AAAAGC-----------------------TGAGGCCC--GCTG-----CTCGTAGGAGTTAATTAGACTGCGGAGGTGTACCACGG-CCCCAG----------------------------------------A---G--------------------------AGTGGAGC----GATCTCCGACCcaagcc-----gatc-----------cgatcc----gg--c---GTCGTGTTCGCTTTCAAGTCAAGCCCCAGCTATTAGTCGCTCAATATTACGCG-TTT-------GCCCG---------AC-AAcattgtttt-gtattttttctgttt----tctc------------------tg-------------------------------------------------------------------------------------tttttttgtt--ctgagAGATCTTGAGTtctggatggatg--g--tgga-cgg------cgga---------------tg-------gtggatgggtggggga-----------------------------------gtggtggcagcgggg----aca--------agg---ctgctgctgttcacaCGCTGCTCATCAACAATTGCTGTCACGAATTTTCCACTCGGCGCTTTTTGCGCGCGCTActtgtttgtattttaaaatttatttatttgtgcagcATCcaca s droWil2.CH963894 1323467 575 + 2843958 attaat--------ataatttatattattatttgtgttttgt-ac---------------------ACTGCCCACATGTCGGCGGTGACGGCAAct----------tgattgt-----tgttgcttgtgttATTGGTCTTTAatatacatttgattc--gtt-----atat-----------------------------------at-agtacatac--------aaatatataagtgtataaatttatatatatg------------tttgtatataagagta--t-GTGCgccttaatt--------aaaaat-----------------------tgctgTGT--GCTGACTGACTCGTAGGAGTTAATTAGATTGCGGAGGTGTTTTGTGG-GTTGATTTCTC-----------------------------------T---C---------------------------------T-----------------------------------------CCGTCG----AT--T---GTC--GTTCGCTTTCAAGTCAAGTTTTAGCTATTAGTCGCTCAATATTACGCGTTTT-------GCTGT---------AC-AGCATTGTG---------------TTT----TAGT------------------GA-------------------------------------------------------------------------------------TC-TCGAGTT--CT------TTCTGAGGG----GTAGAGG--G--TGAG-GAA------GTGG---------------TGAGTGGTCACAAGTGGGAGGG------------------GTGGGTGG-----CAgactgatgctgctgctgctg----ctg--ctgctgctg---ctgctgctgttcacACGCTGCTCATCAACAATTGCTGTCACGAATTTTCCACTCGGCGCTTTTTGCGCGCGCTActtgtttgtattttaaaatttatttatttgtgcagcatccaca s droVir3.scaffold_12875 7363574 627 + 20611582 --TTGTATTTAGCAGCACGCTGCGCATTTCG-------------------CGCTGGA--------AGCTGCCCACTCTCAGT-------------T--CGTCAACTTGATTGTTTTGCTGTTGTTATTGTGGC------TTAATATACATCTGATTCTTGtatata-atat-----------------------a-----------gagtatatatat--------agatatatata--tagt----a-tgtatata--------taGGTATTGAAACATAAGCA--T-GTACGCCTTAATT---------AAAACTCgtgcgtgtgtgtgtgtgtgtgtgtgtgtg--tgtg-----tgtgtAGGAGTTAATTAGACTGCGGAGGTGT---ACGG-CCCCAGTCTCT-----------------------------------T---G------------------------GGTCCGGGGTCTCCGAATGTGTCTCC--GTC-----GAGTCGC--------TGGCCA--------T---TTC--GTTCGCTTTCAAGTCAAGTTTCAGCTATTAGTCGCTCAATATTACGCG-TTT-------TGCTGCTGT-----ACAAACATTCATAt-tgt---------tgt----tgtt------------------gt-------------------------------------------------------------------------------------tgttgttgtt-gct--gtGATCTTGAGTT----CTTGTTGTAT--TGTATGGGGCCTTCTGGT---------------CC--------------------------------------CGGGGCCTATGCTACAATATCGATACGTACCGGGG----CCGTTC-----GGT---CTGCT-CTGTTCACACGCTGCTCATCAACAATTGCTGTCACGAATTTTCCACTCGGCGCTTTTTGCGCGCGCTACTTGTTTGtattttaaaatttatttatttGTGCAGCATCcaca s droMoj3.scaffold_6496 26159473 681 + 26866924 --tAGT------CAGTGTATTGGTCTTTTGGTTCCA--TTCC----ATTTCGTTGGA--------TGCTGCCCACTCTGAAC-------------T--TGAGAATTTGATTGTTTT-------Tta--------------tattatata---------tatatatatatat-----------------------a-----------ca-cgtatatat--------agatatatataATTAGTTGAGG-CGCACATGACATAGTTTAAATACCTCTACAGATGTATTT-GTGTACCTTAATT---------AAAAC--------------------GTGTGTGTGTG--CTCG-----CTCGTAGGAGTTAATTAGACTGCGGAGGTGT---ACGG-CCCGAGTTACT-----------------------------------T---G----------------------CAGAGCTGGGCTCTTCGATTGTGTCTCC--GTC-----GAGTCGC--------TGGCCA--------TTCGTTC--GTTCGCTTTCAAGTCAAGTTTCAGCTATTAGTCGCTCAATATAACGCG-TTT-------TGCTGCTGC-----TCGAATATGCGTAT-GTG---------TGT----GTGT------------------GTAAACAGTGCTAACACACatacatattatatacatgtacatatccacatatatatatatatatatatatatatatatatataaatgtatTGTTGCTGGCT--ATGATCTTGAGTT----CTTGCTG--G--CGTA-GGGGCCTTCTGGC---------------CC---------------------------------------------------GCAATATCGGTACGGACCGGGG----CCGTTC-----GGT---CTGCT-CTGTTCACACGCTGCTCATCAACAATTGCTGTCACGAATTTTCCACTCGGCGCTTTTTGCGCGCGCTACTTGTTTGtattttaaaatttatttatttGTGCAGCATCCACA s droGri2.scaffold_15245 914500 678 + 18325388 --GTATTATTATTATTTTGCTGCTTTTGTAGCTGCT--TGGT----TTTTAACTGAA--------TGCTGCCCACTCTCGAG-------------TTGTGTCAACTTGATTGTTTTGCTGCTGCTG-------------TTAATATACATTTGATTCGTGTATATT-ATATACTCAGtatatatcgtacatataa-----------ta-tatatatgt--------gtgtatgtata------------tgtataca--------tatGTGCTTAAACATAAGCA--T-TTGCGCCTTAATT---------AAAAC-------TTGATGTGTGAGTGAGTGTGTACG--CTGG-----CTCGTAGGAGTTAATTAGACTGCGGAGGTGT---ACGGCCCCCAGTTTCT-----------------------------------T---AGGCATCGGTTCggggtcggggttggggttggggtCTTTGAATGTGTCTCC--GTCTCCGAGAGTCGT--------TGGCCA--------T---TTC--GTTCGCTTTCAAGTCAAGTTTCAGCTATTAGTCGCTCAATATTACGCG-TTTCTGCTGCTGCTGCTGCTGTGTACAAACATTTATATATAG---------TAT----TGTT------------------GT-------------------------------------------------------------------------------------TGTTGTTGCT-G-T--GTGATCTTGAGTT----CTT--------------GGGGCCTTCTGGT---------------CT------------------------------------------CTCCACAGTACAGCATCGATCTGAGTAGTGGGGCCCCGTTC-----GGTCTGCTGCT-CTGTTCACACGCTGCTCATCAACAATTGCTGTCACGAATTTTCCACTCGGCGCTTTTTGCGCGCGCTACTTGTTTGtattttaaaatttatttatttGTGCAGCATCcaca a score=-3473.000000 s dm6.chr2R 24366956 1 + 25286936 G s droSim1.chr2R 18705350 1 + 19596830 G s droSec1.super_23 125024 1 + 989336 G s droEre2.scaffold_4845 21612561 1 + 22589142 G s droAna3.scaffold_13266 5717784 1 - 19884421 A s droBip2.KB464407 1967828 1 + 2915140 A s droEug2.KB465067 609660 1 + 1515531 A s droEle2.KB458573 532515 1 - 5320397 G s droTak2.KB461535 151281 1 - 669855 G s droRho2.KB449310 47144 1 - 65043 A s droFic2.KB457177 89884 1 + 995874 G s droPse3.chr3 1359401 1 - 19787792 c s droPer1.super_34 548254 1 - 916997 C s droMir2.chr3 1400451 1 - 20862834 c s droWil2.CH963894 1324042 1 + 2843958 c s droVir3.scaffold_12875 7364202 1 + 20611582 a s droGri2.scaffold_15245 915179 1 + 18325388 a a score=-395989.000000 s dm6.chr2R 24366957 58 + 25286936 CCTGCA-----CA---------GTCC-CAGAAGCTG------------------------------------------TGGAGCTCTTT------------AGCTCTGGA----TCTCA-GAGGCCTCCACA-------------- s droSim1.chr2R 18705351 63 + 19596830 CCGGCAGCCTCCA---------GTCC-CAGAAGCTG------------------------------------------CGGAGCTCTTT------------AGCTCTGGA----TCTCA-GAGGCCTCCACA-------------- s droSec1.super_23 125025 63 + 989336 CCTGCAGCCTGCA---------GTCC-CAGAAGCTG------------------------------------------TGGAGTTCTTT------------AGCTCTGGA----TCTCA-GAGGCCTCCACA-------------- s droYak3.chr2R 20214805 50 + 21139217 ----------------------GTCT-CAAAAGCTG------------------------------------------TGGAGCTCTTT------------AGCTCTGGA----TCTCA-GAGGCCTCCATA-------------- s droEre2.scaffold_4845 21612562 67 + 22589142 CCTCCA-----CAACCTCCACTGTCT-CGGAAGCTG------------------------------------------TGGAGCTCTTT------------AGCTCTGGA----TCTCA-GAGGCCTCCACA-------------- s droBia2.KB462602 806331 30 + 3129309 -----------CA---------GTCCACAGAAGC---------------------------------------------------------------------------------CTCC-ACAGCCTCCACA-------------- s droSuz1.KI419649 12051871 30 - 14502029 -----------CA---------GTCCACAGAAGC---------------------------------------------------------------------------------CTCC-AAAGCCTCCACA-------------- s droBip2.KB464407 1967829 90 + 2915140 --------------------------ACACatgacgataata-atgacgataataacgatgatg-------atggtgatgggGATCCTC---GTGAAAAAGAGTTCTGTG----CCACA-GTAGAGTCTATA-------------- s droEug2.KB465067 609661 15 + 1515531 -------------------------------------------------------------------------------------------------------------------CTCGCACAGCCTCCA---------------- s droEle2.KB458573 532516 24 - 5320397 ------------------------------------------------------------------------------------------------------cctccaca-----caca-caaacacacaca-------------- s droKik2.KB459527 286500 8 - 1234237 ----------------------------------------------------------------------------------------------------------------------------cacacaca-------------- s droTak2.KB461535 151282 29 - 669855 ------------------------------------------------------------------------------------------------------TCTCGGAAGCCTCCACA-GAAGCCTCCACA-------------- s droRho2.KB449310 47145 17 - 65043 ------------------------------------------------------------------------------------------------------------------CCTCC-ACAgcctccaca-------------- s droFic2.KB457177 89885 17 + 995874 ------------------------------------------------------------------------------------------------------------------CCTCC-ACAgcctccaca-------------- s droPse3.chr3 1359403 90 - 19787792 --------------------------------------ggtacacgggcacacgggcactcgggcacacacacggagagggatccctctcctctctctcatGGATCCGAT----CCTCATGGATACTCTGCT-------------- s droPer1.super_34 548256 90 - 916997 --------------------------------------GGTACACGGGCACACGGGCACTCGGGCACACACACGGAGAGGGATCCCTCTCCTCTCTCTCATGGATCCGAT----CCTCATGGATACTCTGCT-------------- s droMir2.chr3 1400453 82 - 20862834 --------------------------------------ggtacacgggcaca--------cgggcacacacacggagagggatccctctcctctctctcatGGATACGAT----CCTCATGGATACTCTGCT-------------- s droWil2.CH963894 1324044 16 + 2843958 -------------------------------------------------------------------------------------------------------------------caca-cacacacacaca-------------- s droVir3.scaffold_12875 7364203 30 + 20611582 -------------------------------------------------------------------------------------------------------------------caca-cacacacacatgcgctcgcgcacaca s droGri2.scaffold_15245 915180 28 + 18325388 -------------------------------------------------------------------------------------------------------------------caca-cacacacccataca--tacgcacaca a score=28788.000000 s dm6.chr2R 24367015 31 + 25286936 CACA------------TG-A-------T---GGGGATCCTCTC--------------------------G--TGGAGTGAAG s droSim1.chr2R 18705414 31 + 19596830 CACA------------TG-A-------T---GGGGATCCTCTC--------------------------G--TGGAGTGAAG s droSec1.super_23 125088 31 + 989336 CACA------------TG-A-------T---GGGGATCCTCTC--------------------------G--TGGAGTGAAG s droYak3.chr2R 20214855 43 + 21139217 CACACGGGTTGGGGATCG-A-------T---GGGGATGCTCTC--------------------------g--tggagtgaag s droEre2.scaffold_4845 21612629 31 + 22589142 CACA------------TG-A-------T---GGGGATCCTCTC--------------------------G--TGGAGTGAAG s droBia2.KB462602 806361 31 + 3129309 CACA------------TG-A-------T---GGGGATCCTCGC--------------------------G--TGGAGTGAAC s droSuz1.KI419649 12051901 31 - 14502029 CACA------------TG-A-------T---GGGGATCCTCGC--------------------------G--TGGAGTGAAC s droEug2.KB465067 609676 28 + 1515531 CACA------------TG-A-------T---GGGGATCCTCTC--------------------------G--TGGAGTG--- s droEle2.KB458573 532553 31 - 5320397 caca------------tg-g-------t---gGGGATCCTCTC--------------------------G--TGGAGTGGAG s droKik2.KB459527 286508 40 - 1234237 caca------------tg-atgGGTACT---GGGGATCCTCCT--------------------------GGCTGGAGTGCCT s droTak2.KB461535 151311 31 - 669855 CACA------------TG-A-------T---GGGGATCCTCGC--------------------------G--TGGAGTGAGC s droRho2.KB449310 47170 28 - 65043 cgca------------tg-A-------T---GGGGATCCTCtc--------------------------g--tggagtg--- s droFic2.KB457177 89904 31 + 995874 caca------------cg-a-------tgGCGGGGATCCTCtc--------------------------g--tggagtg--- s droPse3.chr3 1359493 30 - 19787792 CACT------------CC-T-------T---G----TTCTTT-----------------------CAggg--cggagcggag s droPer1.super_34 548346 43 - 916997 CACT------------CC-T-------C---G----TTCTTTCGGAGT----------agcagagcagag--cggagcggag s droMir2.chr3 1400535 53 - 20862834 CACT------------CC-T-------C---G----TTCTTTCGGagtagcagagcagagcagagcggag--cggagtggag s droWil2.CH963894 1324078 28 + 2843958 caca------------tata-------c---acaGATCC------------------------------A--TAGAgtggtt s droVir3.scaffold_12875 7364233 18 + 20611582 ------------------------------------cacacgc--------------------------a--caGAGAGAAC s droGri2.scaffold_15245 915208 13 + 18325388 ------------------------------------cacacac--------------------------a--cCGAG----- a score=-78284.000000 s dm6.chr2R 24367046 17 + 25286936 TGGAGTGGA----------------------------TCG--------------TCGGC--- s droSim1.chr2R 18705445 17 + 19596830 TGGAGTGGA----------------------------TCG--------------TCGGC--- s droSec1.super_23 125119 17 + 989336 TGGAGTGGA----------------------------TGG--------------TCGGC--- s droYak3.chr2R 20214898 32 + 21139217 tggagtggagtggagtg-------------gagtggatcG--------------TACGC--- s droEre2.scaffold_4845 21612660 32 + 22589142 TGCAGTGGATCGGATCG-------------GATCGGGTCG--------------TCCGC--- s droBia2.KB462602 806392 32 + 3129309 TGAGCCgaagtggagtg-------------gagtggatcG--------------TCCGC--- s droSuz1.KI419649 12051932 32 - 14502029 TGAACTgaagtggagtg-------------gagtggatcG--------------TCCGC--- s droAna3.scaffold_13266 5717873 45 - 19884421 TGGAGTGGCTCGTATGaccaaccaaccaaccaaccgacca--------------accaC--- s droEug2.KB465067 609704 10 + 1515531 -----------------------------------GATCG--------------TCCGC--- s droEle2.KB458573 532584 17 - 5320397 ----------------------------TTGAGTGGATCG--------------TCCGC--- s droKik2.KB459527 286548 19 - 1234237 TGGAGTGGAGTGGA----------------------------------------TCCAC--- s droTak2.KB461535 151362 17 - 669855 TGGAGTGGA----------------------------TCG--------------TCCGC--- s droRho2.KB449310 47198 15 - 65043 ------------------------------gagtggatcG--------------TCCGC--- s droFic2.KB457177 89935 15 + 995874 ------------------------------gagtggatcG--------------TCCGC--- s droPse3.chr3 1359523 18 - 19787792 ----------------------------tggagtggatcgA-------------TCCGC--- s droPer1.super_34 548389 18 - 916997 ----------------------------cggagtggaTCGA-------------TCCGC--- s droMir2.chr3 1400588 18 - 20862834 ----------------------------tggagtggatcgA-------------TCCGC--- s droWil2.CH963894 1324108 16 + 2843958 ----------------------------ttttgttgttgt--------------tctg---- s droVir3.scaffold_12875 7364251 22 + 20611582 ----------------------------------------ACAGATATACACACTCAATGAG s droGri2.scaffold_15245 915221 8 + 18325388 ------------------------------------------------------TCGATGGG a score=-20932.000000 s dm6.chr2R 24367063 8 + 25286936 GC---------GTAGTG-- s droSim1.chr2R 18705462 8 + 19596830 GC---------GTAGTG-- s droSec1.super_23 125136 8 + 989336 GC---------GTAGTG-- s droYak3.chr2R 20214930 8 + 21139217 GC---------GTAGTG-- s droEre2.scaffold_4845 21612692 8 + 22589142 GC---------GTAGTG-- s droBia2.KB462602 806424 17 + 3129309 ACGGAGTATGGGCAGTG-- s droSuz1.KI419649 12051964 17 - 14502029 ATGGAGTATGGGGAGTG-- s droAna3.scaffold_13266 5717918 6 - 19884421 TT---------GGAG---- s droEug2.KB465067 609714 8 + 1515531 AC---------GGAGTG-- s droEle2.KB458573 532601 8 - 5320397 AC---------GGAGTG-- s droKik2.KB459527 286567 8 - 1234237 AT---------GGAGTG-- s droTak2.KB461535 151379 8 - 669855 TC---------GGAGTA-- s droRho2.KB449310 47213 8 - 65043 AC---------GGAGTG-- s droFic2.KB457177 89950 8 + 995874 AC---------GGAGTG-- s droPse3.chr3 1359541 10 - 19787792 AC-------ACACagtg-- s droPer1.super_34 548407 10 - 916997 AC-------ACACAGTG-- s droMir2.chr3 1400606 10 - 20862834 AC-------ACACagtg-- s droWil2.CH963894 1324124 6 + 2843958 -----------ttAGTG-- s droVir3.scaffold_12875 7364276 8 + 20611582 -----------GCAGAGGC s droMoj3.scaffold_6496 26160264 8 + 26866924 -----------gcagcagc s droGri2.scaffold_15245 915229 2 + 18325388 -----------------GC a score=2030579.000000 s dm6.chr2R 24367071 137 + 25286936 TG-TGTGCTCCTCCTGGAGCGCACTGAAGAATGCATTTGATCAGATAATGTAATTCGCATTTTAAATTGAGGCGCATTCCCAGTTATACTTCTTCTCACATGCA-TTTACCTG---------------------GC-CGT-CGCA-------GG----CATCCTTCGA---TT-----------TGC s droSim1.chr2R 18705470 137 + 19596830 TG-TGTGCTCCTCCTGGAGCGCACTGAAGAATGCATTTGATCAGATAATGTAATTCGCATTTTAAATTGAGGCGCATTCCCAGTTATACTTCTTCTCACATGCA-TTTACCTG---------------------GC-CGT-CGCA-------GG----CATCCTTCGA---TT-----------TGC s droSec1.super_23 125144 137 + 989336 TG-TGTGCTCCTCCTGGAGCGCACTGAAGAATGCATTTGATCAGATAATGTAATTCGCATTTTAAATTGAGGCGCATTCCCAGTTATACTTCTTCTCACATGCA-TTTACCTG---------------------GC-CGT-CGCA-------GG----CATCCTTCGA---TT-----------TGC s droYak3.chr2R 20214938 137 + 21139217 TG-TGTGCTCCTCCTGGAGCGCACTGAAGAATGCATTTGATCAGATAATGTAATTCGCATTTTAAATTGAGGCGCATTCCCAGTTATACTTCTTCTCACATGCA-TTTACCTG---------------------GC-CGT-CGCA-------GG----CATCCTTCGA---TT-----------TGC s droEre2.scaffold_4845 21612700 137 + 22589142 TG-TGTGCTCCTCCTGGAGCGCACTGAAGAATGCATTTGATCAGATAATGTAATTCGCATTTTAAATTGAGGCGCATTCCCAGTTATACTTCTTCTCACATGCA-TTTACCTG---------------------GC-CGT-CGCA-------GG----CATCCTTCGA---TT-----------TGC s droBia2.KB462602 806441 137 + 3129309 TG-TGTGCTCCTCCTGGAGCGCACTGAAGAATGCATTTGATCAGATAATGTAAttcgcattttaaattgaggCGCATTCCCAGTTATACTTCTTCTCACATGCA-TTTACCTG---------------------GC-CAT-CACA-------GG----CATCCTTCGA---TT-----------TGC s droSuz1.KI419649 12051981 137 - 14502029 TG-TGTGCTCCTCCTGGAGCGCACTGAAGAATGCATTTGATCAGATAATGTAATTCGCATTTTAAATTGAGGCGCATTCCCAGTTATACTTCTTCTCACATGCA-TTTACCTG---------------------GC-CAT-CACA-------GG----CATCCTTCGA---TT-----------TGC s droAna3.scaffold_13266 5717937 131 - 19884421 TG-TATACTCCTCCTGGAGCGCACTGAAGAATGCATTTGATCAGATAATGTAATTCGCATTTTAAATTGAGGCGCATTCCCAGTTATACTTCTTCTCACATGCA-TTTACCTT---------------------G--TGC-CTCC-------G---------TTTGGA---TC-----------GAC s droBip2.KB464407 1967992 120 + 2915140 TG-TATACTCCTCCTGGAGCGCACTGAAGAATGCATTTGATCAGATAATGTAATTCGCATTTTAAATTGAGGCGCATTCCCAGTTATACTTCTTCTCACATGCA-TTTACCCA---------------------GC-CGC-CACC------------------------------------------ s droEug2.KB465067 609729 134 + 1515531 TG-CGAGCTCCTCCTGGAGCGCACTGAAGAATGCATTTGATCAGATAATGTAATTCGCATTTTAAATTGAGGCGCATTCCCAGTTATACTTCTTCTCACATGCA-TTTACCTG---------------------GC-CAT-C----------GG----CATCCTTCGA---TT-----------TGC s droEle2.KB458573 532609 140 - 5320397 TG-TGTGCTCCTCCTGGAGCGCACTGAAGAATGCATTTGATCAGATAATGTAATTCGCATTTTAAATTGAGGCGCATTCCCAGTTATACTTCTTCTCACATGCA-TTTACCTC---------------------GG-CCT-CGCC----ATTGG----CATCCTTCGA---TT-----------CTC s droKik2.KB459527 286575 131 - 1234237 TG-TGCGCTCCTCCTGGAGCGCACTGAAGAATGCATTTGATCAGATAATGTAATTCGCATTTTAAATTGAGGCGCATTCCCAGTTATACTTCTTCTCACATGCA-TTTACCTC---------------------------------------GA----CATCCTTCTGTCCTC-----------CGT s droTak2.KB461535 151403 137 - 669855 tg-tgtgctcctCCTGGAGCGCACTGAAGAATTCATTTGATCAGATAATGTAATTCGCATTTTAAATTGAGGCGCATTCCCAGTTATACTTCTTCTCACATGCA-TTTACCTG---------------------GG-CAT-CACA-------GG----CATCCTTCGA---TT-----------TGC s droRho2.KB449310 47221 128 - 65043 TG-TGTGCTCCTCCTGGAGCGCACTGAAGAATGCATTTGATCAGATAATGTAATTCGCATTTTAAATTGAGGCGCATTCCCAGTTATACTTCTTCTCACATGCA-TTTACCTC---------------------------------------GG----CATCCTTCGA---TT-----------CGC s droFic2.KB457177 89958 164 + 995874 AG-TGTGCTCCTCCTGGAGCGCACTGAAGAATGCATTTGATCAGATAATGTAATTCGCATTTTAAATTGAGGCGCATTCCCAGTTATACTTCTTCTCACATGCA-TTTAccagtggccagtggccagtggACCAGC-CAT-CATCCAGCATCGG----CATCCTT-GG---CC-----------CGC s droPse3.chr3 1359553 136 - 19787792 tgctgtgctcctCCTGGAGCGCACTGAAGAATGCATTTGATCAGATAATGTAATTCGCATTTTAAATTGAGGCGCATTCCCAGTTATACTTCTTCTCACATGCA-TTTACTGC---------------------ccgcct-ccct-------gc----ctccctgcca---ct-------------- s droPer1.super_34 548419 147 - 916997 TGCTGTGCTCCTCCTGGAGCGCACTGAAGAATGCATTTGATCAGATAATGTAATTCGCATTTTAAATTGAGGCGCATTCCCAGTTATACTTCTTCTCACATGCA-TTTACTGC---------------------CCGCCT-CCCT-------GC----CACTCTGCCA---CCCTGCTCCCTGC--- s droMir2.chr3 1400618 129 - 20862834 tgctgtgctcctCCTGGAGCGCACTGAAGAATGCATTTGATCAGATAATGTAATTCGCATTTTAAATTGAGGCGCATTCCCAGTTATACTTCTTCTCACATGCA-TTTACTGC---------------------CCGCCt-ccct-------gc----cactc------------------------ s droWil2.CH963894 1324133 138 + 2843958 TC-TTTCGTCCTCCTGGAGCGCAGTGAAGAATGCATTTGATCAGATAATGTAATTCGCATTTTAAATTGAGGCGCATTCCCAGTTATACTTCTTCTCACATGCATTTTACCTT---------------------TA-CCT-GGCT-------TA----CCTCCTCGGT---CT-----------TGG s droVir3.scaffold_12875 7364284 139 + 20611582 AG-AGTCGTCCTCCTGGAGCGCACCAAAGAATGCATTTGATCAGATAATGTAATTCGCATTTTAAATTGAGGCGCATTCCCAGTTAGACTTCTTCTCACATGCA-TTTACCGT-------------------GCGC-GCTGCGTA-------GG--CCCATCCTTCAG---AC-------------- s droMoj3.scaffold_6496 26160272 138 + 26866924 ag-AGTCGTCCTCCTGGAGCGCACC-AAGAATTCATTTGATCAGATAATGTAATTCGCATTTTAAATTGAGGCGCATTCCCAGTTAGACTTCTTCTCACATGCA-TTTGCCGT---------------------GC-GCTGCGTA-------GGCCCCCATCCTTCTG---GC-------------- s droGri2.scaffold_15245 915231 138 + 18325388 AG-AGTCGTCCTCCTGGAGCGCACCAAAGAATGCATTTGATCAGATAATGTAATTCGCATTTTAAATTGAGGCGCATTCCCAGTTAGACTTCTTCTCACATGCA-TTTACCGT-------------------GCGC-GCT-CACT-------GC--TCGCTCCTTCGG---GC-------------- a score=-123326.000000 s dm6.chr2R 24367208 41 + 25286936 ---GAGGCGGAG----GAGTACGA--CT---GCTG-----------GACTG--GGCTGGATGGCCC----- s droSim1.chr2R 18705607 29 + 19596830 ---GAGGCGGAG----GAGTACGA--CT---GCCG-----------GACTG--G----------------- s droSec1.super_23 125281 29 + 989336 ---GAGGCGGAG----GAGTACGA--CT---GCCG-----------GACTG--G----------------- s droYak3.chr2R 20215075 36 + 21139217 ---GAGGCGGAG----GAGTACGA--CT---GCTG-----------GACTG-------CTGGgctc----- s droEre2.scaffold_4845 21612837 41 + 22589142 ---GACGCGGAG----GAGTACGA--CT---GCTG-----------GACTG--GGCTACTGGGCTG----- s droBia2.KB462602 806578 35 + 3129309 ---GAGGCGGAG----GAGTAGGA--TC---GCCG-----------GGCTG--G------CGATGG----- s droSuz1.KI419649 12052118 42 - 14502029 ---GAGGCGGAG----GAGTAAGA--TC---GCTGCACTG----AAGACTG--G------AGACGG----- s droAna3.scaffold_13266 5718068 27 - 19884421 ---G--GAGGAG----GAGTGCTC--CT---CC-------------GCTTGAAG----------------- s droBip2.KB464407 1968112 21 + 2915140 ---------GAG----GAGTGCTC--CT---CC-------------GCCTG--G----------------- s droEug2.KB465067 609863 29 + 1515531 ---CAGGCGGAG----GAGTACGA--AT---GCTG-----------AACTG--G----------------- s droEle2.KB458573 532749 29 - 5320397 ---GAGGCGGAG----GAGTACGA--AT---GCTG-----------GACTG--G----------------- s droKik2.KB459527 286706 39 - 1234237 ---GGAGCGGAG----GAGTACGA--CTTtaactgcgact----gcgactg--g----------------- s droTak2.KB461535 151540 31 - 669855 ---GAGGCGGAG----GAGTACGA--AT---GCCG-----------GACTG--G----------AG----- s droRho2.KB449310 47349 29 - 65043 ---AAGGCGGAG----GAGTACGA--AT---GCTG-----------GACTG--G----------------- s droFic2.KB457177 90122 29 + 995874 ---GAGGCGGAG----GAGTGCGA--GT---GCCG-----------GGCTG--G----------------- s droPse3.chr3 1359689 22 - 19787792 --------------------------ct---gccaccctgctccctgcctc-------------------- s droMir2.chr3 1400747 29 - 20862834 -------------------tgccactct---gccacccTGCTCCCTGCCTC-------------------- s droWil2.CH963894 1324271 12 + 2843958 ------------------GGGCCA--AT---CCCT------------------------------------ s droVir3.scaffold_12875 7364423 31 + 20611582 CA-GGCTCTGTG----------GA--CTC--CCCG-----------GCCTG--G------------CCAGC s droMoj3.scaffold_6496 26160410 39 + 26866924 CG-GGCTCAGTGCACAGTGGACAA--CTCGACCCG-----------GCCTG--G------------C---- s droGri2.scaffold_15245 915369 31 + 18325388 GACTACTCAGTG----------GA--CTC--CCCG-----------GCCTG--A------------C-CGC a score=574693.000000 s dm6.chr2R 24367249 208 + 25286936 AG-----------CTCctccag---------ctccagctc-cagct-------ccagcCT------CATCTTC--T-------------------CCAGAGGAGCCCCAC----------G------ACCA---------------------------------TTCCGAA---------CC---AACATTGCGGGCGTTGCATTATTACGCACAAGTAAATCATCGA------------------------------AAGACGTC----------------------GCTGC------------------T-------G---------------T-------C----CACCGTC---------GA----AAGCCAAC-------------------------GGCTTGTTAAGTAATTTAGTTGGCCTT----TTTT-------G----------------------------CCAA-CTCTCTC-GGCGCA--------TTTT-----GC-------TTTTTCT s droSim1.chr2R 18705636 186 + 19596830 -------------------------------------------GCT-------CCAGCCT------CATCTTC--T-------------------CCAGAGGAGCCCCAC----------G------ACCA---------------------------------TTCCGAT---------CC---AGCATTGCGGGCGTTGCATTATTACGCACAAGTAAATCATCGA------------------------------AAGACGTC----------------------GCTGT------------------T-------G---------------T-------C----CACCGTC---------GA----AAGCCAAC-------------------------GGCTTGTTAAGTAATTTAGTTGGCCTT----TTTT-------G----------------------------CCAA-CTCTCTC-GGCGCA--------TTTT-----GC-------TTTTTCT s droSec1.super_23 125310 177 + 989336 -------------------------------------------GCA-------CCAGCCT------CATCTTC--T----------------------------CCCCAC----------G------ACCA---------------------------------TTCCGAT---------CC---AGCATTGCGGGCGTTGCATTATTACGCACAAGTAAATCATCGA------------------------------AAGACGTC----------------------GCTGC------------------T-------G---------------T-------C----CACCGTC---------GA----AAGCCAAC-------------------------GGCTTGTTAAGTAATTTAGTTGGCCTT----TTTT-------G----------------------------CCAA-CTCTCTC-GGCGCA--------TTTT-----GC-------TTTTTCT s droYak3.chr2R 20215111 212 + 21139217 cacatcca-catccacatccag---------ctccagctc-cagct-------ccaaccT------CATCTTC--T-------------------CCAGAGGAGCCCCAC----------G----------------------------------------------------------------AACATTGCGGGCGTTGCATTATTACGCACAAGTAAATCATCGA------------------------------AAGACGTG----------------------GCCAC------------------TGTCCACAG---------------T-------C----CACCATC---------GA----AAGCCAAC-------------------------GGCTTGTTAAGTAATTTAGTTGGCCTT----TTTT-------G----------------------------CCAA-CTCTCTC-GGCGCA--------TTTT-----GC-------TTTTTCT s droEre2.scaffold_4845 21612878 190 + 22589142 GA---------------------------------------CGGGG-------CCAGCCT------CATCTCC--T-------------------CCAGAGGAACCCCAC----------G------ACCA---------------------------------TTCCGAT---------CC---AACATTGCGGGCGTTGCATTATTACGCACAAGTAAATCATCGA------------------------------AAGACGTC----------------------GCTGC------------------T-------G---------------T-------C----CGCCGTC---------GA----AAGCCAAC-------------------------GGCTTGTTAAGTAATTTAGTTGGCCTT----TTTT-------G----------------------------CCAA-CTCTCTC-GGCGCA--------TTTT-----GC-------TTTTTCT s droBia2.KB462602 806613 157 + 3129309 GG-------------------------------------------------------------------CTCC--T-------------------CC-----------------------------------------------------------------------AGT---------CG---AGCATTGCGGGCGTTGCATTATTACGCACAAGTAAATCATCGA------------------------------AAGACGTC----------------------GCT-C------------------T-------G---------------T-------C----CTCCGTC---------GA----AACCCAGC-------------------------GGCTTGTTAAGTAATTTAGTTGGCCTT----TTTT------------------------------------CCAA-CTCGCCCTGGTGCA--------TTTT-----GCC-TGGC-TTTTTCT s droSuz1.KI419649 12052160 190 - 14502029 GA-------------------------------GAAGCCC-CATCT-------CCAGATT------CATCTCC--T-------------------CTGGAGAGG----------------------------------------------------------------AGG---------CC---AACATTGCGGGCGTTGCATTATTACGCACAAGTAAATCATCGA------------------------------AAGACGTC----------------------GCTCC------------------T-------G---------------T-------C----CACCATC---------GA----AACCCAGC-------------------------GGCTTGTTAAGTAATTTAGTTGGCCtt----tttt-------t---------------------------CCCAA-CTCTCCCCGGTGCA--------TTTT-----GCC-TTGCTTTTTTCT s droAna3.scaffold_13266 5718095 163 - 19884421 -----------------------------------------------------------------------CT--T-------------------TTGGAGAAGCCCCACT---------G------ACCA---------------------------------GGCCGAGAGCTCAGATCCGAGAGCATTGCGGGCGTTGCATTACTACGCACAAGTAAATCATCC-------------------------------AAGACGTC----------------------GTTG-------------------T-----------------------------------------CC---------CA----GGCCCAGC-------------------------GGCTTGTTAAGTAATTTAGTTGGCCGT----TTTT-------G----------------------------CCAAGATTTC--------------------------GA-------TTCTTTT s droBip2.KB464407 1968133 189 + 2915140 -----------------------------------------------------------------------CT--T-------------------TTGGAGAAGCCCCACT---------G------GCCACTG--------------------GAATG-ATTTGGCCTGG---------CCGAGAGCATTGCGGGCGTTGCATTACTACGCACAAGTAAATCATCG-------------------------------AAGACGTC----------------------GCGA-------------------T-------g---------------t-------c----ccaggcc---------ca----ggcccagc-------------------------gGCTTGTTAAGTAATTTAGTTGGCCGt----tttttttGACCA----------------------------TCGAGGTCTCCT-TGGGC------------T-----CC-------TTCTTTT s droEug2.KB465067 609892 216 + 1515531 -----------AGAAGCCCCAG---------CCTCAGCCCTCAGCC-------CCAACTTGTGCTCCATCTCC--T-------------------CTCGAGGAGCCCCAC----------G------ACCA---------------------------------GTCCCGA---------CC---AACATTGCGGGCGTTGCATTATTACGCACAAGTAAATCATCG-------------------------------ACGACGTC----------------------GCCGC------------------T-------G---------------T-------C----CACCATC---------GC----AGCCCAAC-------------------------GGCTTGTTAAGTAATTTAGTTGGCCTT----TTTT-------G---------------------------CCCAA-CTCTCCTCGGAGCA--------TCTT-----GC-------TTTTTCT s droEle2.KB458573 532778 204 - 5320397 ---------------------------------AGAAGCTTCAGCT-------CCAGTCA------CAGCTCC--C-------------------CTGGAGCAGCCCCAC----------G------ATCA---------------------------------TTCCGG----------CC---AGCATTGCGGGCGTTGCATTATTACGCACAAGTAAATCATCG-------------------------------ACGACGTCCACCAACG--------------TTCAA------------------C-------G---------------T-------C----CAACGTC---------GA----AAGCCAAC-------------------------GGCTTGTTAAGTAATTTAGTTGGCCTT----TTTT-------G---------------------------CCCAA-CTCTCTTCGGTgca--------tttc-----gc-------ttttttt s droKik2.KB459527 286745 200 - 1234237 --------------------------------------------aC-------CTGGCTA------TGGCTCTGGT-------------------CGGAAGGAGACCCACT---------G------TCCG-------------------------------------------------CC---AGCATTGCGGGCGTTGCATTATTACGCACAAGTAAATCATCG-------------------------------ACGACGTC----------------------GTTGT------------------C-------G---------------TCCCTGTCC----CAACGTC---------G-----GGTCCAAC-------------------------GGCTTGTTAAGTAATTTAGTTGgccct----tttt-------tt----------------------gttgcttaa-cTCTCCGCGTTGCA--------TTTG-----GCCTTTGCTTTTTTCT s droTak2.KB461535 151571 233 - 669855 AAGCCCCATCTCCCATCTCCAG-------GCTTCCAGCTACCAGCTC------CCAGCTC------CATCTCC--T-------------------CTGGAGAGAT---------------G------AGGA--------------------------------------GG---------CC---AACATTGCGGGCGTTGCATTATTACGCACAAGTAAATCACCGA------------------------------GAGACGTC----------------------GCTGC------------------T-------G---------------T-------C----CACTGTCCACCATCCAGA----AGCCCAGC-------------------------GGCTTGTTAAGTAATTTAGTTGGCCTT----TTTT-------C------------------------AAACCCAA-CTCTCTTCGCTGCA--------TTGA-----GC-CTTGCTTTTTTCT s droRho2.KB449310 47378 227 - 65043 --------------------AGAGGCTCCATCTCCAGCTCCAAACT-------CCAACTC------CTGCTCC--T-------------------CTGGAGCTGCCCCAC----------G------ATCA---------------------------------TTCCGG----------CC---AGCATTGCGGGCGTTGCATTATTACGCACAAGTAAATCATCG-------------------------------TCGACGTC----------------------GTCGTCCAACGTCCAATGTCCAAT-------G---------------T-------C----CAACGTC---------GA----AACCCAAC-------------------------GGCTTGTTAAGTAATTTAGTTGGCCTT----TTTT-------G---------------------------CCCAA-CTCTCTTCGGtgca--------tttt-----cc-------ttttttt s droFic2.KB457177 90151 183 + 995874 ---------------------------------------AGGATCT-------CCAGCGA------AA----C--C-------------------CTGGAGGAG-CCCAC----------G------ACCA-----------------------------------CTCGG---------CC---GGCATTGCGGGCGTTGCATTATTACGCACAAGTAAATCATCG-------------------------------ACGACGTC----------------------GCTGT------------------C-------G---------------T-------C----CTCCATC---------G-----AGCCCAAC-------------------------GGCTTGTTAAGTAATTTAGTTGGCCTT----TTTT-------G---------------------------CCCGG-CTCTCCTCGGGCCA--------TTTG-----GC-------TTTTTct s droPse3.chr3 1359723 302 - 19787792 ----------------------------------------------gccatcgtcatcgt------catcgtc--cggaggagcaggagcttcTGCAGGAGTAGACCCACT-------Tcg------actgcccctg----------ccactgccactg-ccatggcctGG---------CC---AGCATTGCGGGCGTCGCATTATTACGCACAAGTAAATCATCGA-CATCGTAgtcctcgtct------------tcgtcgtc----------------------gtcgt------------------t-------g---------------t-------c----caGCCCC---------GAGCCGAGCTCAGCCGCTG--------------------GGCTTGTTAAGTAATTTAGTTGGCTTT----TTCT-------GTCCTCCCCCTGGCCACCTGCCCCTGGGCGCTC-CTCTCTCTGGTCTGCCAATATCTTTT-----GC--CTGATTTTTTGT s droPer1.super_34 548608 278 - 916997 -------------------------------------------------------------------AGCTTC--TGCAGGA------------------GGAGACCCACT-------TCG------actgccactg----------ccactgccactg-ccaTGGCCTGG---------CC---AGCATTGCGGGCGTCGCATTATTACGCACAAGTAAAtcatcga-catcgtagtcctcgtcttcg---tcggcgtcgtcgtc----------------------gtcgt------------------t-------g---------------t-------c----CAGCCCC---------GAGCCGAGCTCAGCCGCTG--------------------GGCTTGTTAAGTAATTTAGTTGGCTTT----TTCT-------GTCCTCCCCCTGGCCACCTGCCCCTGGGCGCTC-CTCTCTCTGGTCTGCCAATATCTTTT-----GC--CTGATTTTTTGT s droMir2.chr3 1400776 320 - 20862834 ----------------------------------------------GGCAttgccatcgt------catcgtc--cggaggagcaggagcttcTGCAGGAGGAGACCCACt-------tcgactgccactgccactg----------ccactgccactg-ccatggcctgg---------cc---aGCATTGCGGGCGTCGCATTATTACGCACAAGTAAATCATCGA-CATCGTAgtcctcgtcttcgtcttcgtcgtcgtcgtc----------------------gtcgt------------------t-------g---------------t-------c----caGCCCC---------GAGCCGAGCTCAGCCGCTG--------------------GGCTTGTTAAGTAATTTAGTTGGCTTT----TTCT-------GTCCTCCCCCTGGCCACCTGCCCCTGGGCGCTC-CTCTCTCTGGTCTGCCAATATCTTTT-----GC--CTGATTTTTTGT s droWil2.CH963894 1324283 216 + 2843958 ----------------------------------------------------------------------------------------------------------------------------------------GGCTCTCTTGTCTTCTGTCTGTGTCTGGGTCTTGG---------CC---AGCATTGCGGGCGTTGCATTATTACGCACAAGTAAATCATCGTCCaacgttgtcgtcg---------------tcgtcgtc----------------------gtcat------------------c-------g---------------t-------c----atcggtc---------gG----AGTCCTCCTTTTGGTCGTTGTTTCCATCCAACTGGCTTGTTAAGTAATTtagttgacttt----tttt-------t----------------------------tca--ttctcctcattgtt--------tttt-----ct-------tctatat s droVir3.scaffold_12875 7364454 204 + 20611582 -------------------------------------------------------TCTCA------TCTCTGC--T-------------------CTGGACTGTGGCCATTCCTCTGCTTG------TCT--------------------------------TT-GCCGTT---------CC---AGCGTTGCGGGCGTTGCATTATTACGCACAAGTAAATCATCC-------------------------------CAGACGAc----------------------gtcgt------------------c-------gtcgtcgtcgtcgtcTT-------C----CAGCCGC---------A-----GCCTCAAC-------------------------GGCTTGTTAAGTAATTTAGTTGGCTTCTTGGTTTT-------T----------------------------TTTT-CGCTCAC-----TC--------TCGG-----CC-------TTTTTCT s droMoj3.scaffold_6496 26160449 176 + 26866924 ---------------------------------------------------------------------CTGG--T-------------------ATGGACTCTGCCCAGTCCTCGACTCG------GCT--------------------------------TTCGCCGTT---------CC---AGCGTTGCGGGCGTTGCATTATTACGCACAAGTAAATCATCG-------------------------------CAGAGGAC----------------------GTCCT------------------C-------G---------------T-------C----CAACGGC---------T-----GGCTGAAC-------------------------GGCTTGTTAAGTAATTTAGTTGGCTTC---GTTTT-------T----------------------------GTTG-GACCCA----------------TCTG-----GC-------TTTTCCC s droGri2.scaffold_15245 915400 245 + 18325388 -------------------------------------------------------GActg------tctctgt--c-------------------tctgtctctgtctgtgtgtctgtGTG------TCTG-------------------TGGACCATCCTCTTGGCCGTT---------CC---AGCGTTGCGGGCGTTGCATTATTACGCACAAGTAAATCATCG-------------------------------CAGACGACTTTTGCCTCgttgcttgttgttgttgt------------------t-------gttgttgttgtcgtCTT-------CCAAACAGCAGC---------A-----GCCTCAAC-------------------------GGCTTGTTAAGTAATTTAGTTGGCTTC----TTTT-------T----------------------------TCAT-CTCTCTC-----GC--------TCTGCTGGCCT-------TTTTTCT a score=90765.000000 s dm6.chr2R 24367457 10 + 25286936 ATATGGCATT- s droSim1.chr2R 18705822 10 + 19596830 ATATGGCATT- s droSec1.super_23 125487 10 + 989336 ATATGGAATT- s droYak3.chr2R 20215323 10 + 21139217 ATATGGCATT- s droEre2.scaffold_4845 21613068 10 + 22589142 ATATGGCATT- s droBia2.KB462602 806770 10 + 3129309 ATATTGCATT- s droSuz1.KI419649 12052350 10 - 14502029 ATATTGCATT- s droBip2.KB464407 1968326 10 + 2915140 AAACTTTATT- s droEug2.KB465067 610108 10 + 1515531 ATATTGCATT- s droEle2.KB458573 532984 10 - 5320397 ATATTGCATT- s droKik2.KB459527 286947 10 - 1234237 ATGTTGCATT- s droTak2.KB461535 151804 10 - 669855 ATATTGCATT- s droRho2.KB449310 47607 10 - 65043 atattgCATT- s droFic2.KB457177 90334 10 + 995874 atattgcatt- s droPse3.chr3 1360029 10 - 19787792 ATATTGCATT- s droPer1.super_34 548890 10 - 916997 ATATTGCATT- s droMir2.chr3 1401100 10 - 20862834 ATATTGCATT- s droWil2.CH963894 1324499 10 + 2843958 ttatttcagt- s droVir3.scaffold_12875 7364658 10 + 20611582 ATATAATA-TG s droMoj3.scaffold_6496 26160625 11 + 26866924 AGATGATATTA s droGri2.scaffold_15245 915645 11 + 18325388 ATATGATATTA a score=1033443.000000 s dm6.chr2R 24367467 102 + 25286936 ------------------------------------------------------T-------GGCATATTTGTTTAAAG----AGCTTC---T-----TGTGAGCTGAATTTGTTATTGTCTCTATAAACGTAATAAATTGGCATTCAATTAGGCCA----------AAGGTGTTTTGTTCTCTG s droSim1.chr2R 18705832 102 + 19596830 ------------------------------------------------------T-------GGCATATTTGTTTAAAG----AGCTTC---T-----TGTGAGCTGAATTTGTTATTGTCTCTATAAATGTAATAAATTGGCATTCAATTAGGCCA----------AAGGTGTTTTGTTCTCTG s droSec1.super_23 125497 102 + 989336 ------------------------------------------------------T-------GGCATATTTGTTTAAAG----AGCTTC---T-----TGTGAGCTGAATTTGTTATTGTCTCTATAAATGTAATAAATTGGCATTCAATTAGGCCA----------AAGGTGTTTTGTTCTCTG s droYak3.chr2R 20215333 102 + 21139217 ------------------------------------------------------T-------GGCATATTTGTTTAAAG----AGCTTC---T-----TGTGAGCTGAATTTGTTATTGTCTCTATAAACGTAATAAATTGGCATTCAATTAGGCCA----------AAGGTGTTTCGTTCTCTG s droEre2.scaffold_4845 21613078 102 + 22589142 ------------------------------------------------------T-------GGCGTATTTGTTTAAAG----AGCTTC---T-----TGTGAGCTGAATTTGTTATTGTCTCTATAAATGTAATAAATTGGCATTCAATTAGGCCA----------AAGGTGTTTTGTTCTCTG s droBia2.KB462602 806780 102 + 3129309 ------------------------------------------------------T-------GGCATATTTGTTTAAAG----AGCTTC---T-----TGTGAGCTGAATTTGTTATTGTCTctataaatgcaataaattggcattcaATTAGGCCA----------AAGGTGTTTTGCTCTTCG s droSuz1.KI419649 12052360 102 - 14502029 ------------------------------------------------------T-------GGCATATTTGTTTAAAG----AGCTTC---T-----TGTGAGCTGAATTTGTTATTGTCTctataaatgcaataaattggCATTCAATTAGGCCA----------AAGGTGTTTTGCTCTTTG s droEug2.KB465067 610118 102 + 1515531 ------------------------------------------------------T-------GGCATATTTGTTTAAAG----AGCTTC---T-----TGTGAGCTGAATTTGTTATTGTCTctataaatgcaataaattggCATTCAATTAGGCCA----------AAGGTGTTTCGTACTTCG s droEle2.KB458573 532994 102 - 5320397 ------------------------------------------------------T-------Ggcatatttgtttaaag----agCTTC---T-----TGTGAGCtgaatttgttattgtttctataaatgcaataaattggCATTCAATTAGGCCA----------AAGGTGTTTTGTGCTGTG s droKik2.KB459527 286957 103 - 1234237 ------------------------------------------------------T-------GGTGTATTTGTTTAAAG----AGCTTC---T----CTGTGAGCtgaatttgttattgtttctataaatgcaataaattggCATTCAATTAGGCTA----------AAGGTGTTTTGATCCTTG s droTak2.KB461535 151814 102 - 669855 ------------------------------------------------------T-------GGCATATTTGTTTAAAG----AGCTTC---T-----TGTGAGCTGAATTTGTTATTGTCTctataaatgcaataaattggCATTCAATTAGGCCA----------AAGGTGTTTTGCTCTTTG s droRho2.KB449310 47617 102 - 65043 ------------------------------------------------------T-------GGCATATTTGTTTAAAG----AGCTTC---T-----TGTGAGCtgaatttgttattgtttctataaatgcaataaattggCATTCAATTAGGCCA----------AAGGTGTTTTGTTCTTTG s droFic2.KB457177 90344 101 + 995874 ------------------------------------------------------t-------ggcatatttgtttaaag----aGCTGA---T-----TGTGAGctgaatttgttattgtttctaTAAACGCAATAAATTGGCATTCAATTAGGCCA----------AAGGTGTTTTGCTCT-TG s droPse3.chr3 1360039 107 - 19787792 ------------------------------------------------------T-------GGCATATTTGCTTAAAG----AGCTGC---CCTGCCTGTGAGCTGCATTTGATATTGTTTCTATAAATGCTATAAATTGGCATTCAATTAGGGAA----------GAGGTGTTTTATTCTTTG s droPer1.super_34 548900 107 - 916997 ------------------------------------------------------T-------GGCATATTTGCTTAAAG----AGCTGC---CCTGCCTGTGAGCTGCATTTGATATTGTTTCTATAAATGCTATAAATTGGCATTCAATTAGGGAA----------GAGGTGTTTTATTCTTTG s droMir2.chr3 1401110 107 - 20862834 ------------------------------------------------------T-------GGCATATTTGCTTAAAG----AGCTGC---CCTGCCTGTGAGCTGCATTTGATATTGTTTCTATAAATGCTATAAATTGGCATTCAATTAGGGAA----------GAGGTGTTTTATTCTTTG s droWil2.CH963894 1324513 112 + 2843958 ------------------------------------------------------t-------ggcatatatatttgttgtttctgtttc---t-----ttgtggctttttttCTGATTGTTCATAT----GCAATAAATTGGCATTCAATTAGGCAATGCGTGAGAGAAGGTGTTTGATAATTTG s droVir3.scaffold_12875 7364668 128 + 20611582 TATAATATT--ATTTTCTGTTTTTCTTTCTT-------TTATGTTGCTTTGCAGA-------TACGCGCTTGTTT--------GCCTTG---C---------------ATTTGTTATTGTTTATAT----GCATTAAATTGGTTTTCAATTAGGC-A----------AAGGTGTTTTCTAATTTG s droMoj3.scaffold_6496 26160636 142 + 26866924 TGTATTATT--TTTGTCGCAGTTTCTCTCCTTGGCTCATTTCGTTGTCTGTCAGCGTGTTTTGGCATATTTGTGT--------GGCTCG---C---------------ATTTGTTACTGTTCATAC----GCATTAAATTGGCCTTCAATTAGGC-A----------TAGGTGTCCTCTAATTTG s droGri2.scaffold_15245 915656 133 + 18325388 TGTATTAtttgtttttctcttcttttttccat------ttatgtt--ttggcttt-------ggcatatttgttt--------aggttattct---------------tttttttgtttttTGTAT----GCATTAAATTGGCATTCAATTAGGCAA----------AAGGTGTTTTCTAATTTG a score=14444.000000 s dm6.chr2R 24367569 2 + 25286936 GT s droSim1.chr2R 18705934 2 + 19596830 GT s droSec1.super_23 125599 2 + 989336 GT s droYak3.chr2R 20215435 2 + 21139217 GT s droEre2.scaffold_4845 21613180 2 + 22589142 GT s droBia2.KB462602 806882 2 + 3129309 GT s droSuz1.KI419649 12052462 2 - 14502029 GT s droEug2.KB465067 610220 2 + 1515531 GT s droEle2.KB458573 533096 2 - 5320397 GT s droTak2.KB461535 151916 2 - 669855 GT s droRho2.KB449310 47719 1 - 65043 G- s droFic2.KB457177 90445 2 + 995874 GT s droPse3.chr3 1360146 2 - 19787792 GT s droPer1.super_34 549007 2 - 916997 GT s droMir2.chr3 1401217 2 - 20862834 GT s droWil2.CH963894 1324625 2 + 2843958 AT s droVir3.scaffold_12875 7364796 2 + 20611582 AT s droMoj3.scaffold_6496 26160778 2 + 26866924 AT a score=11099.000000 s dm6.chr2R 24367571 1 + 25286936 G s droSim1.chr2R 18705936 1 + 19596830 G s droSec1.super_23 125601 1 + 989336 G s droYak3.chr2R 20215437 1 + 21139217 G s droEre2.scaffold_4845 21613182 1 + 22589142 G s droBia2.KB462602 806884 1 + 3129309 G s droSuz1.KI419649 12052464 1 - 14502029 G s droEug2.KB465067 610222 1 + 1515531 G s droEle2.KB458573 533098 1 - 5320397 G s droKik2.KB459527 287060 1 - 1234237 A s droTak2.KB461535 151918 1 - 669855 G s droRho2.KB449310 47720 1 - 65043 A s droFic2.KB457177 90447 1 + 995874 G s droPse3.chr3 1360148 1 - 19787792 G s droPer1.super_34 549009 1 - 916997 G s droMir2.chr3 1401219 1 - 20862834 G s droWil2.CH963894 1324627 1 + 2843958 G s droVir3.scaffold_12875 7364798 1 + 20611582 G a score=18388.000000 s dm6.chr2R 24367572 2 + 25286936 GG s droSim1.chr2R 18705937 2 + 19596830 GG s droSec1.super_23 125602 2 + 989336 GG s droYak3.chr2R 20215438 2 + 21139217 GG s droEre2.scaffold_4845 21613183 2 + 22589142 GG s droBia2.KB462602 806885 2 + 3129309 GG s droSuz1.KI419649 12052465 2 - 14502029 GG s droEug2.KB465067 610223 2 + 1515531 GG s droEle2.KB458573 533099 2 - 5320397 GG s droKik2.KB459527 287061 2 - 1234237 GC s droTak2.KB461535 151919 2 - 669855 GT s droRho2.KB449310 47721 2 - 65043 GG s droFic2.KB457177 90448 2 + 995874 GG s droPse3.chr3 1360149 2 - 19787792 GG s droPer1.super_34 549010 2 - 916997 GG s droMir2.chr3 1401220 2 - 20862834 GG s droWil2.CH963894 1324628 2 + 2843958 AG a score=-314130.000000 s dm6.chr2R 24367574 85 + 25286936 TAGAAGT-GCTCGCTCGGCTCTCGA--------CAGTTGAT------------------------------------------------------------CAAGAGAT-------------------------ATGA---------TCGGGTGA-------AATTA--------TGGGAGG-----------------------------------------------ATTTT-------ATGCG-----------AACATTATGTA s droSim1.chr2R 18705939 67 + 19596830 TAGAAGT-GCTCGCTCGG--CTCGA--------CAGTTGAT------------------------------------------------------------CAA-------------------------------------------------GA-------AATTA--------TGGGAGG-----------------------------------------------ATTTT-------ATGAA---------ATAGCATTAT--- s droSec1.super_23 125604 67 + 989336 TAGAAGC-GCTCGCTCGG--CTCGA--------CAGTTGAT------------------------------------------------------------CAA-------------------------------------------------GA-------AATTA--------TGGGAGG-----------------------------------------------GTTTT-------ATGAA---------ATAGCATTAT--- s droYak3.chr2R 20215440 91 + 21139217 TAGAAGT-GCTTCTTCGG--CTTGGCAGTTGATCAGTTGAT------------------------------------------------------------CAGGAAAT-------------------------GTGA---------TCGGGTGA-------AATGC----------GAAGG-----------------------------------------------ACTTT-------CTTAT---------AAATAACaaacta s droEre2.scaffold_4845 21613185 72 + 22589142 TAGAAGT-GCTCGTTCGG--CTCGG--------CAGTTGAT------------------------------------------------------------CAGGAAAT----------------------ATGATGA---------TGGGTTGA-------AAT------------GAAGG---------------------------------------------------------------------------AGGACGATCTA s droBia2.KB462602 806887 73 + 3129309 TAGAAGCAGCTCTCTTGG---------------TAGGTGAt------------------------------------------------------------tgaaaaa--------------------------atgg---------------ga-------aatga------aaCAGGaag-----------------------------------------------atttt-------aacaa-----atatatagcG------- s droSuz1.KI419649 12052467 81 - 14502029 TAGCAGTAGCTCTCTTGG---------------CAGATGAt------------------------------------------------------------cggaaaa--------------------------atggga-------aaggaTGA-------AATGG------AGCAGGAAG-----------------------------------------------ATTTT-------AACAA-----AGATATTGTA------- s droEug2.KB465067 610225 65 + 1515531 TAGAAGGAACTCTCATGG---------------CAGATGGT------------------------------------------------------------TAGAGGGT-------------------------ATGATAA---T--TATAGCTT-------AATTA------ACTAACTAG-----------------------------------------------A-------------------------------------- s droEle2.KB458573 533101 85 - 5320397 TAGAAGTGGCTCTCTTGG---------------CAGATgat------------------------------------------------------------caaaaaat-------------------------ttgaaaagatt--ttatCTGA-------GATTTT---TCTATAGACTG-----------------------------------------------CCCAC-------ATTAA-----GTGCA------------ s droKik2.KB459527 287063 73 - 1234237 AAAAAGGAGATGTTTTAA--CACAA--------CATCAAAC------------------------------------------------------------CAGaagat-------------------------atat---------tttgaaaa-------aatcc--------tTACagt-----------------------------------------------ttttc-------cttca---------------------- s droTak2.KB461535 151921 70 - 669855 TC------TCTCTTTGGG---------------AAGATGAT------------------------------------------------------------CACAGAA--------------------------ATGG---------AACGGGGA-------GACTA----------TCTAG-----------------------------------------------ATTTT-------ATGCAT-ACTTGATATG---------- s droRho2.KB449310 47723 74 - 65043 TAGAAGTTGCTCTCTTGG---------------CAGATGAT------------------------------------------------------------CAAAAAAT-------------------------ATGA---------AGAGGTGA-------GGGTA--------------G-----------------------------------------------ATTTT-------ATCTACGATTTTTTAAA---------- s droFic2.KB457177 90450 170 + 995874 TAGAAGTCCCTCTCTTGG---------------CAGATGGTCTGACTAACTagattttgtgcatttttttgGGTTCAGTATAGGTTTTTGACAATATCTAACAAAAAACCGATCGGACTGTCAAGTTAATCaagattaaaaaattcaaaatatgt-------GATTACCAACTGTTTTGCAG-----------------------------------------------AACTA-------ATGTG---------------------- s droPse3.chr3 1360151 80 - 19787792 --------ATTCGCAcag----------------agacgag------------------------------------------------------------agagagag-------------------------aagggag------cagagcga-------gagTC----CtgattgaaaatcaatttgatcGTA---------------------------------ATTCC-------ATTTG---------------------- s droPer1.super_34 549012 80 - 916997 --------ATTCGCTCAG----------------AGACGGG------------------------------------------------------------AGAGAGAG-------------------------AAGGGAG------CAGAGCGA-------GAGTC----CTGATTGAAAATCAATTTGATCGTA---------------------------------ATTCC-------ATTTG---------------------- s droMir2.chr3 1401222 120 - 20862834 --------ATTCGCAGAG----------------AGACGGG------------------------------------------------------------AGGGAGAG-------------------------AAGGGAG------CAGAGCGAGTGTCttgat-----------tgaaaatcaatttgatcgtaattccatttttatttcacaGCTTTTAAAGCAAGATCCTTATCGTGATCTA---------------------- a score=-143391.000000 s dm6.chr2R 24367659 14 + 25286936 TTGTCTAAGA----------------------------------------------------AATT s droSim1.chr2R 18706006 6 + 19596830 --------GA----------------------------------------------------AATG s droSec1.super_23 125671 6 + 989336 --------GA----------------------------------------------------AATG s droYak3.chr2R 20215531 13 + 21139217 tt------tat------------------------aatt-----------------------tatt s droEre2.scaffold_4845 21613257 8 + 22589142 CT------GA----------------------------------------------------CATT s droBia2.KB462602 806996 23 + 3129309 ----------TTGTGT------GCA----ATCGTTGCtt-----------------------gatt s droEug2.KB465067 610290 14 + 1515531 TTTTATAGGA----------------------------------------------------AATT s droEle2.KB458573 533186 17 - 5320397 ----------------------CTG----TTTATGGGCT-----------------------TATT s droKik2.KB459527 287136 14 - 1234237 -----------------------------ttttcaAAGC-----------------------AATT s droTak2.KB461535 151991 9 - 669855 ----------------------------------TGgct-----------------------gatt s droRho2.KB449310 47797 6 - 65043 -------------------------------------CT-----------------------ACCT s droFic2.KB457177 90620 26 + 995874 -------------TTTTCTAAACTT----TGTCAAAATA-----------------------GATT s droPse3.chr3 1360231 31 - 19787792 -----------------------TA----TTTCACAGCT-------TTTAAAACAAGATCCTTAT- s droPer1.super_34 549092 5 - 916997 -----------------------TA-------------------------------------TTT- s droMir2.chr3 1401342 34 - 20862834 -----------------------TAGAATTATTGAAGCTTGTGTTCTTTGCGAT--------TAT- a score=1662.000000 s dm6.chr2R 24367673 8 + 25286936 CATTTTCT s droSim1.chr2R 18706012 8 + 19596830 CACGTTCT s droSec1.super_23 125677 8 + 989336 CATATTCT s droYak3.chr2R 20215544 8 + 21139217 cacACTAT s droEre2.scaffold_4845 21613265 5 + 22589142 CGTAT--- s droBia2.KB462602 807019 8 + 3129309 tataatat s droEug2.KB465067 610304 8 + 1515531 CCTCTTCT s droEle2.KB458573 533203 8 - 5320397 TATCTCTT s droTak2.KB461535 152000 8 - 669855 tgtttttt s droRho2.KB449310 47804 8 - 65043 CATTTTAT s droFic2.KB457177 90647 8 + 995874 caattctt s droPse3.chr3 1360262 8 - 19787792 CGTGATCT s droPer1.super_34 549097 8 - 916997 CACAGCTT s droMir2.chr3 1401376 8 - 20862834 TTTTGTCT a score=-81642.000000 s dm6.chr2R 24367681 14 + 25286936 CA------------------AAAA-----------ATTAAGGA---------------------- s droSim1.chr2R 18706020 2 + 19596830 CA--------------------------------------------------------------- s droSec1.super_23 125685 2 + 989336 CA--------------------------------------------------------------- s droYak3.chr2R 20215552 6 + 21139217 GA------------------ACTA----------------------------------------- s droEug2.KB465067 610312 25 + 1515531 CT------------------AGGTCGGACAGTCCTAGTAAGCA---------------------- s droEle2.KB458573 533211 24 - 5320397 TATTCTTTCTGTAAAATCTAAGAT----------------------------------------- s droRho2.KB449310 47812 13 - 65043 ------------------------------GCACTGTTTATGG---------------------- s droFic2.KB457177 90655 14 + 995874 ----------------------------taataatttttggt----------------------- s droPse3.chr3 1360270 21 - 19787792 -------------------------------------GTAGAATTATTGATGCT-------GTGT s droPer1.super_34 549105 23 - 916997 -------------------------------------TTAAAACAA--GATCCTTATC---GTGA s droMir2.chr3 1401384 26 - 20862834 -------------------------------------TCAGAAAAA--TATGTTCATTCGAATGG a score=-24199.000000 s dm6.chr2R 24367695 10 + 25286936 TCTT-------CCTAAT s droSim1.chr2R 18706022 7 + 19596830 ---T-------CTTAAT s droSec1.super_23 125687 7 + 989336 ---T-------CTTAAT s droYak3.chr2R 20215558 5 + 21139217 ---T-------CTTA-- s droEre2.scaffold_4845 21613270 5 + 22589142 ---T-------CTTC-- s droBia2.KB462602 807027 7 + 3129309 ---t-------tttaat s droAna3.scaffold_13266 5718285 10 - 19884421 TTTT-------CTAAAC s droEug2.KB465067 610361 8 + 1515531 tctt-------tcta-- s droEle2.KB458573 533235 10 - 5320397 TTGA-------TCTACT s droRho2.KB449310 47826 7 - 65043 -CAT-------ATTA-- s droFic2.KB457177 90669 8 + 995874 --tt-------tttata s droPse3.chr3 1360291 10 - 19787792 TCTT-------TGcgat s droPer1.super_34 549128 10 - 916997 TCTG-------TAGAAT s droMir2.chr3 1401410 17 - 20862834 TCTAACATTTCTCTGAT a score=3018.000000 s dm6.chr2R 24367705 3 + 25286936 TAT s droSim1.chr2R 18706029 3 + 19596830 TAT s droSec1.super_23 125694 2 + 989336 T-T s droYak3.chr2R 20215563 3 + 21139217 TAT s droEre2.scaffold_4845 21613275 3 + 22589142 TGT s droBia2.KB462602 807034 3 + 3129309 tat s droAna3.scaffold_13266 5718295 3 - 19884421 TTT s droEug2.KB465067 610369 3 + 1515531 tct s droEle2.KB458573 533245 3 - 5320397 TAT s droRho2.KB449310 47833 1 - 65043 T-- s droFic2.KB457177 90677 3 + 995874 tat s droPse3.chr3 1360301 3 - 19787792 tat s droPer1.super_34 549138 3 - 916997 TAT a score=-20459.000000 s dm6.chr2R 24367708 2 + 25286936 ----------AT--- s droSim1.chr2R 18706032 2 + 19596830 ----------AA--- s droSec1.super_23 125696 2 + 989336 ----------AT--- s droYak3.chr2R 20215566 2 + 21139217 ----------GT--- s droEre2.scaffold_4845 21613278 2 + 22589142 ----------GT--- s droBia2.KB462602 807037 2 + 3129309 ----------cg--- s droAna3.scaffold_13266 5718298 2 - 19884421 ----------AT--- s droEug2.KB465067 610372 2 + 1515531 ----------at--- s droRho2.KB449310 47834 2 - 65043 ----------AT--- s droFic2.KB457177 90683 1 + 995874 -----------t--- s droPse3.chr3 1360304 11 - 19787792 t----tttgtattcg s droPer1.super_34 549141 15 - 916997 TGAAGCTTGTGTTCT a score=-78217.000000 s dm6.chr2R 24367710 18 + 25286936 ---TAAC---CATAAT--TTAC----G-------------------------GAA---------------------- s droSim1.chr2R 18706034 18 + 19596830 ---TAGC---CATAAT--TTAC----A-------------------------GAA---------------------- s droSec1.super_23 125698 18 + 989336 ---TAGC---CATAAT--TTAC----A-------------------------GAA---------------------- s droYak3.chr2R 20215568 43 + 21139217 ---ctgc---taaaat--atat----atatatatataattatacagTTTAAAGAT---------------------- s droEre2.scaffold_4845 21613280 15 + 22589142 ---ATAC---TAGAAT--TC--------------------------------GGT---------------------- s droBia2.KB462602 807039 18 + 3129309 ---tTAT---AACAAT--TAAT----C-------------------------AAA---------------------- s droAna3.scaffold_13266 5718300 18 - 19884421 ---TGAT---GATCCT--TTGT----G-------------------------GGA---------------------- s droEug2.KB465067 610374 22 + 1515531 ---ctat---taTCAC--ATATTTTAG-------------------------GAA---------------------- s droEle2.KB458573 533461 18 - 5320397 ---CTAA---CATCAT--TTTG----G-------------------------GGT---------------------- s droRho2.KB449310 47844 8 - 65043 ---TTGC---TAAA--------------------------------------------------------------- s droFic2.KB457177 90688 18 + 995874 ---ctgG---TTTAAG--TTGC----T-------------------------TAA---------------------- s droPse3.chr3 1360315 32 - 19787792 gAAAAATAGGTATGTT--CATT----C-------------------------GAA--------------TGGTCCAA s droPer1.super_34 549156 45 - 916997 TTTCTAT---TATTTTTGTATT----C-------------------------GGAAAAATATGTATGTTCATTCGAA a score=-20237.000000 s dm6.chr2R 24367728 3 + 25286936 CAG--------------- s droSim1.chr2R 18706052 3 + 19596830 CAG--------------- s droSec1.super_23 125716 3 + 989336 CAG--------------- s droYak3.chr2R 20215611 3 + 21139217 CAG--------------- s droEre2.scaffold_4845 21613295 3 + 22589142 CTT--------------- s droAna3.scaffold_13266 5718319 1 - 19884421 --C--------------- s droEug2.KB465067 610414 3 + 1515531 TGG--------------- s droEle2.KB458573 533479 3 - 5320397 TTT--------------- s droRho2.KB449310 47852 3 - 65043 CAA--------------- s droFic2.KB457177 90706 3 + 995874 TAG--------------- s droPse3.chr3 1360347 10 - 19787792 CATTTCGCT--------G s droPer1.super_34 549201 18 - 916997 TGGTCCAACATTTCGCTG a score=-29095.000000 s dm6.chr2R 24367731 34 + 25286936 AATCGGATTTCTAGCGGCTGT------------------ACTATAATTGCTT s droSim1.chr2R 18706055 34 + 19596830 AATCGGATTTCCATCGGCTGT------------------GCTATAATTGCTT s droSec1.super_23 125719 34 + 989336 AATCGGATTTCTATCGGCTGT------------------GCTATAATTGCTT s droYak3.chr2R 20215614 34 + 21139217 AATCCTATTTCTTTCGGCTGT------------------GCTATAATTGCTT s droEre2.scaffold_4845 21613298 23 + 22589142 AATTATTTTTCATTCG-----------------------------ATGGCTG s droAna3.scaffold_13266 5718320 24 - 19884421 AAT---------ATCGCCCAG------------------ACTCTGA-AGCTT s droEug2.KB465067 610417 52 + 1515531 AATATtttgtgtaataaatattttaaggtatTAATGCCAGCCTTCAGTGCTT s droEle2.KB458573 533482 24 - 5320397 TATGATGTTTATAGTGCCTGC--------------------------TGC-- s droRho2.KB449310 48116 21 - 65043 TACCATATTTCGAGTGCCTGC------------------------------- s droFic2.KB457177 90713 43 + 995874 taaaatgtttttggggGCTTA---------TTGAATTTAACCAAGATTATCC s droPse3.chr3 1360357 30 - 19787792 -ATACAATTTTCTTCTCc---------------------attaaaattgttt s droPer1.super_34 549219 30 - 916997 -ATACAATTTTCTTCTCC---------------------ATTAAAATTGTTT a score=2847.000000 s dm6.chr2R 24367765 5 + 25286936 CTTAT s droSim1.chr2R 18706089 5 + 19596830 TTTAT s droSec1.super_23 125753 5 + 989336 TTTAT s droYak3.chr2R 20215648 5 + 21139217 TTTAT s droEre2.scaffold_4845 21613321 5 + 22589142 TTTAT s droSuz1.KI419649 12053567 5 - 14502029 CCTGT s droAna3.scaffold_13266 5718344 5 - 19884421 ATTAC s droEle2.KB458573 533507 5 - 5320397 TTCAT s droRho2.KB449310 48138 4 - 65043 TTCA- s droFic2.KB457177 90759 5 + 995874 TTCGT s droPse3.chr3 1360387 5 - 19787792 caaaT s droPer1.super_34 549249 5 - 916997 CAAAT a score=-125608.000000 s dm6.chr2R 24367770 15 + 25286936 TT----------------ATTT--------------CTCTTTGT----A s droSim1.chr2R 18706094 15 + 19596830 TC----------------ATTT--------------CTCCTTGT----A s droSec1.super_23 125758 15 + 989336 TC----------------ATTT--------------CTCCTTGT----A s droYak3.chr2R 20215653 32 + 21139217 Tcgttttcaatttat---attc--------------CTTTTTGTGCGCA s droEre2.scaffold_4845 21613326 27 + 22589142 ACATTTTCAATTTGC---ATTT--------------CTTTTCGT----- s droSuz1.KI419649 12053572 15 - 14502029 TT----------------CTTT------------AACTAACTG------ s droAna3.scaffold_13266 5718349 29 - 19884421 CCATCCCCAAATGACGAGAACT--------------GTCAATA------ s droEug2.KB465067 610499 20 + 1515531 ------CTGCCTTAA---CTTA--------------CTAACTG------ s droEle2.KB458573 533512 14 - 5320397 TTTCTAGCAAACTG----------------------------------- s droTak2.KB461535 152406 15 - 669855 -------------------ttttt---------taactaactG------ s droRho2.KB449310 48142 15 - 65043 ----------------------TTA------TCTAACAAACTG------ s droFic2.KB457177 90764 27 + 995874 ----------------------TTGGGTGCCTTCATTTCCTTACAGAAA s droPse3.chr3 1360392 12 - 19787792 -------------------------------ATTCACTCCATA------ s droPer1.super_34 549254 12 - 916997 -------------------------------ATTCACTCCATA------ a score=100230.000000 s dm6.chr2R 24367785 32 + 25286936 ---------------ACTTGCGACGCCTTCACTTCGATTT-------CCTGATC s droSim1.chr2R 18706109 32 + 19596830 ---------------ACTTGCGACGCCTTCACTTCGATTT-------CCTGATC s droSec1.super_23 125773 32 + 989336 ---------------ACTTGCGACGCCTTCACTTCGATTT-------CCTGATC s droYak3.chr2R 20215685 32 + 21139217 ---------------ACTTGCGACGCCTTCACTGCGATTT-------CCTGATC s droEre2.scaffold_4845 21613353 32 + 22589142 ---------------AACTGCGACGCCTTCACTTCGATTT-------CCTGATC s droBia2.KB462602 807397 32 + 3129309 ---------------ACTTTCGACGCCTTCACTTCGCTTT-------GCTGATC s droSuz1.KI419649 12053587 32 - 14502029 ---------------ATTTTCGACGCCTGCACTTCTCTTT-------CCTGATC s droAna3.scaffold_13266 5718384 27 - 19884421 ---------------AATTATTTCGCC--CATATTGTTAT-------GCTA--- s droEug2.KB465067 610519 32 + 1515531 ---------------ATTGGCAACGCCTTCAGTTCGCTTC-------CCTGATC s droEle2.KB458573 533526 32 - 5320397 ---------------ATTTGCAACGCCTTCACTTCGCCTT-------TCCGATC s droTak2.KB461535 152421 36 - 669855 ---------------ATTTTCGACGCCTTCACTGCGCTCTTCATTCGCCTA--- s droRho2.KB449310 48157 32 - 65043 ---------------ATTTGCAACGCCTCCACTTCGCTTT-------CCCGATC s droFic2.KB457177 90792 31 + 995874 ---------------AGTTGCAACGCCCCTATTTCACTT--------CCTGATC s droPse3.chr3 1360404 46 - 19787792 TCCATAGACGTTGATCATGGATATGCC-CCAAACTGTTTC-------TTTGATC s droPer1.super_34 549266 46 - 916997 TCCATAGACGTTGATCATGGATATGCC-CCAAACTGTTTC-------TTTGATC a score=-2346.000000 s dm6.chr2R 24367817 3 + 25286936 CC--G s droSim1.chr2R 18706141 3 + 19596830 CC--G s droSec1.super_23 125805 3 + 989336 CC--G s droYak3.chr2R 20215717 3 + 21139217 CC--C s droEre2.scaffold_4845 21613385 3 + 22589142 CC--G s droBia2.KB462602 807429 5 + 3129309 GCATA s droSuz1.KI419649 12053619 5 - 14502029 GCACA s droEug2.KB465067 610551 3 + 1515531 GC--A s droEle2.KB458573 533558 3 - 5320397 gc--a s droRho2.KB449310 48189 3 - 65043 GC--A s droFic2.KB457177 90823 3 + 995874 GC--A s droPse3.chr3 1360493 3 - 19787792 CC--A s droPer1.super_34 549355 3 - 916997 CC--A s droMir2.chr3 1401561 3 - 20862834 CC--A a score=-1003.000000 s dm6.chr2R 24367820 3 + 25286936 --AAA s droSim1.chr2R 18706144 3 + 19596830 --AAA s droSec1.super_23 125808 3 + 989336 --AAA s droYak3.chr2R 20215720 3 + 21139217 --AAA s droEre2.scaffold_4845 21613388 3 + 22589142 --AAA s droBia2.KB462602 807434 3 + 3129309 --AAA s droSuz1.KI419649 12053624 3 - 14502029 --AAA s droAna3.scaffold_13266 5718411 3 - 19884421 --AAT s droBip2.KB464407 1968420 3 + 2915140 --aat s droEug2.KB465067 610556 3 + 1515531 --GGA s droEle2.KB458573 533563 3 - 5320397 --aaa s droTak2.KB461535 152457 3 - 669855 --AAA s droRho2.KB449310 48194 3 - 65043 --AAA s droFic2.KB457177 90828 3 + 995874 --AAA s droPse3.chr3 1360496 3 - 19787792 TCA-- s droPer1.super_34 549358 3 - 916997 TCA-- s droMir2.chr3 1401564 3 - 20862834 TCA-- a score=44567.000000 s dm6.chr2R 24367823 8 + 25286936 TCTTTTGG s droSim1.chr2R 18706147 8 + 19596830 TCTTTTAG s droSec1.super_23 125811 8 + 989336 TCTTTTGG s droYak3.chr2R 20215723 8 + 21139217 TCTTGCGG s droEre2.scaffold_4845 21613391 8 + 22589142 TCTTGTGG s droBia2.KB462602 807437 8 + 3129309 ACTTTCGG s droSuz1.KI419649 12053627 8 - 14502029 ACTTTTGG s droAna3.scaffold_13266 5718414 8 - 19884421 TTTTGGCT s droBip2.KB464407 1968423 8 + 2915140 tatttCGC s droEug2.KB465067 610559 8 + 1515531 ACTTTTGG s droEle2.KB458573 533566 8 - 5320397 acttttgg s droKik2.KB459527 287165 8 - 1234237 ttttttgg s droTak2.KB461535 152460 8 - 669855 ACATTTGG s droRho2.KB449310 48197 8 - 65043 ACTTTTGG s droFic2.KB457177 90831 8 + 995874 AGTTTCGG s droPse3.chr3 1360499 8 - 19787792 ACTTTAGG s droPer1.super_34 549361 8 - 916997 ACTTTAGG s droMir2.chr3 1401567 8 - 20862834 ACTCTTGG a score=19883.000000 s dm6.chr2R 24367831 24 + 25286936 CTACTTGGCCAATCT-TGGTTCGAG s droSim1.chr2R 18706155 24 + 19596830 CTACTTGGCCAATCT-TGGTTCGGG s droSec1.super_23 125819 24 + 989336 CTACTTGGCCAATCT-TGGTTCGGG s droYak3.chr2R 20215731 25 + 21139217 CTACCTGGCCAATCTCTGGTTCGAG s droEre2.scaffold_4845 21613399 24 + 22589142 CTACTTGGCCAATCT-GGGTTCGAG s droBia2.KB462602 807445 17 + 3129309 CTACTTGG--------CATTTCCAG s droSuz1.KI419649 12053635 17 - 14502029 CTACTTGG--------CATTTCCAG s droAna3.scaffold_13266 5718422 22 - 19884421 ACTCCCGGCTAGTC---AGTCCCAT s droBip2.KB464407 1968431 24 + 2915140 CCATATGGTTATGCT-AAGTTTCGT s droEug2.KB465067 610567 17 + 1515531 CTACTTGG--------CATCTACTG s droEle2.KB458573 533574 17 - 5320397 ctACTTGG--------CATTTCCAG s droKik2.KB459527 287173 22 - 1234237 CTACTTGG--TATCG-CATTTCCAT s droTak2.KB461535 152468 17 - 669855 CTACTTGG--------CCTTTCCAG s droRho2.KB449310 48205 17 - 65043 CTACTTGG--------CATTTCCAG s droFic2.KB457177 90839 17 + 995874 CTACTTGA--------CATTTCCAG s droPse3.chr3 1360507 20 - 19787792 CTACTCTC--AAC---ATTTCCCAT s droPer1.super_34 549369 20 - 916997 CTACTCTC--AAC---ATTTCCCAT s droMir2.chr3 1401575 20 - 20862834 CTACTCTC--AAC---ATTTCCCAT s droMoj3.scaffold_6496 26161438 24 + 26866924 CTCCCTGGTCAATTT-GGGATCAAG a score=49463.000000 s dm6.chr2R 24367855 6 + 25286936 GCAAT----C s droSim1.chr2R 18706179 6 + 19596830 GCCAT----C s droSec1.super_23 125843 6 + 989336 GCCAT----C s droYak3.chr2R 20215756 10 + 21139217 CCAATCTGGC s droEre2.scaffold_4845 21613423 6 + 22589142 GCAAT----C s droBia2.KB462602 807462 6 + 3129309 GCAAT----C s droSuz1.KI419649 12053652 6 - 14502029 GCAAT----C s droAna3.scaffold_13266 5718444 6 - 19884421 CCACT----C s droBip2.KB464407 1968455 6 + 2915140 CCACT----C s droEug2.KB465067 610584 6 + 1515531 GCAAT----C s droEle2.KB458573 533591 6 - 5320397 GCAAT----C s droKik2.KB459527 287195 6 - 1234237 CCAAT----C s droTak2.KB461535 152485 6 - 669855 GCAAT----C s droRho2.KB449310 48222 6 - 65043 GCAAT----C s droFic2.KB457177 90856 6 + 995874 GCAAT----C s droPse3.chr3 1360527 6 - 19787792 CCAAT----C s droPer1.super_34 549389 6 - 916997 CCAAT----C s droMir2.chr3 1401595 6 - 20862834 CCAAT----C s droMoj3.scaffold_6496 26161483 6 + 26866924 GCTGC----T s droGri2.scaffold_15245 916532 6 + 18325388 GCAAA----C a score=-5429.000000 s dm6.chr2R 24367861 1 + 25286936 T s droSim1.chr2R 18706185 1 + 19596830 T s droSec1.super_23 125849 1 + 989336 T s droYak3.chr2R 20215766 1 + 21139217 T s droEre2.scaffold_4845 21613429 1 + 22589142 T s droBia2.KB462602 807468 1 + 3129309 A s droSuz1.KI419649 12053658 1 - 14502029 A s droAna3.scaffold_13266 5718450 1 - 19884421 C s droBip2.KB464407 1968461 1 + 2915140 T s droEug2.KB465067 610590 1 + 1515531 A s droEle2.KB458573 533597 1 - 5320397 A s droKik2.KB459527 287201 1 - 1234237 A s droTak2.KB461535 152491 1 - 669855 A s droRho2.KB449310 48228 1 - 65043 A s droFic2.KB457177 90862 1 + 995874 A s droPse3.chr3 1360533 1 - 19787792 A s droPer1.super_34 549395 1 - 916997 A s droMir2.chr3 1401601 1 - 20862834 A s droWil2.CH963894 1325586 1 + 2843958 T s droMoj3.scaffold_6496 26161489 1 + 26866924 T s droGri2.scaffold_15245 916538 1 + 18325388 T a score=3756592.000000 s dm6.chr2R 24367862 497 + 25286936 GGCATTAGCATATCGGTCA--TAAGATCTATAACT---AAACTC---GGCGG-------ACAGTT----GACAG-CTACTCCGCCC------CGCAGACGA---------ATC-----------------AGA----------TTGGATC--------GG---------ACGGTACGGG--------------------AT--------------------------CAT-AT---------------------------------GG-GAT--------------CCGTC---ATGC-----GAA--GA----------GGC------TCGTCCT------GCTTTCTAACGATGGCATTTTTGATATTTGTGACACGCAGATTTTCCATCAGTGTCAACAAGGCATTG-TTCG----------------------GC-----GAACGTCAACGTGGTTGG---------TCTGGGTCCTCCGAC------C--TCCGGTCC-ACCCCGT--------------TCTCCCGA----TCTCTCCCA---------------------------GACTT-CCAA----------CT--------------CCTGACTC-------AACTGACAGACTCGAT-CGGCCGTCCGA--TCG--TCG-------TCGATTTTTC-AGCA--TCAG---AGC--AAAGGCAGGC-AAAG------T-------------------CGGGCCAATGCAAAA--C----C-----GAAT----------GC----AACGCGTACATTTGCATAGAC------------------------------ACAAAATTAT----ATGAGA----CC----GA-ACC---GAGA------------------------C-----------------CGGGCC---C------GAAACGCA-----GCTTCCTGGTC--------------------TTTTTGT-------------------------------------------GTC--TGAAATTTATGTACCCACACAATGG s droSim1.chr2R 18706186 502 + 19596830 GGCATTAGCATATCGGTCA--TAAGATCTATAACT---AAACTC---GGCGG-------ACAGTT----GACAG-CTACTCCGCCC------CGCAGACGG---------ATC-----------------AGA----------TTGGATC--------GG---------ACGGTACGGG--------------------AT--------------------------CAT-AT---------------------------------GG-GAT--------------CCGTC---ATGC-----GAA--GA----------GGC------TCGTCCT------GCTTTCTAACGATGGCATTTTTGATATTTGTGACACGCAGATTTTCCATCAGTGTCAACAAGGCATTG-TTCG----------------------GC-----GAACGTCAACGTGGTTGG---------TCTGGGTCCTCCGAC------C--TGCGGTCC-ACCCCGTC----------CTGTCTCCCGA----TCTCTCCCA---------------------------GACTC-CCAA----------CT--------------CCTGACTC-------AACTGACAGACTCGAT-CGGCCGTCCGA--TCG--TCG-------TCGATTTTTC-AGCA--TCAG---AGC--AAAGGCAGGC-AAAG------T-------------------TGGGCCAATGCAAAA--C----C-----GAAT----------GC----AGCGCGTACATTTGCATAGAC------------------------------ACAAAATTAT----ATGAGA----CC----GAGACC---GCGA------------------------C-----------------CGGGCC---C------GAAACGCA-----GCTTCCTGGTC--------------------TTTTTGT-------------------------------------------GTC--TGAAATTTATGTACCCACACAATGG s droSec1.super_23 125850 502 + 989336 GACATTAGCATATCGGTCA--TAAGATCTATAACT---AAACTC---GGCGG-------ACAGTT----GACAG-CTACTCCGCCC------CACAGACGG---------ATC-----------------AGA----------TTGGATC--------GG---------ACGGTACGGG--------------------AT--------------------------CAT-AT---------------------------------GG-GAT--------------CCGTC---ATGC-----GAA--GA----------GGC------TCGTCCT------GCTTTCTAACGATGGCATTTTTGATATTTGTGACACGCAGATTTTCCATCAGTGTCAACAAGGCATTG-TTCG----------------------GC-----GAACGTCAACGTGGTTGG---------TCTGGGTCCTCCGAC------C--TCCTGTCC-ACCCCGTC----------CTGTCTCCCGA----TCTCTCCCA---------------------------GACTC-CCAA----------CT--------------CCTGACTC-------AACTGACAGACTCGAT-CGGCCGTCCGA--TCG--TCG-------TCGATTTTTC-AGCA--TCAG---AGC--AAAGGCAGGC-AAAG------T-------------------CGGGCCAATGCGAAA--C----C-----GAAT----------GC----AGCGCGTACATTTGCATAGAC------------------------------ACAAAATTAT----ATGAGA----CC----GAGACC---GCGA------------------------C-----------------CGGGCC---C------GAAACGCA-----GCTTCCTGGTC--------------------TTTTCGT-------------------------------------------GTC--TGAAATTTATGTACCCACACAATGG s droYak3.chr2R 20215767 574 + 21139217 GGCATTAGCATATCGGTCA--TAAGATCTATAACT---AAACTC---GACGG-------ACAGTT----GACAGTTTGCTCCGCCCCG----CGGAGTCGA---------ATCGG---------------AGA----------TTGGATC--------GG---------ACGGTACGGGATCACATGGCATCACATGGCAT--------------------------CAT-AT---------------------------------GG-GAT--------------CCGTC---ATGC-----GAGCCTG----------TGC------TCGTCCT------GCTTTCTAACGATGGCATTTTTGATATTTGTGACACGCAGATTTTCCATCAGTGTCAACAAGGCATTG-TTTG----------------------GC-----GAACGTCAACGTGGTTGG---------TCTGGGTCCTCCGGC------CATCCCGATCT-CCCACTCC---------TCCGGCTCCAGA-------CTCCCAAATCCCATATCCCAACTCCCGACCACCGACTC-CCAA----------CT--------------CCCGACTCCTGACTCAACTGACAGACTCGAT-CGGCCGTCCGA--TCG--TCG-------TCGATTTTTC-AGCA--TCAGAGCAGC--AAAGGCAGGCAAAAG------T-------------------CGGGCCAATGCAAAA--C----C-----GAAT----------GC----AGCGCGTACATTTGCATAGAC------------------------------ACAAAATTAT----ATGAGA----CC----AAGACC---GAGA-----------------CCGAGAGC-----------------CGGGCC---G------AAAACGCA-----GCTTCCTGGTC--------------------TTTTTGT-------------------------------------------GTC--TGAAATTTATGTACCCACACAATGG s droEre2.scaffold_4845 21613430 506 + 22589142 GGCATTAGCATATCGGTCA--TAGGATCTATAACT---AAACTC---GACGG-------ACAGTT----GACAGTTTACTCCGCC-------CGCAGACGG---------ATC-----------------AGA----------TTGGATC--------GG---------ACGGTACGGG--------------------AT--------------------------CAT-AT---------------------------------GG-GAT--------------CCGTC---ATGC-----GAA--GA----------GGC------TCGTCCT------GCTTTCTAACGATGGCATTTTTGATATTTGTGACACGCAGATTTTCCATCAGTGTCAACAAGGCATTG-TTTG----------------------GC-----GAACGTCAACGTGGTTGGTCCTGCTCCTCCTGCTCCTCCGAC------CCTCCCGGTCT--CCACTTC---------TCTGACTCCATG-------CTCCAA----------------------------ACTC-CCGA----------CT--------------CCTGACTC----CCCAACTGACAGACTCGAT-CGGCCGTCCGA--TCG--TCG-------TCGATTTTTC-AGCA--TCAG---AGC--AAAGGCAGAC-AAAG------T-------------------CGGGCCAATGCAAAA--C----C-----GAAT----------GC----AGCGCGTACATTTGCATAGAC------------------------------ACAAAATTAT----ATGAGA----CC----GAGGC--------------------------------C-----------------CGGGCC---G-------AAACGCA-----GCTTCCTGGTC--------------------TTTTTGT-------------------------------------------GTC--TGAAATTTATGTACCCACACAATGG s droBia2.KB462602 807469 492 + 3129309 GGCATTAGCATATCGGTCA--TAAGATCTATAACT---AAGCCC---GACGG-------GCAGTT----GACAGTTTTCTCCGCCC------CACAGACGG---------ATC-----------------AGA----------TAGGATC--------GG---------ACGGTATGAG--------------------AT--------------------------CAT----------------------------------------------------------------ATGC-----GAG--GA----------GGC------TCGTCCT------GCTTTCTAACGATTGCATTTTTGATATTTGTGACACGCAGATTTTCCATCAGTGTCAACAAGGCATTG-TTTG----------------------GCGAACGGAACGTCAACGTGGTTGG---------------TCCTCCGT-------C--CTCGATCC-CGAGCTCC----------CAGACTCCCCA------TCCCCTG---------------------ACTTTCGACTC-CCGA----------CT--------------CCTGACTC-------AACTGACAGACTCGAT-CGGCCGTCCGA--TCG--CCG-------TCGATTTTTC-AACA--TCAG---ACC--AAAGTCAGGCCAAAG------T-------------------CGGGCCAATGCAAAA--C----C-----GAAT----------GC----AGCGCGTACATTTGCATAGAC------------------------------ACAAAATTAT----ATGAGA----CC----GAGACC-------------------------------C-----------------AGGACC---C--AC--AAAACGCA-----GCTTCCTGGTC--------------------TTTTTGT-------------------------------------------GTC--TGAAATTTATGTACCCACACAATGG s droSuz1.KI419649 12053659 509 - 14502029 GGCATTAGCATATCGGTCA--TAAGATCTATAACT---AAACCC---TACGG-------ACAGTT----GACAGTTTTCTCCGCCC------CGCAGACGG---------ATC-----------------AGA----------TTGGATC--------GG---------ACGGTATGGG--------------------AT--------------------------CAT-AT---------------------------------GG-GAG--------------CCATCATCATGC-----GAA--GA----------GGC------TCGTCCT------GCTTTCTAACGATTGCATTTTTGATATTTGTGACACGCAGATTTTCCATCAGTGTCAACAAGGCATTG-TTTG----------------------GCGAACGGAACGTCAACGTGGTTGG---------------TCCTCCATCCTCCAAC--CTCAATCC-CGAACTCC----------CAGACTCCTCA-----GTCCCCCG---------------------------GACTC-CCGA----------CT--------------CCTGACTC-------AACTGACAGACTCGAT-CGGCCGTCCGA--TCG--TCG-------TCGATTTTTC-AACA--TCAG---ACC--AAAGTCAGGCCAAAG------T-------------------CGGGCCAATGCAAAA--C----C-----GTAT----------GC----AGCGCGTACATTTGCATAGAC------------------------------ACAAAATTAT----ATGAGA----CC----GAGACC-------------------------------C-----------------AGGACC---C--AC--AAAACGCA-----GCTTCCTGGTC--------------------TTTTTGT-------------------------------------------GTC--TGAAATTTATGTACCCACACAATGG s droAna3.scaffold_13266 5718451 539 - 19884421 CGCATTAGCATATC-GGGA--AAAGATCTATAACC---CAGCGC---GCTGG-------CCAGTT----GACAGTTTTCTCCGCCCCACCCTCGGAATCGG---------ATC-------------------A----------TCAGATC-------------------ACTGAATGGG--------------------GA--------------------------TAT-AT---------------------------------GA-TACGGTAGGGGACATAAGCGTC---ATAG-----AAA--GG---AGAGCCCGGCCTGCGATCGTCCTGACTTCGCTTTCTAACGATTGAATTTTTGATATTTGTGACACGCAGATTTTCCATCAGTGTCAACAAGGCATTG-TTTG----------------------GC----GAAACGTCAACGTGGTTGG---------TC----TCCTCCGTC------C-----------------------------CAGAGCCGGGCAGCGAGTACCCCA---------------------------GACCC-CGGA---------------------------CTGACTC-------AACTGACAGACTTGATCCAATCGTC-----CCG--TCG-------TCGATTTTTC-AACA--TCAG---ACC-------------AAAG------T-------------------CGGGCCAATGCAAAAACC----C---------------------------CGCGTACATTTGCATAGAC------------------------------ACAAAATTAT----ATGAGA----CC----GTGGCC-------------------------------C-----------------AGGACC---G--AC--AAAACGCA-----GCTTCCTGGTCTT------------------TTTTTCTCCTCATCCTCCTCCTTTTTTTT-----TTGTGTTTGGGTTTTGGGT--TGAAATTTATGTACCCACACAATGG s droBip2.KB464407 1968462 486 + 2915140 CGCATTAGCATATCGGGGA--GAAGATCTATAACC---CAGCTCCCAGCTGG-------ACAGCT----GACAGTTTTCTCCGCCCCACCTTCGGAATCGG---------ATC-------------------A----------TCAGATC-------------------AGTGGAT-GG--------------------GA--------------------------TAT-AT---------------------------------GA-TACG-------------GCGTC---ATAG-----AAA--GG---AGAGCCTGGC------TCGTCCTGCCTGCGCTTTCTAACGAttgaatttttgatatttgtGACACGCAGATTTTCCATCAGTGTCAACAAGGCATTGTTTTG----------------------GC----GAAACGTCAACGTGGTTGG---------TC----TCCTCCGTT------C-----------------------------CAGAGCTTCGC-----------------------------------------------------------------------------CAGACTC-------AACTGACAGACTTGATCCAATCGT------CCG--TCG-------TCGATTTTTC-AACA--TCAG---ACC-------------AAAG------T-------------------CGGGCCAATGCAAAAA-C----C---------------------------CGCGTACATTTGCATAGAC------------------------------ACAAAATTAT----ATGAGA----CC----GTGGCC-------------------------------C-----------------AGGACC---G--AC--AAAACGCA-----GCTTCCTGGTC--------------------tttttctcctcctcctcctcgttttt-----------------ggttttgggt--tgAAATTTATGTACCCACACAATGG s droEug2.KB465067 610591 494 + 1515531 GGCATTAGCATATCGGTCA--TAAGATCTATAACT---AAACTC---GACGG-------ACAGTT----GACAGTTACCTCCGCC-------CGCAGACGG---------ATC-----------------GGA----------TTGGATC--------GG---------ACGGCATAAG--------------------AT--------------------------CAT-AT---------------------------------GG-GAT--------------CCGTC---ATGC-----GAA--GA----------GGC------TCGTCCT------GCTTTCTAACGattgcatttttgatatttgTGACACGCAGATTTTCCATCAGTGTCAACAAGGCATTG-TTTG----------------------GC-----GAACGTCAACGTGGTTGG---------------TCCGCCATC------C----TCATCC-------------------CGGACTCCCGA------ACTCCCG----------------------------ACTC-CTGA----------CT--------------CCTGACTC-------AACTGACAGACTCGAT-CGGCCGTCCGA--TCG--TCG-------TCGATTTTTC-AACA--TCAG---ACC--AAAGTCAGGCCAAAG------T-------------------CGGGCCAATGCAAAA--C----C-----GAAT----------GC----AGCGCGTACATTTGCATAGAC------------------------------ACAAAATTAT----ATGAGA----CC----GAGACC-------------------------------C-----------------AGGACC---C--AC--AAAACGCA-----GCTTCCTGGTC--------------------TTTTTGT----------GTCGtttttttG---------------------GGC--TGAAATTTATGTACCCACACAATGG s droEle2.KB458573 533598 566 - 5320397 GGCATTAGCATATCGGTCA--TAAGATCTATAACT---AAACTC---GACGG-------ACAGTT----GACAGTTTTCTCCGCCC------CGCAGACGT---------ATC-----------------Aga----------ttggatt--------gg---------atcatatggg--------------------atgtgggatgtgggatgaggggatatgggat-ct---------------------------------gg-gat--------------CCATC---ATGC-----GAA--GAGAGGGAGGCTGGC------TCGTCCT------GCTTTCTAACGattgcatttttgatatttgtgACACGCAGATTTTCCATCAGTGTCAACAAGGCATTG-TTTG----------------------GC-----GAACGTCAACGTGGTTGG---------TCTGGCTTCACCGTA------C-----------------------------CAAACTCCTTG----------------------------------------GCTGC-CTGG----------CT-------------GCCTGACTC-------AACTGACAGACTCGAT-CGGCCGTCCGA--TCA--TCG-------TCGATTTTTC-AACATCTCAG---ACCAAAAAGTCAGGCCAAAG------T-------------------CGGGCCAATGCTAAA--C----C-----GAATGCAGCGCAGCGC----AGCGCGTACATTTGCATAGAC------------------------------ACAAAATTAT----ATGAGA----CC----GAGACC-------------------------------C-----------------AGGACC---C--AC--AAAACGCA-----GCTTCCTggtc--------------------tttttgt-----gtttatttatttttggttaaatttttttttttttcctgagC--TCAAATTTATGTACCCACACAATGG s droKik2.KB459527 287202 510 - 1234237 GGCATTAGCATATCGGTCA--AAAGATCTATAACT--AAAACCC---GTCGAGC----TGCGGCT----GACAGTTGCCTCCGCCC------CGCCA---------------------------------AGA----------TTGGATCGCTGCGATGG---------ACAGACTGGG--------------------AT--------------------------CAT-AT---------------------------------GG-GAT--------------CCATC---ATATATGAGAAG--GA----------GGC------TCGTCCT------GCTTTCTAACGATTGCATTTTTGATATTTGTGACACGCAGATTTTCCATCAGTGTCAACAAGGCATTG-TTTG----------------------GC-----GAACGTCAACGTGGTTGG---------------TCCTCCATCGTAG--C-----------------------------CCGGCTCCGGG-----CTCGCTCA---------------------------G-----------------------------------ACTGACTC-------AACTGACAGGCTCGAT-CGGCCGTCCGA--TCG--TCgacgattttcgatttttc-aacATCTCAG---ACC-------------AAAG------T-------------------CGGGCCAATGCAAAA--C----C-----GAAT----------GC----AGCGCGTACATTTGCATAGAC------------------------------ACAAAATTAT----ATGAGA----CC----GAGACC-------------------------------C---------CA------AAGACC---G--ACCGAAAACGCA-----GCTTCCTGGTc--------------------ttttttgtgtgattttgtttgttttttttt--------------------gtcgatgAAATTTATGTACCCACACAATGG s droTak2.KB461535 152492 521 - 669855 GGCATTAGCATATCGATCG--TAAGATCTATAACT---AAGCTC---GACGG-------ACAGTT----GACAG----CTCCGCCC------CGCAGTCCGTTTTCCGTCGTC-----------------AGA----------TTGGATC--------GG---------ACGGTATGAG--------------------AT--------------------------CAT-AT---------------------------------GG-GAT--------------CCATCATCATGC-----AAA--GA----------GAC------TCGTCCT------GCTTTCTAACGATTGCATTTTTGATATTTGTGACACGCAGATTTTCCATCAGTGTCAACAAGGCATTG-TTTG----------------------GCGAACGGAACGTCAACGTGGTTGG---------------TCCTCCATC------C---TCAATCC-CGAACTCA----------CAGTTTCCTCA-------TCCCCT---------------------------GGCTC-CCGATGCTCCTCATCT--------------CCTGACTC-------AACTGACAGACTCGAT-CGGCCGTCCGA--TCG--TCG-------ACGATTTTTC-AACATCTCAG---ACC--AAAGTCAGGCCAAAG------T-------------------CGGGCCAATGCAAAA--C----C-----GAAT----------GC----AGCGCGTACATTTGCATAGAC------------------------------ACAAAATTAT----ATGAGA----CCGCGAGAGACC-------------------------------C-----------------AGGACC---C--AC--AAAACGCA-----GCTTCCTGGTC--------------------TTTTTAT-------------------------------------------GTC--TGAAATTTATGTACCCACACAATGG s droRho2.KB449310 48229 553 - 65043 GGCATTAGCATATCGGTCA--TAAGATCTATAACT---AAACTC---GACGGACGACGGACAGTT----GACAGTTTTCTCCGCCC------CGCAAACGG---------ATC-----------------AGA----------TCGGATC--------GA---------ACGGGATGGG--------------------AT--------------------------CAT-ATGGGGATATGAGGATATGGGTATATGGTTATATGGG-GAT--------------CCGTC---ATGC-----GAA--GA---GA-----GGC------TCGTCCT------GCTTTCTAACGATTGCATTTTTGATATTTGTGACACGCAGATTTTCCATCAGTGTCAACAAGGCATTG-TTTG----------------------GC-----GAACGTCAACGTGGTTGG---------------TCCTCCATC------C-----------------------------Cggactcatgg------actcgtg---------------------------gactcgtgga----------ct-------------cCCTGACTC-------AACTGACAGACTCGAT-CGGCCGTCCGA--TCG--TCG-------TCGATTTTTC-AACATCTCAG---ACC--AAAGTCAGGCCAAAG------T-------------------CGGGCCAATGCAAAA--C----C-----GAAT----------GC----AGCGCGTACATTTGCATAGAC------------------------------ACAAAATTAT----ATGAGA----CC----GAGACC-------------------------------C-----------------AGGATC---C--AC--AAAACGCA-----GCTTCCTGgtc--------------------tttttgtgtttatttttttcgtttttcgtttttttt--------------gtc--ttaaatTTATGTACCCACACAATGG s droFic2.KB457177 90863 537 + 995874 GGCATTAGCATATCGGCCT--TAAGATCTATAACT---GAACCC---GACGG-------ACAGTT----GACAGTCTGCTCCGCCC------CGCGGACGG---------ATC-----------------AGA----------TCGCATC--------GG---------ACAGGAGGGG--------------------AG--------------------------CAT-AC---------------------------------GG-GAT--------------CCATC---ATGC-----GAG--GA---GA-----GGC------TCGTCCT------GCTTTCTAACGATTgcatttttgatatttgtgACACGCAGATTTTCCATCAGTGTCAACAAGGCATTG-TTCG----------------------GC-----GAACGTCAACGTGGTTGG---------------tcctccatc------c--cggactcc-cagactcccccgaatcccccgactccccg------acttgca---------------------------aaccc-cgga----------ct----ccccggattccccgGCTC-------AACTGACAGACTCGAT-CGGCCGTCCGA--TCG--TCG-------TCGATCTTTC-AACATCTCAG---ACC--GAACTCAGGCCAAAG------T-------------------CGGGCCAATGCAAAA--TACAGC-----GAAT----------GC----AGCGCGTACATTTGCATAGAC------------------------------ACAAAATTAT----ATGAGG----CC--GAGAGACC-------------------------------C-----------------GGGACC---C--AC--AAAACGCA-----GCTTCCTGGTC--------------------TTTTTGT-----GTCTTTTCGTCCG-------------------------GCC--TCAAATTTATGTACCCACACAATGG s droPse3.chr3 1360534 560 - 19787792 GGCATTAGCATATCAGCCAACAGAGATCTATAACT---C--tct---cacag-------aca-ca----gacag-tgACTCCGGGA------GGACATtgg---------agt-----------------ggt----------gtggagt--------ggagagcggaAACGGAGT-GG--------------------AT--------------------------CAT-AT---------------------------------GGAGAT--------------CCATC---ATACATT--GTA--GA----------GCC------TTGTCCT------GCTTTCTAACGATTgcatttttgatatttgtgACACGCAGATTTTCCATCAGTGTCAACAAGGCATTG-TTCGGG--------------AGAGCAGC-----AGACGTCAACGTGGTTGG---------------TCCGCCATCGCAGA-C--CCCGTTCCGGCCACGTC----------CTGGCCCGCTA------GCCCGCT---------------------------GGCCC-GTTG---------CCC--------------GCTGCCCC---GAAAGACTGACAGACTCGAT-CGGCCGTCCGA--TCG--TCA-------TCGATTTTTC-AACA--TCAG---ACC--AAAGTCgggccaaaa------cgaaacgaaacccagAGTCGCGGGCTAATGCAAAA--C----T-----GAAT----------GCAGCGAGCGCGTACATTTGCATAGAC------------------------------ACAAAATTAT----ATGAGA----CC---CGAGACC--CAGGA------------------------C-----------------AGGACC---CCGAT--CAAACGCA-----GCTTCCTGGtc--------------------ttttttc-------------ggtttg------------------------gtt--tgcaATTTATGTACCCACACAATGG s droPer1.super_34 549396 579 - 916997 GGCATTAGCATATCAGCCAACAGAGATCTATAACT---C--TCT---CACAG-------ACA-CA----GACAG-TGACTCCGGGA------GGACATtgg---------agt-----------------ggtgtggagtggagtggagt--------ggagAGCGGAAACGGAGT-GG--------------------AT--------------------------CAT-AT---------------------------------GGAGAT--------------CCATC---ATACATT--GTA--GA----------GCC------TTGTCCT------GCTTTCTAACGATTGCATTTTTGATATTTGTGACACGCAGATTTTCCATCAGTGTCAACAAGGCATTG-TTCGGG--------------AGAGCAGC-----AGACGTCAACGTGGTTGG---------------TCCGCCATCGCAGA-C--CCCGTTCCGGCCACGTC----------CTGGCCCGCTA------GCCCGCT---------------------------GGCCC-GTTGCCCCGTTGCCCC--------------GCTGCCCC---GAAAGACTGACAGACTCGAT-CGGCCGTCCGA--TCG--TCA-------TCGATTTTTC-AACA--TCAG---ACC--AAAGTCGGGCCAAAA------CGAAACGAAACCCAGAGTCGCGGGCTAATGCAAAA--C----T-----GAAT----------GCAGCGAGCGCGTACATTTGCATAGAC------------------------------ACAAAATTAT----ATGAGA----CC---CGAGACC--CAGGA------------------------C-----------------AGGACC---CCGAT--CAAACGCA-----GCTTCCTGGTC--------------------TTTTTTC-------------GCTTTG------------------------GTT--TGCAATTTATGTACCCACACAATGG s droMir2.chr3 1401602 579 - 20862834 GGCATTAGCATATCAGCCAACAGAGATCTATAACT---C--tct---cacag-------aca-ca----gacag-cgaCTCCGGGA------GGACAttgg---------agt-----------------ggtgtggagtggagtagagt--------ggagagcggaaaCGGAGT-GG--------------------AT--------------------------CAT-AT---------------------------------GGAGAT--------------CCATC---ATACATC--GTA--GA----------GCC------TTGTCCT------GCTTTCTAACGATTGcatttttgatatttgtgACACGCAGATTTTCCATCAGTGTCAACAAGGCATTG-TTCGGG--------------AGAGCAGC-----AGACGTCAACGTGGTTGG---------------TCCGCCATCGCAGA-C--CCCGTTCCGGCCACGTC----------CTGGCCCGCTA------GCCCGCT---------------------------GGCCC-GTTGCCCCGATACCCC--------------GCTGCCCC---GAAAGACTGACAGACTCGAT-CGGCCGTCCGA--TCG--TCA-------TCGATTTTTC-AACA--TCAG---ACC--AAAGTCgggccaaaa------cgaaacgaaacccagaGTCGCGGGCTAATGCAAAA--C----T-----GAAT----------GCAGCGAGCGCGTACATTTGCATAGAC------------------------------ACAAAATTAT----ATGAGA----CC---CGAGACC--CGGGA------------------------C-----------------AGGACC---CCGAT--CAAACGCA-----GCTTCCTGGTC--------------------TTTTTTC-------------GCTATG------------------------GTT--TGCAATTTATGTACCCACACAATGG s droWil2.CH963894 1325587 471 + 2843958 GGCATTAGCATATCGATAT--GCTGATCTATAACT---TGGCTC---AGTTG-------GC----------CAG----CTCCACCC--------------G---------CCT-----------------GGT----------TTATGGT--------TG---------------------------------------AT--------------------------CCTGGT---------------------------------CG-AAG--------------CTTTC---TAAC-----GAT--------------TGc------aattctt------gttgtt-----gttgcttttttgatatttgtgaCACGCAGATTTTCCATCAGTGTCAACAAggcattg-tttttattttttttgctgttgttgttgc-----taacgTCAACGTGGTTGG---------------TCCTCT---------C---------------------------------------A----------------------------------------------TTCA--------------------------GTCGAGTC-------AAC----------GAT-CGTTCGTTTGG--GTT--CAG-------TCGATCGTTCGAGCC--ACAA---AAT--GCAGAAAGCCAAAAGGAAATAT-------------------CAGGCAACAG--AAA--C----CGTTTGGAAC----------AC----GGCGCGTACATTTgcatagacaaaaaaaaaaagaaaaaccaaaaaaaataaaaaaaattat----atgagAGAAGTT----GAGAGA-------------------------------G-----------------ACGACC---G--ACG-GCAACGCAGTTTGGCTTCCTGGTC----------------------------------------------------------------------CTC--TG-GATTTATGTACCCACACAATGG s droVir3.scaffold_12875 7365862 520 + 20611582 GGGATTAGCATATCGGTGT--TCAGATCTATAACTCTGAGCTGC---GCCGG-------AAAACT----GACTG-CGAGACAATTT------GAATGTCAA---------AGTCTTGGCTGGGCTGGTCTGGG----------CTGCAGC--------TG---------GAGTTGCCGG--------------------AT--------------------------CAG-A----------------------------------GG-GAT--------------CGATC---AT---------A--GG----------CTC------TCATAGT-----------TTAACGATTGAA-TTTTGATATTTGTGACACGCAGATTTTCCATCAGTGTCAACAAGGCATTG-TTTG----------------------GC------CACATCAACGTGGTTGG---------------TCCGCCAGC------T-----------------------------CAGTAGGCTGA------CAGGATA---------------------------GACGG-GCAg----------actgactgtctgaatgactgactg----actgactgacggact-gga-ggactgacAGAGTTGA--TCG-------TCGATTTTTC-AACA--TCAG---CCC--GA---------AAAA------T----------------------------GCAAAG-------C-----GAAC----------AC----AACGCGTACATTTGCATAGAC------------------------------ACAAAATTACGACTATAAGA----GC----CGGATCGATAAAA-----------------AAAAAGGC-----------------AAAATGATGG--AA--AAAACGCA----GGCTTCCTGGTGTCCCG---------------TTGCCGT-------------GCTATGTCT---------------------TTT--CTGAATTTATGTACCCACACAATGG s droMoj3.scaffold_6496 26161490 513 + 26866924 GGCATTAGCATATCGCTGC--TGGGATCTATAACTTTGAGCAGT---GCTGG--------GAGCT----CGTTG-CGAGACAATTT------GAATGCCAA---------AGTCTT----------------G----------TGGCAGT--------TG---------GAGCTGCGAG--------------------AT--------------------------GAG-G----------------------------------AG-GAT--------------CGATC---TC-------TGG--GG----------CTC------TCATAGT-----------TTAACGATTGAA-TTTTGATATTTGTGGCACGCAGATTTTCCATCAGTGTCAACAAGGCATTG-TTTG----------------------GC------CCCATCAACGTGGTTGG---------------TCCGCCAGC------T-----------------------------CAGTGGGCTGA------CAGGATA---------------------------GACGG-TCGG----------TC-----------------------------GGCCGACTGACT-GAA-TGACTGACAGAGTTGA--ACG-------TCGATTTTTC-AACA--TCAG---CCC--GA---------AAAA------T----------------------------GCAAAG-------C-----GAAT----------AC----AACGCGTGCATTTGCATAGAC------------------------------ACAAAACTGCGACTTTAAGA----GC----CGGATCGATAAAacacacaaacacacacacacacagacacacacattcacacaATAAAACTAT-G--AA--GAAACGCA----GGCTTCCCGGACTCCCG---------------TTGCCGT-------------GCGATGTCT---------------------TTT--GTGGATTTATGTACCCACACAATGG s droGri2.scaffold_15245 916541 491 + 18325388 GCCATTAGCATATCGGTGC--TGGGATCTATAAAT---------------GG-------GTAACTCAACGACTG-CAACACAATTT------GAATGTCAA---------AGTCTG--------------GAG----------CTGCATC--------TG---------AAGTTT---G--------------------AT--------------------------CAG-A----------------------------------CG-GAT--------------C---------------------GG----------CTC------TCATAGT-----------TTAACGATTGAA-TTTTGATATTTGTGACACGCAGATTTTCCATCAGTGTCAACAAGGCATTG-TTTG----------------------GC------CACATCAACGTGGTTGG---------------TCCACCAGC------T-----------------------------CAGTGGGCTGA------CAGgact---------------------------ggctg-actg----------gc------------tgactgactg----ccagactgccagact-gcc-agactg---GAGTTGATCTCG-------TCGATTTTTC-AACA--TCGG---GCC--GA---------AAAA------T----------------------------GCAAAAA-C----C-----GAAC----------AC----AACGCGTACATTTGCATAGAC------------------------------ACAAAATTAC--------GA----GC----CGAATCGATAAAA----------------GAAAAAAAC---------CGTAAAA-AAAAGTAA-A--GA--AAAACGCA----TGCTTCCTGGTGTCCCGttttttgttttttttttttttt-------------tttttGGCT---------------------TTC--TTGAATTTATGTACCCACACAATGG a score=-325662.000000 s dm6.chr2R 24368359 56 + 25286936 GGT-AACA--AAACAGTTGGAGGAGC-------------------------------------------CC---GT-CTCCGC---TG----------------------------CTGG----------G-GAGCC--G------------------------TG-----------------GGGC---CCGT s droSim1.chr2R 18706688 56 + 19596830 GGT-AACA--AAACAGTTGGAGGAGA-------------------------------------------CC---CG-CTCCGC---TG----------------------------CTGG----------G-GAGCC--G------------------------TG-----------------GGGC---CCGT s droSec1.super_23 126352 56 + 989336 GGT-AACA--AAACAGTTGGAGGAGC-------------------------------------------CC---CG-CTCCGC---TG----------------------------CTGG----------G-GAGCC--G------------------------TG-----------------GGGC---CCGT s droYak3.chr2R 20216341 65 + 21139217 GGT-AACA--AAACAGTTGGAGGAGC------------------------------------------TTC---GT-CTCCGC---TG----------------------------CTGG----------G-GAGCC--G------------------------TGGTGCTTGT---------GGGC---CCGT s droEre2.scaffold_4845 21613936 78 + 22589142 GGT-AAGA--AAACAGTTGGAGGAGC-----------------------C-----------CG----TCTC---CG-CTCCGC---TG----------------------------CTGG----------G-GAGCC--G------------------------TGGGGCCCGCGGGGACGTGGGGC---CCGT s droBia2.KB462602 807961 61 + 3129309 GGT-AACA--AAACAGTTGGAGGAAC-----------------------TGAAC--GCTGGGA----CCCC---GT-CTTCCT---------------------------------------------------GCC--A------------------------TG-----------------GGGC---CCGT s droSuz1.KI419649 12054168 57 - 14502029 GGT-AACA--AAACAGTTGGAGGAAC-----------------------TGAAC--GCTTAGG----CCCC---GT-CTT-------------------------------------------------------CC--A------------------------TG-----------------GGGC---CCAT s droAna3.scaffold_13266 5718990 97 - 19884421 GGT-AAGAAGAAACAGTTGGAGGAATCGACGCTGAAACCGTCGCCGACTTGGTC--GTTTTTG----TGGC---TT-TTTCAG---TG----------------------------CTGG----------C-GAGTCGGG------------------------CG-----------------CTGC---TTGT s droBip2.KB464407 1968948 93 + 2915140 GGCAAAGGAGAAACAGTTGGAGGAAT---CGCTGAAACCGTCGCCGAGTTGGTC-GGTTTTGG----TGGC---TGATTTCAG---TG----------------------------CTG-------------GAGTC--G------------------------CG-----------------CTGC---TTGT s droEug2.KB465067 611085 65 + 1515531 GGT-AACA--AAACAGTTGGAGGAAC-----------------------------CGATGAAG----CCCC---GT-CTCCGCCA-TG----------------------------CTGG----------G-GAGTC----------------------------------------------GGGC---TTAT s droEle2.KB458573 534164 70 - 5320397 GGT-AAGA-GAAACAGTTGGAAGAAT-----------------------CGTCGAAGCCCCGA----CTTC---TG-CTTCGA---TG----------------------------CTGG----------G-GAGTC----------------------------------------------GGGC---CCAT s droKik2.KB459527 287712 81 - 1234237 GGT-AACA--AAACAGTTGAGACCGT-----------------------------------------AGCC---GT-CTCCGTCCTCG----------------------------TTGGGGTCCCAGTTG-GAGCC--GAAGACG--------------GAGTCG-----------------CTGC---TTGT s droTak2.KB461535 153013 57 - 669855 GGT-AACG--AAACAGTTGGAGGAAC-------------------------------------------CG---AA-CGCCGA---GG----------------------------CCAA----------GTCCTCC--A------------------------TG-----------------GGGC---CCAT s droRho2.KB449310 48782 72 - 65043 GGT-AACA-AAAACAGTTGGGGGAAT-----------------------------CGTCGAAG----ACCCGAAGT-CTTCGA---TG----------------------------CCGG----------G-GAGTC--A----------------------GTCG-----------------GAGC---CCAT s droFic2.KB457177 91400 63 + 995874 GGC-AGGA--AAACAGTTGGGGGAAT------------------------------CGCTGGG----GCCC---GT-CTTCGA---TG----------------------------CC------------G-GAGCC--T------------------------CG-----------------TGGC---CCAT s droPse3.chr3 1361094 97 - 19787792 GGT-AACA-AAAACAGTTGGAGGAAt-----------------------------cgtcgtcggagtcgtt---gt-tgtcga---tg----------------------------ctgg------------gagtc--gtcgtcgagcgtcgtcgtcgagcatcg-----------------aggctggtggt s droPer1.super_34 549975 97 - 916997 GGT-AACA-AAAACAGTTGGAGGAAT-----------------------------CGTCGTCGGAGTCGTT---GT-TGTCGA---TG----------------------------CTGG------------GAGTC--GTCGTCGAGCGTCGTCGTCGAGCATCG-----------------AGGCTGGTGGT s droMir2.chr3 1402181 97 - 20862834 GGT-AACA-AAAACAGTTGGAGGAAt-----------------------------cgtcgtcggagtcgtt---gt-tgtcga---tg----------------------------ctgg------------gagtc--gtcgtcgagcgtcgtcgtcgagcatcg-----------------agGCTGGCGGT s droWil2.CH963894 1326058 35 + 2843958 TTT-AAGA-------------------------------------------------------------CT---GG-----GT---TG----------------------------CTTg------------gtgtt--g------------------------ct-----------------tttt---tttt s droMoj3.scaffold_6496 26162003 57 + 26866924 ------------CTGACTGAAAg------------------------------------cccg----gccc---gg-ccaggc---ccgggtctactcggctctcgcttggcctga------------------------------------------------------------------------------ s droGri2.scaffold_15245 917032 36 + 18325388 ------------CCAACAGAGAGGTT-----------------------------GAGACCCG----GCCC---GA-TCTGGC---CA---------------------------------------------------------------------------------------------------------- a score=2913164.000000 s dm6.chr2R 24368415 179 + 25286936 GGTGTTGGCCTAAACACCATTCTAGCGGTTC---GTTT--AGCTTGTTTATTGGCAT-GAAAATCTATCA---AAAATGCATCATGCA-----------TTTTATATTTATTGTACGTAAGTACAAAAATAATGTGCTTGACATTTGACCCG-GCCC--AAACGAC----A-A-------CAG--CGTT---ATG---GCCGT---GCCACATGTTG---CCC------ATGGT s droSim1.chr2R 18706744 179 + 19596830 GGTGTTGGCCTAAACACCATTCTAGCGGTTT---GTTT--AGCTTGTTTATTGGCAT-GAAAATCTATCA---AAAATGCATCATGCA-----------TTTTATATTTATTGTACGTAAGTACAAAAATAATGTGCTTGACATTTGACCCG-GCCC--AAACGAC----A-A-------CGG--CGTT---ATG---GCCGG---GCCACATGTTG---CCC------ATGGT s droSec1.super_23 126408 179 + 989336 GGTGTTGGCCTAAACACCATTCTAGCGGTTC---GTTT--AGCTTGTTTATTGGCAT-GAAAATCTATCA---AAAATGCATCATGCA-----------TTTTATATTTATTGTACGTAAGTACAAAAATAATGTGCTTGACATTTGACCCG-GCCC--AAACGAC----A-A-------CGG--CGTT---ATG---GCCGG---GCCACATGTTG---CCC------ATGGT s droYak3.chr2R 20216406 180 + 21139217 GGTGTTGGCCTAAACACCATTCTAGCGGTTC---GTTT--AGCTTGTTTATTGGCAT-GAAAATCTATCA---AAAATGCATCATgca-----------ctttatatttattgtacgtaaatacaaaaataatgtgcttGACATTTGACCCG-GCCC--AAACGAC----A-A-------CAG--CGCT---ATGGCCGCCGT---GCCACATGTTG---CCA------ATG-- s droEre2.scaffold_4845 21614014 179 + 22589142 GGTGTTGGCCTAAACACCATTCTAGCGGTTC---GTTT--AGCTTGTTTATTGGCAT-GAAAATCTATCA---AAAATGCATCATGCA-----------TTTTATATTTATTGTACGTAAGTACAAAAATAATGTGCTTGACATTTGACCCG-GCCC--AAACGAC----A-A-------CAG--CGTT---ATG---GTCGG---GCCACATGTTG---CCC------ATGGT s droBia2.KB462602 808022 178 + 3129309 GGTGTTGGCCTAAACACCATTCTAGCGGTTC---GTTT--AGCTTGTTTATTGGCAT-GAAAATCTATCA---AAAATGCATcatgca-----------ttttatatttattatacgtaaatacaaaaataatgtgCTTGACATTTGACCCG-GCCC--AAACGAC----A-A-------CAG--CGTT---ATG---GCC-A---GCCACATGTTG---CCG------CTTGC s droSuz1.KI419649 12054225 174 - 14502029 GGTGTTGGCCTAAACACCATTCTAGCGGTTC---GTTT--AGCTTGTTTATTGGCAT-GAAAATCTATCA---AAAATGCAtcatgca-----------ttttatatttattatacgtaaatacaaaaataatgtgCTTGACATTTGACCCG-GCCC--AAACGAC----A-A-------CAG--CGTT---ATG---GCCAA---GCCACATGTTG---Ccg----------- s droAna3.scaffold_13266 5719087 183 - 19884421 GGTGTTGGCCTAAACACCATTCTAGCGGTTC---GTTT--AGCTTGTTTATTGGCAT-GAAAATCTATCA---AAAATGCATCATGCA-----------TTTTATATTTATTGTACGTAAATACAAAAATAATGTGCTTGACATTTGACCCG-GCCC--AAACGAC----AGA-------CAG--CGTT---ATG---GCCGCCGGGCCACATGTTG---CCC------GTTTT s droBip2.KB464407 1969041 182 + 2915140 GGTGTTGGCCTAAACACCATTCTAGCGGTTC---GTTT--AGCTTGTTTATTGGCAT-GAAAATCTATCA---AAAATGCATCatgca-----------ttttatatttattgtacgtaaatacaaaaataatgtgCTTGACATTTGACCCG-GCCC--AAACGAC----AGA-------CAGCCCGCT---ATG---GCCGT---GCCACATGTTG---Ccc------gtttt s droEug2.KB465067 611150 176 + 1515531 GGTGTTGGCCTAAACACCATTCTAGCGGTTC---GTTT--AGCTTGTTTATTGGCAT-GAAAATCTATCA---AAAATGCATCATgca-----------ctttatatttattatacgtaaatacaaaaataatgtGCTTGACATTTGACCCG-GCCC--AAACGAC----A-A------------CGTT---ATG---GCCAA---GCCACATGTTG---CCG------TTTGC s droEle2.KB458573 534234 176 - 5320397 GGTGTTGGCCTAAACACCATTCTAGCGGCTC---GTTT--AGCTTGTTTATTGGCAT-GAAAATCTATCA---AAAATGCATcatgca-----------ttttatatttattatacgtaaatacaaaaataatgtgcTTGACATTTGACCCG-GCTT--CAACGAC----A-A------------CGTT---ATG---GCCAA---GCCACATGTTA---CCC------CTTGC s droKik2.KB459527 287793 176 - 1234237 GGTGTTGGCCTAAACACCATTCTAGCGGTTC---GTTT--AGCTTGTTTATTGGCAT-GAAAATCTATCA---AAAATGCATcatgca-----------ttttatatttattatacgtaaatacaaaaataatgtgCTTGACATTTGACCCG-GCCC--GAACGAC----A-A------------CGTT---ATG---GCCAT---GCCACATGTTG---CCA------GTTAG s droTak2.KB461535 153070 182 - 669855 GGTGTTGGCCTAAACACCATTCTAGCGGTTC---GTTT--AGCTTGTTTATTGGCAT-GAAAATCTATCA---AAAATGCATCatgca-----------ttttatatttattatacgtaaatacaaaaataatgtgCTTGACATTTGACCCG-GCCC--AAACGAC----A-ACGA----CAG--CGTT---ATG---GCCAA---GCCACATGTTG---CCG------GTTGC s droRho2.KB449310 48854 182 - 65043 GGTGTCGGCCTAAACACCATTCTAGCGGTTC---GTTT--AGCTTGTTTATTGGCAT-GAAAATCTATCA---AAAATGCATCatgca-----------ttttatatttattatacgtaaatacaaaaataatgtgCTTGACATTTGACCCG-GCCC--AAACGAC----A-A------------CGTT---ATG---GCCAA---GCCACATgttg---ccattgccggttgg s droFic2.KB457177 91463 176 + 995874 GGTGTTGGCCTAAACACCATTCTAGCGGTTC---GTTT--AGCTTGTTTATTGGCAT-GAAAATCTATCA---AAAATGCATcatgca-----------ttttatatttattgtacgtaaaaacaaaaataatgtgcTTGACATTTGACCCG-GCCC--AAACGAC----A-A------------CGTT---ACG---GCCGA---GCCACATGTTG---CCC------GTTGC s droPse3.chr3 1361191 178 - 19787792 ggtgttggctTAAACACCATTCTAGCGGTTC---GTTT--AGCTTGTTTATTGGCAT-GAAAATCTATCA---AAAATGCAtcatgca-----------ttttatatttattatacgtaaatacaaaaataatgtgCCTGACATTTGACCCG-GCCC--AAACGAC----A---------CAA--CGTT---ATG---GCCCG---GCCACATGTTG---TCT------TCCGA s droPer1.super_34 550072 178 - 916997 GGTGTTGGCTTAAACACCATTCTAGCGGTTC---GTTT--AGCTTGTTTATTGGCAT-GAAAATCTATCA---AAAATGCATCATGCA-----------TTTTATATTTATTATACGTAAATACAAAAATAATGTGCCTGACATTTGACCCG-GCCC--AAACGAC----A---------CAA--CGTT---ATG---GCCCG---GCCACATGTTG---CCT------TCCGA s droMir2.chr3 1402278 178 - 20862834 GGTGTTGGCTTAAACACCATTCTATCGGTTC---GTTT--AGCTTGTTTATTGGCAT-GAAAATCTATCA---AAAATGCATcatgaa-----------ttttatatttattatacgtaaatacaaaaataatgtgCCTGACATTTGACCCG-GCCC--AAACGAC----A---------CAA--CGTT---ATG---GCCCG---GCCACATGTTG---CCT------TCCGA s droWil2.CH963894 1326093 196 + 2843958 tttttttgtttaaacaccATTCTTGTGGTTC---GTTT--AGCTTGTTTATTGGCATGGAAAATctatcaaacaaaaaaaatttggtatttctttttttttttatatttattagacattaatacaaaataaatgtgCTTGACATTTGACCCG-GCCC--CAGCGAC----A-GCGACAACCAG--CAAC---GTG-----------GCCACATGTTGGTTcca------ct--- s droVir3.scaffold_12875 7366448 168 + 20611582 AGTGTTGGCCAAAACACCATTCTAGCGGTTT--AAGCC--AGCTTGTTTATTGGCAT-GAAAATCTATCA---AAAATGCATCATGCA------------TTTATATTTATTATACGTAAACACAAAAATAATGTGCTTGACATTTGACCCG-GCCC--AAACGAC----A-A------------CGTT----TG-----------GCCACATGTTG---CCA------CGT-- s droMoj3.scaffold_6496 26162084 169 + 26866924 AGTGTTGGCTAAAACACCATTCTAGCGGCTG--AAGCC--AGCTTGTTTATTGGCAG-GAAAATCTATCA---AAAGTGCATAAGCTA------------TTCATATTTATTATACATAAACACAAAAATAATGTGCTTGACATTTGACCCG-GCCC--AAACGAC----A-A------------CGTT---GCG-----------ACCACATGTTG---CCA------CGT-- s droGri2.scaffold_15245 917068 183 + 18325388 AGTGTTGGCTAAAACACCATTCTAGCGGTTGTAAAGTCTTTGCTTGTTTATTGGCAT-GAAAATCTATCA---AAAATGCATCATGCA------------TTTATATTTATTATACGTAAACATAAAAATAATGTGCTTGACATTTGACCCGCGCCCCAAAACAACGACAA-A------------CGCTTTGTTG-----------GCCACATGTTG---CCA------CGT-- a score=-381590.000000 s dm6.chr2R 24368594 74 + 25286936 C-------------Tgttgccaatggccaagttgccaag-----at--------------gcca-------------agttgccagg-----ttgccTGCAAGTC-------AGCCAGT--------CTGCAAGTCTAC s droSim1.chr2R 18706923 66 + 19596830 C-------------TGTTGCCAATGGCCAAGATGCCAA----------------------------------------GTCGCCAGG-----TTGCCGGCAAGTC-------TGCCAGT--------CTGCAAGTCTAC s droSec1.super_23 126587 74 + 989336 C-------------TGTTGCCAATGGCCAAGATGCCAAG-----TT--------------GCCA-------------GGTTGCCAGG-----TTGCCGGCAAGTC-------TGCCAGT--------CTGCAAGTCTAC s droYak3.chr2R 20216586 38 + 21139217 ---------------------------------GCCAAG-----TT--------------GCCA-------------GGTTGCCAGG-----TTGCCTGCA-------------------------------AGTCTGC s droEre2.scaffold_4845 21614193 66 + 22589142 C-------------TGTGGCCAATGgccacgttgccacg-----ct--------------gcca-------------cgttgccacg-----ctgccTGCAAGTC-------TACC----------------AGTCTAC s droBia2.KB462602 808200 64 + 3129309 C-------------AGTTGCCTGTTGCCG-GTTGCCAAT-----ag--------------gctt--------------ttggccaag-----ttgcCTGCAAGTC-------TGCC----------------AGACTGC s droSuz1.KI419649 12054399 54 - 14502029 ---------------gttgccagttgcca-gttgccaat-----AG--------------GCTT--------------TTAGCCAAG-----TTGCCTGCAAGT-------------------------------CTGC s droAna3.scaffold_13266 5719270 70 - 19884421 GT------------TGTTTTC---TGCCTGGTGGCTGGT-----GTCTTGGGGCTTTTTCGCTT--------------TTGGCCA------------GCTATGCC-------TGCC----------------TGCCTGC s droBip2.KB464407 1969223 76 + 2915140 gt--------tttctgttttctgttgtttGGTGGCTGGT-----GTCTTGGG--------GCTT--------------TTGGCCA------------TCCAAGACTAGCCTGTGCT----------------AGTCCTC s droEug2.KB465067 611326 42 + 1515531 C-------------GGTTGCTAGTTGCCT-------------------------------G-----------------TTGGCCAAG-----TTGCCTGCA-------------------------------AGTCTGC s droEle2.KB458573 534410 73 - 5320397 C--------------CCTGCCAGTTGGCA-GTTGCCTGT-----TG--------------GAAG--------------TTGGCAATGGTCTATTGCCAGCAAGTTT------TGCC------------CGCAAGTCTGC s droKik2.KB459527 287969 65 - 1234237 CTAGCT----AGCCTGTTGCCTGTTGTTA-GCTGCCTTT-----TA--------------GCCT-------------GTAAGCCAGG-----CTTTTGGC--------------------------------CGCCTGC s droTak2.KB461535 153252 46 - 669855 C-------------GGTTGCCAATAGACC-------------------------------GTTT-------------GTTGGCCAAG-----TTGCCTGCA-------------------------------AGTCTGC s droRho2.KB449310 49036 83 - 65043 c-------------agttgtctgttgcca-gttgccagt-----tt--------------gcca-------------gttggcagtGGTCTATTGCCTGTTGGCC-------TGCAAGTTT---TGCCGGCAAGTCTGC s droFic2.KB457177 91639 79 + 995874 C-------------AGTTGCTCGCTGTTT-GTTGGCAGT---------------------Gcct-------------gttggccaag-----ttgccTGCGAGTC-------GGCGAATCCACGAGTCTGAAAGTCTGC s droPse3.chr3 1361369 58 - 19787792 G-------------CCTTGCCA-----CAGCCTGCCACA---------------------GGCT-------------GTTGGTTGT------TGGCCTGCCGGGC-------AGGC----------------AGTCTGC s droPer1.super_34 550250 60 - 916997 G-------------CCTTGCCA-----CAGCCTGCCACA---------------------GGCT-------------GTTGGCTGT------TGGCCTGCCGGGC-------AGGCTA--------------GGTCTGC s droMir2.chr3 1402456 65 - 20862834 G-------------CCTTGCCA-----CAGCCTGCCAcaggctgtt--------------ggct-------------gttggctgt------tggcctgccaggc-------aggc----------------agtctGC s droVir3.scaffold_12875 7366616 59 + 20611582 ----CTTTTAGGCTGATTATGAAACGGCTTtctgtttgt-----tt--------------gtct-------------ctctgtctgt-----ttgtttgt--------------------------------------- s droMoj3.scaffold_6496 26162253 64 + 26866924 ----CTTTT-GGCTGATTAAGAAACGGctttctgtttct-----ct--------------gtgt-------tgccagctttgtcggt-----ttgtctgt--------------------------------------- s droGri2.scaffold_15245 917251 72 + 18325388 ----CTTTTGGGCTGATTATGAAACCGCTTTCCgttcgt-----ct--------------gtttgtctgtttgtcagttttgtctgt-----tagtttgt--------------------------------------- a score=2900809.000000 s dm6.chr2R 24368668 449 + 25286936 CAG---------TCC-------------CGACTGAT--------TATGAAACTGG----CTGCTTTGTCGGTA-----------------T-C-CG--------------------------GGG--------------------ATATT--TG--GTTATTGTCTTC-------------------------G---------GACTTGCATTCTAACACAAATCAAAA--------------------------C-GGG-CAACAG-----CA--ATCCCAACACTCGCCACTTAAACGCTCGTTTATAATGTTGTTAAAATACAATAAATAGCCAGGACTCGCAGCAGGCGGTTTTC--------------------------------------------------------ACTG---C---CT----CTC------------------------------------------CGACCCCAG-CAGCCCA-------------T-----------TTCCAT------------------------------------------------------TGC----------------------------------TCATGCTGATTTATGAAATGTGGAC---------------------------GCCGATGTGGC-GGCCCACAA--------CCGCAAGCAGAA---------CCC-----------CCA-----CCCCGGCTA---------------------------------AGGCCA------GCTCTC----CTCTGGCCAGGCTTAGACTCAGTCCTGGGTACTGGGTGCTCGG---------------------TACTCGATTCCA----------GGGGCCT-CTAACTGGGC--AAAGCCGGCA--------------------------GG--GGTGAT--TG-----------TGTGATTGTGG--GCCGGTGATTGA---GTTGTCGGCCTGCTGGGCTACT-------GTTTG s droSim1.chr2R 18706989 448 + 19596830 CAG---------TCC-------------CGACTGAT--------TATGAAACTGG----CTGCTTTGTCGGTA-----------------T-C-CG--------------------------GGG--------------------ATATT--TG--GTTATTGTCTTC-------------------------G---------AACTTGCATTCTAACACAAATCAAAA--------------------------C-GGG-CAACAG-----CA--ATCCCAACACTCGCCACTTAAACGCTCGTTTATAATGTTGTTAAAATACAATAAATAGCCAGGACTCGCAGCAGGCGGTTTCC--------------------------------------------------------TCTG---C---CT----CTC------------------------------------------CGACCCCAG-CAGCCCA-------------T-----------TTCCAT------------------------------------------------------TGC----------------------------------TCATGCTGATTTATGAAATGTGGAC---------------------------GCCGATGTGGC-GGCCCACAA--------CCGCAAGCAGAA---------CCC-----------CCA-----CCCCGGCTG---------------------------------AGGCCA------GCTCTC----CTCTGGCCAGGCTTAGACTCAGTCCTGGGCACTGGGTGCTCGG---------------------TACTCGATTCCA----------GGGGCCT-CTAACTGGGC--AAAGCCGGCA--------------------------AG--GGTGAT--TG-----------TGTGATTGTGG--GCCGGTGATTGA---GTTGTCGG-CTGCTGGGCTACT-------GTTTG s droSec1.super_23 126661 444 + 989336 CAG---------TCC-------------CGACTGAT--------TATGAAACTGG----CTGCTTTGTCGGTA-----------------T-C-CG--------------------------GGG--------------------ATATT--TG--GTTATTGTCTTC-------------------------G---------GACTTGCATTCTAACACAAATCAAAA--------------------------C-GGG-CAACAG-----CA--ATCCCAACACTCGCCACTTAAACGCTCGTTTATAATGTTGTTAAAATACAATAAATAGCCAGGACTCGCAGCAGGCGGTTTTC--------------------------------------------------------TCTG---C---CT----CTC------------------------------------------CGACCCCAG-CAGCCCA-------------T-----------TTCCAT------------------------------------------------------TGC----------------------------------TCATGCTGATTTATGAAATGTGGAC---------------------------GCCGATGTGGC-GGCCCACAA--------CCGCAAGCAGAA---------CCC-----------CCA-----CCCCGGCTG---------------------------------AGGCCA------GCTCTC----CTCT-----GGCTTAGACTCAGTCCTGGGCACTGGGTGCTCCA---------------------TACTCGATTCCA----------GGGGCCT-CTAACTGGGC--AAAGCCGGCA--------------------------GG--GGTGAT--TG-----------TGTGATTGTGG--GGCGGTGATTGA---GTTGTCGGCCTGCTGGGCTACT-------GTTTG s droYak3.chr2R 20216624 485 + 21139217 AAG---------TCC-------------CGACTGAT--------TATGAAACTGG----CTGCTTTGTCGGTG-----------------T-C-CG--------------------------GGG--------------------ATATT--TG--GTTATTGTCTTC-------------------------G---------GACTTGCATTCTAACACAAATCAAAA--------------------------C-GGG-CAACAG-----CA--ATCCCAACACTCGCCACTTAAATGCTCGTTTATAATGTTgttaaaatacaataaatagCCAGGACTCGCAGCAGGCGGTTCTC--------------------------------------------------------ACTG---C---CT--CACTG---------------------------------CCTCTCCGCCGACCC----GAGCACA-------------T-----------TTCCAT------------------------------------------------------TGC----------------------------------TCATGCTGATTTATGAAATGTGGAC---------------------------GCCGATGTGGC-GGCCCACAA-------GCCGCAAACAGAG--------CCCC-----------CCA-----CCCCGCCTA---------------------------------AGGCCATGGTGTACT-------TTCTAGCCAGGCTTAGACCCGGCACTGGATACTGGGTACTGGGTACTGGGTAGTGAGTACTCGATACTCGATGCCA----------GGGGCCT-CTAACTGGGC--AAAGTCGGCA--------------------------GG--GGTGATTGTG-----------TGTGATTGTGG--GCCCGTGATTGA---GTTGTCGGCCTGCTGGGCTACT-------GTTTG s droEre2.scaffold_4845 21614259 450 + 22589142 CAG---------TCC-------------CGACTGAT--------TATGAAACTGG----CTGCTTTGTCGGTG-----------------T-C-CG--------------------------GGG--------------------ATATT--TG--GTTATTGTCTTC-------------------------G---------GACTTGCATTCTAACACAAATCAAAA--------------------------C-GGG-CAACAG-----CA--ATCCCAACACTCGCCACTTAAATGCTCGTTTATAATGTTGTTAAAATACAATAAATAGCCAGGACTCGCAGCAGGCGGTTTTC--------------------------------------------------------ACTG---G---CT----CTG------------------------------------------CGACCC----GAGCCCA-------------T-----------TTCCAT------------------------------------------------------TGC----------------------------------TCATGCTGATTTATGAAATGTGGAC---------------------------GCCGATGTGGC-GGCCCACAA-------GCCGC-AGCAGAA---------CCC-----------CCA-----CCCCGGCTG---------------------------------CGGCCA------GCT-------TTCTGGCCAGGCTTAGACCCGGCACTGGGAACTGGGAACTGGGTACTGAG--------------TACTCGATTCCA----------GGGGCCT-CTAGCTGGGC--AAAGTCGGCA--------------------------GG--GGCGAC--TG-----------TGTGATTGTGG--GCCCGTGATTGA---GTTGTCGGCCCGCTGGGCTACT-------GTTTG s droBia2.KB462602 808264 467 + 3129309 CAG---------TCCCG--A--------CGACTGAT--------TATGAAACGGC----TCGCTTTGTCGGTA-----------------T-C-CGAGTATCGAAGTACCC--AAGTATCCGGGG--------------------ATATT--TG--GTTATTGTCTTT-------------------------G---------ATTTTGCATTCTAACACAAATCAAAA--------------------------C-GGC-CAACAG-----CA--ATCCCAACACTCGCCACTTAAATGCTCGTTTATAACGTtgttaaaatacaataaatagcCAGGACTCGCAGCAGGCGGTTTTC--------------------------------------------------------ACTA---G---CCAGCGCTC------------------------------------------CGAAGGC---GAACACA-------TACCCCT-----------TTCCAT---------TTCCCC--------------------------------------CTGC----------------------------------TCATGCTGATTTATGAAATGTGGAC---------------------------GCCGATGTGGCGGGCCCACAA-------GCCGCAAACAGCG---------CCC-----------CAA-----CCCCCTTTG----------------------------------GGCCA------GCT-------CCCTGACCAGGCTAAGACTC------------------------------------------------CGGTCC------------GGGGCCG-CTCACTGGGC--AAAGTCGGCA--------------------------GG--GGTGAT--TG-----------TGTGATTGTAG--GCCCGTGATTGA---GTTGTCGGCCTGCTGGGCTACTGTTTGCCGTTTG s droSuz1.KI419649 12054453 454 - 14502029 CAG---------TCCCG--A--------CGACTGAT--------TATGAAACTGC----CTGCTTTGTCGGTA-----------------T-C-CG--------AGTACCC--AAGTATCCGGGG--------------------ATATT--TG--GTTATTGTCTTT-------------------------G---------ATTTTGCATTCTAACACAAATCAAAA--------------------------CGGGC-CAACAG-----CA--ATCCCAACACTCGCCACTTAAATGCTCGTTTATAACGTtgttaaaatacaataaatagcCAGGATTCGCAGCAGGCGGTTTTC--------------------------------------------------------ACTA---G---CCGGCTCTC------------------------------------------CGAAGGC---GAacaca-------------t-----------ttccat---------ttccct--------------------------------------ctGC----------------------------------TCATGCTGATTTATGAAATGTGGAC---------------------------GCCGATGTGGCGGGCCCACAA-------GCCGCAAACAGAG---------CCC-----------CAA-----CCCCCTTTT----------------------------------GGCCA------GCT-------CTCTGACCAGGCTAAGACTC------------------------------------------------CGATCC------------GGGGCCT-CTAACTGGGC--AAAGTCGGCA--------------------------GG--GGTGAT--TG-----------TGTGATTGTAG--GCCCGTGATTGA---GTTGTCGGCCTGCTGGGCTACTGTTTGCCGTTTG s droAna3.scaffold_13266 5719340 493 - 19884421 TAG---------TCC-------------CGACTGAT--------TATGAAAC--------GGCTTTGTCGGTA-----------------T-C-AG---AGGGGGATATCG--GATATT---GGG--------------------ATATT--TG--GTTATTGTCTTT-------------------------C---------AGTTTGCATTCTAACACAAATCAAAA--------------------------C-GGG-------------------CCAACACTCGCCACTTAAACGCTCGTTTATAATGTTGTTAAAATACAATAAATAGCCAGGACTCGCAGCAGGCGGTTTTC--------------------------------------------------------ACCA---G---CC--GGCCA-------ATCCAGCCAGCCAGCTAGGGAGCCTATCTATCTATCGATGGCGA-ACACACA-------------T-----------TTCCAT---------TTCCATTAAC-----------CGAG---------AGTGCCTTGACTGT----------------------------------TCGTGCTGATTTATGAAATGTGGCC-GGGCCCGTCCTGACTCGGACGCGGACGTCGCAGTGGCGGGCCCACAA-------AACG--AGCGAAC---------CCA-----------ATA------------------------------------------------GGCCA------A---------CTCTGGC-------------------------------------------------------------CTATTGAA--------AGGTGGCCC-CCGGGTTCCC-------CTCCT--------------------------GG--TGTGAT--TGCATTGGTTGATTGTGATTGTGG--GCCTGTGATTGA---GTTGTCGGCCTGCTGGGCTACT-------GTTTG s droBip2.KB464407 1969299 516 + 2915140 TAG---------TCC-------------CGACTGAT--------TATGAAACT------TGGCTTTGTCGGTA-----------------T-C--G---CGGGGGATATC-------------GG--------------------ATATT--TG--GTTATTGTCTTT-------------------------C---------GGCTTGCATTCTAACACAAATCAAAA--------------------------C-GGGCCAACAG-----CA--ATACCAACACTCGCCACTTAAACGCTCGTTTATAATGTtgttaaaatacaataaatagcCAGGACTCGCAGCAGGCGGTTTTC--------------------------------------------------------acca---g---cc--agctagccagtcagccagccagtcatCCAGCTAGCCTATCTATCTATCGATGGCGA-ACacaca-------------t-----------ttccat---------ttccattaac-----------CGAGCCTTATGCCAGTGCCTTGACTGT----------------------------------TCGTGCTGATTTATGAAATGTGGCCGGGGCCTGTCCTGGTT-----------GCCGCAGTGGCGGGCCCACAA-------AACG--AACGAAC---------CCA-----------ATA------------------------------------------------GGCCA------ATACTGCCAGCTCTGGCC----------------------------------------------------------TTCTATTAAA--------AGGGGCCCC-CTCGTTGCCC-------CTCCT--------------------------GG--TGCGAT--TGCATTGGTTGATTGTGATTGTAG--GCCTGTGATTGA---GTTGTCGGCCTGCTGGGCTACT-------GTTTG s droEug2.KB465067 611368 447 + 1515531 CAG---------TCG-------------CGAGTGAT--------TATGAAAC--------TGCTTTGTCGGTA-----------------T-C-CG--------------------------GGG--------------------ATATT--TG--GTTATTGTCTTT-------------------------G---------ATTTTGCATTCTAACACAAATCAAAA--------------------------C-GGGCCAACAG-----CA--ATCCCAACACTCGCCACTTAAATGCTCGTTTATAATGTTgttaaaatacaataaatagcCAGGACTCGCAGCAGGCGGTTTTC--------------------------------------------------------ACCA---G---CT----CTC------------------------------------------CAAGGCGAACGAacaca-------------t-----------ttccat---------ttccctcgGCCG----C--TGCGAC--------------------TGC----------------------------------TCATGCTGATTTATGAAATGTGGAC---------------------------GCCGATGTGGCGGGCCCACAGACCACAAGCCGCAAACAGAA---------CCC-----------CAA-----CCCCTTG------------------------------------GGCCA------GCT-------CTCTGGCCAGGCTAAGACCAAGACTAAGGACCC-----------------------------------------------------CGGGCCT-CTAACTGGGC--AAAGTCGGCA--------------------------GG--GGTGAT--TG-----------TGTGATTGTAG--GCCCGTGATTGA---GTTGTCGGCCTGCTGGGCTACT-------GTTTG s droEle2.KB458573 534483 449 - 5320397 CAG---------TCC-------------CGACTGAT--------TATGAAAC--------GGCTTTGTCGGTA-----------------T-CGCG--------------------------GGG--------------------ATATT--TG--GTTATTGTCTTC-------------------------G---------ATTTTGCATTCtaacacaaatcaaaa--------------------------c-gGGCCAACAG-----CA--ATCCCAACACTCGCCACTTAAATGCTCGTTTATAATGttgttaaaatacaataaatagcCAGGATTCGCAGCAGGCGGTTTTC--------------------------------------------------------ACCA---G---CT----CGC------------------------------------------CAAGGCGAACGAGCAcaatttccattgccat-----------ttccat---------ttcccccgACCG----CTTTGCAACTG------------------CGC----------------------------------TCATGCTGATTTATGAAATGTGGAC---------------------------GCCGATGTGGCGGGCCCACAA------------ACACGAAA---------CCC-----------CAA-----CCCCTTTTG----------------------------------GGCCA------GAT-------CTCTGACCAGGCCAA-------------------------------------------------TACTCGATTCGC----------TGGGCCT-CTAACTGGGC--CCAGTCGGCA--------------------------GG--GGTGAT--TG-----------TGTGATTGTAG--GCCCGTGATTGA---GTTGTCGGCCTGCTGGGCTACT-------GTTTG s droKik2.KB459527 288034 469 - 1234237 TAG---------TCTCGCCG--------CGACTGAT--------TATGAAAC--------GGCTTTGTCGGTA-----------------T-C-GG--------GA----------------GGG--------------------ATATT--TG--GTTATTGTCTTC-------------------------G---------ATTTTGCATTCTAACACAAATCATGG--------------------------C-CGGCCAGCAG-----CAATATCCCAACACTCGCCACTTAAATGCTCGTTTATAAtgttgttaaaatacaataaatagcCAGGACTCGCAGCAGGCGGTTTCC--------------------------------------------------------CCCA---A---Ct----cgc------------------------------------------tgtc------tctctct-------------c-----------tcccag---------gCT------------------------------------------CTC----------------------------------CCATGCTGATTTATGAAATGTGGCC---------------------------GCCGCTGTGGC-GGCCCACAA-------AACGCAGGCCCAA---------CCA-----------CAA-----CCACGGATCCAAAGCAAAGCGAACCAAACCCCCAACCCCAATAAGCCA------ACTCTGA---CTCTGGCTAGGT----------------------------------------------------CCCCCGGCCAGG--------CCGACGACT-CTAACTGGGCCCAGAGTCGGCA--------------------------GG--GGTGAT--TG---TGATTG--TGTGATTGCAGCAGCCGGTGATTGA---GTTGTCGGCATGCTGGGCTACT-------GTTTG s droTak2.KB461535 153298 465 - 669855 CAG---------TCCCGA----------CGACTGAT--------TATGAAACTGC---TTGGCTTTGTCGGTA-----------------T-C-CCAGTATCTAAATATCCGAGAGTATCCGGGG--------------------ATATT--TG--GTTATTGTCTTT-------------------------G---------ATTTAGCATTCTAACACAAATCAAAA--------------------------C-GGGCCAATAG-----CA--ATCCCAACACTCGCCACTTAAATGCTCGTTTataatgttgttaaaatacaataaatagccAGGACTCGCAGCAGGCGGTTTTC--------------------------------------------------------ACTG---G---CTGGCTCTC------------------------------------------CGAAGGC---GAacaca-------------t-----------ttccat---------ttccctc--------------------------------------gGC----------------------------------TCATGCTGATTTATGAAATGTGGAC---------------------------GCCGATGTGGCGGGCCCACAA-------ACCGCAAACAGAA---------CCC-----------CGACCAACCCCCTTCTA----------------------------------AGCCA------GCT-------CCCTGACCAGGCTAAGACTC------------------------------------------------CAAAGCCG----------GGGGCCT-CTAACTGGGC--AAAATCGGCA--------------------------GG--GGTGAT--TG-----------TGTGATTGTGG--GCCCGTGATTGA---GTTGTCGGCCTGCTGGGCTACT-------GTTTG s droRho2.KB449310 49119 429 - 65043 CAG---------TCC-------------CGACTGAT--------TATAAAAC--------GGCTTTGTCGGTA-----------------T-CGCG--------------------------GGG--------------------ATATT--TG--GTTATTGTCTTT-------------------------G---------ATTTTGCATTCTAACACAAATCAAAA--------------------------C-GGGCCAACAG-----CA--ATCCCAACACTCGCCACTTAAATGCTCGTTTATAATGTtgttaaaatacaataaatagcCAGGACTCGCAGCAGGCGGTTTTC--------------------------------------------------------ACTG---G---CT----CAC------------------------------------------CAAGGC----GAAcaca------------at-----------ttccat---------ttccctcgCTCG----TTTTGCGAC--------------------TGC----------------------------------TCATGCTGATTTATGAAATGTGGAC---------------------------GCCGATGTGGCGGGCCCACAG------------CCACAGAA---------CCC-----------CAA-----CCC---------------------------------------------------CCT-------TTTTGACCAGGCCAAGACG-------------------------------------------------CGATTCCC----------GGGGCCCACTAACTGGGC--CCAGTCGGCA--------------------------GG--GGTGAT--TG-GGTGATTG--TGTGATTGTAG--GCCCGTGATTGA---GTTGTCGGCCTGCTGGGCTACT-------GTTTG s droFic2.KB457177 91718 380 + 995874 CAG---------TCCCC-----------CGACTGAT--------TATGAAAC--------GGCTTTGTCGGTG-----------------T-CTCT--------------------------GGG--------------------ATATT--TG--GTTATTGTCTTC-------------------------G---------ATTTTGCATTCTAACACAAATCAAAA--------------------------C-GGGCCAGCAG-----CA--GTCCCAACACTCGCCACTTAAATGCTCGTTTATAATGTtgttaaaatacaataaatagccaGGATTCGCAGCAGGCGGTTTTC--------------------------------------------------------ACTG---G---CT----CTC------------------------------------------CGAGGC----GAACACA-------------T-----------TTCCCT---------CGTT-----------------------------------------CGC----------------------------------TCATGCTGATTTATGAAATGTGGAC---------------------------GCCGAAGTGGC-GGCCCACAA--------ACGGATCCCCAT---------CCC-----------CGA-----ACCCCTTTG----------------------------------GGCCG------AGT-------ATCTGGCCGGGCCAAGACT-------------------------------------------------CGCTTCC-----------CGGGCCT-CTAACTGGGC--CCAGTCGGCA--------------------------G-----------TA----------------------------------------------GCCTGCTGGGCTACT-------GTTTG s droPse3.chr3 1361427 498 - 19787792 TAGGAAAGCCTCTCCTCTT---------CGAGTGAT--------TATGAAAC--------GGCTTTGTCGGTA-----------------TTC-CG--------------------------GGgatatatggatatggatatggatatt--cG--GTTATTGTCTTG-------------------------G---------CTTTCGAATtctaacacaaatcaaaa--------------------------c-gGCCTAACAG-----CA--ATCCCAACACTCGCCACTTAAATGCTCGTTTATAATGTtgttaaaatacaataaatagtCGGGATTCGCAGCAggcggttgct--------------------------------------------------------gctgcaag---cT----GCA------------------------------------------CG--------CTGCACT-------------G-----------TTCCAC---------CTTTTGCTC------------------------------------CGC----------------------------------TCATGCTGATTTATGAAATGTGGAC---------------------------GCCGTCTTGGCGGTCCCACAA--------ACGGACTtggac---------tccgactctgactgcga-----ctgcgactg------------------agactgggactccAAAGGCCA------GC--------CTCTGATCGGG---------------------------------------------------------CGAGCCTT----------GAGGCCT-CTGACTGGGC--TCCGTCTGGCtctcagtcgcagtctcagCCCGAGTCGG--CGTGAT--TG-----------TGTGATTGTAG--GCCTTTGATTGA---GTTGTCGGCATGCTGGGCTACT-------GTTTG s droPer1.super_34 550310 484 - 916997 TAGGAAAGCCTCTCCTCTT---------CGAGTGAT--------TATGAAAC--------GGCTTTGTCGGTA-----------------TGC-CG--------------------------GGG--ATATGGATATGGATATGGATATT--CG--GTTATTGTCTTG-------------------------G---------CTTTCGAATTCTAACACAAATCAAAA--------------------------C-GGCCTAACAG-----CA--ATCCCAACACTCGCCACTTAAATGCTCGTTTATAATGTTGTTAAAATACAATAAATAGTCAGGATTCGCAGCAGGCGGTTGCT--------------------------------------------------------GCTGCAAG---CT----GCA------------------------------------------CG--------CTGCACT-------------G-----------TTCCAC---------CTTTTGCTC------------------------------------CGC----------------------------------TCATGCTGATTTATGAAATGTGGAC---------------------------GCCGTCTTGGCGGTCCCACAA--------ACGGACTTGgac---------tgc------gactgaga-----ctgagactg------------------agactgggactCCAAAGGCCA------GC--------CTCTGATCGGG---------------------------------------------------------CGAGCCTT----------GAGGCCT-CTGACTGGGC--TCCGTCTGGC------TCGAAGTCTCAGCTCGAGTCGG--CGTGAT--TG-----------TGTGATTGTAG--GCCTTTGATTGA---GTTGTCGGCATGCTGGGCTACT-------GTTTG s droMir2.chr3 1402521 490 - 20862834 TAGGAAAGCCTCTCCTCTT---------CGAGTGAT--------TATGAAAC--------GGCTTTGTCGGTA-----------------TGC-Cg--------------------------ggg--atatggatatggatatggatatt--cG--GTTATTGTCTTC-------------------------G---------CTTTCGAATTCtaacacaaatcaaaa--------------------------c-gGCCTAACAG-----CA--ATCCCAACACTCGCCACTTAAATGCTCGTTTATAATGTtgttaaaatacaataaatagtCGGGATTCGCAGCAggcggttgct--------------------------------------------------------gctgcaag---cT----GCA------------------------------------------CG--------CTGCACT-------------G-----------TTCCAC---------CTTTTGCTC------------------------------------CGC----------------------------------TCATGCTGATTTATGAAATGTGGAC---------------------------GCCGTCTTGGCGGTCCCACAA--------ACGGACTtggac---------tccgactctgactgcga-----ctgcgactg------------------agactgggactccAAAGGCCA------GC--------CTCTGATCGGG---------------------------------------------------------CGAGCCTT----------GAGGCCT-CTGACTGGGC--TCCGTCTGGC------TCGCAGTCTCAGCCCGAGTCGG--GGTGAT--TG-----------TGTGATTGTAG--GCCTTTGATTGA---GTTGTCGGCATGCTGGGCTACT-------GTTTG s droWil2.CH963894 1326341 437 + 2843958 -------------------CAAAAT---CGATTGAT--------TATGAAAC-----------------GGCA-----------------T-T-TG--------------------------GAG--------------------GCTTT--TGTCGGTATTGTCTTG-------------------------G---------AATTTGCATTCTAACACAAATCAAAA--------------------------C-AGG----------------CTTTCAACACTCGCCACTTAAATGCTCGTTTATAATGTTgttaaaatacaataaatagcCAGGACTCTCAGCAGGCGGCATtcgtacatacatgtatatcgtatatatctacagatatatatatatgtatgtacctagtGCTA---C---CC----CCA------------------------------------------CT--------CACAAGA-------------G-----------TTTCAGACTAAAGAGTTCTCTAGCCTG----CTGGCCTG---------------------TGA----------------------------------TCATGCTGATTTATGAAATGTGGAC---------------------------GCCGACATGGC-GGtcaacaa------------------aa---------cta-----------aaa------------------------------------------------ggcGA------ACC-------AT------AGGTTTAGTCC-------------------------------------------------AGACTCTT----------TGGACCT-ctctctgagt--------------------------------------g-----------tg-----------tgtgattgtAA--ATCTTTGAttgagttgttgttggcatGCTGAGCTact-------gtttg s droVir3.scaffold_12875 7366675 450 + 20611582 -----------------------at---tggctgct-------ttgtcggtctgtctgtctgC----------------CCCCCCCTCCCT-C-TG--------------------------GCA--------------------GGCAGC-CT--GGCATTGTCTTT-GGCCCGTTTGGA------------GTCTCGGTGTATTTTGCATTCTAACACAAATCAAATG-------------------------C-GGCCCCACTC-----GA--CACTCGCCACTCGCCACTTAAACGCTCGTTTATAATGTTGTTAAAATACAATAAATAGCCAGGATTCGCAGCAGGCGG-TTTC--------------------------------------------------------ATAG---CGAAAC----GGC------------------------------------------AA--------ACGCACA-------------G---------ATCTCCCG---------CTCCCTCCCCCTCACAC----------------------------TGC----------------------------------ACATGCTGATTTATGAAATGTGGAC---------------------------GCCGACTTGGC-GGCCAACCA-------AAGGC---CAAAT---------CCC-----------CCA-----CTGCACTCC----------------------------------AGCTA------GCC-------AGAT-------CTGAGACCAACTGCTTActg----ctgctg--------------------------------------------------ct-gctgctgctg-------ctgct--------------------------gc--GGTGAT--TG-------TG--TGTGATTGCAA--GTCTTTGATTGA---GTTGTCCGCGTGCTGGGCTACT-------GTTTA s droMoj3.scaffold_6496 26162317 519 + 26866924 -----------------------ctgtctgactgct------------gtcctccccctccgctct---------cgctctccctctccct-c-tG--------------------------CTG--------------------CTTAACGCT--GCCATTGTCTTT-GTCCCGTTTGCA------------GTCGCGATGTATTTTGCATTCTAACACAAATCAAATGC--CTCACCTCTCGCCACTCGCCCCC-GGCCCCCCGCCTCCGGC--CACTCGCCACTCGCCACTTAAACGCTCGTTTATAATGTTGTTAAAATACAATAAATAGCCAGGATTCGCAGCAGGCGG-TTCC--------------------------------------------------------ATTG---CGATAC----GGC------------------------------------------CA--------ACGCACA-------------G-----------CTCTCG---------CTCTCTCGCGCT----C----------------------------CGC----------------------------------GCATGCTGATTTATGAAATGTGTCC---------------------------GGCCAGTTGGC-GGCCAACCA-------AAGGC---CAAAT---------CCC-----------CCA-----CTGCACTCG----------------------------------GTCTA------GCTCGGG---GGCC-------CCGAGACCAACTGCTGGCTGCCAACTGCTGCAGGCTGC-------------------CGACTCCTGACTGGTGACTGCATct-gctgctgctg-------ctgct--------------------------gctTGGTGAG--TG-------TG--TGTGATTGCAG--CTCTCTGATTGA---GTTGTCCGTGTGTTGGGCTTCT-------GTTTA s droGri2.scaffold_15245 917323 572 + 18325388 -----------------------ttatttgtttgcttgtttgtttgCCTTTCTGCCTGCCAGCTTTGTCGGCCCACCATCCCCATTCCCCT-C-CG--------------------------CTC--------------------CTTAT--TG--GCCATTGTCTTTGGGCCTGTTTCGGTGTGCGCAGCGTGTCTCGCCGTATTTTGCATTCTAACACAAATCAAACGCGAGCCCCACTccgatacccgatacc-cgatacccgatactcga--tactcgatTCTCGCCACTTAAACGCTCGTTTATAATGTTGTTAAAATACAATAAATAGCCAGGATTCGCAGCAGGCGGTTTTC--------------------------------------------------------AACG---C---AC----CGC------------------------------------------CA--------GCGAGCT-------------CTGTCTCTCTATCTCCAT---------CTCTCTCCCGTCTCCAC----------------------------CGCCATCTCCATCTCCTCCATCTTGCGCGCTAGAGAAAAATGCTGATTTATGAAATGTGGAC---------------------------GACGACTTGGC-GGCCAACCA-------AAGGC---CAAATCTTAAATCCCCC-----------CCA-----CTGCAATGC----------------------------------AGTCA------ACCTAA----ATCT-------TAAAGACCAACTGTTGACTACCAActg-----------------------------------------------------ct-gctgctgctg-------ctgct--------------------------gT--GGCAAC--TG-------GC--TGTGATTGCAA--TTCTTTGATTGA---GTTGTCCGTGTGCTGGGCTACT-------GTTTA a score=27960.000000 s dm6.chr2R 24369117 2 + 25286936 CA s droSim1.chr2R 18707437 2 + 19596830 CA s droSec1.super_23 127105 2 + 989336 CA s droYak3.chr2R 20217109 2 + 21139217 CA s droEre2.scaffold_4845 21614709 2 + 22589142 CA s droBia2.KB462602 808731 2 + 3129309 CA s droSuz1.KI419649 12054907 2 - 14502029 CA s droAna3.scaffold_13266 5719833 2 - 19884421 CA s droBip2.KB464407 1969815 2 + 2915140 CA s droEug2.KB465067 611815 2 + 1515531 CA s droEle2.KB458573 534932 2 - 5320397 CA s droKik2.KB459527 288503 2 - 1234237 CA s droTak2.KB461535 153763 2 - 669855 CA s droRho2.KB449310 49548 2 - 65043 CA s droFic2.KB457177 92098 2 + 995874 CA s droPse3.chr3 1361925 2 - 19787792 GA s droPer1.super_34 550794 2 - 916997 GA s droMir2.chr3 1403011 2 - 20862834 GA s droVir3.scaffold_12875 7367125 2 + 20611582 CA s droMoj3.scaffold_6496 26162836 2 + 26866924 CA s droGri2.scaffold_15245 917895 2 + 18325388 CA a score=17100.000000 s dm6.chr2R 24369119 1 + 25286936 G s droSim1.chr2R 18707439 1 + 19596830 G s droSec1.super_23 127107 1 + 989336 G s droYak3.chr2R 20217111 1 + 21139217 G s droEre2.scaffold_4845 21614711 1 + 22589142 G s droBia2.KB462602 808733 1 + 3129309 G s droSuz1.KI419649 12054909 1 - 14502029 G s droAna3.scaffold_13266 5719835 1 - 19884421 G s droBip2.KB464407 1969817 1 + 2915140 G s droEug2.KB465067 611817 1 + 1515531 G s droEle2.KB458573 534934 1 - 5320397 G s droKik2.KB459527 288505 1 - 1234237 G s droTak2.KB461535 153765 1 - 669855 G s droRho2.KB449310 49550 1 - 65043 G s droFic2.KB457177 92100 1 + 995874 G s droPse3.chr3 1361927 1 - 19787792 G s droPer1.super_34 550796 1 - 916997 G s droMir2.chr3 1403013 1 - 20862834 G s droVir3.scaffold_12875 7367127 1 + 20611582 G a score=273208.000000 s dm6.chr2R 24369120 46 + 25286936 T-----------------TTG-----CCGAG--TGGCTTATCTT-GCGGT---GCATCGCAGCTGT--TCGACCAG s droSim1.chr2R 18707440 45 + 19596830 T-----------------TCG------CGAG--TGGCTTATCTT-GCGGT---GCATCGCAGCTGT--TCGACCAG s droSec1.super_23 127108 46 + 989336 T-----------------TCG-----CCGAG--TGGCTTATCTT-GCGGT---GCATCGCAGCTGT--TCCACCAG s droYak3.chr2R 20217112 45 + 21139217 T-----------------TCG-----CCGCG--TGGCTTATCTT-GCGGT---GCATCGCAGCTGC--TCGCCCA- s droEre2.scaffold_4845 21614712 45 + 22589142 T-----------------TCG-----CTGAG--TGGCTTATCTC-GCGGT---GCATCGCAGCTGT--TCGGCCA- s droBia2.KB462602 808734 47 + 3129309 C-----------------TCG-----CTGAG--TGGCTTATCTTGGCGGT---GCATCGCAGCTGT--TCGACTAC s droSuz1.KI419649 12054910 47 - 14502029 T-----------------TCG-----CTGAG--TGGCTTATCTTAGCGGT---GCATCGCAGCTGT--TCGACTAG s droAna3.scaffold_13266 5719836 47 - 19884421 T-----------------TCG-----CCGAG--TGGCTTATCTGGCCTAT---GCATCCCAGCTGT--TCGGTTAG s droBip2.KB464407 1969818 47 + 2915140 T-----------------TCG-----CCGAG--TGGCTTATCTGGCCTTT---GCATCCCAGCTGT--TCGGTTAC s droEug2.KB465067 611818 47 + 1515531 T-----------------GCG-----CTGAG--TGGCTTATCTTGGCGGT---GCATCGCAGCTGC--TCGACTAG s droEle2.KB458573 534935 49 - 5320397 T-----------------TCG-----CTGAG--TGGCTTATCTTGGCGGT---GCATCGCAACTGTTCTCGACTAG s droKik2.KB459527 288506 56 - 1234237 T-----------------TTGGAGAACTGAGAATGGTTTATCTT-TTGCTTCGGAATCGCAGCTGT--TGGGAAAG s droTak2.KB461535 153766 64 - 669855 TTTTCAGCTTGCAGTGAGTCG-----CTGAG--TGGCTTATCTTAGCGGT---GCATCGCAGCTGT--TCGACTAG s droRho2.KB449310 49551 50 - 65043 T-----------AGT---GCG-----GTGAG--TGGCTTATCTTAGCAGT---GCATCGCAGCTGT--TCGACTAG s droFic2.KB457177 92101 47 + 995874 T-----------------TCG-----CTGAG--TGGCTTATCGCGGCGGT---GCATCGCGGCCAT--TCGAACAG s droPse3.chr3 1361928 40 - 19787792 T-----------------TCT-----TTGAG--TGGGCTATCTATTAGTA---GAATCACAGCTTT--T------- s droPer1.super_34 550797 40 - 916997 T-----------------TCT-----TTGAG--TGGGCTATCTATTAGTA---GAATCACAGCTTT--T------- s droMir2.chr3 1403014 40 - 20862834 T-----------------TCT-----TTGAG--TGGGCTATCTATTAGTA---GAATCAGAGCTTT--T------- a score=28154.000000 s dm6.chr2R 24369166 14 + 25286936 CCTGCCAGTTGTCT s droSec1.super_23 127154 3 + 989336 CCT----------- s droBia2.KB462602 808781 14 + 3129309 TCTGGCATTATTCC s droSuz1.KI419649 12054957 14 - 14502029 CCTGGCATTATTCT s droAna3.scaffold_13266 5719883 14 - 19884421 TCGGCCATAATTTC s droBip2.KB464407 1969865 14 + 2915140 TCGGccataatttc s droEug2.KB465067 611865 14 + 1515531 CCTGGTATTACTCT s droEle2.KB458573 534984 14 - 5320397 TCGGCCATAATTCT s droKik2.KB459527 288562 14 - 1234237 TCGGGCTTTATTCT s droTak2.KB461535 153830 14 - 669855 TCTGGCTCTATTCT s droRho2.KB449310 49601 14 - 65043 TCGGCTATTATTCT s droFic2.KB457177 92148 14 + 995874 GCTGGCATTACTCT s droPse3.chr3 1361968 12 - 19787792 --GGCTATAGCTCC s droPer1.super_34 550837 12 - 916997 --GGCTATAGCTCC s droMir2.chr3 1403054 12 - 20862834 --GGCTATAGCTCC a score=188039.000000 s dm6.chr2R 24369180 34 + 25286936 GCCGCCTCCACTTATCATGGTC---CAGG-AGGGGTCA s droSim1.chr2R 18707838 34 + 19596830 GCACCCTCCACTTATCACGGTC---CAGG-AGGGGTCA s droSec1.super_23 127157 27 + 989336 -------CCACTTATCACGGTC---CAGG-AGGGGTCA s droYak3.chr2R 20217157 35 + 21139217 ---GCCTCCACTTATCACGGCCTGGCAGGAAGGGGTCA s droEre2.scaffold_4845 21614757 34 + 22589142 ---GCCCCCACTTATCACGGCTTAGCAGG-AGGGGTCA s droBia2.KB462602 808795 34 + 3129309 GCCGCCTTCACTTATCACGGCC---TGCC-AGGGGTCA s droSuz1.KI419649 12054971 34 - 14502029 GCCGCCTTCACTTATCACGGCC---TAGA-AGGGGTCA s droAna3.scaffold_13266 5719898 34 - 19884421 ATTTTGGGAGCTTATCATTGGT---CTAT-AAAGGTCA s droBip2.KB464407 1969880 34 + 2915140 tttttggtaACTTATCATTGGA---CTAT-AAAGGTCA s droEug2.KB465067 611879 34 + 1515531 GCCGCCTTCACCTATCACAGCT---TAGA-AGAGGTCA s droEle2.KB458573 534998 34 - 5320397 GCCGCCTGCACTTATCATTGGT---CAGA-AGGGGTCA s droKik2.KB459527 288577 32 - 1234237 AGTTCGGCGA--TATCGGGGGT---CTTG-AGGGGTTA s droTak2.KB461535 153844 34 - 669855 GCCGCCTTCACTTATCACGGCC---TAGA-AGGGGTCA s droRho2.KB449310 49615 36 - 65043 GCCGCCTGCACTTATCCAGGCTTA-TAGA-AGGGGTCA s droFic2.KB457177 92162 34 + 995874 GCCGCCTGCACTTATCACGGCT---TAGA-AGGGGTCA s droPse3.chr3 1361980 34 - 19787792 GCAGCCTTAGCTTATCACTATT---TTAA-AGGGGTCA s droPer1.super_34 550849 34 - 916997 GCAGCCTTGGCTTATCACTGGT---TTAA-AGGGGTCA s droMir2.chr3 1403066 34 - 20862834 GCAGCCTTGGCTTATCACTGGT---TTAA-AGGGGTCA a score=-6538.000000 s dm6.chr2R 24369214 2 + 25286936 -TG s droSim1.chr2R 18707872 2 + 19596830 -AG s droSec1.super_23 127184 2 + 989336 -AG s droYak3.chr2R 20217192 2 + 21139217 -AG s droEre2.scaffold_4845 21614791 2 + 22589142 -AG s droAna3.scaffold_13266 5719932 2 - 19884421 -GG s droBip2.KB464407 1969914 2 + 2915140 -GG s droEug2.KB465067 611913 2 + 1515531 -AG s droEle2.KB458573 535032 2 - 5320397 -AG s droRho2.KB449310 49651 2 - 65043 -AG s droFic2.KB457177 92196 2 + 995874 -AG s droPse3.chr3 1362014 2 - 19787792 CA- s droPer1.super_34 550883 2 - 916997 CA- s droMir2.chr3 1403100 2 - 20862834 CA- a score=8006.000000 s dm6.chr2R 24369216 4 + 25286936 G-GTT s droSim1.chr2R 18707874 5 + 19596830 GCGTT s droSec1.super_23 127186 4 + 989336 G-GTT s droYak3.chr2R 20217194 4 + 21139217 G-ATT s droEre2.scaffold_4845 21614793 4 + 22589142 G-ATT s droAna3.scaffold_13266 5719934 4 - 19884421 G-AAT s droBip2.KB464407 1969916 4 + 2915140 G-AAT s droEug2.KB465067 611915 4 + 1515531 G-AGT s droEle2.KB458573 535034 4 - 5320397 G-ATT s droRho2.KB449310 49653 4 - 65043 G-ATT s droFic2.KB457177 92198 4 + 995874 G-ATT a score=1135.000000 s dm6.chr2R 24369220 1 + 25286936 A s droSim1.chr2R 18707879 1 + 19596830 A s droSec1.super_23 127190 1 + 989336 A s droYak3.chr2R 20217198 1 + 21139217 A s droEre2.scaffold_4845 21614797 1 + 22589142 A s droAna3.scaffold_13266 5719938 1 - 19884421 G s droBip2.KB464407 1969920 1 + 2915140 G s droEug2.KB465067 611919 1 + 1515531 G s droRho2.KB449310 49657 1 - 65043 G s droFic2.KB457177 92202 1 + 995874 G a score=-13779.000000 s dm6.chr2R 24369221 10 + 25286936 CG---ACTGCAC-----------------------C s droSim1.chr2R 18707880 11 + 19596830 AGA--AATGCAC-----------------------C s droSec1.super_23 127191 10 + 989336 CG---ACTGCAC-----------------------C s droYak3.chr2R 20217199 33 + 21139217 CG---GCTGCCCTGGCACACGGAAAGTGTCTGAGTC s droEre2.scaffold_4845 21614798 33 + 22589142 CG---ATTGCACTGGCACACCGAAAGTGTCTGAGTC s droBip2.KB464407 1969923 10 + 2915140 CT---ACTAGAT-----------------------G s droEug2.KB465067 611920 10 + 1515531 --A-TCTAGCAC-----------------------C s droRho2.KB449310 49660 10 - 65043 CG---AGTGCAC-----------------------C s droFic2.KB457177 92203 11 + 995874 --AGTGCTACAC-----------------------C a score=1302.000000 s dm6.chr2R 24369231 1 + 25286936 G s droSim1.chr2R 18707891 1 + 19596830 G s droSec1.super_23 127201 1 + 989336 G s droYak3.chr2R 20217232 1 + 21139217 G s droEre2.scaffold_4845 21614831 1 + 22589142 G s droBip2.KB464407 1969933 1 + 2915140 T s droRho2.KB449310 49670 1 - 65043 G s droFic2.KB457177 92214 1 + 995874 G a score=-8637.000000 s dm6.chr2R 24369232 32 + 25286936 GGCACACAGCCCCCA------------------TCCACCCAACGTGCGGA s droSim1.chr2R 18707892 39 + 19596830 GGCACACAGCCCCCATCTGTG-----------CTCCACTGAACGTATGGA s droSec1.super_23 127202 42 + 989336 GGCACACAGCCCCCATCTGTA--------CTCCTCCACTCAACGTGTGGA s droYak3.chr2R 20217233 23 + 21139217 GAAACTCAGCTG-----------------------CATTCA----GTGCT s droEre2.scaffold_4845 21614832 39 + 22589142 GAAACTCAGCCGCCTTCAGTG-----------CTCCACTTAACGTGTGGA s droBip2.KB464407 1969934 41 + 2915140 GAAATGTGGCAC-----TGTAG----TAATTTATTAACCAAACTTGTAAG s droFic2.KB457177 92225 46 + 995874 AGCCGGTAACCCACACTATTAACTCTTAGAGAGGCCAGTCAAGGCA---- a score=-18965.000000 s dm6.chr2R 24369264 49 + 25286936 TCATATGATACAGCAGGTGGTAGGAGAAGAG---ATGTTTACTGTCTTACAG-- s droSim1.chr2R 18707931 49 + 19596830 TCATATGATACAGCAGGTGGTAGGAGAAATG---ATGTTTACTGCCTTGCAG-- s droSec1.super_23 127244 49 + 989336 TCATATGGTACAGCAGGTGGTAGGAGAAATG---ATGTTTACTGCCTTGCAG-- s droYak3.chr2R 20217256 28 + 21139217 CCACTTAATGATGT--TTACTATCTGAGAC------------------------ s droEre2.scaffold_4845 21614871 30 + 22589142 TGATCTAATACAGCAGATAGTAGGGGAAAC------------------------ s droAna3.scaffold_13266 5719986 52 - 19884421 TAGTAGGAGAGACCACGGTGAAGGAGACCTAGATATGGTTTCTCGGAAAAAA-- s droBip2.KB464407 1969975 30 + 2915140 ----------------------AGAGACATGGATTTTGGGTTTAGTTAGGAA-- s droFic2.KB457177 92271 48 + 995874 CCGCAGAATATAG---GTAGTATTTTAAGCA---GACGGTTCTAATTCAAACGG a score=4871.000000 s dm6.chr2R 24369313 3 + 25286936 AGT s droSim1.chr2R 18707980 3 + 19596830 AGT s droSec1.super_23 127293 3 + 989336 AGT s droYak3.chr2R 20217284 3 + 21139217 AGC s droEre2.scaffold_4845 21614901 3 + 22589142 AGT s droAna3.scaffold_13266 5720038 3 - 19884421 AGG s droBip2.KB464407 1970005 3 + 2915140 GGT s droKik2.KB459527 288903 3 - 1234237 AGT s droFic2.KB457177 92319 3 + 995874 ACT a score=3664.000000 s dm6.chr2R 24369316 4 + 25286936 ----AATA s droSim1.chr2R 18707983 4 + 19596830 ----AATA s droSec1.super_23 127296 4 + 989336 ----AATA s droYak3.chr2R 20217287 4 + 21139217 ----ACTA s droEre2.scaffold_4845 21614904 4 + 22589142 ----AATA s droSuz1.KI419649 12055484 4 - 14502029 ----aata s droAna3.scaffold_13266 5720042 4 - 19884421 ----CAGA s droBip2.KB464407 1970009 4 + 2915140 ----CTTC s droKik2.KB459527 288906 4 - 1234237 ----ATTA s droFic2.KB457177 92322 8 + 995874 AAAAAATA a score=1971.000000 s dm6.chr2R 24369320 2 + 25286936 TT s droSim1.chr2R 18707987 2 + 19596830 TA s droSec1.super_23 127300 2 + 989336 TA s droYak3.chr2R 20217291 2 + 21139217 TT s droEre2.scaffold_4845 21614908 2 + 22589142 TT s droSuz1.KI419649 12055488 2 - 14502029 tt s droAna3.scaffold_13266 5720046 2 - 19884421 CT s droBip2.KB464407 1970013 2 + 2915140 TT s droKik2.KB459527 288910 2 - 1234237 TT s droFic2.KB457177 92330 2 + 995874 AC s droMir2.chr3 1403201 2 - 20862834 TT a score=-140418.000000 s dm6.chr2R 24369322 74 + 25286936 TGCCCAA----TCTATA-----CCT--AATACCTAA--TGT-ATCCCCTTAA-----------------AGAATCCCG---TACTAATTGCCACTCCTT-----AGATACAGT s droSim1.chr2R 18707989 82 + 19596830 AGCCCAA----TCTATA-----CAT--AATACCTAA--TGT-ATTCCATTAAAGTTGTG---------CAGGTATCTG---CTCTAATTGCCACTCCTT-----AGATACAGT s droSec1.super_23 127302 82 + 989336 AGCCCAA----TCTATA-----CCT--AATACCTAA--TGT-ATTCCATTAAAGTTGTG---------CAGGTATCTG---CTCTAATTGCCACTCCTT-----AGATACAGT s droYak3.chr2R 20217293 46 + 21139217 AGCTC----------------------AATACCCAA--TAT-ATCC-----------------------------------CAC--ATGGTCACTCCTT-----AGCCACAAT s droEre2.scaffold_4845 21614910 85 + 22589142 AGCCCAG----ACTATC-----TATCTAATGCCTAA--TAG-ATCCT-CAAAAGCTGTG---------CGAGTATCCCA-GCACTAATTGTCACTCCTT-----AGATACGGT s droSuz1.KI419649 12055490 81 - 14502029 taagcat----tttata-----CAT--AGCTATAAT--CAG-CTTCCCATGAAATAATA------AATCGATTACCTC---CAC--AATTTCACAATTT-----AAGTAAT-- s droAna3.scaffold_13266 5720048 84 - 19884421 TGAACAC----TTTTTT-----CAA--AATGACATA--TATCAATTTATGAAAGCCAAG------ACAAAAGTGTTTCTCTCTTTAATATTATTTTTTT-----AAAC----- s droBip2.KB464407 1970015 87 + 2915140 TCATTACAAAATCAGag-----caa--aataatata--aaccaCTCTATGAAAACCAAG------ACCAAAGCTTATCACACTTAAACCATTCTTTTTT-----AAA------ s droKik2.KB459527 288912 97 - 1234237 CACTCAA----TCGTTAACCTTTTT--AATACTCAAATTGT-AAACTTCAAAAGCCGCTTTAAattcacaaataatta---tatttacactTACTTTCT-----AAgtatag- s droFic2.KB457177 92332 86 + 995874 GGTTTAGAGAATCT--------TCT--ACTTTTATA--TAA-GTAATCTCCAACTGaag---------aaacttttccaattacCAACAGGCACGACTTACGGCAGAC----- s droPse3.chr3 1362117 88 - 19787792 TACCCAT----TAGATGATCTTCTC--AACTATAAA--GCA-CTttcttaaacattttt---------cact--tGTTGTCTTCAAAATTTGacttatt-----taataaaaa s droPer1.super_34 550986 90 - 916997 TACCCAT----TAGATGATCTTCTC--AACTATAAA--GCA-CTTTCTTAAACATTTTT---------CACTTGTGTTTTCTTCaaaattttacttatt-----taataaaaa s droMir2.chr3 1403203 90 - 20862834 TACCCAT----TAGATGATCTTCTC--AACTATAAG--GCA-CTttcttaaacattttt---------cacttgtgttttcttcaaaattttacttatt-----taatacaaa a score=-34415.000000 s dm6.chr2R 24369396 22 + 25286936 TGCAATGTACCA-----------------CCAAGTAGCG s droSim1.chr2R 18708071 22 + 19596830 TGCATCGCAACA-----------------CCATGTCTTA s droSec1.super_23 127384 22 + 989336 TGCATCGCAACA-----------------CCATGTCTTA s droYak3.chr2R 20217339 2 + 21139217 TG------------------------------------- s droEre2.scaffold_4845 21614995 22 + 22589142 TGCCCTGCACCA-----------------CTTGGAAGCG s droAna3.scaffold_13266 5720132 17 - 19884421 -TTCTCTTATCA-----------------ACACAT---- s droBip2.KB464407 1970102 15 + 2915140 ---CTCTTATCA-----------------acacat---- s droTak2.KB461535 154270 22 - 669855 TGCACTATTTca-----------------ccatttaaaa s droFic2.KB457177 92418 39 + 995874 TATCttgtacaaataaaatcttaaagttTCCAAGTAATT s droPse3.chr3 1362205 15 - 19787792 tataatgcaTAT-----------------ACA------- s droPer1.super_34 551076 15 - 916997 tataatGCATAT-----------------ACA------- s droMir2.chr3 1403293 15 - 20862834 tataatgcATAT-----------------ACA------- a score=2548.000000 s dm6.chr2R 24369418 1 + 25286936 T s droSim1.chr2R 18708093 1 + 19596830 T s droSec1.super_23 127406 1 + 989336 T s droEre2.scaffold_4845 21615017 1 + 22589142 T s droEle2.KB458573 535665 1 - 5320397 T s droKik2.KB459527 289009 1 - 1234237 t s droTak2.KB461535 154292 1 - 669855 t s droFic2.KB457177 92476 1 + 995874 T a score=-12350.000000 s dm6.chr2R 24369419 6 + 25286936 CTTAT------C s droSim1.chr2R 18708094 6 + 19596830 CTTAT------C s droSec1.super_23 127407 6 + 989336 CTTAT------C s droYak3.chr2R 20217341 4 + 21139217 --CAT------T s droEre2.scaffold_4845 21615018 6 + 22589142 CTCAT------T s droBia2.KB462602 809321 6 + 3129309 CTTAT------C s droSuz1.KI419649 12055573 6 - 14502029 TTAAA------C s droAna3.scaffold_13266 5720149 12 - 19884421 TTTATAAAAAAC s droBip2.KB464407 1970117 11 + 2915140 tttat-aaaaac s droEle2.KB458573 535666 6 - 5320397 TTcac------a s droKik2.KB459527 289010 5 - 1234237 ttaat------- s droTak2.KB461535 154293 6 - 669855 ------ataaac s droFic2.KB457177 92478 5 + 995874 TTAGC------- s droPse3.chr3 1362220 6 - 19787792 CTTAC------C s droPer1.super_34 551091 6 - 916997 CTTAC------C s droMir2.chr3 1403308 6 - 20862834 CTTAC------C a score=-52517.000000 s dm6.chr2R 24369425 96 + 25286936 ACTT--AGT---ATGC-----CT--TA---------------CTCACCCA-TGACT--AGGTGCCAGCCGGTCTTGTCCAGATCTTCT--TCAGA--TCTCCTTCCCAGCATCCGCTATC---------------ACCC--CGATCA s droSim1.chr2R 18708100 94 + 19596830 ACTT--AGT---ATGC-----CT--TA---------------CTCACCCA-TGACT--AGGTGCCAGCCGGTCTTGTCCAGATCTTCC--TC--A--TCGCCTTCCCAGCATCCGCGATC---------------ACCC--CGATCA s droSec1.super_23 127413 94 + 989336 ACTT--AGT---ATGC-----CT--TA---------------CTCACCCA-TGACT--AGGTGCCAGCCGGTCTTGTCCAGATCTTCC--TC--A--TCGCCTTCCCAGCATCCGCGATC---------------ACCC--CGATCA s droYak3.chr2R 20217345 96 + 21139217 ACTT--AGT---ATGC-----CA--TA---------------CTCACCCA-TAAGT--AGGTGCCAGCTGGTCTTGTCCAGATCTTCCAGCT--A--TCTCCTTCCCAGCATCCGCGATC---------------ACCC--CGATCA s droEre2.scaffold_4845 21615024 95 + 22589142 ACTT--AGT---ATGC-----TCATTA---------------CTCACCCG-TAACT--AGGTGCCAGCTGGTCTTGTCCAGATCTTCC--TC--A--TCTCCTT-CCAGCATCCGCGATC---------------ACCC--CGATCA s droBia2.KB462602 809327 94 + 3129309 A--T--TAA---AGTC-----TT--TA---------------CTTACCCG-TAATT--AAGTGCCAGCCAATGGAATACACTTCTTTC--TT--G--TCTCTTTGAAAACAGTGATGATC---------------ACCAAGTGATCC s droSuz1.KI419649 12055579 94 - 14502029 G--T--AAT---ATTT-----TC--CA---------------CTTACCCA-TAACT--AAGTGCCAGCCAATCGAATACATTTCTTCC--TT--A--TCTCTTTGCAAACAGCCATGATC---------------ACTGAGTGATCC s droAna3.scaffold_13266 5720161 100 - 19884421 ACTCTAATT---TTAAATATTCT--TA---------------CTCACCCG-TTTTTT-AAACTCAAGC---TTAGGCCTCGCTCTCCA--TT--A--TTATGTT-CCACAAACCCAGATC---------------ACCATGTGATCA s droBip2.KB464407 1970128 96 + 2915140 acttAAAGT---ATGA-----CT--TA---------------CTCaccca-ttttttgaaattcaagC---TTAGGCATCACTTTCCA--TA--A--TTAAGTT-CCATTAAACCAGACC---------------ACTGTGTGATGA s droEug2.KB465067 612349 78 + 1515531 actt--aac---attt-----tc--ca---------------cttACCTA-TGTTT--AAGTGCC---------TGTTTAGTTCCTCA--TT--A--TC---------ACAGCCATGATC---------------GGTGTGTGATCA s droEle2.KB458573 535672 99 - 5320397 attt--agtttaattt-----tt--ga---------------ctTACCTA-TATTT--AAGCGAGTGTTAATTTAACACAGATCTTTT--TT--A--TCTCCTTGCCAGCAGTCATGATC---------------ACTGTGCAATCA s droKik2.KB459527 289015 92 - 1234237 attt--aat---tcca-----AA--CA---------------CTTACCCATTTAAT--TAgtcttattaatttaaaaacggATCTTCC--AA--G--TCGGTTTCCCACCAAGGCTGCTT---------------CCCA-----GCA s droTak2.KB461535 154299 94 - 669855 ------att---ttct-----tg--cA---------------CTTACCCA-TAATT--AAGAGACAGTCAATCTGATAGAAATCATCC--TT--AACTCTTGTTGCAAACAACCATGATC---------------ACTGTGTGACCC s droRho2.KB449310 50202 96 - 65043 acta--aat---attt-----at--aa---------------cttacCCA-TATTT--AAGCGAGTACTAATTAAATACAGATCTTCC--TT--A--TCTCTTTGCCAGCAGTCAAGATC---------------GCTGGGCGATCA s droFic2.KB457177 92522 106 + 995874 ATTC--ACT---CCTC-----CA--CACGTTTCACATTTTTACTTACCCA-TATCA--AA-----AGCTCGCTTAAGACAGTTCTTCC--GT--A--TATCTTTTCCAAGATCATTGATC---------------ACTGCGTGATCA s droPse3.chr3 1362226 82 - 19787792 -----------------------------------------------CAT-TAATG--AAATCGAATCAAGTTAGGGATCTACCGTCC--AC--A--GCACAGC-TGTGCCTCCTCGATC--------GGCAGGCAGCATTCGATCA s droPer1.super_34 551097 83 - 916997 -----------------------------------------------CAT-TAATG--AAATCGAATCAAGTTAGGGATCTACCGTCC--AC--A--GCACAGC-TGTGCCTCGGCGGGC-------AGGCAGGCAGCATTCGATCA s droMir2.chr3 1403314 90 - 20862834 -----------------------------------------------CAT-TAAGG--AAATCGAATCAAGTTAGGGATCTACCGTCC--AC--A--GCACAGC-TGTGCCTCCTCGAtcggcgggcaggcaggcagcattcGATCA a score=327479.000000 s dm6.chr2R 24369521 50 + 25286936 AGTC-------TCAAG-TATTCAAGTCACCATCTTGCTATGT---GTCCATACA-ATTTTCT s droSim1.chr2R 18708194 50 + 19596830 AGTC-------TCAAG-TATTCAAGTCACCATCTTGCGATGT---GTCCGTACA-ATTTTCT s droSec1.super_23 127507 50 + 989336 AGTC-------TCAAG-TATTCAAGTCACCATCTTGCGATGT---GTCCGTACA-ATTTTCT s droYak3.chr2R 20217441 55 + 21139217 GGTCTCAG--GTCAGG-TATTCAAGTCACCATCTTCCGATGT---GTCCGTACG-ATTTTCT s droEre2.scaffold_4845 21615119 50 + 22589142 GGTC-------TCAAG-TATTCAAGTCACCATCGTTCGACGT---GTCCGTACA-ATTTTCT s droBia2.KB462602 809421 50 + 3129309 TAAC-------TCAAG-TACTCAAGTCACCATCTTGCAATGt---tcttgtatt-attttct s droSuz1.KI419649 12055673 51 - 14502029 TGAC-------TCAAG-TATTCATGTCACCATCTTGTAATgt---tcttttattaattttct s droAna3.scaffold_13266 5720261 51 - 19884421 CCTC-------TTTGGAGTTTCAAGTCACCATCTTTTAAGTT---CTTTAATCA-ATTTTCT s droBip2.KB464407 1970224 54 + 2915140 CTCC-------TCAGGATTTTCAAGTCACCATCttcaaagttttctttttgtaa-attttct s droEug2.KB465067 612427 51 + 1515531 AGTC-------TCCAG-TATTCAAGTCACCATCTTTCAATGT---TCTTGTACTAATTTTCT s droEle2.KB458573 535771 46 - 5320397 AGTC-------TCAAG-TATTCAAGTCACCATCTTTCAATGT---TCtcg-----atttaat s droKik2.KB459527 289107 51 - 1234237 GATC-------TTATG-TATTCAAGTCACCATCTTTCAGTGT---tctcttattaattttct s droTak2.KB461535 154393 51 - 669855 GGAC-------TCAAG-TACTCAAGTCACCATCTTTCAATGT---TCTCGTATTAATTTTCT s droRho2.KB449310 50298 51 - 65043 AGTC-------TCAAG-TATTCAAGTCACCATCTTTCAATGT---TCTCGAATTAATTTTCT s droFic2.KB457177 92628 51 + 995874 AGTC-------TCGGG-TAATCAAGTCACCATCTTTCAATGT---TCTCGAACTAATTTTCT s droPse3.chr3 1362308 58 - 19787792 AGTCGTAGCTCTTAAG-CATTCAAGTCACCATCTTTCAATGT---actgtaattaattttct s droPer1.super_34 551180 58 - 916997 AGTCGTAGCTCTTAAG-CATTCAAGTCACCATCTTTCAATGT---ACTGTAATTAATTTTCT s droMir2.chr3 1403404 58 - 20862834 TGTCGTAGCTCTTAAG-CATTCAAGTCACCATCTTTCAATGT---actgtaattaattttct s droVir3.scaffold_12875 7368024 45 + 20611582 AGGC-------TTAAG-TCTTAGAG------ATTTATTATTT---GTACACAGCAACTTTAT a score=174041.000000 s dm6.chr2R 24369571 11 + 25286936 T----------CACACACTTT s droSim1.chr2R 18708244 11 + 19596830 T----------CACACACTTT s droSec1.super_23 127557 11 + 989336 T----------CACACACTTT s droYak3.chr2R 20217496 11 + 21139217 T----------CACACACTTT s droEre2.scaffold_4845 21615169 11 + 22589142 T----------CACACACTTT s droBia2.KB462602 809471 11 + 3129309 t----------caCACACTTT s droSuz1.KI419649 12055724 11 - 14502029 t----------cacacacttt s droAna3.scaffold_13266 5720312 11 - 19884421 T----------CACACACTTT s droBip2.KB464407 1970278 11 + 2915140 t----------cacacacttt s droEug2.KB465067 612478 11 + 1515531 T----------CACACACTTT s droEle2.KB458573 535817 21 - 5320397 taatattaatacacACACTTT s droKik2.KB459527 289158 11 - 1234237 t----------cacACACTTT s droTak2.KB461535 154444 11 - 669855 T----------CACACACTTt s droRho2.KB449310 50349 11 - 65043 T----------CACACACTTT s droFic2.KB457177 92679 11 + 995874 T----------CACACACTTT s droPse3.chr3 1362366 11 - 19787792 t----------caCACACTTT s droPer1.super_34 551238 11 - 916997 T----------CACACACTTT s droMir2.chr3 1403462 11 - 20862834 t----------caCACACTTT s droVir3.scaffold_12875 7368080 11 + 20611582 T----------CACACACTTG s droMoj3.scaffold_6496 26163429 11 + 26866924 T----------CACACACTCG a score=-27075.000000 s dm6.chr2R 24369582 7 + 25286936 C------CAG-CCA- s droSim1.chr2R 18708255 7 + 19596830 C------CAG-TCA- s droSec1.super_23 127568 7 + 989336 C------CAG-TCA- s droYak3.chr2R 20217507 13 + 21139217 CCAGTTTCAG-TTC- s droEre2.scaffold_4845 21615180 7 + 22589142 C------CAG-TTC- s droBia2.KB462602 809482 8 + 3129309 CC-----CAG-TTT- s droSuz1.KI419649 12055735 9 - 14502029 cc-----cagtttt- s droAna3.scaffold_13266 5720323 8 - 19884421 -----TCCAG-TAC- s droEug2.KB465067 612489 8 + 1515531 -----CCCAG-TTT- s droEle2.KB458573 535838 8 - 5320397 -----CCCAG-TTC- s droKik2.KB459527 289171 7 - 1234237 ------CCAG-TTC- s droTak2.KB461535 154455 8 - 669855 -----cccag-ttt- s droRho2.KB449310 50360 8 - 65043 -----CCCAG-TTC- s droFic2.KB457177 92691 7 + 995874 ------CTAG-TTC- s droPse3.chr3 1362377 7 - 19787792 ------CCAG-CTC- s droPer1.super_34 551249 7 - 916997 ------CCAG-CTC- s droMir2.chr3 1403473 7 - 20862834 ------CCAG-CTC- s droVir3.scaffold_12875 7368091 7 + 20611582 -------CCG-TACA s droMoj3.scaffold_6496 26163440 7 + 26866924 -------CCG-GGCA a score=86311.000000 s dm6.chr2R 24369589 21 + 25286936 TC-----------ACTGATTGAC--CACACTGTT s droSim1.chr2R 18708262 21 + 19596830 TC-----------ACTGATTGAT--CACACTGTT s droSec1.super_23 127575 21 + 989336 TC-----------ACTGATTGAT--CTCACTGTT s droYak3.chr2R 20217520 21 + 21139217 TC-----------ACTGATTGAT--CACACTGTT s droEre2.scaffold_4845 21615187 21 + 22589142 TT-----------ACTGATTGAT--CACACTGTT s droBia2.KB462602 809490 22 + 3129309 TC----------TTTTGATTGAT--CGCACTTTT s droSuz1.KI419649 12055744 23 - 14502029 tc----------ttttgattgat-ccacactttt s droAna3.scaffold_13266 5720331 21 - 19884421 TT-------------TGAATATTTCTGAACTTTT s droEug2.KB465067 612497 21 + 1515531 CT-----------TTTGATTGAT--CACACTTTT s droEle2.KB458573 535846 21 - 5320397 TT-----------ATTGATTGAT--CACACATTT s droKik2.KB459527 289178 21 - 1234237 TT-----------GGCGATTGAT--CACACTTTT s droTak2.KB461535 154463 27 - 669855 tttttt-----cttttgattgAT--CACACTTTT s droRho2.KB449310 50368 23 - 65043 TT---------TTTCTGATCGAT--CACACTTTT s droFic2.KB457177 92698 21 + 995874 TC-----------GCTGATCGAT--TACACTTTT s droPse3.chr3 1362384 32 - 19787792 TTTTCTGTCTGTTCTTGTTCGGT--CACACTTTT s droPer1.super_34 551256 32 - 916997 TTTTCTGTCTGTTCTTGTTCGGT--CACACTTTT s droMir2.chr3 1403480 32 - 20862834 TTTTCTGTCTGTTCTTGTTTGGT--CACACTTTT s droWil2.CH963894 1328415 19 + 2843958 -------------TCACTTTAAA--TGAACATTT s droVir3.scaffold_12875 7368098 18 + 20611582 ------------TTTTGATCGGC----CACTTTT s droMoj3.scaffold_6496 26163447 18 + 26866924 ------------CTTCGGTCGGT----CACTTTT a score=2854209.000000 s dm6.chr2R 24369610 488 + 25286936 CACGTATTT----C------AATC-----------ACTG----------------------A-----------------------AGCA-AGAAGCC--------GAGGA---------------------------TC--GT----TCCTCGT---TCGTCGTGCAGGTC------ACGCAGTTGCTCACAGACTGAAAACGTAACCCCAGCGGTCGCACCTCTTGAG-TC--------------TCGAG-CC------------GG---AGAAACCCGA-G---GAGAAACCCGTTTGGAGGGG--------------CTTAAGAG------CA-----C--GAT-CC-GCACTGAAGG----CG----ATGGG--G---ATGGGTGCGATAGGGAGGC-----G-------C--TATACGTTCGATCCGCTTG---CACCTTC---GAG------------CCGCT-CTCTT------C---GG-TACTCTCTTAAG--CC-------GGCTCTCTCTC-----------GCTGCCTATT----------AGGCA--CAGGCACCC----------------------------------------------ATAT--------TCCATATTCCACATAGGAGGACTATG----TATGTAGC--GA--TGATCTGTGGGCGGGACTTGT-----------------------GGCT-------G-----------------------------CT--------------------------------------------------CGTG-----TGCGTATTAGATTTTAT-----------AGACCCGC-------------TTGC-GACTT-------GCTCGC-CAAGTCCA-TTTTGGGCCGGGC-CTATGTAC-ATTGGC--T------GCGT---GGG-------GACGG--------------------------------ATGGGCAAACAA--------------A------TGAGTGG----------------TCCCCGGT-- s droSim1.chr2R 18708283 483 + 19596830 CACGTCTTT----C------AATT-----------ACTG----------------------A-----------------------AGCA-AGAAGCC--------GAGGA---------------------------TC--GC----TCCTCGT---TCGTCGTGCGGGTC------ACGCAGTTGCTCACAGACTGAAAACGTAACCCCAGCGGTCGCAACTCTTGAG-TC--------------CCGAG-CC------------GG---AGAAACCCGA-G---GAGAAACCCGTTTGGAGGGG--------------CTTAAGAG------CA-----C--GAT-CC-GCACTGAAGG----CG----ATGGG--G---ATGGGTGCGATAGGGAGGC-----G-------C--TATACGGCCGATCCGCTTG---CACCTTC---GAG------------CCGCT-CTCTT------C---GG-GGCTCTCTTAAG--CC-------GGCGCTCTCTC-----------GCTGCCTATT----------AGGCA--CAGGCACCC----------------------------------------------ATAT--------TCCATATTCCACATAG-----TCCTC----CATGTAGC--GC--CGATCTGTGGGCGGGACTTGT-----------------------GGCT-------G-----------------------------CT--------------------------------------------------CGTG-----TGCGTATTAGATTTTAT-----------AGACCCGC-------------TTGC-GACTT-------GCTCGC-CAAGTCCA-TTTTGGGCCGGGC-CTATGTAC-ATTGGC--T------GCGT---GGG-------GACAG--------------------------------ATGGGCAAACAA--------------A------TGAGTGG----------------TCCCCGGT-- s droSec1.super_23 127596 484 + 989336 CACGTCTTT----C------AATC-----------ACTG----------------------A-----------------------AGCA-AGAAGCC--------GAGGA---------------------------TC--GC----TCCTCGT---TCGTCGTGCAGGTC------ACGCAGTTGCTCACAGACTGAAAA-GTAACCCCAGCGGTCGCAACTCTTGAG-TC--------------CCGAG-CC------------GG---AGAAACCCGA-G---GAGAAACCCGTTTGGAGGGG--------------CTTAAGAG------CA-----C--GAT-CC-GCACTGAAGG----CG----ATGGG--G---ATGGGTGCGATAGGGAGGC-----G-------C--TATACGGCCGATCCGCTTG---CACCTTC---GAG------------CCGCT-CTCTT------C---GG-GGCTCTCTTAAG--CC-------GGCGCTCTCTC-----------GCTGCCTATT----------AGGCAGCGAGGCACCC----------------------------------------------ATAT--------TCCATATTCCACATAG-----TCCTC----CATGTAGC--GC--CGATCTGTGGGCGGGACTTGT-----------------------GGCT-------G-----------------------------CT--------------------------------------------------CGTG-----TGCGTATTAGATTTTAT-----------AGACCCGC-------------TTGC-GACTT-------GCTCGC-CAAGTCCA-TTTTGGGCCGGGC-CTATGTAC-ATTGGC--T------GCGT---GGG-------GACAG--------------------------------ATGGGCAAACAA--------------A------TGAGTGG----------------TCCCCGGT-- s droYak3.chr2R 20217541 491 + 21139217 CACGTCTTT----C------AATC-----------ACTG----------------------AAGTCCAGAATGCCAGTAGCCAGAAGCC-AGAAGCC--------GAGGA---------------------------TC--GC----TCCTCGA---TCGTCGTGCAGGTC------ACGCAGTTGCTCACAGACTGAAAACGGAACCCCGGCGATCGGAGCTCTTGAG-TC--------------CCGAG-CC------------GG---AGAAACCCGA-G---GAGAAACCCGTTTGGAGGGG--------------CTTAAGAGCAGCACTG-----C--GAT-CC-GCACTGGAGG-----------------A---ACGGGTGCGACAGGGAGGC--------------------------------------CACCTTT---CAG------------CCGCT-CTCTT------T---CG-GTCTCTCTTAAG--CC--------------------------------GCCTATT----------AGGCA--------CCT----------------------------------------------ATAC--------CTTATAT-----ACAG-----TACTC----CATGTAGC--CC--CGAGATGTGGGCGGGACTTGT-----------------------GGCC-------G-----------------------------CT--------------------------------------------------CGTG-----TGCGTATTAGATTTTAT-----------AGACCCGC-------------TTGT-GACTC-------GCTCAC-CAATTCCA-TCTTGGGCCTGGT-CTATGTAC-ATTGGC--T------GCGT---GGg-------gacacatggacacatggacagatggacagatggGTAGATGGGCACACAA--------------A------TGAGTGG----------------TCCCCGGT-- s droEre2.scaffold_4845 21615208 489 + 22589142 CACGTCTTT----C------AGTC-----------ACTG----------------------A----------------AGCCAGAAGCA-GAAAGCC--------GAGGA---------------------------TC--GC----TCCCCGA---TCGTCGTGCAGGTC------ACGCAGCTGCTCACAGACTG-AAACGTAACCCCAGCGGTCGGGACTCTTGAG-TCGCAACTCTTGAGTGCCGAG-CC------------GG---AGAAACCCGA-G---GAGAAACCCGTTTGGCGGGG--------------CTTAAGAG------TA-----C--GAT-CC-GCACTGGCGGGAGTCG----GTGGGTCG---ATGGGTGCGATAGGGAGGC-----C-------A--TGTGCGGCCGATCCGCTTG---CACCTTC---GGG------------CCGCT-CTCTT------C---GA-GCCTCTCTTAAG--CC--------------------------------GCCTGTT----------AGGCA--------GCT----------------------------------------------ATAT--------CTCATAT-------AG-----TCCTC----CCTGGAGC--GC--CGATCTGTGGGCGGGACTTGT-----------------------GGCC-------G-----------------------------CT--------------------------------------------------CGTG-----TGCGTATTAGATTTTAT-----------AGACCCGC-------------TTGT-GACTT-------GCTCAG-CAATTCCA-TTTTGGGCCGGGC-CTATGTAC-ATTGGC--T------GCGT---GGG-------GACAGATGGGCA-------------------------ATGGGCAAGCAA--------------A------TGAGTGG----------------TCCCCGGT-- s droBia2.KB462602 809512 447 + 3129309 CACGTCTTT----C------AATC-----------GCTC----------------------A-----------------------AGCA-AAGAGCC---------AAGA---------------------------TC--GC----TCCTCGA---TCGTCGTGCAGGTC------ACGCAGTTGCTCACAGACTGAAAACGTAGACCCAGCGGTGGAAACTCTTGAG-TC--------------TCGAG-CTGGAGAAACCTGGGG---AGAAACCTGA-G---AAGAAACCCGTTTTGAGGAG-A------------CTTAAGAG------TG-----C--GAT-CG----------------------------------------------GAGGC-----T-------A--TGTACTGGCGATCCGCTTG---CACCCTG---GAG------------CCGCA-CTCTT------C----G-GGCTCTCTTAAG--CG--------CGACTCTC-C-----------GGGTTTCATT----------AGgca--------ctt----------------------------------------------atat--------tttatac-------ag-----tCCTC----CACATAGC--GG--CGGCCTGTGGGCGGGACTTGC-----------------------GGCT-------G-----------------------------CT--------------------------------------------------CGTG-----TGCGTATTAGATTTTAT-----------AGACTCGC-------------CTGT-GACTT-------GCTCAC-CAATTCCA-TTTTGGGCCGGGC-CTATATAC-ATTGGC--T------GCGT---GGG-------GACAA--------------------------------ATGGGCAAACAA--------------A------TGAGTGG----------------TCCCCGGT-- s droSuz1.KI419649 12055767 467 - 14502029 cacGTCTTT----C------AATC-----------GCTC----------------------A-----------------------AGCAGAAGAGCC--------AAAGA---------------------------TC--GC----TCCTCGA---TCGTCGTGCAGGTC------ACGCAGTTACTCACAGACTGAAAACGTAACCCTAGCGGTCGGGACTCTTGAG-TC--------------TTGAG-TT------------GG---AGAAAACTGA-G---AAGAAACCCGTTCTGTGGGG-A------------CTTAAGAG------TA-----C--GAT-CG-GAACTTGAGG----C------------G---ATAGGTGCGATAGAGAGGC-----T-------A--CATACAGCCGATCCGCTTG---CACCTTT---GAG------------CCGCA-CTCTT------C---GG-GGTTCTCTTAAG--CC--------CGACTCTCTC-----------GGGTTTTATT----------AGGca--------ctt----------------------------------------------atat--------tttatat-------ag-----tcGTC----CATATAGC--GG--CGATCTGTGGGCGGGACTTGC----------------------TGGCT-------G-----------------------------CT--------------------------------------------------CGTG-----TGCGTATTAGATTTTAT-----------AGACTCGC-------------TTTT-GACTT-------GCTCAC-CAATTCCA-TTTTGGGCCGGGCTCTATATAC-ATTGGC--T------GCGT---GGG-------GACAA--------------------------------ATGAGCAAACAA--------------A------TGAGTGG----------------TCCCCGGT-- s droAna3.scaffold_13266 5720352 495 - 19884421 CACGTCTTT----C-----GAAAT-----------GCCG----------------------A-----------------------AGCA-AAAATCA--------AAAGA---------------------------CCCAGC----TCCTCGA---TCGTCGCTA----C------TCAAAGTTACTCACAGACTGAAAACGAATCCGTCGGATACGCAACTCTTGAG-TC----------------GGA-AC------------TG---AGAGACCCGA-G---GAGAAACCCGTTTTGGGGCA-A------------CTTAAGAG------AA-----C--GAT-CC-CGACTTGAGG-----------------AGCCCTGAGCCCGAACGAAAAGA-----T-------A--TATAGTGCCAGTCCAGTCC---CACCCAT---AGG------------CCGCTGCTCTTGCCACAT---GG-GGCTCTCTTAAG--CC--------CGACTCCCGC-----------CGATTTGATT----------AGGCA--------CTT----------------------------------------------ATAT--------TTTATAT-------AG-----TCGTTCCTACATAAAGCTAGC--CGACCTGTGGGCGGGACTTGC----------------------GGGCTGCTC---G-----------------------------CT--------------------------------------------------CGTG-----TGCGTATTAGATTTTAT-----------AGACTCACTGAGTCTTGAGAGCTGA-AACTT-------GCTCAG-CAATTCCA-TTTTGGGCCGGGCTTTATATAC-ATTGGC--T------GCGT---GGG-------GACAA--------------------------------ATGGGCAAACAA--------------A------TGAGTGG----------------TCCCAGTC-- s droBip2.KB464407 1970321 464 + 2915140 cACGCCTTT----C-----AAAAT-----------GCCG----------------------a-----------------------agca-aaaatca--------aaaga---------------------------cttaGC----TCCTCGA---TCGTCGCTA----C------TCAAAGATACTCACAGACTGAAAACGAATCCGTCGGATGCGCAACTCCTGAG-TC----------------GGC-TG------------TG---AGAGACCCGA-G---GAGAAACCAGTTTTGAGGCA-A------------CTTAAGAG------AA-----C--GATCCC-CGACTTGAGG-----------------G--------------------------------------------GCCAGTCCAGTCC---CACCCAT---AGG------------CCGGTGCTCTGGCCGT-T---GG-GACTCTCTTAAG--CC--------CGACTCCCGC-----------CGATTTGATT----------AGGca--------ctt----------------------------------------------atat--------tttatat-------ag-----tcGTCCATACATAAAGCTAGC--CGAGCTGTGGGCGGGACTTGC----------------------TGGCTGCTC---G-----------------------------CT--------------------------------------------------CGTG-----TGCGTATTAGATTTTAT-----------AGACTGGCAGCGTCTT--GAGTTGAGAGCCA-------GCTCAG-CAATTCCA-TTTTGGGCCGGGCTCTATATAC-ATTGGC--T------GCGT---GGG-------GACAA--------------------------------ATGGGCAAACAA--------------A------TGAGTGG----------------TCCCAGTC-- s droEug2.KB465067 612518 465 + 1515531 CACGTCTTT----C------AATC-----------GCTC----------------------A-----------------------AGAAAAGAAGCC--------AAAGA---------------------------TC--GC----TCCTCGA---TCGTCGTGCAGGTC------ACGCAGTCGCTCACAGACTGAAGACGTAACCCCAGCGGTCGAAACTCTTGAG-TC--------------CCG---CT------------GG---AGAAACCTGA-G---AAGAAACCCGTTTGGCGCGG-A------------CTTAAGAG------CA-----C--GCT-TG-CCCCTTGAGG----T------------G---GTGAGTGCGACAGAGAGGA-----T-------G--TATGCAGCCGATCCGCTCG---CACCTTA---GAG------------CTGCA-CTCTT------C---GG-CGTTCTCTTAAGGTCT--------TCACTCTCCC-----------GGGTTTTATT----------AGGca--------ctt----------------------------------------------atat--------tttatat-------ag-----tcGTC----CATATAGC---C--CGATCTGTGGGCGGGACTTGC----------------------TGGCC-------G-----------------------------CT--------------------------------------------------CGTG-----TGCGTATTAGATTTTAT-----------AGACTCGC-------------TTTT-GACTT-------GCTCAC-CAATTCCA-TTTTGGGCCGGGC-TTATATAC-ATTGGC--T------GCGT---GGG-------GACAA--------------------------------ATGAGCAAACAA--------------A------TGAGTGG----------------TCCCCGGT-- s droEle2.KB458573 535867 499 - 5320397 CACGTCTTT----CCATCGCAACC-----------ATCG----------------------A-----------------------GGCAAAAAAGCT--------GAAGA---------------------------TC--GC----TCCTCGA---TCGTCGTGCAGGTC------ACGCAGTTGCTCACAGACTGAAAACGTAGCCCCAGCGATCGCAACTCTTGAG-TT--------------CCG---CT------------GG---AGAAACCTGA-G---AAGAAACCCGTTTGCGGAGA--------------CTTAAGAG------TG-----C--GAT-CG-GCACTTGAGG----C------------G---ACTAGTGCGACAGggaagcaaatat-------a--tataaaaccgATCCGTTTGCACCACCATT---GAT------------CCACA-CTCTT------CAAAGC-GGTTCTCTTAAG--CC--------GCACTCTCTC-----------GGGTTTTATT----------AGgca--------ctt----------------------------------------------atat--------tttatat--actatGG-----TCCTC----CATATAGC--GA--CGATCTGTGGGCGGGACTTAC----------------------TGTTTGCTCGATG-----------------------------CT--------------------------------------------------CGTG-----TGCGTATTAGATTTTAT-----------AGACTCGC-------------TTTT-GACTT-------GCTCAG-CAATTCCA-TTTTGGGCCGGGCTTTATATAC-ATTGGC--T------GCGT---GGG-------gacaa--------------------------------ataagcaaacaa--------------atgaGTGTGAGTGG----------------TCCCCGGT-- s droKik2.KB459527 289202 495 - 1234237 CACGTCTTT----C------AATC-----------ACTG----------------------A-----------------------GGC--AAAAGCT--------AA--A---------------------------TC--GC----TCCTCGA---TCGTCGTGCAGGTC------ACGCAGTTGCTCACAGACTGAAACCGTGTCTCTGGCTGTTGCAACTCTTGAG-TG----------------GCG-CT------------GG---AGAAACCCGA-G---AAGAAACCAGTTTGGAGGAG-A------------CTTAAGAG------CA-----A--GAC-CCGGCACTGGGAA----C------------G---ATGAGTGCGAGGGAGAAGC-----T-------GATCGCACAACCTATCCACTCG---CACTTAT---TGT------------TGGGAACTCTT------T---AA-AGTTCTCTTAAG--CC--------CgactctcgctctctctcggGGCTTTTCATT----------AGGca--------ctt----------------------------------------------atat--------tttatat-------ag-----tcgTTCA--TATATAGC--CA--CGATCTGTGGGCGGGACTTGCAG-------------------CGGGTC-------G-----------------------------CT--------------------------------------------------CGTG-----TGCGTATTAGATTTTAT-----------AGACTCGC-------------TCGC-GACTCGCGGCTGGCTCAC-CAATTCCA-TTTTGGGCCGGGCCTTATATAC-CTGGGC--T------GCGT---GGG-------GACAT-TGGACAA------------------------ATGGGCAAACAA--------------A------TGAGTGG----------------TTCCAGGC-- s droTak2.KB461535 154490 465 - 669855 CACGTCTTT----C------AATC-----------GGCC----------------------A-----------------------AGCAAAAGAGCC--------AAAGA---------------------------TC--GC----TCCTCGA---TCGTCGTGCAGGTC------ACGCAGTTGCTCACAGACTGAAAACGTAGCCCCAGCGGTCGAAACTCTTGAG-TC-------------TTCGAG-CC------------GG---AGAATCTGGA-G---AAGAAACCCGTTTTGAGGAG-A------------CTTAAGAG------TA-----C--GAT-CG-CGACTTGAGG----T------------G---ATAAGTGCGACAGAAAGGC-----T-------A--TATACAGCCGATCCGCTTG---CACCTTT---GAG------------CCGCA-CTCTT------C---GG-AGCTCTCTTAAG--TC--------GCACACTCTC-----------GTGTTTTATT----------AGGCA--------CCT----------------------------------------------ATAT--------TGTACAT-------AG-----TCGTC----CATATAGC--GA--CGATCTGTGGGCGGGACTTGC----------------------TGGCT-------G-----------------------------CT--------------------------------------------------CGTG-----TGCGTATTAGATTTTAT-----------AGACTCGC-------------TTTT-GACTT-------GCTCAC-CAATTCCA-TTTTGGGCCGGGCTCTATATAC-ATTGGC--T------GCGT---GGG-------GACAA--------------------------------ATGAGCAAACAA--------------A------TGAGTGG----------------TCCc---t-- s droRho2.KB449310 50391 493 - 65043 CACGTCTTT----C------AATT-----------GGCC----------------------A-----------------------AGCAAAAAAGCC--------AAAGA---------------------------TC--GC----TCCTCGA---TCGTCGTGCAGGTC------ACGCAGTTACTCACAGACTGAAAACGTAAGCCCAGCGGTCGGAACTCTTGAG-TC----------------CAG-CT------------GG---AGAAACCTGA-G---AAGAAACCCGTTTCAAAGGGGA------------CTTAAGAG------AA-----CGAGAT-CG-GTACCTGGGG----C------------G---ATAAGTGCGACAGGGAGGC-----A-------GAATGTGCAGCCGATCCGCTTG---CACCTTCTTGGGG------------CCTTA-CTCTTATCACAG---TC-GGCTCTCTTAAG--CC--------CGACTCTCTCTCTC-------GGGTTTTATT----------AGGca--------ctt----------------------------------------------atat--------tttatat-------ag-----taCTC----CATATAGC--GA--CGATCTGTGGGCGGGACTTGCTGGC-----------------TTGGCC-------G-----------------------------CT--------------------------------------------------CGTG-----TGCGTATTAGATTTTAT-----------AGACTCGC-------------TTTT-GACTT-------GCTCAC-CAATTCCA-TTTTGGGCCGGGC-TTATATAC-ATTGGC--CACATTGGCGT---GGG-------GACAA--------------------------------ATGAGCAAACAA--------------A------TGAGTGG----------------TCCCCGGT-- s droFic2.KB457177 92719 461 + 995874 CACGTCTTT----C------AATC------------CCC----------------------A-----------------------AGAA-AAGAAAC--------ACAGA---------------------------TC--GC----TCCTCGA---TCGTCGTGCAGGTC------ACGCAATCGCTCACAGACTGAAAGCGAAGCCCCAGCTGTCGGAGCTCTTGGG-TC--------------CCG---CC------------GA---GGAAACCTGG-C---AAGGAACTCGTTTCGGGGAA--------------CTTAAGAG------TA-----A--GAT-CG-CCACTGGGGG----C------------G---ACGAGTGCGACAGAGAGGT-----T-------G--CATAGCTCCGATCCGCTCG---CACCTCA---GAG------------CTGCA-CTCTT------T---GG-CGCTCTCTTAAG--CC--------GCGCTCTCGC-----------AGGTTTTATT----------AGGca--------ctt----------------------------------------------atat--------t-tatat-------ag-----ccGAG----CATATAGC--GC--CGATCTGTGGGCGGGACTTGC----------------------TGGCC-------G-----------------------------CT--------------------------------------------------CGTG-----TGCGTATTAGATTTTAT-----------AGACTCGC-------------TTTT-GACTT-------GCTCAC-CAATTCCA-TTTTGGGCCGGGCTTTATATAC-ATTGGC--T------GCGT---GGG-------gacaa--------------------------------ataagcaaacaa--------------a------tgagTGG----------------TCCCCGGT-- s droPse3.chr3 1362416 593 - 19787792 CACGTCTTC----C------GATCGTTCTGCAACGGCCG----------------------A-----------------------AG---GAAAGCC--------GAAGAAGATCGATCCCATCCAGCAGCGGTCGTGC--GA----TCCTCGA---TCGTCGTGCAGGTCACGCAGACGCAGTTACTCAAAGACTGAAAACGTAGCTGCATCGCATGGGTCTCTTGAG-TC--------------GCTGC-TC------------GGGC-AGAAACCTGA-G---TAGAAACTCGTTTGTGGGGC-GACATTT-----TCTTAAGAG------AA-----C--ACC-CG-CCACTGGGGA----C------------T---GTGAGT------GAGAGGG-----A-------G--CAAACAGATATCTTACATT---CCCTCCA---AAG------------C-----TCTTT------T---GG-Ggctctcttaag--cccagctctgacactctctc-----------gcgcgctctcgcgctctcgtgcgct--------cgt--gctctccctctctctctct------ggggttTCATTAGGCAGttatat--------tttatgt--------g-----tg-------tatatagg-AGA--CGACCTGTGGGCGGGACTTGT-----------------------GCCG-------GTGCG-----------------------ATCG--------------------------------------------------TGTG-----TGCGTATTAGATATTATAGACACACTGCAGACTCGC-------------CTGT-GACTT-------GCTCAG-CAATGCCA-TTTTGGGCCGGGCTCTATATAC-ATTGGC--T------GCGT--GGGG-------GACAA--------------------------------ATGAGCAAACAA--------------A------TGAGCGGcaatttatgtgtgttttctcCGAA-- s droPer1.super_34 551288 591 - 916997 CACGTCTTC----C------GATCGTTCTGCAGCGGCCG----------------------A-----------------------AG---GAAAGCC--------GAAGAAGATCGATCCCATCCAGCAGCGGTCGTGC--GA----TCCTCGA---TCGTCGTGCAGGTCACGCAGACGCAGTTACTCAAAGACTGAAAACGTAGCTGCATCGCATGGGTCTCTTGAG-TC--------------GCTGC-TC------------GGGC-AGAAACCTGA-G---TAGAAACTCGTTTGTGGGGC-GACATTT-----TCTTAAGAG------AA-----C--ACC-CG-CCACTGGGGA----C------------T---GTGAGT------GAGAGGG-----A-------G--CAAACAGATATCTTGCATT---CCCTCCA---AAG------------C-----TCTTT------T---GG-GGCTCTCTTAAG--CCCAGCTCTGACACTCTCTC-----------GCGCGCTCTC----------GCGCT--------CTCGTGCGCTCGTGCTCTCCCTCTCTCTCTGGGGTTTTATTAGGCAGTTATAT--------TTTATGT--------G-----TG-------TATATAGG-AGA--CGACCTGTGGGCGGGACTTGT-----------------------GCCG-------GTGCG-----------------------ATCG--------------------------------------------------TGTG-----TGCGTATTAGATATTATAGACACACTGCAGACTCGC-------------CTGT-GACTT-------GCTCAG-CAATGCCA-TTTTGGGCCGGGCTCTATATAC-ATTGGC--T------GCGT--GGGG-------GACAA--------------------------------ATGAGCAAACAA--------------A------TGAGCGGCAATTTATGTGTGTTTTCTCCGAT-- s droMir2.chr3 1403512 591 - 20862834 CACGTCTTC----C------GATCGTTCTGCAGCGGCCG----------------------A-----------------------AG---GAAAGCC--------GAAGAAGATCGATCCCATCCAGAAGCGGTCGTGC--GA----TCCTCGA---TCGTCGTGCAGGTCACGCAGACGCAGTTACTCAAAGACTGAAAACGTAGCTGCATCGCATGGGTCTCTTGAG-TC--------------GCTGC-TC------------GGGC-AGAAACCTGA-G---GAGAAACTCGTTTGTGGGGC-GACATTT-----TCTTAAGAG------AA-----C--GCC-CG-CCACTGGGGA----C------------T---GTGAGT------GAGAGGG-----A-------G--CAAACAGATATCTTGCATT---CCCTCCA---AAG------------C-----TCTTT------T---GG-Ggctctcttaag--cccagctctgacactctctc-----------gcgcgctctc----------gcgct--------ctcgtgcgctcgtgctctccctctctctctggggttTCATTAGGCagttatat--------tttatgt--------g-----tg-------tatatagg-AGA--CGACCTGTGGGCGGGACTTGT-----------------------GCCC-------GTGCG-----------------------ATCG--------------------------------------------------TGTG-----TGCGTATTAGATATTATAGACACACTGCAGACTCGC-------------CTGT-GACTT-------GCTCAG-CAATGCCA-TTTTGGGCCGGGCTCTATATAC-ATTGGC--T------GCGT--GGGG-------GAcaa--------------------------------atgagcaaacaa--------------a------tgagcggcaatttatgtgtgttttctccgat-- s droWil2.CH963894 1328434 527 + 2843958 CACGTCTTTGTTGC------AATT-----------GCAC----------------------G-----------------------ATCGATTGAATC--------AATCG---------------------------AT--TC----TCCTCAA---TCGTCGTGCAGCTC------ACGCAGTTACTCACAGACTGAAAACGTGGCCAGAAAATCACCGACTCTTGAG-TC-------------CTCCAG-TT------------GGCTGAGAAGTCCAA-GTATGAGAAACTTGTTTGTTGCCA--------------CTTAAGAG------CAAAGATC--GCC-TG-GCAGTCAAGT----CAGGCcatgtgtct---gtatgtgtgagAGAGATAC-----T-------C--TCT--------TCTGTTTA---CAATTTA------------------------CTCTT------A---AA--------TTTGT--CT--------CCCTGCTCAC-----------CATTTTGATT--------AGAGAca--------ctt----------------------------------------------atat--------tttatat--------a-----cattt----tatatacC------TGAATTGTGGGCGTGACTTGGAGTCGACTTGACTTGAGTTggctggct-------ggatggctgAGTTACTAGTCGGGCTTGCAGTT--------------------------------------------------CGTGTGTGCTGCGTATTAGATTTTAT-----------AGACTCGC---------------------TT-------GCTCACACATTTCCA-TTTTGGGCCGTGGCTTATATACAATTGGC--TGAACT-GCGT--GGGG-------GACAA--------------------------------ATGAGCAAACAA--------------A------TGAGCGA----------------CAATTTAT-- s droVir3.scaffold_12875 7368116 533 + 20611582 AACGTCTTT----C----CCTATG-----------GCGTGCACTTAACTTCAGGCAC----G-----------------------ATCA---GCACG--------ATCGT---------------------------TC--GCTGATTCGTTGA---TCGTCGTGCGGCTC------ACGCAGCTGCTCACAGACTGAAAACGCAATCCGAGCCGTTGCGACTCTTGAGTCC--------------GTCCGCGT------------TT---CGATCTCTCTGA---GAAAAACTTGTTTCAAATGG-GTTCTGCACAATTTTTAAGAG------CA-----C--GAT-CG-TCAACTTGCC----TG-----------C---CTGTGTGGGAGTGCAATGG-----CGCATGTGG--TGCGCGTGCGCGCT-CTCT---CTCTTTC---TAGCATGTTTCAA-GCCACG-CTCTT------T---GCTTGCGCTCTTAAG--TT--------GAGTTTTTAT--------------------T----------AGGCA--------CTT----------------------------------------------CAGCG-------CTTATAT-------TG--------------TATATAGC--CA---CAGCTGTGGGCGTGACTTGT-----------------------GGCC-------G-----------------------------CT--------------------------------------------------GGTGTG---TGCGTATTAGATTTTAT-----------AGACTCGC-------------TTTT-GACTT-------GCTTA--CATGTCCA-TTTTGGGCCGGGCCTTATGTAC-ATTGGC--C------GTTT-GGGGGCTGACGCGACAA--------------------------------ATGAGCAAACAAATGAGCGCCAATTTA------TGAGTTT----------------TTTGCGAGTT s droMoj3.scaffold_6496 26163466 461 + 26866924 AACGTCTTT----C----GACATG-----------GGGC-------------TGCAC----G-----------------------ATCG---AGGCGGTGCGCTCGTCGT---------------------------TC--GCTGATTCGTCGA---TCGTCGTGCGACTT------ACGCAGCTGCTCACAGACTGAAGGCGCAATCCGAGTCGCTGCGACTCTCGAG-CC--------------GCGCTGAT------------TG---CGATCTCT---G---AGAAAACCCGTTTCTCGCAG-TCGCAGCTCAA-CTTTAAGAG--------------------------------C----TG-----------C---CTGTGTGGGAGTGCAATGG-----C-------G--TGctctctccctct-ctct---ctctctc---t--------------cccta-tctgt------c---tctctctctctcAGT--CC--------GCGCTCTTCG--------------------C----------TGACT--------CT-----------------------------------------------------------CTTA----------AG--------------TACATAGC--CA---GGGCTGTGGGCGTGACTTGC-----------------------AGCA-------G-----------------------------CT--------------------------------------------------TGTGGC---TGCGTATTAGATTTTAT-----------AGACTCGC-------------TTTT-GACTT-------GCTTA--CCTGTCCATTTTTGGGCCGGGCCTTATGTAC-ATTGGC--C------GTTC---GGGCTGGCGCGACAA--------------------------------ATGAGCAAACAA--------------A------TGAGTTT----------------CTTTCAAG-C s droGri2.scaffold_15245 918707 594 + 18325388 --------------------CACT-----------GTGC------ACTTTCAGGCACACGAG-----------------------ATCA-ATGCACG--------ATCGT---------------------------TC--GCTGATTCGTGGATTGTCGTCGTGCGACTC------ACGCAGTTGCTCACAGACTGAAAACGCAATCGCAGCTGCTGCAGCTCTCAAG-CC--------------ACAAT-GC------------GT---CGATCTCTGC-G---AGCAAACGAGTTTC-AACAT-ATTCTTTTCG--TTTTAAGAG------CA-----C---AT-TA-CCCATTTGAT----TG-----------C---GTGCGTGTGAGCGAGATGG-----TGCATATTG--TGCG-------------CT---CTCTCTC---TTGCGTGGCTCAATTTGGTG-CTCTT------T---GGCGGCGCTCTTAAG--TT--------GGGTTTTTGGTGCTTCTTCT-TCTTCATGTT----------AGGCA--------CTT----------------------------------------------ATCTGCTGTTGCTTTATATTGTGTGGAG--------------TAAATAGC--CAGTTGAGCTGTGGGCGTGACTTGT-----------------------GCCT-------G-----------------------------GTTGCTCGTTGCTGGTTGCGCTGTGTTGTTGgtgtgtgtgtgtatgtgtgtgtgtgtg---tgcgtATTAGATTTTAT-----------AGACTCGC-------------TTTT-GACTT-------GCTTA--CATGTCCA-TTTTGGGCCGGGCCTTATGTAC-ATTGGCCAC------GTTTGGGGGGCTGACGCGACAA--------------------------------ATGAGCAAACAAATGAGCGCCAATTTA------TGAGTTT----------------CTTTCCAG-T a score=-89589.000000 s dm6.chr2R 24370098 18 + 25286936 C-----------------GCAGCG-----------------G-------------------------GCATGAAAAT s droSim1.chr2R 18708766 18 + 19596830 C-----------------GCAGCG-----------------G-------------------------GCATGAAAAT s droSec1.super_23 128080 18 + 989336 C-----------------GCAGCG-----------------G-------------------------GCATGAAAAT s droYak3.chr2R 20218032 18 + 21139217 C-----------------GCAGCG-----------------G-------------------------Gcatgaaaat s droEre2.scaffold_4845 21615697 18 + 22589142 C-----------------GCAGCG-----------------G-------------------------GCATGAAAAT s droBia2.KB462602 809980 18 + 3129309 G-----------------GCCCTG-----------------G-------------------------Gcatgaaaat s droSuz1.KI419649 12056241 18 - 14502029 G-----------------GCCCTG-----------------G-------------------------Gcatgaaaat s droAna3.scaffold_13266 5720847 22 - 19884421 C-----------------TCCTCT-TC------------GCG-------------------------GCATGAAAAT s droBip2.KB464407 1970785 22 + 2915140 C-----------------TCCTCA-TC------------GCG-------------------------Gcatgaaaat s droEug2.KB465067 612983 18 + 1515531 C-----------------GCTCTG-----------------G-------------------------gcatgaaaat s droEle2.KB458573 536366 23 - 5320397 T-----------------GCTTTGGTC------------GGG-------------------------gcatgaaaat s droKik2.KB459527 289697 34 - 1234237 C-----------------TCTCGA-TCCCCTTTCCCGGGGCG-------------------------gcatgaaaat s droTak2.KB461535 154955 8 - 669855 ---------------------------------------------------------------------atgaaaat s droRho2.KB449310 50884 18 - 65043 T-----------------GCTCTG-----------------G-------------------------Gcatgaaaat s droFic2.KB457177 93180 18 + 995874 T-----------------GCCCGG-----------------G-------------------------gcatgaaaat s droPse3.chr3 1363009 48 - 19787792 CCGATCCGCtcggctctggctatg-----------------g------------ctatggctctgttGTATGAGAAT s droPer1.super_34 551879 54 - 916997 CCGATCCGCTCGGCTCTGGCTATG-----------------G------ATATGTCTCTGGCTCCGTTGTATGAGAAT s droMir2.chr3 1404103 60 - 20862834 ccgatccgctcggctctggctatg-----------------gctatggctatggctctggctccgttGTATGAGAAT s droVir3.scaffold_12875 7368649 28 + 20611582 -------------------------------------------------TGTTGTCTTTGTTGTTGCATATGAGCAT s droMoj3.scaffold_6496 26163927 28 + 26866924 -------------------------------------------------CGATGTTGTGGACGTCTGAGCTGAGTAT s droGri2.scaffold_15245 919301 22 + 18325388 -------------------------------------------------TGATGT------TGTTGCATATGAGCAT a score=1079122.000000 s dm6.chr2R 24370116 179 + 25286936 TCAATTTACACCAACCT--GCTACAAAA----TGACGTATCTCT---------------------------------GCATGT----ATTTAGTGGAATTTATTCA-----------------GCA----TATA---C----------------------TCGGATA--TCTGCGA-CG---------------------GGT-----------ACT----CCG-------------------------TTG---TTGGGTGTAACCAGTT---------------CTCG-------------AGC-----AA---AAA--------ATATGAAATCAGCGA---TCGAATATT----TCG--------TA--TTCCGCTTGTGGGCGTGGGCACG s droSim1.chr2R 18708784 179 + 19596830 TCAATTTACACCAACCT--GCTACAAAA----TGACGTATCTCT---------------------------------GCATGT----ATTTGCTGGAATTTATTCA-----------------GCA----TATA---C----------------------TCGGATA--TCTGCGG-CG---------------------GGT-----------ACT----TCG-------------------------TTG---TTGGGTGTAACCAGTT---------------CTCG-------------AGC-----AA---AAA--------ATATGAAATCAGCGA---TCGAATATT----TCG--------TA--TTCCGCTTGTGGGCGTGGGCACG s droSec1.super_23 128098 178 + 989336 TCAATTTACACCAACCT--GCTACAAAA----TGACGTATCTCT---------------------------------GCATGT----ATTTGCTGGAATTTATTCA-----------------GCA----TATA---C----------------------TCGGATA--TCTGCGG-CG---------------------GGT-----------ACT----TCG-------------------------TTG---TTGGGTGTAACCAGTT---------------CTCG-------------AGC------A---AAA--------ATATGAAATCAGCGA---TCGAATATT----TCG--------TA--TTCCGCTGGTGGGCGTGGGCACG s droYak3.chr2R 20218050 194 + 21139217 tcaatttacacCAACCT--GCTACAAAA----TGACGTATCTCT---------------------------------GCATGT----ATTTACTGCGATTTATTCACTACtatacat-atc-tata----tata---t----------------------atagata--tatgcaG-CG---------------------GGT-----------ACT----TCG-------------------------CTG---TTGGGTGTAACCAGTT---------------CTCG-------------AGC-----AA---CAA--------ATATGAAATCAGCGa---ttgaatatt----ttg--------ta--ttccgctggtgggcgtgggcaCG s droEre2.scaffold_4845 21615715 187 + 22589142 TCAATTTGCACCAACCT--GCTACAAAA----TGACGTATCTCT---------------------------------GCATGT----ATTTACTGGAATTTATTCA---------GT-ATA-CTCG----TACA---A----------------------GTAGATG--TATAAAGTCG---------------------GATGG---------ATA----TCG-------------------------TTG---TTGGGTGTAACCAGTT---------------CTCG-------------AGC-----AA----AA--------ATATGAAATCAGCGA---TTGAATATT----TTG--------TA--TTCCGCTTGTGGGCGTGGGCACG s droBia2.KB462602 809998 192 + 3129309 tcaatttacacCAACCT--GCTACAAAA----TGACGTATCTCT---------------------------------GCatgt----atttattgaaatttattca----------------atta----tata---C----------------------TGAGATA--TCTGCGG-CG---------------------GAT-----------ACT----TCGTTCTCCG-------------GCGATTTG---TTGGGTGTAACCAGTT---------------TTCG-------------CGT-----AA---GAA--------ATATGAAATCAGCGA---TTGAATATT----TCT--------TC--TTTGGCTTGTGGGCGTGGGCACA s droSuz1.KI419649 12056259 193 - 14502029 tcaatttacacCAACCT--GCTACAAAA----TGACGTATCTCT---------------------------------GCatgt----atttattgaaatttattca----------------atta----taTA---C----------------------AGAGATA--TCTGCAG-CG---------------------GAT-----------ACT----TCGTTCTCCA-------------GCGATTTG---TTGGGTGTAACCAGTT---------------Ttcg-------------ctt----aaa---aaa--------atatgaaatcagcga---ttgaatatt----ttt--------tc--tttcgcttgtgggcgtgggcaCA s droAna3.scaffold_13266 5720869 213 - 19884421 TCAATTTACACCAGCCC--GCTACAAAA----TGACGTATCTCTTTATATCTCTCCATAGTATACCCCCTATATGTAGTATAT----ATTTGATGAAATTTATTCA---------------------------------------------------------------------G-AC---------------------GTT----------------------------------------------TGG---TTGGGTGTAACCAGTTTATTTTTTTGCAAAATACAAAATAAAAAACACAAA-----AA---AAT--------GTATGAAATCAGCAA---TGGAAATAT----TTT--------AC--TTTCGGTTGTGGGCGTGGGCACG s droBip2.KB464407 1970807 181 + 2915140 tcaatttacacCAGCCC--GCTACAAAA----TGACGTATCTCTTTATATCTCTA-------------------GTAGTATAT----ATTTGATGAAATTTATTCA---------------------------------------------------------------------G-AC---------------------GTT----------------------------------------------TGG---TTGGGTGTAaccagtttgtttttttgcaaaaccca-------------gaa-----aa---aat--------gtatgaaatcagcaa---tggaaatat----ttt--------ac--tttCGGTTGTGGGCGTGGGCACg s droEug2.KB465067 613001 179 + 1515531 tcaatttacaccAACCT--GCTACAAAA----TGACGTATCTCT---------------------------------GCAtgt----atttattgaaatttattca----------------acta----tata---c-------------------------aata--tatatat-tc---------------------gat-----------cCC----CAG---------------------CGATTTG---TTGGGTGTAACCAGTT---------------CTCG-------------CGT----------AAA--------ATATGAAATCAGCGA---TTGAATATT----TCG--------TC--TTTGGCTGGTGGGCGTGGGCACG s droEle2.KB458573 536389 194 - 5320397 tcaatttacacCAACCT--GCTACAAAA----TGACGTATCTCT---------------------------------GCatgt----atttattgaaatttattca---------atcATATGGTA----TATA---T----------------------ACAGATA--TCTTCGT-TC---------------------CGT-----------TCT----CCA--------------------ACAATTTG---TTGGGTGTAACCAGTTTGGCg----------ctca---------------------aa---aaa--------atatgaaatcagcga---ttgaatatt----ttt--------tc--tttcgcttgtgggcgtgggcacg s droKik2.KB459527 289731 206 - 1234237 tcaatttacacCAACCT--GCTACAAAA----TGACGTATGTTTCGCTCTCTGTCT---------------------GTgtgt----atttattgaaatttattca----------------atCG----CAGAGATC----------------------CAAGTTA--TATATGT-TT---------------------CTT-----------TCG----CTG---------------------CGATTTG---TTGGGTGTAACCTGTt---------------tttg-------------cacacacaaa---aaa--------atatgaaatcagcga---ttgaatatt----ttt--------tcgatttgaactGTGGGCGTGGGCACG s droTak2.KB461535 154963 194 - 669855 tcaatttacacCAGCCT--GCTACAAAA----TGACGTATCTCT---------------------------------GCatgt----atttattgaaatttattca----------------atta----caTA---C----------------------AGAGATATCTCTGCAG-TG---------------------GAT-----------ATT----TCGTTTCGCA-------------GCGATTTG---TTGGGTGTAACCAGTT---------------TTCg-------------cgt-----aa---aaa--------atatgaaatcagcga---ttgaatatt----ttt--------tc--tttcgcttgTGGGCGTGGGCACG s droRho2.KB449310 50902 211 - 65043 tcaatttacacCAACCT--GCTACAAAA----TGACGTATCTCT---------------------------------GCatgt----atttattgaaatttattca----------------atta----tatA---C------------------------AGATA--CCTATAG-TG---------------------GAT-----------ATA----TCTTTCTCCGTTCCGTTCTCCATCAAATTTG---TTGGGTGTAACCAGTt---------------tttg-------------agc-----aa---aaaaaaataacatatgaAATCAGCga---ttgaatatt----ttt--------ca--ttttgcttGTGGGCGTGGGCACG s droFic2.KB457177 93198 201 + 995874 tcaatttacaccAGCCC--GCCACAAAA----TGACGTATCTCT---------------------------------GCATGT----ATTTATTGAAATGTATTCC----------------ATTA----TATA---C------------------------GGACA--GCTATAG-TG---------------------GATGTTCTTTCTCCGTT----CCGTTCTGCA-------------GCGATTTG---TTGGGTGTAACCAGTT---------------TTCG-------------CGT-----AA---GAA--------ATATGAAATCAGCGA---Ttgaatatt----tgt--------ta--tttcgcTGGTGGGCGTGGGCACG s droPse3.chr3 1363057 252 - 19787792 TCAATTGACACCAACCT--GCTACAAAA----TGACGTATCTCCCGC------------------------------ttatgt----atttattgaaatttattca----------------atta----tata---cgacttactatatacatatctatctagata--tgtatat-gtatatacatatatgtatgtatatgt-----------aca----ccc--------------------aacctttggctttgggtgtAACCAGTT---------------TTTA---GCACactcaaaaa-----aa---gaa--------atatgaaatcagcga---ttgaatatt----tttgttatttctc--CATCGATTGTGGGCGTGGGCACG s droPer1.super_34 551933 246 - 916997 TCAATTGACACCAACCT--GCTACAAAA----TGACGTATCTCCCGC------------------------------TTATGT----ATTTATTGAAATTTATTCA----------------ATTA----TATA---CGACTTACtatatacatatctatctagata--tatgtac-gt------atgtatgtacatatatgt-----------aca----CCC--------------------AACCTTTGGCTTTGGGTGTAACCAGTT---------------TTTA---GCACACTCAAAAA-----AA---GAA--------ATATGAAATCAGCGA---TTGAATATT----TTTGTTATTTCTC--CATCGATTGTGGGCGTGGGCACG s droMir2.chr3 1404163 242 - 20862834 CCAATTGACACCAACCT--GCTACAAAA----TGACGTATCTCCCGc------------------------------gtatgt----atttattgaaatttattca----------------atta----tata---cgactgactatatacatatctatctagata--tatgtac-at----------atatatgtatatgt-----------aca----ccc--------------------aacctttggctttgggtgtAACCAGTT---------------TTTA---GCACactcaaaaa-----aa---gaa--------atatgaaatcagcga---ttgaatatt----tttgttatttctc--cATCgattgtgggcgtgggcaCG s droWil2.CH963894 1328974 204 + 2843958 TCGACTTGCACACGTCTCAGTCataaagtttttgctttgcttttc--------------------------------gcttgg----ttttat--aaattaattca----------------atcAAACCTATATtcc----------------------acaaata--tatgtat-tt---------------------gcc-----------tGC----CTG-----------------------TTTGG---TTGGGTGTAACCAGTT---------------TTCT-------------CGA-----AATTCGCT--------ATATGAAATCAgcgaatttcaaattttagtcttt--------tt--gtttttttgtgggcGTGGGCACA s droVir3.scaffold_12875 7368677 150 + 20611582 TTAATTTACACGAATTT--GTTATAAGA----TCACGTCTGTAA---------------------------------ATATATACAGATTT-------------TG-------------------A----TTTC---A-------------------------GCTG--GGTGTAA-CC---------------------AGT-----------TTT----TCT---------------------TTATTTT---TT-TGTGAAAT---TT---------------GCCG-------------TGC-----AC---AAA--------ATATGAAATCAGCT----TTGA---------TTT--------TG-----------TGGGCGTGAGCACG s droMoj3.scaffold_6496 26163955 140 + 26866924 TT----------AATTT--GTTATAGGA----TCTCGTCTGTGT---------------------------------GTGTAT----ATTT-------------CA-------------------A----TTAG---C-------------------------GCTG--AGTCTAA-CC---------------------AGT-----------TTTATTGTTT---------------------TTGTTTT---TTATGTGAGAT---TG---------------G-CG-------------TGC-----AC---AAA--------ATATGAAATCAGCT----TTGA---------TTT--------TG-----------TGGGCGTGAACACG s droGri2.scaffold_15245 919323 139 + 18325388 TTAATTTACACGAATTT--GTTATAAGA----TCACGTATACAT---------------------------------ATATAT----ATAT----------------------------------A----TACA---C-------------------------GTTG--GGTGTAA-CC---------------------AGT-----------TTG-------------------------------GTTT---TT-TGTGAAAT---TT---------------GCCG-------------TGC-----AC---AAA--------ATATGAAATCAGCT----TCGA----T----TTT--------TG-----------TGGGCGTGAACACG a score=167620.000000 s dm6.chr2R 24370295 55 + 25286936 C-----T---------CCATTCC----------TATAGATGGTCTT------GGCTTTGTGTTTGA---------------------TCA---TTTTTGT--AAAATGACA s droSim1.chr2R 18708963 55 + 19596830 C-----T---------CCGTTCC----------TATCTATGGTCTT------GGCTTTGTGTTTGA---------------------TCA---TTTTTGT--AAAATGACA s droSec1.super_23 128276 55 + 989336 C-----T---------CCGTTCC----------TATCTATGGTCTT------GGCTTTGTGTTTGA---------------------TCA---TTTTTGT--AAAATGACA s droYak3.chr2R 20218244 76 + 21139217 C-----T---------CCGGTCC----------TATAGATGGtctt------ggctttgtttttgctcatttggtgctgattttttgtca---tttttgt--aaaATGACA s droEre2.scaffold_4845 21615902 55 + 22589142 C-----T---------CCGGTCC----------TATAGATGGTCTT------GGCTTTGCTTTTGT---------------------TCA---TTTTTGT--AAAATGACA s droBia2.KB462602 810190 54 + 3129309 C-----T---------CCGATCC----------TATAGATGG-GTT------TGCTTGGCGGTGgt---------------------tca---tttttgt--aaaatgacA s droSuz1.KI419649 12056452 55 - 14502029 C-----T---------CCGTTCC----------TATAGATGGTTTT------TGCTTAGCGTCTgt---------------------tca---tttttgt--aaaatgacA s droAna3.scaffold_13266 5721082 71 - 19884421 C-----T---------CCGATCCGATCGAATTTTATAGATGCCTTTCTGTCATGTGTTGGATTTGT---------------------TCA---TTTTTGT--AAAATGACA s droBip2.KB464407 1970988 76 + 2915140 ctccgat---------ccgatccgatcgcATCTTATAGATGTCTTTCTGTCATGTGTTCGATTTgt---------------------tca---tttttgt--aaaatgaca s droEug2.KB465067 613180 54 + 1515531 C-----T---------CCAATCC----------TATAGATGC-CTT------TGCCGTGcttttgt---------------------tcg---tttttgt--GAAATGAca s droEle2.KB458573 536583 35 - 5320397 c------------------------------------------ttt------tgct-----tttgt---------------------tcattttttttgt--aaaatgacA s droKik2.KB459527 289937 66 - 1234237 C-----TCCCCGATCGCCCATTC----------GATGGATGCTTTT------TGCTCAGCCTGTGT---------------------TCA---TTTTAGTCAGAAATGACa s droTak2.KB461535 155157 55 - 669855 C-----T---------CCAATAC----------TATAGATGGTTTT------TGCTTGggttttgt---------------------tca---tttttgt--gaaatgaca s droRho2.KB449310 51113 50 - 65043 C-----T---------CCGTACC----------TATAGAtggtttt------tgct-----tttgt---------------------tca---tttttgt--aaaatgacA s droFic2.KB457177 93399 55 + 995874 C-----T---------CCGATCC----------TATAGATggtttt------tgctttgcttttgt---------------------tcg---TTTTTCT--AAAATGACA s droPse3.chr3 1363309 34 - 19787792 C---------------GAGATCC----------AACAGAT---CTT------TG---------------------------------GGC---TTTTTGT--GAca----- s droPer1.super_34 552179 34 - 916997 C---------------GAGATCC----------AACAGAT---CTT------TG---------------------------------GGC---TTTTTGT--GACA----- s droMir2.chr3 1404405 34 - 20862834 C---------------GAGATTC----------AACAGAT---CTT------TG---------------------------------GGC---TTTTTGT--GACA----- s droWil2.CH963894 1329178 44 + 2843958 C-----G---------CAAGATC----------TGTTGTctttttt------tgc--------------------------------tca---tttttgt--AAAATGACA s droVir3.scaffold_12875 7368837 52 + 20611582 -----TT---------CAGTCTA----------TATATAT---TGT------ATTATTTTTTTTGC---------------------TCA---TTTTTGT--CGAATGACA s droGri2.scaffold_15245 919490 51 + 18325388 -----CT---------Ctttttt----------tatata----tat------atatatGTTTTTGT---------------------TCA---TTTTTGT--CGAATGACA a score=53580.000000 s dm6.chr2R 24370350 3 + 25286936 CAA s droSim1.chr2R 18709018 3 + 19596830 CAA s droSec1.super_23 128331 3 + 989336 CAA s droYak3.chr2R 20218320 3 + 21139217 CAA s droEre2.scaffold_4845 21615957 3 + 22589142 CAA s droBia2.KB462602 810244 3 + 3129309 CAA s droSuz1.KI419649 12056507 3 - 14502029 CAA s droAna3.scaffold_13266 5721153 3 - 19884421 CAA s droEug2.KB465067 613234 3 + 1515531 caa s droEle2.KB458573 536618 3 - 5320397 CAA s droKik2.KB459527 290003 3 - 1234237 caa s droTak2.KB461535 155212 3 - 669855 caa s droRho2.KB449310 51163 3 - 65043 CAA s droFic2.KB457177 93454 3 + 995874 CAA s droPse3.chr3 1363343 3 - 19787792 caa s droPer1.super_34 552213 3 - 916997 CAA s droMir2.chr3 1404439 3 - 20862834 CAA s droWil2.CH963894 1329222 3 + 2843958 CAA s droVir3.scaffold_12875 7368889 3 + 20611582 CAA s droGri2.scaffold_15245 919541 3 + 18325388 CAA a score=572101.000000 s dm6.chr2R 24370353 77 + 25286936 TTAAAT-TATTTCC---AAACAGTTCTCGGCT------TGGTCTTTGACTAATGATGAAAGC----------------CCCTGGAACTGATTTGTCAGTTAGT s droSim1.chr2R 18709021 77 + 19596830 TTTAAT-GATTTCC---AAACAGTTCTCGGCT------TGGTCTTTGACTAATGATGAAAGC----------------CCCTGGAACTGATTTGTCAATTAGT s droSec1.super_23 128334 77 + 989336 TTTAAT-GATTTCC---AAACAGTTCTCGGCT------TGGTCTTTGACTAATGATGAAAGC----------------CCCTGGAACTGATTTGTCAATTAGT s droYak3.chr2R 20218323 74 + 21139217 TTTAGC-GA--TCC---AAACAGTTCTCGGCT------TGGTCTTTGACTAATGATGAAGG-----------------CGCTGGAACTGATTTGTCAATTAGT s droEre2.scaffold_4845 21615960 76 + 22589142 TTTAAT-GATTTCC---AAACAGTTCTCGCCT------TGGTCTTTGACTAATGACGAAGG-----------------CGCTGGAACTGATTTGTCAATTAAT s droBia2.KB462602 810247 88 + 3129309 TTTAAT-GAAATCC---AAACAATTCTCGACA------TGGTCTTTGACTAATGATGAACGC-GCCGATCGGA----GTGCTGGAACcgatttttcaattagt s droSuz1.KI419649 12056510 88 - 14502029 TTTAAT-GAAATCC---AAACAATTCTCGACA------TGGTCTTTGACTAATGATGAAGGC-GCCGATCGGA----GTGCTGGAACCGATTTTTCAATTAGT s droEug2.KB465067 613237 88 + 1515531 tttaat-gaaatcc---AAACAGTTCTCGGCT------TGGTCTTTGACTAATGGTGAAGGT-GCCAATCGCA----CTGCTGGAACTGatttttcaattagt s droEle2.KB458573 536621 88 - 5320397 TTTAAT-GAAATCC---AAAGAATTCTCGACT------TGGTCTTTGACTAATGATGAAGGC-GCTGTTCGAA----GTGCTGgaactgatttttaaattagt s droKik2.KB459527 290006 91 - 1234237 tttaat-gaaatcc---AAACAATTCTCATCTTGG---TGGTTTTTGACTAATGACGAAAGGTGGTGATCGGA----GTGCCGAAATAGATTTTTCAATTAG- s droTak2.KB461535 155215 88 - 669855 tttaat-gaaatCC---AAACAATTCTCGACT------TGGTCTTTGACTAATGATGAAGGC-GCCGATCGGA----GTGCTGGAACCGATTTTTCAATTAGT s droRho2.KB449310 51166 88 - 65043 TTTAAT-GAAATCC---AAAAAATTCTCGACT------TGTTCTTTGACTAATGATGAAGGC-GCTGTTCGAA----GTGCTGGAACTGATTTTTCAATTAGT s droFic2.KB457177 93457 94 + 995874 TTTAAT-GAAATCC---AAACAGTTCTCGACTTGGACTTGGTCTTTGACTAATGATGAAGGC-GCTGGTCGGA----GTGCTGGAACtgatttttcaattagt s droPse3.chr3 1363346 92 - 19787792 tttaat-gaaattt---aaacaattcTAGACT------TGGTGTTTGACTAATGATCAATGC-GCCGGCCGGACAGGGTGCTGAAACtgatttttcaattagt s droPer1.super_34 552216 92 - 916997 TTTAAT-GAAATCC---AAACAATTCTAGACT------TGGTGTTTGACTAATGATCAATGC-GCCGGCCGGACAGGGTGCTGAAACTGATTTTTCAATTAGT s droMir2.chr3 1404442 92 - 20862834 TTTAAT-GAAATCC---AAACAATTCTAGACT------TGGTGTTTGACTAATGATCAATGC-GCCGGCCGGACAGGGTGCTGAAACtgatttttcaattagt s droWil2.CH963894 1329225 67 + 2843958 TTCAATAGAAATCT----------------TT------TGGTG-TTGACTAATGATTggtac-acaaaaaaaa------------tttgattttcaaattaGT s droVir3.scaffold_12875 7368892 82 + 20611582 TTTGAT-GAAATCTGTTAAAAAGCGCTG----------CTGGACTTGCCTAATGAGCAGAGA----AGTCAAG-----CTTAGAAATTGATTTTGATATTGT- s droGri2.scaffold_15245 919544 76 + 18325388 TTCGAT-GAAATCT-TTCAAGATTACTG----------CGAGCCTTGTCTAATGATCGGCAA-------CAGT-----CGCCAAGTGTGTTTTTG--TTTGT- a score=14166.000000 s dm6.chr2R 24370430 4 + 25286936 CTTG- s droSim1.chr2R 18709098 4 + 19596830 CTTG- s droSec1.super_23 128411 4 + 989336 CTTG- s droYak3.chr2R 20218397 4 + 21139217 TTTG- s droEre2.scaffold_4845 21616036 4 + 22589142 TTTG- s droBia2.KB462602 810335 4 + 3129309 ctTA- s droSuz1.KI419649 12056598 4 - 14502029 CTTA- s droEug2.KB465067 613325 4 + 1515531 tttc- s droEle2.KB458573 536709 4 - 5320397 tttg- s droKik2.KB459527 290097 3 - 1234237 -TTG- s droTak2.KB461535 155303 4 - 669855 TTTA- s droRho2.KB449310 51254 4 - 65043 TTTG- s droFic2.KB457177 93551 4 + 995874 tttg- s droPse3.chr3 1363438 4 - 19787792 ttcG- s droPer1.super_34 552308 4 - 916997 TTCG- s droMir2.chr3 1404534 4 - 20862834 tttg- s droVir3.scaffold_12875 7368974 4 + 20611582 -TTTT s droGri2.scaffold_15245 919620 4 + 18325388 -TTAC a score=-245471.000000 s dm6.chr2R 24370434 69 + 25286936 CAGTCGA-CTG---TAA-----------TGGCTGT-GGTCGATCTTGGTACCGTTT------ACAGGGGG-GTTTCCATTT------------------TGTCAG--------ATTGG s droSim1.chr2R 18709102 49 + 19596830 CAGTCGG-CTG---TAA-----------TGGCTGT-GGTCGATTTTGGTA---------------------------ATTT------------------TGTCAG--------ATTGG s droSec1.super_23 128415 49 + 989336 CAGTCGG-CTG---TAA-----------TGGCTGT-GGTCGATTTTGGTA---------------------------ATTT------------------TGTCAG--------ATTGG s droYak3.chr2R 20218401 63 + 21139217 GAGTCGA------------------------CTGT-GCTCGATTTTTGTAAAATGT------ACAGGGGG-TTTCA-ATTAGCGA--------------TTTCAG--------GTTGG s droEre2.scaffold_4845 21616040 56 + 22589142 G------------------------------CTGT-GGTCGATTTTGGTGACGTTT------ACAGGGGG-TTTCG-ATTGGCGA--------------TATC-G--------GTTGG s droBia2.KB462602 810339 92 + 3129309 GAGTCGGACAG---TAAAAACT-----GAGGCACT-GGTCGCCTTCACCTAGATTT------ATAGCCGT-TTTAA-ATTAGCTGAGATA---------TTTCAATTATCCACGTAGG s droSuz1.KI419649 12056602 93 - 14502029 GAGTCGGACAG---TAAAACTT-----GTGGCTCT-GATCGACATTACCTAGATTT------ATAGCGGT-TTTAA-ATTAGCAGATATATATCAATTTTGTCAG--------attgg s droEug2.KB465067 613329 76 + 1515531 GAGTTGGCCGG---TGG-----------AAGCTGT-GATCGACTTCGACTAGATTT------ATAGTGGT-TTTAA-ATTAGCACATT-----------TGTCAG--------CTTGG s droEle2.KB458573 536713 77 - 5320397 caGTT-----------------------TGGCAGT---TTGGACTGAATTagattt------atagttttaattaa-attagcacAGATATATCCATTTTGTCAG--------CTTGG s droKik2.KB459527 290100 55 - 1234237 GAGTTGA---------------------------T-GGTTGAGCATTGCAAAGTTT------GGTCTTAT-TTTGA-GAT-------------------CTTAAT--------ATTTG s droTak2.KB461535 155307 96 - 669855 GAGCCAAGCAG---TAAAAATTGT--GGCAGCTGG-GATCGACTTTTCTTAGATTT------ATAGCCGT-TTTAA-ATTAGCACAGATATATCAATTTTGTCAG--------CTTGG s droRho2.KB449310 51258 101 - 65043 GAGTTTGGCAG-CTTGAAACCTACTGACAGTTTTC-GATCGAATTGCGTTAGATTT------ATAGtttgaattaa-attagcaCAGAAATATCTATTTTGTCAA--------ATAGG s droFic2.KB457177 93555 40 + 995874 gAGTCGGGCAGTTTTGAAAGTT--------------------TTCCTATTAGATTT------ATAG---------------------------------------------------- s droPse3.chr3 1363442 65 - 19787792 TGGCTAAACTG------------------GATTGCAGTTTACATTCGATTCGATATCTga--aaaattgc-tttta-attg------------------gGTGGA------------- s droPer1.super_34 552312 64 - 916997 TGGCTAAACTG------------------GATTGC-GTTTACATTCGATTCGATATCTGA--AAAATTGC-TTTTA-ATTG------------------TGTGGA------------- s droMir2.chr3 1404538 65 - 20862834 tggCTAAACTG------------------GATTGCAGTTTATATTCGATTCGATATCTga--aaaattgc-tttta-attg------------------ggTGGA------------- s droGri2.scaffold_15245 919624 58 + 18325388 ---------------------------AATTCATT-AGTTGGCCTCTCTAAAGATTTTTAATGAAGTCGT-TTTCA-AGCTGCA---------------TTTG--------------- a score=-361891.000000 s dm6.chr2R 24370503 44 + 25286936 TGTC-TTAT------------------------------------------ATTTGCACTTGAA---TATGGCACATA-------------------TATAGG----GTATTC s droSim1.chr2R 18709151 58 + 19596830 GTTC-TTAT------------------------------------------ATTTGCACTTGAA---TATGACACATATCT---------CGTTCGTTATATAAACTTAGGTC s droSec1.super_23 128464 44 + 989336 GTTC-TTAT------------------------------------------ATTTGCACTTGAA---TATCGCACATA-------------------CATGTA----TAAGTC s droYak3.chr2R 20218464 55 + 21139217 GTTT-----------------------------------------------ATATACAATTACA---TATATCAGTTTAAGCTG--TTATCTTTC--TAAATA----GAATCT s droEre2.scaffold_4845 21616096 51 + 22589142 GTTT-TCAAA-----------------------------------------ATTTGCACATGAA---TATGACATTTCTAG-----------TTC--TAAATA----TAATCA s droBia2.KB462602 810431 6 + 3129309 GTTT-TT---------------------------------------------------------------------------------------------------------- s droSuz1.KI419649 12056695 6 - 14502029 gttt-tt---------------------------------------------------------------------------------------------------------- s droEug2.KB465067 613405 54 + 1515531 GTTTATTATGGTTATTCTCTTTTCTGTTAATGAT---TTCT----------ATATTCAATCCAA---TTT------------------------------------------- s droEle2.KB458573 536794 38 - 5320397 GTCT-CTGT------------------------------------------GATTGcctttcaaaattataaaatgttttt-------------------------------- s droKik2.KB459527 290155 31 - 1234237 GTTA-TA--------------------------------------------ATTAGCGGAGATA---TATTAACTTTGT---------------------------------- s droTak2.KB461535 156238 45 - 669855 --------------------tGTATTTTATCTGC-CATTTT----------CTTTTCcctcaaa---aataatttgttt---------------------------------- s droRho2.KB449310 51377 67 - 65043 ---------------tgtcataaattttaaatttgttgttt----------attaatcACTACG---TACACtttttttGGGAGCATAATTTACC------------------ s droFic2.KB457177 93595 40 + 995874 ----------------------------------------------------TGTGCTAAAAAT---TAGCACAGATATGACAACTTTGCCGGTC------------------ s droPse3.chr3 1363507 41 - 19787792 ----------------------------AACCATACAGTTTCTG---GTGGACTAGAACTTTAG---CAATGCTC-------------------------------------- s droPer1.super_34 552376 41 - 916997 ----------------------------AACCATACAGTTTCTG---GTGGACTAGAACTTTAG---CAATGCTC-------------------------------------- s droMir2.chr3 1404603 41 - 20862834 ----------------------------AACCATACAGTTTCTG---GTGGACCAGAACTTAAG---CAATGCTC-------------------------------------- s droGri2.scaffold_15245 919682 48 + 18325388 -----------------------------------------CAGCATATTCAATTCCTCTTAAA---TACCACAATCTTATCCAAATTGTTT--------------------- a score=9675.000000 s dm6.chr2R 24370547 3 + 25286936 TAG s droSim1.chr2R 18709267 3 + 19596830 CAG s droSec1.super_23 128621 3 + 989336 TAG s droYak3.chr2R 20218567 3 + 21139217 CAA s droEre2.scaffold_4845 21616211 3 + 22589142 CAG s droEug2.KB465067 613459 3 + 1515531 TAG s droEle2.KB458573 536832 3 - 5320397 tat s droKik2.KB459527 290186 3 - 1234237 CAG s droTak2.KB461535 156283 3 - 669855 cag s droRho2.KB449310 51444 3 - 65043 TAT s droFic2.KB457177 93635 3 + 995874 TAG s droPse3.chr3 1363548 3 - 19787792 TAT s droPer1.super_34 552417 3 - 916997 TAT s droMir2.chr3 1404644 3 - 20862834 TAT s droGri2.scaffold_15245 919730 3 + 18325388 CAC a score=-20242.000000 s dm6.chr2R 24370550 9 + 25286936 TTTTTATCT s droSim1.chr2R 18709270 9 + 19596830 TTTCTATCT s droSec1.super_23 128624 9 + 989336 TTTCTATCT s droYak3.chr2R 20218570 9 + 21139217 GAGCTATTT s droEre2.scaffold_4845 21616214 9 + 22589142 CTCCTATCT s droBia2.KB462602 810437 7 + 3129309 --TGTttcc s droSuz1.KI419649 12056701 7 - 14502029 --tgttttc s droEug2.KB465067 613462 9 + 1515531 CTTTTCTTT s droEle2.KB458573 536835 9 - 5320397 gatCGTTCT s droKik2.KB459527 290427 9 - 1234237 TTCTTAATT s droTak2.KB461535 156286 8 - 669855 -ttctaaat s droRho2.KB449310 51447 9 - 65043 TTTCCATAT s droFic2.KB457177 93638 7 + 995874 GCTTTAA-- s droPse3.chr3 1363551 6 - 19787792 TTTCTT--- s droPer1.super_34 552420 6 - 916997 TTTCTT--- s droMir2.chr3 1404647 6 - 20862834 TTTCTT--- s droGri2.scaffold_15245 919733 5 + 18325388 TTTTT---- a score=-45818.000000 s dm6.chr2R 24370559 3 + 25286936 T--------------------------CA s droSim1.chr2R 18709279 3 + 19596830 T--------------------------CA s droSec1.super_23 128633 3 + 989336 T--------------------------CA s droYak3.chr2R 20218579 29 + 21139217 GCGACTGTTTCTTGGACTTCAAAATTTAA s droEre2.scaffold_4845 21616223 3 + 22589142 G--------------------------AA s droBia2.KB462602 810444 3 + 3129309 c--------------------------ca s droSuz1.KI419649 12056708 3 - 14502029 c--------------------------at s droEle2.KB458573 536844 3 - 5320397 --------------------------TTA s droKik2.KB459527 290436 3 - 1234237 --------------------------TCT s droTak2.KB461535 156295 11 - 669855 ------------------ttttattgaat s droRho2.KB449310 51458 3 - 65043 --------------------------TAT s droFic2.KB457177 93645 3 + 995874 --------------------------TCA s droPse3.chr3 1363557 3 - 19787792 --------------------------TCC s droPer1.super_34 552426 3 - 916997 --------------------------TCC s droMir2.chr3 1404653 3 - 20862834 --------------------------TCC a score=3061.000000 s dm6.chr2R 24370562 7 + 25286936 CAATACT s droSim1.chr2R 18709282 7 + 19596830 CAATACT s droSec1.super_23 128636 7 + 989336 CAATACT s droYak3.chr2R 20218608 7 + 21139217 CATGACC s droEre2.scaffold_4845 21616226 7 + 22589142 CAAGACC s droBia2.KB462602 810447 7 + 3129309 aaaaata s droSuz1.KI419649 12056711 7 - 14502029 aaaaata s droEle2.KB458573 536847 7 - 5320397 Caagatt s droKik2.KB459527 290439 7 - 1234237 AGTTGCT s droTak2.KB461535 156306 7 - 669855 caTAATC s droRho2.KB449310 51461 7 - 65043 CCATTTT s droFic2.KB457177 93648 7 + 995874 ATTAATC s droPse3.chr3 1363560 7 - 19787792 CAATGCT s droPer1.super_34 552429 7 - 916997 CAATGCT s droMir2.chr3 1404656 7 - 20862834 CAATGCT s droGri2.scaffold_15245 919738 4 + 18325388 ---TATT s anoGam1.chr2R 35548098 7 + 62725911 CAAATCG a score=-72374.000000 s dm6.chr2R 24370569 32 + 25286936 ---AATGACATTATCG--------------TCTTT------GATAATG---------CTTAGCG s droSim1.chr2R 18709289 32 + 19596830 ---AATTCCATTTTCG--------------TCTTT------CACAATT---------CTTGACG s droSec1.super_23 128643 32 + 989336 ---AATGCCATTATTG--------------TCTAT------GACAGTG---------CTTGACG s droYak3.chr2R 20218615 32 + 21139217 ---AATGTCATTTTGG--------------TGTTT------GGCAACG---------CTTGACC s droEre2.scaffold_4845 21616233 32 + 22589142 ---AATGTCATTATCG--------------GGTTT------GGCTTCG---------CTTGACC s droBia2.KB462602 810454 32 + 3129309 ---tatttcaattctT--------------TATCA------AAAAATC---------TGCGAAG s droSuz1.KI419649 12056718 40 - 14502029 ---tatttcaattccC------ATTCTGCATATTa------acgtatt---------ttttata s droKik2.KB459527 290446 32 - 1234237 ---TATATTATACAAA--------------TCTTT------AAACCTT---------ATTAGTA s droTak2.KB461535 156316 38 - 669855 ---CATAACATAAGTC--------------TTTGttaaagcaaaaata---------tttcagc s droRho2.KB449310 51468 46 - 65043 ---AAGGTCATCTTAGTCTCAACTTTtatatttcg------aaaattt---------ttttaaa s droFic2.KB457177 93655 28 + 995874 ---AATGTAATAAACA--------------ACTCA------AAtaatt---------ctt---- s droPse3.chr3 1363567 41 - 19787792 ---AAAAGCACTATCT--------------TTTAT------GGGTTTTGAGTACCAGCTTGATC s droPer1.super_34 552436 41 - 916997 ---AAAAGCACTATCT--------------TTGAT------GGGTTTTGAGTACCAGCTTGATC s droMir2.chr3 1404663 41 - 20862834 ---AAAAGCAGTATCT--------------TTTAT------GGGTTTTGAGTCCCAGCTTGATC s droGri2.scaffold_15245 919745 32 + 18325388 ---TATAACACTTTGC--------------ACGTT------TTCAATG---------ATTAAAA s anoGam1.chr2R 35548105 32 + 62725911 AAAAAAACAACCGTCT--------------TTATC------GGGGCCT---------CTCT--- a score=16215.000000 s dm6.chr2R 24370601 3 + 25286936 CTC s droSim1.chr2R 18709321 3 + 19596830 CTC s droSec1.super_23 128675 3 + 989336 CTC s droYak3.chr2R 20218647 3 + 21139217 ATC s droEre2.scaffold_4845 21616265 2 + 22589142 -TC s droBia2.KB462602 810486 3 + 3129309 TTC s droSuz1.KI419649 12056758 3 - 14502029 atc s droEug2.KB465067 613811 3 + 1515531 ctt s droKik2.KB459527 290478 3 - 1234237 CTC s droTak2.KB461535 156355 2 - 669855 -tt s droRho2.KB449310 51518 3 - 65043 ctt s droPse3.chr3 1363619 3 - 19787792 CTC s droPer1.super_34 552487 3 - 916997 CTC s droMir2.chr3 1404714 3 - 20862834 CTC s droGri2.scaffold_15245 919784 3 + 18325388 ATC s anoGam1.chr2R 35548137 3 + 62725911 ATC a score=-14278.000000 s dm6.chr2R 24370604 3 + 25286936 TGT s droSim1.chr2R 18709324 3 + 19596830 TAT s droSec1.super_23 128678 3 + 989336 TAT s droYak3.chr2R 20218650 3 + 21139217 TAC s droEre2.scaffold_4845 21616267 3 + 22589142 TAT s droBia2.KB462602 810489 3 + 3129309 TTT s droSuz1.KI419649 12056761 3 - 14502029 ttt s droEug2.KB465067 613814 3 + 1515531 tct s droEle2.KB458573 537141 3 - 5320397 tgt s droKik2.KB459527 290481 3 - 1234237 cac s droTak2.KB461535 156358 3 - 669855 taa s droRho2.KB449310 51521 3 - 65043 tgc s droFic2.KB457177 93683 3 + 995874 tat s droPse3.chr3 1363628 1 - 19787792 T-- s droPer1.super_34 552496 1 - 916997 T-- s droMir2.chr3 1404723 1 - 20862834 T-- s droGri2.scaffold_15245 919789 1 + 18325388 T-- s anoGam1.chr2R 35548140 3 + 62725911 TGT a score=-1702.000000 s dm6.chr2R 24370607 1 + 25286936 -C s droSim1.chr2R 18709327 1 + 19596830 -C s droSec1.super_23 128681 1 + 989336 -C s droYak3.chr2R 20218653 1 + 21139217 -C s droEre2.scaffold_4845 21616270 1 + 22589142 -C s droBia2.KB462602 811139 1 + 3129309 -C s droSuz1.KI419649 12057209 1 - 14502029 -C s droEle2.KB458573 537144 1 - 5320397 -t s droKik2.KB459527 290484 1 - 1234237 -t s droTak2.KB461535 156361 1 - 669855 -c s droRho2.KB449310 51524 1 - 65043 -t s droFic2.KB457177 93686 1 + 995874 -t s droPse3.chr3 1363629 1 - 19787792 -C s droPer1.super_34 552497 1 - 916997 -C s droMir2.chr3 1404724 1 - 20862834 -C s droGri2.scaffold_15245 919790 1 + 18325388 -C s anoGam1.chr2R 35548143 1 + 62725911 G- a score=-8919.000000 s dm6.chr2R 24370608 15 + 25286936 CAATTA---------------AAAT---------------GAGTT s droSim1.chr2R 18709328 15 + 19596830 CAATTA---------------AAAT---------------GAGTT s droSec1.super_23 128682 15 + 989336 CAATTA---------------AACT---------------GAGTT s droYak3.chr2R 20218654 15 + 21139217 CAATTA---------------AAAT---------------GAGTT s droEre2.scaffold_4845 21616271 15 + 22589142 CAATTA---------------AAAT---------------GAGTT s droBia2.KB462602 811140 15 + 3129309 CAATTA---------------AAGT---------------GACTT s droSuz1.KI419649 12057210 15 - 14502029 CAATTA---------------AAGT---------------GGCTA s droBip2.KB464407 1971064 15 + 2915140 caattt---------------taat---------------gaaat s droEug2.KB465067 613818 15 + 1515531 aaattt---------------taat---------------caCTC s droEle2.KB458573 537145 15 - 5320397 caatta---------------aaat---------------gactt s droKik2.KB459527 290485 9 - 1234237 -tattt---------------aatt-------------------- s droTak2.KB461535 156362 15 - 669855 caatta---------------aaat---------------taata s droRho2.KB449310 51525 15 - 65043 taaaaa---------------tcat---------------aaatc s droFic2.KB457177 93687 12 + 995874 ---aaa---------------aaag---------------aagtT s droPse3.chr3 1363632 30 - 19787792 AGATCAAAGCTAAAAGCCCTCAAGG---------------GAGTA s droPer1.super_34 552500 30 - 916997 AGATCA---------------AAGCTAAAAGCCCTCAACGGAGTA s droMir2.chr3 1404727 30 - 20862834 AGATCAAAGCTTAAAGCCCTCATGG---------------GAGTA s droGri2.scaffold_15245 919791 15 + 18325388 ---------------GACAACAGAT---------------GAGTA s anoGam1.chr2R 35548144 15 + 62725911 CCATTA---------------ACAT---------------AGCTT a score=-158816.000000 s dm6.chr2R 24370623 31 + 25286936 TCTTAA--------AGGACAAAACA----------------AGCATT--TTAAA---------ATT s droSim1.chr2R 18709343 31 + 19596830 TCTTAA--------ATGACAAAACA----------------ACCATT--TAAAA---------ATT s droSec1.super_23 128697 31 + 989336 TCTTAA--------ATGACAAAACA----------------ACCATT--TTAAA---------ATA s droYak3.chr2R 20218669 31 + 21139217 TCTCAA--------ATGACAAAACA----------------AACGCT--TTAGA---------ATT s droEre2.scaffold_4845 21616286 31 + 22589142 TCTAAA--------ATGACAAAACA----------------AACATT--TTAAA---------ATT s droBia2.KB462602 811155 36 + 3129309 TATAAA--------ATGACAAAGGA----------------ATCATT--TTAAGTTAA----TACT s droSuz1.KI419649 12057225 36 - 14502029 TATTAA--------ATGacaaagaa----------------aacatt--ttaaattga----tata s droAna3.scaffold_13266 5721158 29 - 19884421 TTAAAG--------GGGCTGAAACT----------------GATTTT--TCA-----------ATT s droBip2.KB464407 1971093 27 + 2915140 ATCCAG--------GTGTCGAAACT----------------GTTTCC--TTA-----------A-- s droEug2.KB465067 613833 29 + 1515531 --TATA--------ATGACCAAAGT----------------AAcaat--tgaaa---------ttt s droEle2.KB458573 537160 10 - 5320397 --------------------------------------------att--tgata---------aa- s droKik2.KB459527 290494 14 - 1234237 -----------------------------------------acttta--tttaa---------ttc s droTak2.KB461535 156378 30 - 669855 attttt--------tctattatgcA----------------AGCATT--TCTA----------ATT s droRho2.KB449310 51555 56 - 65043 TTGAAA--------AagataaaacaatttattatgtCTAAGATTATT--TTGAACCCAATTTAAAT s droFic2.KB457177 93700 33 + 995874 CTTAAA--------ATCTCCACACT----------------AGTTTCCATTGCT---------GAT s droPse3.chr3 1363663 43 - 19787792 CTTCAAATGGCCTGCTGGGATATAC----------------GTATCT--TAATACCCC-----ATA s droPer1.super_34 552531 26 - 916997 CTTCAA--------ATGGCCTGCTG----------------GGATAT----------------ACG s droMir2.chr3 1404758 26 - 20862834 CTTCAA--------ATGGCCTGCTG----------------GGATAT----------------ACG s droGri2.scaffold_15245 919811 27 + 18325388 Cattaa--------attttaatatt----------------attatt------a---------att s anoGam1.chr2R 35548159 31 + 62725911 CTTTTA--------TCGACTTAGAA----------------ATTATT--AGAAA---------TTT a score=13279.000000 s dm6.chr2R 24370654 8 + 25286936 GATTTATT s droSim1.chr2R 18709374 8 + 19596830 GATTTATT s droSec1.super_23 128728 8 + 989336 TATTTATT s droYak3.chr2R 20218700 8 + 21139217 GATTTATA s droEre2.scaffold_4845 21616317 8 + 22589142 GATTTATA s droBia2.KB462602 811191 7 + 3129309 GAAGTAT- s droSuz1.KI419649 12057261 7 - 14502029 aaaGTAT- s droAna3.scaffold_13266 5721187 8 - 19884421 GGTTTTTT s droEug2.KB465067 613862 8 + 1515531 gatttata s droKik2.KB459527 290508 8 - 1234237 gaTTCATT s droTak2.KB461535 156408 8 - 669855 GATTTAAG s droRho2.KB449310 51611 8 - 65043 gacttatt s droFic2.KB457177 93733 8 + 995874 AATTTATA s droPse3.chr3 1363706 8 - 19787792 GATCTGAA s droPer1.super_34 552557 8 - 916997 TATCTGAA s droMir2.chr3 1404784 8 - 20862834 TATCTGAA s droGri2.scaffold_15245 919838 8 + 18325388 actttatt a score=-165816.000000 s dm6.chr2R 24370662 51 + 25286936 ----------CGTCC---G-------TA-----------AT----------GAAAC--------TATATCAAC----ACGACCAT-----GGCACGCATT---CAATGG----------------GCT s droSim1.chr2R 18709382 55 + 19596830 ----------ACTAC---G-------TA-----------AT----------GAAAC--------TATAACAACTATAGCGACCAT-----GGCACGCATT---CAATGG----------------GCT s droSec1.super_23 128736 55 + 989336 ----------CCTAC---G-------TA-----------AT----------GAAAC--------TATATCAACTATAGCGACCAT-----GGCACGCATT---CAATGG----------------GCT s droYak3.chr2R 20218708 57 + 21139217 AGATCCCT-CCCTCC------------------------AT----------GGAAC--------TTTATCAGA----GCCACCGA-----GGCACGCATT---CAATGG----------------GTT s droEre2.scaffold_4845 21616325 56 + 22589142 AG--------CCTCCAACG-------AG-----------AT----------GGAAC--------TTTATCAAA----GCCACCAT-----GGCACGCATT---CAATGG----------------GAT s droBia2.KB462602 811198 59 + 3129309 ----------CCTTC---G-------TA-----------GT----------GCAAAAAGTAAAGTTTATCTAG----TCCCACAT-----GACATACATT---CAATTG----------------GCT s droSuz1.KI419649 12057268 51 - 14502029 ----------CCTTC---G-------TA-----------AT----------GCAGC--------TTTATCTAG----TCCTACAT-----GACATACATT---CAATTG----------------GGT s droAna3.scaffold_13266 5721195 55 - 19884421 GGGC------CTAAT------------------------AT----------ATAGT--------CTCTAATAC----TAAATCAT-----TAAATACCCCTTTTCTTGT----------------AGT s droBip2.KB464407 1971120 43 + 2915140 ----------CTTTT------------------------AT----------CTAAC--------TATTAATAG----TTAACCAT-----TAAATGGCTC--------T----------------GAT s droEug2.KB465067 613870 55 + 1515531 aata------tccCT---G-------TA-----------GA----------GCACC--------TCTGTCTAA----AATTACAT-----AACAAGCATT---CAATGG----------------GCT s droEle2.KB458573 537170 51 - 5320397 ----------tattt---g-------ta-----------at----------accAC--------TTAATCTAA----GCATCTGT-----AGCCAGCATT---CAATTA----------------TCT s droKik2.KB459527 290516 38 - 1234237 ----------CGATT-------------------------------------------------CCCATCTAA-------AAATT-----GTCAAGAATT---GGGTCT----------------GCA s droTak2.KB461535 156416 52 - 669855 CAAAA-----CCTTC---G-------AA-----------AT----------ACAAG------------TCTAG----TCCCCCAT-----GGCAGGCATT---CAATGG----------------GTC s droRho2.KB449310 51619 61 - 65043 taataattatttctc---a-------TA-----------TT----------GCAAC--------TTAATCTAA----GCATCTTT-----AGCCAGCATT---CAATTG----------------GCT s droFic2.KB457177 93741 49 + 995874 ----------CGAAT---A------TTA-----------AA----------ACGAG--------TTCAGTTAT----ACAACTCT-----AG---GCAAC---CAATAG----------------gtt s droPse3.chr3 1363714 78 - 19787792 TAAC------CGTTC---GACT-----------------A-----------GCCGC--------TTCATCTGA--GAGGAGCCGTCGATAGGCAGGCATT---CAATGGCTGAGGAGCTTCTGTTGCA s droPer1.super_34 552565 95 - 916997 TACC------CCATA---GATCTGAATAACCTTTCGACTA-----------GCCGC--------TTCATCTGA--GAGGAGCCATCGATAGGAAGGCATT---CAATGGCTGAGGAGCTTCTGTTGCA s droMir2.chr3 1404792 95 - 20862834 TACC------CCATA---GATCTGAATA-----------ACCTTTCGACTAGCCGC--------TTCATTTGA--GAGGAGCCATCGATAGGCAGGCATT---CAATGGCTGAGGAGCTTCTGTTGCA a score=-10288.000000 s dm6.chr2R 24370713 8 + 25286936 -TCC------------CAGCA s droSim1.chr2R 18709437 8 + 19596830 -TCC------------CAGCA s droSec1.super_23 128791 8 + 989336 -TCC------------CAGCA s droYak3.chr2R 20218765 8 + 21139217 -GCC------------CAGCA s droEre2.scaffold_4845 21616381 8 + 22589142 -GCC------------CAGCA s droBia2.KB462602 811257 8 + 3129309 -TTC------------CAGAG s droSuz1.KI419649 12057319 8 - 14502029 -TTC------------CAGAG s droAna3.scaffold_13266 5721250 8 - 19884421 -CTC------------TTAAG s droBip2.KB464407 1971163 8 + 2915140 -GTC------------TTAGG s droEug2.KB465067 613925 8 + 1515531 -TTT------------CAGAG s droEle2.KB458573 537221 20 - 5320397 -tctgagttttttttatagag s droKik2.KB459527 290554 8 - 1234237 -TTT------------CAAAA s droTak2.KB461535 156468 8 - 669855 -TAC------------CAGCG s droRho2.KB449310 51680 20 - 65043 -TCTGACTCTGTTTTTCGGAA s droFic2.KB457177 93790 8 + 995874 -gca------------ttaaa s droPse3.chr3 1363792 8 - 19787792 -TTC------------TAGAG s droPer1.super_34 552660 8 - 916997 -TTC------------TAGAG s droMir2.chr3 1404887 8 - 20862834 -TTC------------TAGAG s droVir3.scaffold_12875 7370169 8 + 20611582 TCGC------------CGGT- a score=484067.000000 s dm6.chr2R 24370721 56 + 25286936 TTTAATCGCTGTCAGGGGC--------------T--------CCAGATTGT-TTTCTCAGTTACGG--ACCTTCTTC----------GGCT s droSim1.chr2R 18709445 66 + 19596830 TTTAATCGCTGTCAGGGGC--------------T--------CCAGATTGT-TTTCTCAGTTAGGG--ACCTTCTTCGACTTCGCTTGGCT s droSec1.super_23 128799 66 + 989336 TTTAATCGCTGTCAGGGGC--------------T--------CCAGATTGT-TTTCTCAGTTAGGG--ACCTTCTTCGACTTGGCTTGGCT s droYak3.chr2R 20218773 66 + 21139217 TTTAATCGCTGTCAGGGGC--------------T--------CCAGATTGT-TTGCTCAGTTAGGG--ACCTTCTGCGGCTTGGCTTGGCC s droEre2.scaffold_4845 21616389 66 + 22589142 CTTAATCGCTGTCAGGGGC--------------T--------CCAGATTGT-TTTCTCAGTTAGGG--ACCTTCTTCGGTTTGGCCTGGCC s droBia2.KB462602 811265 56 + 3129309 CTTAATCGCTGTCAGTGGC--------------T--------CGAGATTGT-TTGGTTAGTTAGGA--CCCTTCTTC----------GAAT s droSuz1.KI419649 12057327 56 - 14502029 TTTAATCGCTGTCAGTGGC--------------T--------CCAGATTGT-TTGGCTAGTTAAAG--GCCTTCTTC----------GAAT s droAna3.scaffold_13266 5721258 60 - 19884421 TTTACACGCTGTCAGTGGC--------------T--------CCAGATTGT-ATGGTTAGTTAG--------TCGGAGATGTCCACAGTTT s droBip2.KB464407 1971171 60 + 2915140 TCTAATCGCTGTCAGTAGC--------------T--------CCAGATTGT-ATGGTTAGTTAG--------TCGGCAATGTCCACTGTTT s droEug2.KB465067 613933 56 + 1515531 TCTAATCGCTGTCACCGTC--------------T--------CCAGATTGC-TTAGCTAGTTAGGA--GCCTCCTTC----------GGCC s droEle2.KB458573 537241 56 - 5320397 tTTAATCGCTGTCAGTGGT--------------T--------CCAGATTGT-TTGCTTAGTTAGGG--ACCTTCTTC----------GGCT s droKik2.KB459527 290562 58 - 1234237 TCTAATCGCTGTCAATAGC--------------T--------CCAGATTGT-ATGACCCGTTTAGGGTACCCCCTGC----------CCCT s droTak2.KB461535 156476 56 - 669855 TTTAATCGCTGTCAGTGGC--------------T--------CCAGATTGT-TTGCCTAGTTAGGG--GCCTTCTTC----------GGTT s droRho2.KB449310 51700 56 - 65043 TTTAATCGCTGTCAGTGGC--------------T--------CCAGATTGT-TTGGTTAGTTAGGG--GCCTTCTTC----------GGTT s droFic2.KB457177 93798 56 + 995874 tttaatcgcTGTCAGTGGC--------------T--------CGAGATTGT-TTGCCTAGTTAGGG--GCCTTCTTC----------GGAT s droPse3.chr3 1363800 56 - 19787792 TTTAATCGCTGTCAGCGGC--------------T--------CCAGATTGT-ATGGGCAGTTAGGG--GCCTTCTTT----------GCTT s droPer1.super_34 552668 56 - 916997 TTTAATCGCTGTCAGCGGC--------------T--------CCAGATTGT-ATGGGCAGTTAGGG--GCCTTCTTT----------GCTT s droMir2.chr3 1404895 56 - 20862834 TTTAATCGCTGTCAGCGGC--------------T--------CCAGATTGT-ATGGGCAGTTAGGG--GCCTTCTTT----------GCTT s droWil2.CH963894 1331468 62 + 2843958 tttaatcGCTGTCATTGGA--------------TACGAGATACCAGATTCT-ATGGTCAGTTTACG----TGGCTTT----------TGTT s droVir3.scaffold_12875 7370177 63 + 20611582 TCTAATCGCTGTCAGAGTACACACTGTACAGTGT--------ACAGATTGTAATGGCCAGTTACGC----------C----------GCTT a score=405651.000000 s dm6.chr2R 24370777 113 + 25286936 TGGCTAAATCTAGCCAAA--CATC------GA---ACTCAGTTG---GTT------------------------GG--G---CACCCACATCAGG---GA------------ACCC------CTCCTCCATCCTTCCAATCGGAGG--CACTTTACATA--------CGCC----------G-------AGTT-GAGATCTT---GTA s droSim1.chr2R 18709511 113 + 19596830 TGGCTAAATCTAGCCAAA--CATC------GA---ACTCAGTTG---GTT------------------------GG--G---CACCCACATCAGC---GA------------ACCC------CTCCTCCATCTTTCCAATCGGAGG--CACTTTACATA--------CGCC----------G-------AGTT-GAGATCTT---GTA s droSec1.super_23 128865 113 + 989336 TGGCTAAATCTAGCCAAA--CATC------GA---ACTCAGTTG---GTT------------------------GG--G---CACCCACATCAGC---GA------------ACCC------CTCCTCCATCCTTCCAATCGGAGG--CACTTTACATA--------CGCC----------G-------AGTT-GAGATCTT---GTA s droYak3.chr2R 20218839 120 + 21139217 TGGCTAAATCTAGCCAAA--CATC------GA---acccagttgccagttggct--------------------GG--G---CACCCACATCAGC---AT------------CCTT------CCCTTGCAGCCTTCCAATCGGAGG--CACTTAACATA--------CGCC----------G-------AGTT-GAGATCTT---GTA s droEre2.scaffold_4845 21616455 111 + 22589142 CAA--ACATCTAGCCAAA--CATC------GA---ACTCAGTTG---GCTGG----------------------GG--G---CACCCACATCAGC---GA------------AC--------CCCTTGCATCCTTCCAATCGGAGG--CACTTAACATA--------CGCC----------G-------AGTT-GAGATCTT---GTA s droBia2.KB462602 811321 110 + 3129309 TGGCAAAATCAAGCTAAA--CATC------GA---ATTCAGTTT---GTCG-----------------------GG--G---CACCCACATCGGC---ATC-----------ATTC------CCCCTCCAAACCCTCGATT-------CACTTAACATA--------CGCC----------G-------AGTG-GAGATCTT---GTA s droSuz1.KI419649 12057383 110 - 14502029 TGGCTAAATCTAGCTAAA--CATC------GA---ATTCAGTTT---GCCG-----------------------GG--G---CACCCACATCAGT---ATC-----------AGCC------CCCCTCCAAACCTTCGATT-------CACTTAACATA--------CGCC----------G-------AGTT-GAGATCTT---GTA s droAna3.scaffold_13266 5721318 145 - 19884421 TTCCTAAATCTAGCTAAA--CATC------GA---ACTCACTTT---GTCCTCTGGAAGGGGCGGTGGGACAGGGGCTG---CACCCACATCGAA---AACACA----CTAGGTCC------CCACCACTGTCCTTCGGTT-------CACTTAACATA--------CGCC----------G-------AGCT-GAGCTCCTGCGGTA s droBip2.KB464407 1971231 130 + 2915140 TTGCTAAATCTAGCTAAA--CATC------GA---ACCCACTTT---GTCGTCTGAAAGGGGCGCTGGGACGGGGGCTG---CACCCACATCGGT---AGCTCG--------------------------GTCCTTTGGTT-------CACTTAACATA--------CGCC----------G-------AGCTGGAGCTCCTGCGGTA s droEug2.KB465067 613989 103 + 1515531 CAGCTAAATCTTGCTAAA--CATC------GA---ACTCAGTTT---GTCT-----------------------GG--G---CACCCACATCAGC---------------------------CTCCCCCAGTCCTTCGAGT-------CACTTAACATA--------CGCC----------G-------AGTT-GAGATCTT---GTA s droEle2.KB458573 537297 109 - 5320397 TGGCTAAATCTAGCCAAA--CATC------GA---ACTCAGTTT---GTCT-----------------------GG--G---CACCCACATGAGT---AG------------TCAA------CCCCGCCAGTCCTTCGACT-------CACTTAACATA--------CGCC----------G-------AGTT-GAGATCTT---GTA s droKik2.KB459527 290620 137 - 1234237 TAACTAAATCCAGCTAAA--CATT------GA---ACTCA-------ACT------------------------GG--G---CACCCACATTGGT---ATACAATATCCGCAATCCGTGGAGCCTCCCTCTCCCTTCGATTGGACC--AGCTTAACATA--------CGCcaagctgagctg-------agct-gagctccT---GTA s droTak2.KB461535 156532 110 - 669855 CGGCTAAATCTAGCTAAA--CATC------GA---ATTCAGTTG---GTCG-----------------------AG--G---CACCCACATCAGT---ATT-----------ATTC------CCCCTCCAAACCTTCGACT-------CACTTAACATA--------CGCC----------G-------AGTT-GAGATCTT---GTA s droRho2.KB449310 51756 107 - 65043 CGGCTAAATCTAGCTAAA--CATC------GA---ACTCAGTTT---GTCT-----------------------GG--G---CACCCACATGAGT-----------------GGTC------CCCCTCCAGTCCTTCGACT-------CACTTAACATA--------CGCC----------G-------AGTT-GAGATCTT---GTA s droFic2.KB457177 93854 118 + 995874 TGG-TAAATCTAGCTAAA--CATC------GA---ACTCAGTTT---GTCC-----------------------GG--G---CACCCACATCAGg---atccccctcctc--ctcc------tcctcccagTCCATCGGTC-------CACTTAACATA--------CGCC----------G-------AATT-GAGCTCTT---GTA s droPse3.chr3 1363856 127 - 19787792 TGGCTAAATCTAGCTAAA--CATC------GAACTACTAGCTTT---GTCC-----------------------GG--G---CACCCACATGGTG---CTCCTACTCcgcatcctc------ctccttctacCCCTGGAC--------CGCTTTGGACA----------------------GAGTAcgaagtacgagtacga---gta s droPer1.super_34 552724 123 - 916997 TGGCTAAATCTAGCTAAA--CATC------GAGCTACTAGCTTT---GTCC-----------------------GG--G---CACCCACATGGTGctcctcctcctcctcatcctc------ctccttctACCCCTGGAC--------CGCTTTGGACA----------------------G-------AGTACGAGTACGA---GTA s droMir2.chr3 1404951 114 - 20862834 TGGCTAAATCTAGCTAAA--CATC------GAGCTACTAGCTTT---GTCC-----------------------GG--G---CACCCACatggtg---ctcctcctcctcatcctc------ctccttctacCCCTGGAC--------CGCTTTGGaca----------------------g-------------agtacga---gta s droWil2.CH963894 1331530 146 + 2843958 TGCCTAAATCTAGCCAAAAGCATTCGCGGGGC---AGGCAGCTT---GTTG-----------------------TT--GTCTCATCCACCCCCAC---CTCTTCCATCTACTCGTC------CTTCTTCACAAGACTGTTTCA-----CATGTTGCACAGAAGGAGGCACCTAGT------G-------AACT-GGACTCTC---GTT s droVir3.scaffold_12875 7370240 85 + 20611582 TGGC-------GGCTAAC--CAGC------GA---A--------------------------------------AT--G---CACCCACATGAGC-----------------TGCC------AGTTTTGTGGTTAGCAACT-------CGTTTAA---A--------TGCA----------A-------AACA-GATACTCG---ATA s anoGam1.chr2L 39578153 110 - 48795086 TGCCTGAAAGCAGGCTGA--AATC------GA---AAGTGAACG---CTT------------------------TT--G---AACGCCAGTAAAC-----------------GGCC------AAGCACCATCTATGCGATAATATGCAAGCCCTGAACG--------GGCC----------A-------TGTT-GAACACCT------ a score=8997.000000 s dm6.chr2R 24370890 3 + 25286936 TT--C- s droSim1.chr2R 18709624 3 + 19596830 TT--C- s droSec1.super_23 128978 3 + 989336 TT--C- s droYak3.chr2R 20218959 3 + 21139217 TT--C- s droEre2.scaffold_4845 21616566 3 + 22589142 TT--C- s droBia2.KB462602 811431 3 + 3129309 TT--C- s droSuz1.KI419649 12057493 3 - 14502029 TT--C- s droAna3.scaffold_13266 5721463 3 - 19884421 TC--C- s droBip2.KB464407 1971361 3 + 2915140 TC--C- s droEug2.KB465067 614092 3 + 1515531 TT--C- s droEle2.KB458573 537406 3 - 5320397 TT--C- s droKik2.KB459527 290757 3 - 1234237 TT--C- s droTak2.KB461535 156642 3 - 669855 TT--C- s droRho2.KB449310 51863 3 - 65043 TT--C- s droFic2.KB457177 93972 3 + 995874 TT--C- s droPse3.chr3 1363983 5 - 19787792 ttcgc- s droPer1.super_34 552847 5 - 916997 TTCGC- s droMir2.chr3 1405065 5 - 20862834 ttcgc- s droWil2.CH963894 1331676 3 + 2843958 TA--C- s droVir3.scaffold_12875 7370333 3 + 20611582 CC--G- s droMoj3.scaffold_6496 26165256 3 + 26866924 TT--C- s anoGam1.chr2L 39578263 2 - 48795086 ----CC a score=45639.000000 s dm6.chr2R 24370893 2 + 25286936 GT s droSim1.chr2R 18709627 2 + 19596830 GT s droSec1.super_23 128981 2 + 989336 GT s droYak3.chr2R 20218962 2 + 21139217 GT s droEre2.scaffold_4845 21616569 2 + 22589142 GT s droBia2.KB462602 811434 2 + 3129309 GT s droSuz1.KI419649 12057496 2 - 14502029 GT s droAna3.scaffold_13266 5721466 2 - 19884421 GT s droBip2.KB464407 1971364 2 + 2915140 GT s droEug2.KB465067 614095 2 + 1515531 GT s droEle2.KB458573 537409 2 - 5320397 GT s droKik2.KB459527 290760 2 - 1234237 GT s droTak2.KB461535 156645 2 - 669855 GT s droRho2.KB449310 51866 2 - 65043 GT s droFic2.KB457177 93975 2 + 995874 GT s droPse3.chr3 1363988 2 - 19787792 GT s droPer1.super_34 552852 2 - 916997 GT s droMir2.chr3 1405070 2 - 20862834 gt s droWil2.CH963894 1331679 2 + 2843958 GT s droVir3.scaffold_12875 7370336 2 + 20611582 GT s droMoj3.scaffold_6496 26165259 2 + 26866924 GT s droGri2.scaffold_15245 920640 2 + 18325388 GT s anoGam1.chr2L 39578265 2 - 48795086 GC a score=1340383.000000 s dm6.chr2R 24370895 124 + 25286936 -ATAATTGCAATTTCCATTCAACTGTTTGTTCG--------------CCGCCGG-TCTGTGT-CC-GACT----CCGTTTCATTTG---------------------TTTGGCTAG------------T---------TT--TGCGG-TTGTTAGTGCCCATCATAAATTGCAGAA--------GCGGC-CAGGGGAA-------CC s droSim1.chr2R 18709629 123 + 19596830 -ATAATTGCAATTTCCATTCAACTGTTTGTTCG--------------CCGCCGG-TCTGTGT-CC-GACT----CCGTTTCATTTG---------------------TTTGGCTAG----------------------TT--TGCGG-TTGTTAGTGCCCATCATAAATTGCAGAA--------GCGGC-CAGGGGAT-------CC s droSec1.super_23 128983 123 + 989336 -ATAATTGCAATTTCCATTCAACTGTTTGTTCG--------------CCGCCGG-TCTGTGT-CC-GACT----CCGTTTCATTTG---------------------TTTGGCTAG----------------------TT--TGCGG-TTGTTAGTGCCCATCATAAATTGCAGAA--------GCGGC-CAGGGGAT-------CC s droYak3.chr2R 20218964 124 + 21139217 -ATAATTGCAATTTCCATTCAACTGTTTGTTCG--------------CCGCCGC-TCTGTGT-CC-GAGT----CCGTTTCATTTG---------------------TTTGGCTAG------------T---------TT--TGCGG-TTGTTAGTGCCCATCATAAATTGCAGAA--------GCCGT-GAGGGGAT-------CC s droEre2.scaffold_4845 21616571 124 + 22589142 -ATAATTGCAATTTCCATTCAACTGTTTGTTCG--------------CCGCCGC-TCTGTGT-CC-GACT----CCGTTTCATTTG---------------------TTTGGCTAG------------T---------TT--TGCGG-TTGTTAGTGCCCATCATAAATTGCAGAG--------GCGGC-CAGGGGAT-------CC s droBia2.KB462602 811436 127 + 3129309 -ATAATTGCAATTTCCATTCAACTGTTTGTTCG--------------CCGCCGG-TTTGTGC-TC-GACt----ccatttcatttg---------------------tttggctAG------------T---------TT--TGCGG-TTGTTAGTGCCCATCATAAATTGCCGGAATT-----GGGGT-AAGGAGTC-------CT s droSuz1.KI419649 12057498 127 - 14502029 -ATAATTGCAATTTCCATTCAACTGTTTGTTCG--------------CCGCCGG-TTTGTGT-CC-AACT----CCATTTCATTTG---------------------TTTGGCTAG------------T---------TT--TGCGG-TTGTTAGTGCCCATCATAAATTGCCGGAATT-----GGGGT-AAGGAGTC-------CT s droAna3.scaffold_13266 5721468 124 - 19884421 -ATAATTGCAATTTCCATTCAACTGTTTGTTCG-------------CCCGCTTG-TTTGCGT-CC-GACT----TCATTTCATTTGT--------------------TTTGGCCAGG-----------T---------TT--TGCGG-TTGTTAGTGCCCATCATAAATTGCAGGA--------ATTAA-GGGGGGG---------- s droBip2.KB464407 1971366 127 + 2915140 -ATAATTGCAATTTCCATTCAACTGTTTGTTCG-------------CCCGCTTG-TTTGCGT-CC-GAct----tcatttcatttgt--------------------tttggccaGG-----------T---------TT--TGCGG-TTGTTAGTGCCCATCATAAATTTCAGGA--------ATTAA-gggggggA-------GT s droEug2.KB465067 614097 127 + 1515531 -ATAATTGCAATTTCCATTCAACTGTTTGTTCG--------------CCGCCGG-TTTGTGT-cc-aatt----ccatttcatttg---------------------tttggctaG------------T---------TT--TGCGG-TTGTTAGTGCCCATCATAAATTGCGGGAACT-----GGGGC-AGGGGGCT-------CT s droEle2.KB458573 537411 129 - 5320397 -ATAATTGCAATTTCCATTCAACTGTTTGTTTG-------------CCCGCCGG-TTTGTGT-CC-GACt----ccatttcatttg---------------------tttggctAG------------T---------TT--TGTGG-TTGTTAGTGCCCATCATAAATTGCGGCAATC----GGTGGC-AAGGAGCT-------CC s droKik2.KB459527 290762 141 - 1234237 -ATAATTGCAATTTCCATTCAACTGTTTGTTCG--------------CCGCCGGTTTTGTGT-CC-AACT----CCGTTTCATTTG---------------------TTTGGCCAGT-----------T---------GC--TGCGG-TTGTTAGTGCCCATCATAAATTGCAAGAATTAGGTGGAGGT-GGGGAGCTTGGGCCGCC s droTak2.KB461535 156647 127 - 669855 -ATAATTGCAATTTCCATTCAACTGTTTGTTTG--------------CCGCCGG-TTTGTGT-CC-AACT----CCATTTCATTTG---------------------TGTGGCTAG------------T---------TT--TGCGG-TTGTTAGTGCCCATCATAAATTGCCTGAATT-----GTGGT-AAGGAGCT-------CC s droRho2.KB449310 51868 129 - 65043 -ATAATTGCAATTTCCATTCAACTGTTTGTTAG-------------CCCGCCGG-ATTGTGT-CC-AACt----ccatttcatttg---------------------tttggcTAG------------T---------TT--TGCGG-TTGTTAGTGCCCATCATAAATTGCGCCAATTG----TGGGC-GAGGAGCT-------CC s droFic2.KB457177 93977 128 + 995874 -ATAATTGCAATTTCCATTCAACTGTTTGTTCG-------------CCCGCCGG-ATTGTGT-CC-AACT----CCATTTCATTTG---------------------TTCGGCTAG------------T---------TT--TGCGG-TTGTTAGTGCCCATCATAAATTGCGGGAACT-----GGGGT-AGGGAGCT-------CC s droPse3.chr3 1363990 141 - 19787792 -ATAAttgcaatttccattgaaCTGTTTGTTCGTTTTGTGGGCCTCTGTGTCCC-TCTGTGC-CT-caat----tcattt-gtttg---------------------tttggcttg------------t---------tT--TGCGG-TTGTTAGTGCCCATCATAAATTGCAGGAATTG----GGAGC-TATGGGTG-------CT s droPer1.super_34 552854 141 - 916997 -ATAATTGCAATTTCCATTCAACTGTTTGTTCGTTTTGTGGGCCTCTGTGTCCC-TCTGTGC-CT-CAAT----TCATTT-GTTTG---------------------TTTGGCTTG------------T---------TT--TGCGG-TTGTTAGTGCCCATCATAAATTGCAGGAATTG----GGAGC-TATGGGTG-------CT s droMir2.chr3 1405072 141 - 20862834 -ataattgcaatttccattcaacTGTTTGTTCGTTTTGTGGGCCTCTGTGTCCC-TCTGTGC-Ct-caat----tcattt-gtttg---------------------tttggcttg------------t---------tT--TGCGG-TTGTTAGTGCCCATCATAAATTGCAGGAATTG----GGAGC-TATGGGTG-------CT s droWil2.CH963894 1331681 132 + 2843958 -ATAATTGCAATTTCCATTCaactgtttgtttg-----------tttgttcggt-tttgtgg-ccaaact----tcatttcatttg---------------------tttggtttt------------ttgcttgtactt--tgCGGTTTGTTAGTGCCCATCATAAATTGC------------TGGAT-TAAAAGAT--------- s droVir3.scaffold_12875 7370338 120 + 20611582 -ATAATTGCAATGCCCATTCAACTGTTTGTTTG--------------CGGCCAA-GTT--------CATT----TCATTTCGTTTC-----GTTTCAGCTGGA----TTTGGCT--------------T---------CTGGGCCCG-TTGTTAGTGCCCATCATAAA----------------TTTGC-GGAAAGCG--------- s droMoj3.scaffold_6496 26165261 100 + 26866924 -ATAATTGCAATGTCCATTCAACTGTTTGTTTG--------------CGGCCAA-GTT--------CACT----TCAT-----------------------------TTTGGCT--------------T---------TT-AACCCG-TTGTTAGTGCCCATCATAAAT---------------TTTGC-GGAAGGCG--------- s droAlb1.JH854640 327051 136 + 406291 -ataattgcaatttgcattcaaCTGTTTGTTTG--------------CGGTCAA-GTT--------GATT----ACATTTGTTCCCCT---GACtcggcttgg----cttggcttggccaAGGCTTGCT---------TT-ATGCCG-TTGTTAGTGGCcttcataaa----------------tttgcaaaaaaatg--------- s droGri2.scaffold_15245 920642 128 + 18325388 -ATAATTGCCATGTCCATTCAACTGTTTGTTTG--------------CGGCCAA-Gtt--------catt----tcatttcgtttcgtttcgtttcgtttGCAGCTTTTTGGCT--------------T---------TT-AGGCCG-TTGTTAGTGCCCATCATAAA----------------TTTGC-GGAAAGCG--------- s anoGam1.chr2L 39578267 121 - 48795086 TTAAACTCC--TTTGCTTACAACAGTTGGCATA----------------------CCCGTGTACC-AACTACACCCGTTTCCCAAA---------------------GTGAACTGG------------T---------TT--TGCAG-TTGGCCCTGCCTTTCATACCCCTCTGGT--------TCCGC-GACGGAAA-------CC a score=358423.000000 s dm6.chr2R 24371019 114 + 25286936 CCTCCTAGTGCCTGGCC----ATGCGGACCGGCAGG--------------AGTG-----------GCCG--------------------------GAG--GCAGC---GGCACAGGCTAATCGGTGGCGTTTCATCTG--CGGCCTGCTG----------TCCTGTTGTCC-----------------------TGTT--GCCTCTTGTTC s droSim1.chr2R 18709752 114 + 19596830 CCTCCCAGTGCCTGGCC----ATGCGGACCGGGAGG--------------AGTG-----------GCCG--------------------------GAG--GGAGC---GGCACAGGCTAATCGGTGGCGTTTCATCTG--CGGCCTGCTG----------TCCTGTTGTCC-----------------------TGTT--GCCTCTTGTTC s droSec1.super_23 129106 114 + 989336 CCTCCCAGTGCCTGGCC----ATGCGGACCGGGAGG--------------AGTG-----------GCCG--------------------------GAG--GGAGC---GGCACAGGCTAATCGGTGGCGTTTCATCTC--CGACCTGCTG----------TCCTGTTGTCC-----------------------TGTT--TCCTCTTGTTC s droYak3.chr2R 20219088 158 + 21139217 CCTCC-AGCCACTGGGC----ATGCGGACCAGGAGGAGTGGCCA------AGTGGAGCAGGGGAAGCCATGGAAGCAGGGGGAGTAGAGGGAGTAGAG--GGAGC---GGCACAGGCTAATCGGTGGCGTTTCATCTG--CGGCCTGCTG----------TCCTGTTGTCC-----------------------TGTT--GCCTCTTGTTC s droEre2.scaffold_4845 21616695 97 + 22589142 CCTCC--------------------------GGAGGAGTGG---------AGTG-----------GCCA------------------GGGGCGCAGAG--GGAGC---GGCACAGGCTAATCGGTGGCGTTTCATCTG--CGGCCTGC------------------TGTCC-----------------------TGTT--GCCTCTTGTTC s droBia2.KB462602 811563 96 + 3129309 CCTCC-AGCCGCTGGTG----ATGTGG-----------------------ACTG-----------GACG--------------------------GAG--GGAGC---GGCACAGGCTAATCGGTGGCGTTTCATCTG--CGGCCTGC------------------TGTCC-----------------------TGTT--GCCTCTTGTTC s droSuz1.KI419649 12057625 96 - 14502029 CCTCC-GGCGCCTGGTG----ATGTGG-----------------------ATAG-----------GACG--------------------------GAG--GGAGC---GGCACAGTCTAATCGGTGGCGTTTCATCTG--CGGCCTGC------------------TGTCC-----------------------TGTT--GCCTCTTGTTC s droAna3.scaffold_13266 5721592 90 - 19884421 ---------------------CCCAGTACCAGTAGGGC------------AGTG-----------GCTA----------------------------------------GCAGAAGCTAATCGGTGGCGTTTCATCTC--AGGCCTGCTG----------TCCTGCTATCC-----------------------TGTG--GCGGCTTGTTC s droBip2.KB464407 1971493 111 + 2915140 TGTACCAGTATCAGTACCAGTACCATTACCAGTAGGGC------------AGTG-----------GCTA----------------------------------------GCCGAGGCTAATCGGTGGCGTTTCATCTC--AGGCCTGCCG----------TCCTGCTGTCC-----------------------TGTG--GCGGCTTGTTC s droEug2.KB465067 614224 91 + 1515531 CCTCCGACGGCCGGGGG---------------------------------AGTG-----------GACA--------------------------GAG--GGAGC---GGCACAGGCTAATCGGTGGCGTTTCATCTG--CGGCCTGC------------------TGTCC-----------------------TGTT--GCCTCTTGTTC s droEle2.KB458573 537540 106 - 5320397 CCTCC-AGCGGCTAAGG----ATGTGGAACGGGAGGA-------------GGGG-----------GGCA--------------------------GAG--GGAGC---GGCATAGGCTAATCGGTGGCGTTTCATCTG--CGGCCTGC------------------TGTCC-----------------------TGTT--GCCTCTTGTTC s droKik2.KB459527 290903 104 - 1234237 CCTCC-AGGGGATCAGG----ATAAGCACGTTGCGA--------------TGGG-----------AGCA--------------------------GTG--GGAGT---GG-GCAGGCTAATCGGTGGCGTTTCATCTG--TGAACTGC------------------TGTCC-----------------------TGTT--GCGGCTTGTTC s droTak2.KB461535 156774 116 - 669855 CCTCC-AGCGCCTGGTG----ATGTGGCATTGGGGGAGAAGC--------GGCG-----------GCTG---------------------GGACAGAG--GGAGC---GGCACAGGCTAATCGGTGGCGTTTCATCTG--CAGCCTGC------------------TGTCC-----------------------TGTT--GCCTCTTGTTC s droRho2.KB449310 51997 119 - 65043 CCTCC-AGCGGCAAAGG----ATGCTGAATAGGCGGAGTGGGGAGTGAAGAGGG-----------GGCA--------------------------GAG--GGAGC---GGCACAGGCTAATCGGTGGCGTTTCATCTG--CGGCCCGC------------------TGTCC-----------------------TGTT--GCCTCTTGTTC s droFic2.KB457177 94105 104 + 995874 CCTCC-AGCGGCTCAGG----ATGTGG-CAAGGAGG--------------AGTT-----------CGCC--------------------------GAG--GGAGC---GGCACAGGCTAATCGGTGCCGTTTCATCTG--CGACCCGC------------------TGTCC-----------------------TGTT--GCCTCTTGTTC s droPse3.chr3 1364131 99 - 19787792 CTTGG-cgaggtggggt---------------gggg--------------gggg-----------gtaA--------------------------GGT--GCAGCTATGCCCCTTGCTAATCGGTGGCGTTTCATCTG--CGGCCTGC------------------TGTCC-----------------------TGTTCGGGGGCTTGTTC s droPer1.super_34 552995 97 - 916997 CTTGG-CGAGGTGGGGT-----------------GG--------------GGGG-----------GTAA--------------------------GGT--GCAGCTATGCCCCTTGCTAATCGGTGGCGTTTCATCTG--CGGCCTGC------------------TGTCC-----------------------TGTTCGGGGGCTTGTTC s droMir2.chr3 1405213 98 - 20862834 CTtgg-tggggcggggt----------------ggg--------------gggg-----------gtaa--------------------------GGT--GCAGCTATGCCCCTTGCTAATCGGTGGCGTTTCATCTG--CGGCCTGC------------------TGTCC-----------------------TGTTCGGGGGCTTGTTC s droWil2.CH963894 1331813 126 + 2843958 ------Ggtgaagaagg----aggaggaggcagaGG--------------ACAA-----------GATG--------------------------GAGGAGGATT---GGC---GGCTAATCGGTGGCGTTTCATCTGAATACTCTGCGGTTGCTACTGTTCCTGATGTTCCTCTA------------------TGTTCACTAGCTTGTTT s droVir3.scaffold_12875 7370458 95 + 20611582 ------GGCGCCTGGCC---------------------------------AAAC-----------GCCA-------------------------------G-------------GGCTAATCGGTGGCGTTTCATCTG--ACTGCGCT------------------TAGTCCTCTTCCCTGCGCCTCTTTGATGTGTC--GCCCCTCTTCT s droMoj3.scaffold_6496 26165361 73 + 26866924 ------GGCGCCTGGAC---------------------------------AAAC-----------GCCA-------------------------------G-------------GGCTAATCGGTGGCGTTTCATCTG--ACTGCGCT------------------TGGTCC----------------------CGCC--AACTCTTTCCT s droAlb1.JH854640 327187 72 + 406291 ------gGCGCCTTGCC---------------------------------AAAC-----------GCCA---------------------------------------------GGCTAATCGGTGGCTTTTCATCTG--CTTCTGGT------------------CGTACCTC--------------------TACT--ACCTCTACT-- s droGri2.scaffold_15245 920770 77 + 18325388 ------GGCGCCTGGCC---------------------------------AAAC-----------GCCA---------------------------------------------GGCTAATCGGTGGCGTTTCATCTG--ACTGCGCC------------------TGCTCAGCGTT-----------------TGTC--CTCCCCCCTCA a score=48134.000000 s dm6.chr2R 24371133 3 + 25286936 GCC s droSim1.chr2R 18709866 3 + 19596830 GCC s droSec1.super_23 129220 3 + 989336 GCC s droYak3.chr2R 20219246 3 + 21139217 GCC s droEre2.scaffold_4845 21616792 3 + 22589142 GCC s droBia2.KB462602 811659 3 + 3129309 GCC s droSuz1.KI419649 12057721 3 - 14502029 GCC s droAna3.scaffold_13266 5721682 3 - 19884421 GCC s droBip2.KB464407 1971604 3 + 2915140 GGC s droEug2.KB465067 614315 3 + 1515531 GCC s droEle2.KB458573 537646 3 - 5320397 GCC s droKik2.KB459527 291007 3 - 1234237 GCC s droTak2.KB461535 156890 3 - 669855 GCC s droRho2.KB449310 52116 3 - 65043 GCC s droFic2.KB457177 94209 3 + 995874 GCC s droPse3.chr3 1364230 3 - 19787792 GGC s droPer1.super_34 553092 3 - 916997 GGC s droMir2.chr3 1405311 3 - 20862834 GGC s droWil2.CH963894 1331939 3 + 2843958 GGC s droVir3.scaffold_12875 7370554 3 + 20611582 GCC s droMoj3.scaffold_6496 26165435 3 + 26866924 GTC s droAlb1.JH854640 327259 3 + 406291 GCC a score=439996.000000 s dm6.chr2R 24371136 28 + 25286936 TGTCGGCGCACGCATAATTAGGCCTGAG s droSim1.chr2R 18709869 28 + 19596830 TGTCGGCGCACGCATAATTAGGCCTGAG s droSec1.super_23 129223 28 + 989336 TGTCGGCGCACGCATAATTAGGCCTGAG s droYak3.chr2R 20219249 28 + 21139217 TGTCGGCGCACGCATAATTAGGCCTGAG s droEre2.scaffold_4845 21616795 28 + 22589142 TGTCGGCGCACGCATAATTAGGCCTGAG s droBia2.KB462602 811662 28 + 3129309 TGTCGGCGCACGCATAATTAGGCCTGAG s droSuz1.KI419649 12057724 28 - 14502029 TGTCGGCGCACGCATAATTAGGCCTGAG s droAna3.scaffold_13266 5721685 28 - 19884421 TGTCGGCGCACGCATAATTAGGCCTGAG s droBip2.KB464407 1971607 28 + 2915140 TGTCGGCATACGCATAATTAGGCCTGAG s droEug2.KB465067 614318 28 + 1515531 TGTCGGCGCACGCATAATTAGGCCTGAG s droEle2.KB458573 537649 28 - 5320397 TGTCGGCGCACGCATAATTAGGCCTGAG s droKik2.KB459527 291010 28 - 1234237 TGTCGGCACACGCATAATTAGGCTTGAG s droTak2.KB461535 156893 28 - 669855 TGTCGCCGCACGCATAATTAGGCCTGAG s droRho2.KB449310 52119 28 - 65043 TGTCGGCGCACGCATAATTAGGCCTGAG s droFic2.KB457177 94212 28 + 995874 TGTCGGCGCACGCATAATTAGGCCCGAG s droPse3.chr3 1364233 28 - 19787792 TGTCGTCGCACGCATAATTAGGCCTGAG s droPer1.super_34 553095 28 - 916997 TGTCGTCGCACGCATAATTAGGCCTGAG s droMir2.chr3 1405314 28 - 20862834 TGTCGTCGCACGCATAATTAGGCCTGAG s droWil2.CH963894 1331942 28 + 2843958 TGTCGGCTCACGCATAATTAGGCCTGAC s droVir3.scaffold_12875 7370557 13 + 20611582 ---------------TTTCTAGCCGATA s droMoj3.scaffold_6496 26165438 13 + 26866924 ---------------TGATAGGCCttgt s droAlb1.JH854640 327262 10 + 406291 ---------------TAT---GCCTATG s droGri2.scaffold_15245 921232 28 + 18325388 tgtCGGCGCACGCATAATTAGGCCTGGG a score=161183.000000 s dm6.chr2R 24371164 33 + 25286936 GACAAT-CGTTTTGGCCGCTGCACTGCGAGAAAT s droSim1.chr2R 18709897 33 + 19596830 GACAAT-CGTTTTGGACGCTGCACTGCGAGAAAT s droSec1.super_23 129251 33 + 989336 GACAAT-CGTTTTGGCCGCTGCACTGCGAGAAAT s droYak3.chr2R 20219277 33 + 21139217 GACAAT-CGTTTTGCTcgctgcactgcgagaaac s droEre2.scaffold_4845 21616823 33 + 22589142 GACAAT-CGTTTTGGTGGCTGCACTGCGAGAAAT s droBia2.KB462602 811690 33 + 3129309 GACAAT-CGTTTTGGAAGCTCCACTGCGGGAAAT s droSuz1.KI419649 12057752 33 - 14502029 GACAAT-CGTTTTGGAAGCTGCACTTCAGGAAAT s droAna3.scaffold_13266 5721713 33 - 19884421 GACAAT-CGTTTTGGTTGTTGCATCAAAAGAAAT s droBip2.KB464407 1971635 33 + 2915140 GACAAT-CGTTTTGGTTGTTGCATCAAAAGAAAT s droEug2.KB465067 614346 33 + 1515531 GACAAT-CGTTTTGGCTTCTGCACTGCGGGAAAT s droEle2.KB458573 537677 33 - 5320397 GACAAT-CGTTTTGGCTGACACACTGcgggaaaa s droKik2.KB459527 291038 33 - 1234237 GACAAT-CGCTATGGCGAGTGCACTGGGGAAAAA s droTak2.KB461535 156921 33 - 669855 GACAAT-CGTTTCGGCCGCAGCACTGCGGGaaat s droRho2.KB449310 52147 33 - 65043 GACAAT-CGTTTTGGCTTTCACACTGCGGAAAAT s droFic2.KB457177 94240 33 + 995874 GACAAT-CGCTTTACTAGCTCCACTGCGGAAAAT s droPse3.chr3 1364261 24 - 19787792 GAcaat-cgtttcg----tttcgctccGT----- s droPer1.super_34 553123 24 - 916997 GACAAT-CGTTTCG----TTTCGCTCCGT----- s droMir2.chr3 1405342 24 - 20862834 GAcaat-cgtttcg----tttcgctccGT----- s droWil2.CH963894 1331970 30 + 2843958 GACAAT-CGCAAAATACACTGCAACACAAAA--- s droVir3.scaffold_12875 7370570 24 + 20611582 ---Agt-tgtcgttgtcgttgttgttgt------ s droMoj3.scaffold_6496 26165451 24 + 26866924 ---cgt-tgttgttgttgttgccattgt------ s droAlb1.JH854640 327272 25 + 406291 ---AGTGCATCtgagtatctgtatctgt------ a score=-404288.000000 s dm6.chr2R 24371197 43 + 25286936 TGGAGCGAG-----CTGATT------------AACATA----TA--------------TGTCA--CAACCAATGC-----------------------------------------------------------------------------------TAGCC--- s droSim1.chr2R 18709930 47 + 19596830 TGGAGCGAG-----CTGATT--------TATATACATA----TA--------------TGTCA--CAAGAAATGC-----------------------------------------------------------------------------------TAACC--- s droSec1.super_23 129284 43 + 989336 TGGAGCTAG-----CTGATT------------TACATA----TA--------------TGTCA--CAACAAATGC-----------------------------------------------------------------------------------TAGCC--- s droYak3.chr2R 20219310 40 + 21139217 tAGTGCGAG-----CTGATT------------TGCATA--------------------TGTCA---CACAGATAC-----------------------------------------------------------------------------------TAGAC--- s droEre2.scaffold_4845 21616856 47 + 22589142 TAGGGCGAG-----CTGATT------------TGCATACATGTG--------------CATCA--CCACAAACAC-----------------------------------------------------------------------------------TAGAC--- s droBia2.KB462602 811723 123 + 3129309 TGGTGGAA--------GATC------------CATGTT----TA--------------TAtca--ccaaaaattaaataataaatttaaaacatttattggttttatcgtctaataaatgtatctgtttatttattgaccATTTCGGTAACCCTTAAGAAGTA--- s droSuz1.KI419649 12057785 41 - 14502029 TAATGGGA--------GATT-----------ACATAGG----TA--------------TATca--ccaaaaatta-----------------------------------------------------------------------------------aagaa--- s droAna3.scaffold_13266 5721746 10 - 19884421 ------------------------------------------------------------CTA--CTACCAA---------------------------------------------------------------------------------------------- s droEug2.KB465067 614379 45 + 1515531 TAATAGGAT-----atagaa------------taaata----tt--------------tctcgATTTAAGAACAT-----------------------------------------------------------------------------------TGAAA--- s droEle2.KB458573 537710 41 - 5320397 taataatag-------tatt------------tgtata----ta--------------tatta--ccAAAAATGC-----------------------------------------------------------------------------------TGAAC--- s droKik2.KB459527 291075 31 - 1234237 -----------------------------Cgaaaagaa----ta--------------taata--atataaagtt-----------------------------------------------------------------------------------tAGAG--- s droTak2.KB461535 156954 33 - 669855 ---------------aaatg------------ggaaaa----ta--------------tatca--ccaaaaatta-----------------------------------------------------------------------------------aagaa--- s droRho2.KB449310 52180 41 - 65043 TAATGGcgg-------aata------------tattaa----ta--------------tatta--ccAGAATTGC-----------------------------------------------------------------------------------CCGAC--- s droFic2.KB457177 94275 56 + 995874 TTGGGCAACC----CCGACTGAGTCCCTTAGATGCTGG----Ac--------------tattt--ctaaaaatta-----------------------------------------------------------------------------------tcCAA--- s droPse3.chr3 1364285 39 - 19787792 ---------TTCGGCCCACT------------GAAAGA----AA--------------TACCT--GCAACCGGGT-----------------------------------------------------------------------------------TGGAG--- s droPer1.super_34 553147 39 - 916997 ---------TTCGGCCCACT------------GAAAGA----AA--------------TACCT--GCAACCGGGT-----------------------------------------------------------------------------------TGGAG--- s droMir2.chr3 1405366 39 - 20862834 ---------TTCGGCCCACT------------GAAAGA----AA--------------TACCT--GCAACCGGGT-----------------------------------------------------------------------------------TGGAG--- s droWil2.CH963894 1332000 20 + 2843958 ----------------------------------------------------------GGCTA--AAATAGATAA-----------------------------------------------------------------------------------TAAAT--- s droVir3.scaffold_12875 7370594 40 + 20611582 ----------------------------------------cgtagttgttgttgtcgttgtcg--ttgtcgttgt-----------------------------------------------------------------------------------cCCTGGC- s droMoj3.scaffold_6496 26165475 41 + 26866924 ----------------------------------------cgttgtcgttgtcgtagttgtcg--ttgtcgttgt-----------------------------------------------------------------------------------cgctgGCC s droAlb1.JH854640 327297 25 + 406291 ----------------------------------------ccTG--------------TATCA--GAATC--TGT-----------------------------------------------------------------------------------CCACTGCG a score=-76427.000000 s dm6.chr2R 24371240 10 + 25286936 --TTTTTT-CTAA s droSim1.chr2R 18709977 10 + 19596830 --TTTTTA-CTAA s droSec1.super_23 129327 10 + 989336 --TATTTC-ATAA s droYak3.chr2R 20219350 10 + 21139217 --GAGCTG-AATG s droEre2.scaffold_4845 21616903 3 + 22589142 --TAG-------- s droBia2.KB462602 811846 10 + 3129309 --TGAGTT-TCAA s droSuz1.KI419649 12057826 10 - 14502029 --tgtttt-tcaa s droEug2.KB465067 614424 10 + 1515531 --GATTCC-GTGA s droEle2.KB458573 538035 10 - 5320397 --tttttt-ctaa s droKik2.KB459527 291126 9 - 1234237 --tttttc-atG- s droTak2.KB461535 156987 10 - 669855 --catttt-aaaa s droRho2.KB449310 52221 10 - 65043 --TCTCTC-CCAA s droFic2.KB457177 94339 10 + 995874 --TTTATT-TTAG s droPse3.chr3 1364325 9 - 19787792 --TTCCTT-GGA- s droPer1.super_34 553187 9 - 916997 --TTCCTT-GGA- s droMir2.chr3 1405406 9 - 20862834 --TTCCTT-GGA- s droWil2.CH963894 1332028 9 + 2843958 --TGTTTA-GTA- s droVir3.scaffold_12875 7370634 7 + 20611582 -TTGTTCT----- s droMoj3.scaffold_6496 26165516 8 + 26866924 GTTGTTCT----- s droAlb1.JH854640 327322 9 + 406291 ACTGTCCTG---- a score=-207463.000000 s dm6.chr2R 24371250 26 + 25286936 ----------TCATATTT--ATACTGCTC--------CTAGATTGA s droSim1.chr2R 18709987 26 + 19596830 ----------TCATATTC--GTACAGCTC--------CTAGATTAA s droSec1.super_23 129337 26 + 989336 ----------TCATATTC--GTTCAGCTC--------CTAGATTGG s droYak3.chr2R 20219360 34 + 21139217 ----------ATTCATTC--GTATAGCTCTAGATTTACTAGATTGA s droEre2.scaffold_4845 21616906 28 + 22589142 ----------------GG--GTACAGCAGTAGATCGAGTAGATTGA s droBia2.KB462602 811856 26 + 3129309 ----------TCCtgatt--atattataa--------gaagatata s droAna3.scaffold_13266 5721756 19 - 19884421 -----------CAAAATA--ATA--------------CAAAATTAA s droEug2.KB465067 614440 26 + 1515531 ----------TCAAATAA--ACTCTGGCA--------GTAAATCAA s droEle2.KB458573 538045 23 - 5320397 -------------tgaaA--ATACTTGAA--------TGTAATTTG s droKik2.KB459527 291135 28 - 1234237 ----------TCGAATTT--GGTCAAAAATG------acagtttta s droTak2.KB461535 156997 22 - 669855 --------------agat--ctaATGGTC--------CTAATTCAA s droFic2.KB457177 94349 24 + 995874 ------------TCAGAA--ATGGTAATA--------ATGTATTCA s droPse3.chr3 1364340 10 - 19787792 ----------TCCGCTGC--GT------------------------ s droPer1.super_34 553202 10 - 916997 ----------TCCGCTGC--GT------------------------ s droMir2.chr3 1405421 10 - 20862834 ----------TCCGCTGC--GT------------------------ s droWil2.CH963894 1332037 11 + 2843958 ----------GCAAGCTT--ATA----------------------- s droVir3.scaffold_12875 7370641 21 + 20611582 -GTTGTCTTGGCGCACGC--ATAA---------------------- s droMoj3.scaffold_6496 26165524 21 + 26866924 -GTTGTCTTGGCTCACGC--ATAA---------------------- s droAlb1.JH854640 327331 24 + 406291 AGCTGTCCCAGCGTTAGCCGATAa---------------------- a score=-474005.000000 s dm6.chr2R 24371276 46 + 25286936 G-----------TTGCTAAG---------------TTTGGTTTTC-----------------------ATCT------------------CATGTACAAT----------------------------------------------------------------GTTCCACA--------GCAAT s droSim1.chr2R 18710013 46 + 19596830 G-----------TTGCTAAG---------------TTTGGTTTTC-----------------------ATTT------------------CATGTACAAT----------------------------------------------------------------GCTCCACA--------GCAAT s droSec1.super_23 129363 42 + 989336 T-----------TTG----G---------------TTTGATTTTC-----------------------ATCT------------------TATGTACAAT----------------------------------------------------------------GTTCTACA--------GCAAT s droYak3.chr2R 20219394 52 + 21139217 G-----------TGTAGAAG---------------CATGTTGTATTCTA------------AAGTCATATTT------------------CCTTTTCAAT----------------------------------------------------------------GTAGTACA------------- s droEre2.scaffold_4845 21616934 76 + 22589142 GATCTATATTGATATAGAAG---------------CATGTTTCTTTCTG------------ATGTCAAATTT------------------CCTGTTCAAT----------------------------------------------------------------GTAGCATGAGATGTGCTCATT s droBia2.KB462602 811882 79 + 3129309 t-----------ttaacaaaacatTGCATTCCTACTATGCCCTTTTCTG------------AGTTTAGATCTTGG-----------AATATATTTGAAAG----------------------------------------------------------------ATTATTTA--------GGAAG s droAna3.scaffold_13266 5721775 21 - 19884421 G------------------G------------------------------------------------ATAT----------------------TCCAAA----------------------------------------------------------------GCAGTAAA--------G---- s droEug2.KB465067 614466 42 + 1515531 C-----------TTTATTAG------------------ATACTTA-----------------------ATCT---------------AAGCTATTCCAAT----------------------------------------------------------------ATATGAAA--------G---- s droEle2.KB458573 538068 49 - 5320397 A-----------ATCAAAAG---------------CTTCTAATTTTctgca-----aaacaattaaacatat----------------------tttaat----------------------------------------------------------------gt------------------- s droKik2.KB459527 291163 133 - 1234237 a-----------ttgaaaaa---------------ctagTCTTGAATAATAtctattaacaaatttaaatta------------------tatttccaatttctaaaataatttacacatTAAACCATGTGGATATCTACTTAAATTCCTAAACTAAATACTAAACTACACa--------gcaat s droFic2.KB457177 94379 48 + 995874 ------------------------------------------------------------GCgtctatattt---------------aaatattttcgatcgataatata------------------------------------------------------attttaca--------atttg s droPse3.chr3 1364350 22 - 19787792 --------------------------------------------------------------------------GCCTCT----CCGTGGGGTTTTCGGC------------------------------------------------------------------------------------- s droPer1.super_34 553212 22 - 916997 --------------------------------------------------------------------------GCCTCT----CCGTGGGGTTTTCGGC------------------------------------------------------------------------------------- s droMir2.chr3 1405431 22 - 20862834 --------------------------------------------------------------------------GCCTCT----TCGTGGGGTTTTCGGC------------------------------------------------------------------------------------- s droWil2.CH963894 1332048 19 + 2843958 -------------------------------------------------------------------GGTTT------------------TTTGTCAAGT----------------------------------------------------------------GTAT----------------- s droVir3.scaffold_12875 7370662 26 + 20611582 ----------------------------------------------------------TTAGGCCTGGTTCT--CCT--------------AGTCGCAGC------------------------------------------------------------------------------------- s droMoj3.scaffold_6496 26165545 40 + 26866924 ----------------------------------------------------------TTAGGCCTGGTTCT--GCTTCTGCTGCTACTCCAGGCTCTGC------------------------------------------------------------------------------------- s droAlb1.JH854640 327355 42 + 406291 ----------------------------------------------------------gttgtcgtagttgttggcttgttttgtttgggcCATCGCAGC------------------------------------------------------------------------------------- a score=-22417.000000 s dm6.chr2R 24371322 4 + 25286936 CT---AC-- s droSim1.chr2R 18710059 4 + 19596830 CT---AC-- s droSec1.super_23 129405 4 + 989336 CT---AC-- s droYak3.chr2R 20219446 2 + 21139217 -----AC-- s droEre2.scaffold_4845 21617010 7 + 22589142 CGAGTAC-- s droBia2.KB462602 811961 1 + 3129309 C-------- s droKik2.KB459527 291296 4 - 1234237 tcaa----- s droTak2.KB461535 157497 4 - 669855 ---CTac-- s droFic2.KB457177 94434 4 + 995874 ---gtac-- s droVir3.scaffold_12875 7370688 2 + 20611582 -----GT-- s droMoj3.scaffold_6496 26165585 2 + 26866924 -----AT-- s droAlb1.JH854640 327397 4 + 406291 -----GCAC a score=-6327.000000 s dm6.chr2R 24371326 5 + 25286936 ATTTT s droSim1.chr2R 18710063 5 + 19596830 ATTTA s droSec1.super_23 129409 5 + 989336 ATTTA s droYak3.chr2R 20219448 5 + 21139217 ATATC s droEre2.scaffold_4845 21617017 5 + 22589142 ACCTC s droBia2.KB462602 811962 5 + 3129309 ATCTT s droSuz1.KI419649 12058328 5 - 14502029 ACCCT s droAna3.scaffold_13266 5721798 3 - 19884421 GTC-- s droEug2.KB465067 614508 5 + 1515531 AACAC s droEle2.KB458573 538117 5 - 5320397 attta s droKik2.KB459527 291300 3 - 1234237 --att s droTak2.KB461535 157501 5 - 669855 gcttt s droFic2.KB457177 94438 5 + 995874 atttt s droWil2.CH963894 1332067 4 + 2843958 -TTTA s droMoj3.scaffold_6496 26165587 3 + 26866924 --CTA s droAlb1.JH854640 327401 5 + 406291 GCATA a score=1137.000000 s dm6.chr2R 24371331 1 + 25286936 A s droSim1.chr2R 18710068 1 + 19596830 A s droSec1.super_23 129414 1 + 989336 A s droYak3.chr2R 20219453 1 + 21139217 A s droEre2.scaffold_4845 21617022 1 + 22589142 A s droBia2.KB462602 811967 1 + 3129309 A s droSuz1.KI419649 12058333 1 - 14502029 T s droEug2.KB465067 614513 1 + 1515531 T s droEle2.KB458573 538122 1 - 5320397 a s droKik2.KB459527 291303 1 - 1234237 a s droTak2.KB461535 157506 1 - 669855 t s droRho2.KB449310 52606 1 - 65043 A s droFic2.KB457177 94443 1 + 995874 a s droWil2.CH963894 1332071 1 + 2843958 A s droMoj3.scaffold_6496 26165590 1 + 26866924 G s droAlb1.JH854640 327406 1 + 406291 A a score=15541.000000 s dm6.chr2R 24371332 3 + 25286936 TTT- s droSim1.chr2R 18710069 3 + 19596830 TTT- s droSec1.super_23 129415 3 + 989336 TTT- s droYak3.chr2R 20219454 3 + 21139217 TTT- s droEre2.scaffold_4845 21617023 3 + 22589142 TTT- s droBia2.KB462602 811968 3 + 3129309 TTT- s droSuz1.KI419649 12058334 3 - 14502029 TTT- s droEug2.KB465067 614514 3 + 1515531 TTT- s droEle2.KB458573 538123 3 - 5320397 ttt- s droKik2.KB459527 291304 3 - 1234237 ttt- s droTak2.KB461535 157507 3 - 669855 ttt- s droRho2.KB449310 52607 3 - 65043 TTT- s droFic2.KB457177 94582 3 + 995874 TTT- s droWil2.CH963894 1332072 3 + 2843958 CTT- s droMoj3.scaffold_6496 26165591 3 + 26866924 -TTC s droAlb1.JH854640 327407 3 + 406291 -TTA a score=4571196.000000 s dm6.chr2R 24371335 700 + 25286936 GGC---TAAGTGCACT----------------AGTAGCAGGTTA--CCC----------CTCG-----------CAA--------------TTT-G------GCCAAATAATTGGT-AACCGA-AAACAATAAG-----------------CTC-----------GTTCCT--------CGT----------------A--CT--------CCC------------------G-GCCAATCGTGGCATCCTAATGC---GGCC----CAGACATTTAAATAGATGCTAATTC---C--CATCATAACTGGCT--------------GGAGA---------------------CCCCATTTCCCGTTC-TC--------------------------------GGGTCC--------AA--ATGAACTA--ATGAATT------------------TGAACCC-----GCC-----------------------ACT--CGA-TT------------GTGG-----CAGA----------------------CTC--ACGA-----CGAT----------TGGAGG-----C----------GACTGCCA------------------------------------ACTTCCTG---------CTGGCCGCTTTCTTT-GCGCGTGAATCCGTGTAACCGCAAC---------------------CC----------------------------GCACCAGA--G----AAAA------------GACACAAAACTGTGATTTGCCCAAA---AACAG-AAAGCC-------GGCCAGAAAGCCTC-------------------------GCTTTGCGGATATAAACGCT-TTAAAA------CTCCATA--TTGT-------GGCC-----------TGGCCCGGATGCGA---------------------------------------CGACAATTGTGAA---GA----C--GACC-AAAT---------------------GGCCA-AA-------TC------CG-----ACTCCGAGT-------TTAGCT-------------------GGCAAA--TGTCTACGCAGTGTTGTC---GCTTCTGCC----GCTTTTGTTGC---C----CTGCGCT------GTTGCCA-----GATGCCAgt----------tggttgttg--gtagtt-ggtagttgcttgt-tggttgt--tcgcttgttgC------------------CGCTTCGTGTCAACT-------GACT-TCTGCCTC--------------------------------------------------AGCTTTC--------------GGCTTTTGTTTCGTCG-----TGGCAAGCCGCCCCATTTTGCTTAGCC------------A----------------------GCCA------------------AGCCAT---------------CCCATAACATTTTCCCCAACGTTTCCTGC s droSim1.chr2R 18710072 688 + 19596830 GGC---TAAGTGAACT----------------AGTAGCAGGTTA--CCC----------CTCG-----------CAA--------------TTT-G------GCCAAATAATTGGT-AACCGA-AAACAATAAG-----------------CTC-----------GTTCCT--------CGT----------------A--CT--------CCC------------------G-GCCAATCGTGGCATCCTAATGC---GGCC----CAGACATTTAAATAGATGCTAATTC---C--CATCATAACTGACT--------------GGAGA---------------------CCCCGTTTCCCGTTC-TC--------------------------------GGGTCC--------AA--ATGAACTA--ATGAATT------------------TGAACCC-----GCC-----------------------ACT--CGA-TT------------GTGG-----CAGA----------------------CTC--ACGA-----CGAT----------TGGAGA-----C----------GACTGCCA------------------------------------ACTTCCTG---------CTGGCCGCTTTCTTT-GCGCGTGAATCCGTGTAACCGCAAC---------------------CC----------------------------GCACCAGA--G----AAAA------------GGCACAAAACTGTGATTTGCCCAAA---AACAG-AAAGCC-------GGCCAGAAAGCCTC-------------------------GCTTTGCGGATATAAACGCT-TTAAAA------CTCCATA--TTGT-------GGCC-----------TGGCCCGGATGCGA---------------------------------------CGACAATTGTGAA---GA----C--GACC-AAAT---------------------GGCCA-AA-------TC------CG-----ACTCCGAGT-------TTAGCT-------------------GGCAAA--TGTCTACGCAGTGTTGTC---GCTTCTGCC----GCTTTTGTTGC---C----CTGCGTT------GT------------TGCCAGT----------TGGTTGTTG--GTAGTT-GGTAGTCGCTTGT-TGGTTGT--TCGCTTGTTGC------------------CGCTTCGTGTCAACT-------GACT-TCTGCCTC--------------------------------------------------AGCTTTC--------------TGCTTTTGTTTCCTCG-----TGGCAAGCCGCCCCATTTTGCTTAGCC------------A----------------------GCCA------------------ACCCAT---------------AACA-----TTTTCCCCAACGTTTCCTGC s droSec1.super_23 129418 676 + 989336 GGC---TAAGTGCACT----------------AGTAGCAGGTTA--CCC----------CTCG-----------CAA--------------TTT-G------GCCAAATAATTGGT-AACCGA-AAACAATAAG-----------------CTC-----------GTTCCT--------CGT----------------A--CT--------CCC------------------G-GCCAATCGTGGCATCCTAATGC---GGCC----CAGACATTTAAATAGATGCTAATTC---C--CATCATAACTGACT--------------GGAGA---------------------CCCCGTTTCCCGTTC-TC--------------------------------GGGTCC--------AA--ATGAACTA--ATGAATT------------------TGAACCC-----GCC-----------------------ACT--CGA-TT------------GTGG-----CAGA----------------------CTC--ACGA-----CGAT----------TGGAGG-----C----------GACTGCCA------------------------------------ACTTCCTG---------CTGGCCGCTTTCTTT-GCGCGTGAATCCGTGTAACCGCAAC---------------------CC----------------------------GCACCAGA--G----AAAA------------GACACAAAACTGTGATTTGCCCAAA---AACAG-AAAGCC-------GGCCAGAAAGCCTC-------------------------GCTTTGCGGATATAAACGCT-TTAAAA------CTCCATA--TTGT-------GGCC-----------TGGCCCGGATGCGA---------------------------------------CGACAATTGTGAA---GA----C--GACC-AAAT---------------------GGCCA-AA-------TC------CG-----ACTCCGAGT-------TTAGCT-------------------GGCAAA--TGTCTACGCAGTGTTGTC---GCTTCTGCC----GCTTTTGTTGC---C----CTGCGTT------GT------------TGCCAGT----------TGGTTGTTG--GTAGTT--------GCTTGT-TGGTTGT--TCGCTTGTTGC------------------CGCTTCGTGTCAACT-------GACT-TGTGCCTC--------------------------------------------------AGCTTTC--------------GGCTTTTGTTTCCTCG-----TGGCAAGCCGCCCCATTTTGCTTAGCC------------A----------------------GCGA------------------AGCCAG---------------CCAA----------CCCAACGTTTCCTGC s droYak3.chr2R 20219457 749 + 21139217 AGC---TCAGTGCACT----------------AGTGGCAGGTTA--CCC----------CGCG-----------CAA--------------TTT-G------GCCAAATAATTGGT-AACCGA-AAACAATAAG-----------------CTC-----------GTTTCT--------CGT----------------A--CT--------CCC------------------A-ACCAATCGTGGCATCCTAATGC---GGCC----CAGACATTTAAATAGATGCTAATTC---C--CATCATAACTGACT--------------GGAGACCCCGTCTCCCGTCTCCCGTTCCCCCTTCCCCGTTC-TC--------------------------------GGCTCT--------CG--ATGAACTA--ATGAATT------------------TGAACCC-----GCC-----------------------ACT--CGA-TT------------GTGG-----CAGA----------------------CTC--ACGACGCGGCGAT----------TGGAGG-----C----------GACTTGCA------------------------------------ACTTCCTG---------CTGGCCGCTTTCTTT-GCGCGTGAATCCGTGTAACCGCAACCAGCAACCCGCAATCCGCCATCC----------------------------GCACCAGA--G----AAAA------------GGCACAAAACTGTGATTTGCCCAAA---AACAG-AAAGCC-------GGCCAGAAAGCCTC-------------------------GCTTTGCGGATATAAACGCT-TTAAAA------CTCCATA--TTGT-------GGCC-----------TGGCCCGGATGCGA---------------------------------------CGACAATTGTGAA---GACGACC--GACC-AAAT---------------------GGCCA-AA-------TC------CG-----ACTCCCAGT-------TTAGCT-------------------GGCAAA--TGTCTACGCAGTGTTGTC---GCTTCTGCC----GCTTttgttgc---c----ctgcgtt------gttgcca-----gttgccagt----------tggttgttg--ccagtt-ggtagttgcttgt-tggttgt--tcgcttgttgc------------------cGCTCCGTGTCAACT-------GACT-TTTGCCTC--------------------------------------------------AGCTTTC--------------GGCTTTTGTTTCCACC-----AGC--ACCAGCCCCATTTTGCTTAGCC------------A----------------------GCCA------------------AGCCAT---------------CCCATAACATTTTCCCCAGCGCTTCCTGC s droEre2.scaffold_4845 21617026 723 + 22589142 GGC---TGAGTGCACT----------------GGTAGCAGGTTA--GCC----------CTCG-----------CAA--------------TTC-G------GCCAAATAATTGGT-AAGCCA-AAACAATAAG-----------------CTC-----------GTTTCT--------CGT----------------A--CT--------CCC------------------G-GCCAATCGTGGCATCCTAATGC---GGCC----GAGACATTTAAATAGATGCTAATTC---C--CATCATAACTGACT--------------GGAGA----------------------CCCGTTTCCCGTTC-TC--------------------------------GGGTCC--------AA--ATGAACTA--ATGAATT------------------TGAACCC-----GCC-----------------------ACT--CGA-TT------------GTGG-----CAGA----------------------CTC--ACGA-----CGAT----------TGGAGG-----C----------GACTTCCA------------------------------------ACTTCCTG---------CTGGCCGCTTTCTTT-GCGCGTGAATCCGTGTAACCGCAGC---------------------CC----------------------------GCAGCAGA--G----AAAA------------GACAC-AAACTGTGATTTGCCCAAA---AACAG-AAAGCC-------GGCCAGAAAGCCTCGCTTTGC----------------GGGCTTTGCGGATATAAACGCT-TTAAAA------CTCCATA--TTGT-------GGCC-----------TGGCCCGGATGCGA---------------------------------------CGACAATTGTGAA---GA----C--GACC-AAAT---------------------GGCCA-AA-------TC------CG-----ACTCCGAGT-------TTAGCT-------------------GGCAAA--TGTCTACGCAGTGTTGTC---GCTTCTGCC----GCTTTTGTTGC---C----CTGCGCT------GCTGCCA-----GTCGGTTGT----------TGGTAGTTG--GTTGTT-GGCTGTTGGCTGT-TGGTTGT--TCGCTTGTTGC------------------CGCTTCGTGTCAACT-------GACT-TTTGCCTC--------------------------------------------------AGCTTTC--------------GGCTTTTGTTTCCACC-----AGCCAAGCCGCCCCATTTTGCTTAGCC------------A----------------------GCCGC--CAACCGAGCCATCCCAGCCAT---------------CCCATAACATTTTCCCCAGCGTTTCCTGC s droBia2.KB462602 811971 731 + 3129309 TCGC--CGAGTGCTCT----------------AGTAGCAGGTTA--CCC----------CTCG-----------CAA--------------TTC-G------GCCAAATAATTGGT-AACTGA-AAACAATAAG-----------------CTC-----------GTTTTT--------CGT----------------A--CT--------CCC------------------G-GCCAATCGTGGCATCTTAATGC---GGCC----CTGACATTTAAATAGATGCTAATTC---C--CATCATAACTGACT--------------GGGGG-------------CCCGGGCCCCACAATTCCCGTTCGCC--------------------------------GGGTGG--------GT--CTGAACTA--ATGAATT------------------TGAACCC-----GCC-----------------------ACT--CGA-TT------------GAGA-----CAGA----------------------CTC--ACGA-----CGAC----------CCGACT-----C----------GACTGCGACTCGGAG-------------------------CTCCACTTCCTG---------CTGGCCGCTTTCTTT-GCGCGTGAATCCGTGTAACCGCAGG---------------------CC----------------------------GCAGCGGA--G---AAAAA------------GACACAAAACTGTGATTTGCCCAAA---AACAG-AAAGCC-------GGCAAGAAAGCTCCGCTTCGG-----CTTGCTTTGCCTTGCTTTGCGGATATAAACGCT-TTAAAA------CTCCATA--TTGC-------GGCC-----------TGGCCCGGATGCGA---------------------------------------CGACAATTGTGAA---GA----C--GACC-AAAT---------------------GGCCA-AAC------TC------CG-----ACTCCGAGT-------TTAGCT-------------------GGCAAA--TGTCTACGCAGTGTTGTC---GCTTCTCCC----GCCTttgttgc---c----cgtggtt------gt------------tggctgt----------tggttgttg--gttgtt-ggttgttggatgt-tggttgt--tcgcttgttgC------------------CGCTCCGTGTCAACT-------GAC--TGGGCCTT--------------------------------------------------AGCTTTC--------------GGCTTTTGTTTCCACC-----ATCCGTGCCGCCCCATTTCGCTTA--------------------------------------GCCA------------------AGCCAT---------------CCCATAACATTCGCCCCAACGTTTCCTGT s droSuz1.KI419649 12058337 736 - 14502029 GTG---CGAGTGCATT----------------AGTAGCAGGTTA--CCC----------CTCG-----------CAA--------------TTT-G------GCCAAATAATTGGT-AACTGA-AAACAATAAG-----------------CTC-----------GTTTTT--------CGT----------------A--CT--------CCC------------------G-GCCAATCGTGGCATCTTAATGC---GGCC----CTGACATTTAAATAGATGCTAATTC---C--CATCATAACTGACT--------------GGGGA------------CCCCGAGCTCTACAATTCCCGTTTGCC--------------------------------GGGTGG--------GT--CTGAACTA--ATGAATT------------------TGAACCC-----GCC-----------------------ACT--CGA-TT------------GAGA-----CAGA----------------------CTC--ACGA-----CGAC----------CCAAGT-----C----------GACTTCG-------------------------------------ACTTCCTG---------CTGGCCGCTTTCTTT-GCGCGTGAATCCGTGTAACCGCAAC---------------------CC----------------------------GCATCAGA--G---AAAAA------------GACACAAAACTGTGATTTGCCCAAA---AACAG-AAAGCC-------GGCAAGAAAGCTTCGCTTCggtttgctttgctttgctttgctttgcGGATATAAACGCT-TTAAAA------CTCCATA--TTGT-------GGCT-----------TGGCCCGGATGCGA---------------------------------------CGACAATTGTGAA---GA----C--GACC-AAAT---------------------GGCCA-AAC------TC------CG-----ACTCCCAGT-------TTAGCT-------------------GGCAAA--TGTCTACGCAGTGTTGTC---GCTTCTCCC----GCTTttgttgc---c----catggtt------gt------------tggtagt----------tggttgttg--gctgtt-ggt-------tgt-tggttgt--tcgcttgttgC------------------CGCTTCGTGTCAACT-------GACT-TGGGCCTT--------------------------------------------------AGCTTTC--------------GGCTTTTGTTTCCACA-----AGCCAAGCCGCCCCATTTTGCTTAGCC------------GGG-CCGGCA-------AAGTTGGCCA------------------AGCCAT---------------CCCATAACATTTGCCTCAACGTTTCCTGT s droAna3.scaffold_13266 5721812 775 - 19884421 GGC---TAGATG---T----------------TGCGGCAGGTTA--GCC----------CTCG-----------CAA--------------TTT-G------GCCAAATAATTGCTGAACTGA-AAACAATAAG-----------------CTC-----------GTTTCT--------CGT----------------A--CT--------CTC------------------GCAGCAATCGTGGCATCTTAATGC---GGCC----ATGACATTTAAATAGATGCTAATTC---C--CATCATAACTGACT--------------CGCAG---------------------------TACCCGCTC-CC--------------------------------TG------------AA--CTAAACTA--ATGAATT------------------TGAACTT-----TCC-----------------------ACG--CGA-TTTTTTGGGTG---GAAA-----AAGA----------------------CTC--ACGACTTG-CGAT----------TCGAAT-----T----------GAATCCGAATCCGAATCGGAATCGTAATCGTATTGAGACTCTCTACTTCCTG----TTGGCCTGGCCGCTTTCTTT-GCGCGTGAATCCGTGTAACCACAGA---------------------GC----------------------------AAA-------G----AAAAC-----------AAAAAAAAACAGTGATTTGACCAAA---AACAGAAAAGCC-------GGCAAGAAA------------------------------GCTTTGCGGATATAAACGCT-TTAAAA------CTCCATA--TTGT-------GGCC-G-------CTTGGCCCGGATGCTA--------------CGACGACAACAGTA----------GCGACAATTGTGAAG-AGA----A--GACC-AAAT---------------------GGCCA-AC-------CT------CC-----CCTTGGAGC-------TTAGCT-------------------GGCAAA--TGTCTACGCAGTGTCGTCTTGGCCAGTGTC----GTTCCTGCCTC---T----TTTCATTTTGGTtgttgctacttctgctgccact---------gctgctactg--ctact---gcCTCCGCTGATGTGGTTGT--TCGCTTGTTGC------------------CGTTTCGTGTCAACT-------GACT-TGGGCCTT--------------------------------------------------AGCTTTC--------------GGCTTTTGTTTCCACC----------AGCCGCCCCATTTTGCTAagccagcaagccagcca----------------------gcc-------------------agccaT---------------CCCATAACATTTGCCTTTACGTTTCCTGT s droBip2.KB464407 1971736 769 + 2915140 GGC---TAGTTG---T----------------GGCAGCAGGTTA--GCC----------CTCG-----------CAA--------------TTT-G------GCCAAATAATTGCC-AACTGA-AAACAATAAG-----------------CTC-----------GTTTCT--------CGT----------------A--CT--------CTC------------------GCAGCAATCGTGGCATCTTAATGC---GGCC----CTGACATTTAAATAGATGCTAATTC---C--CATCATAACTGACT--------------CGCAC---------------------------AACTAGCTC-CC--------------------------------TG------------AA--CTAAACTA--ATGAATT------------------TGAACTT-----TCC-----------------------ACg--cgattttttttggtgaaaaaaa-----aaga----------------------ctc--aCGACT---CGAT----------TCGAAT-----TGA----ATTCGAATCCAAATCCGAATCGTAATCGTAATTGTATTGAGACTCTCTACTTCCTG----TTGGCCTGGCCGCTTTCTTT-GCGCGTGAATCCGTGTAACCAcaaa---------------------ga----------------------------aaacagaaacg----aaaataacaaagtaaaaaaaaaaaactgtgatttgaccaaa---aacagaaaagcc-------GGCAAGAAA------------------------------GCTTTGCGGATATAAACGCT-TTAAAA------CTCCATA--TTGT-------GGCC-G-------CCTGGCCCGGATGCTA--------------CGACGACAACAGTA----------GCGACAATTGT------GA----A--GACC-AAAT---------------------GGCCA-AC-------CT------CC-----CC---AAGC-------TTAGCT-------------------GGCAAA--TGTCTACGCAGTGTCGTCTTGGCCACCGCC----GTTCCTGCCTC---T----TTTCATT----ctgttgccactgccacagcca------------ctGTTACTG--CTACT---GCTTCTGGTGATGTGGTTGT--TCGCTTGTTGC------------------CATTTCGTGTCAACT-------GACT-TGGGCCTT--------------------------------------------------AGCTTTC--------------GGCTTTTGTTTCCACC----------AGCCGCCCCATTTTGCTA----------------A----------------------GCC-------------------AGCCAT---------------CCCATAACATTTGCCTTAACGTTTCCTGT s droEug2.KB465067 614517 703 + 1515531 CGT---CGAGTGCATA----------------AGTAGCAGGTTA--CCC----------CTCG-----------CAA--------------TTT-A------GCCAAATAATTGGT-AACTGA-AAACAATAAG-----------------CTC-----------GTTTTT--------CGT----------------A--CT--------CCC------------------G-GCCAATCGTGGCATCTTAATGC---GGCC----CTGACATTTAAATAGATGCTAATTC---C--CATCATAACTGACT--------------CGGGA--------------------CCCCGAGTTCCCGTTTGCC--------------------------------GGGTC--------------TGAACTA--ATGAATT------------------TGAACCC-----GCC-----------------------ACT--CGA-TT------------GAGA-----CTGG----------------------CTC--ACGA-----CGAC----------CCGACT-----CCATTCCATTCGATTACCA------------------------------------ACTTCCTG---------CTGGCCGCTTTCTTT-GCGCGTGAATCCGTGTAACCGCAAC---------------------CC----------------------------GCATCAGA--A----AAAA------------GACACAAAACTGTGATTTGCCCAAA---AACAG-AAAGCC-------GGCAAGAAAGCTTT-------------------------GCTTTGCGGATATAAACGCT-TTTAAA------CTCCATA--TTGT-------GGCC-----------TGGCCCGGATGCGA---------------------------------------CGACAATTGTGAA---GA----C--GACC-AAAT---------------------GGCCA-AA-----------------------CTCCGAGT-------TTAGCT-------------------GGCAAA--TGTCTACGCAGTGTTGTA---GCTTCTCCC----GCT-TTGCGgc---t----ctt-gtt------gt------------tgtgtgt----------tgtatgttg--ccagtt-ggt-------tgt-tggttgt--tcgcttgttgC------------------CGCTTCGTGTCAACC-------GACT-TGGGCCTT--------------------------------------------------AGCTTTC--------------GGCTTTTGTTTCCACA-----AGCCAGGCCGCCCCATTTTGCTTAGCC------------A----------------------GCCAA-GCCAGCAAGCTGGCC-AGCCGT---------------CCCATAACATTTGCTTCAACGTTTCCTGT s droEle2.KB458573 538128 738 - 5320397 ggC-----AGTGCACT----------------AGCAGCAGGTTA--CCC----------CTCG-----------CAA--------------TTT-G------GCCAAATAATTGGT-AACTGA-AAACAATAAG-----------------CTC-----------GTTTTT--------CGT----------------ACTCT--------CCC------------------G-GCCAATCGTGGCATCTTAATGC---GGCG----CAGACATTTAAATAGATGCTAATTC---C--CATCATAACTGACT--------------CGAGG----------------------------CCCCATTC-TC--------------------------------AA--TG--------GT--CTGAACTA--ATGAATT------------------TGAACCC-----GCCGGTCGATTACT-CGGCTGTGGCTGCT--CGA-TT------------GAGA-----CAGA----------------------CTC--ACGA-----AGAA----------TCGACT-----C----------AACTCTCT------------------------------------ACTTCCTG---------CTGGCCGCTTTCTTTAGCGCGTGAATCCGTGTAACCGCAAC---------------------CC----------------------------GCAGCACA--GAAGAAAAA------------GACACAAAACTGTGATTTGCCCAAA---AACAG-AAAGCC-------GGCAAGAaagctttgctttgctttgctctgCTCTGCCTCGCTTTGCGGATATAAACGCT-TTAAAA------CTCCATA--TTGT-------GGCC-----------TGGCCCGGATGCGA---------------------------------------CGACAATTGTGAA---GA----CCAGACC-AAAT---------------------GGCCA-AA-----------------------CTCCCAGT-------TTAGCT-------------------GGCAAA--TGTCTACGCAGTGTTGTC---GCTTCTTCT----GCTTTTGCTGA---t----gtg-gtt------gt------------tggctgt----------tggttgttg--tccgtt-ggc-------tgt-tggttgt--tcgcttgttgC------------------CGCTTCGTGTCAACT-------GAGT-TGGGCCTT--------------------------------------------------AGTTTTC--------------GGCTTTTGGTTTCACA-----AGCCAAGCCGCCCCATTTTGCTTAGCC------------A----------------------CCCAGagccatcgccat-----tgccat---------------cCCATAACATTTGCCTCAACGTTTCCTGT s droKik2.KB459527 291308 707 - 1234237 --------aatgattt----------------atttacttactA--CCCATTTTCGTGACGtg-----------caaatgcaacagcagGTTTA-G------GCCAAATAATTGCC-AACTGA-AAACAATAAG-----------------CTC-----------GTTCTTTTTGTGGCTGT----------------A--CT--------CCCTG----------------G-GCCAATCGTGGCATCTTAATGC---GGCC----CTGACATTTAAATAGATGCTAATTC---C--CATCATAACT----------------------A-------------------------------------CT--------------------------------GA----------------CTGAACTA--ATGAATT------------------TAAACTCTACTGGCG-----------------------ATC--CGA-TT------------GGGG-----CCAAC---------------------CTC--ACGA-----CA-----------------------C----------TGCTCCCA------------------------------------ACTTCCTG---------CTGGCCGCTTTCTTT-GCGCGTGAATCCGTGTAACCGCACA-------------------------------------------------------------G--------------------CACACAAAACTGTGATTTGCCCAAA---AACAG-AAAGCC-------GGCCAGAAA------------------------------GCTTTGCGGATATAAACGCT-TTAAAA------CTCCATA--TTGT-------GGCCTG-------CCTGGCCCGGAtgcga--------------cgacaa-------------------cgacaattGTGAA---GA----C-----C-AAAT---------------------GGCCA-AA-------CT------CG-----ACTCC-------------AGCC-------------------GGCAAA--TGTCTACGCAGCGTTGTC---GCTTCTCCT----TCTTttgttgccg-c----ttctgtt------gc------------tgctgct---------gttgttgctg--atgat---gt-------ggt-tgttgtt--tcgcttgttgc------------------CGCTTCGTGTCAACT-------GACT-TGGGCCTTAGCCTCAGCTCCAGAGTCAGTTCCAGCCCCGGCTACGAGCTACGAGCTACAGCTTTC--------------GGCTTTTGTTTTCACA----------AGCCGCCCCATTTTGCTT----------------A----------------------GCC-------------------AGCCAT---------------CCCATAACATTCGCCCCAACGTTTCCTGT s droTak2.KB461535 157510 774 - 669855 ---tggcaagtgCATT----------------AGTAGCAGGTTA--CCC----------CTCG-----------CAA--------------TTT-G------GCCAAATAATTGGT-AACTGA-AAACAATAAG-----------------CTC-----------GTTTCT--------CGT----------------A--CT--------CCT------------------G-GCCAATCGTGGCATCTTAATGC---GGCC----CTGACATTTAAATAGATGCTAATTC---C--CATCATAACTGAGT--------------CGCGA------------CCCCGAGTTCCAGAGCTCCCGTTT-CCCATTACCCATTTGCCGCTTTGCGGCTCTGGGTGGGTCT--------GACTCTGAACTA--ATGAATT------------------TGAACCC-----GGC-----------------------ACT--CGA-TT------------GAGA-----CAGAC---------------TTTAGACTC--ACGA-----CGACCCAAGTGGAATCGAGT-----T----------GGATGCCA------------------------------------ACTTCCTG---------CTGGCCGCTTTCTTT-GCGCGTGAATCCGTGTAACCGCAAC---------------------CC----------------------------GCATCAGA--G---AAAAA------------GACACAAAACTGTGATTTGCCCAAA---AACAG-AAAGCC-------GGCAAGAAAGCTTCGCTTTGGCTT---------------GCTTTGCGGATATAAACGCT-TTAAAA------CTCCATA--TTGT-------GGCC-----------TGGCCCGGATGCGA---------------------------------------CGACAATTGTGAA---GA----C--GACC-AAAT---------------------GGCCA-AA-------CT--CCGACG-----ACTCCGAGT-------TTAGCT-------------------GGCAAA--TGTCTACGCAGTGTTGTC---GCTTCTCCA----GCTTTTGCTGC---T----CAtggtt------gt-----------------------------tggttgttg--gctgtttggt-------tgt-tggttgt--tcgcttgttgC------------------CGCTTCGTGTCAACT-------GAGT-TGGGCCTT--------------------------------------------------AGCTTTC--------------GGCTTTTGTTTCCACCATCCAAGCCAAACCGCCCCATTTTGCTTAGCC------------AGG-CCAGCA-------AAGTTGGCCC------------------AGCCAT---------------CCCATAACATTTGCCTCAACGTTTCCTGT s droRho2.KB449310 52610 719 - 65043 ---TCCCAAGTGCACT----------------GGCAGCAGGTTA--CCC----------CTCG-----------CAA--------------TTT-G------GCCAAATAATTGGT-AACTGA-AAACAATAAG-----------------CTC-----------GTTTTT--------CGT----------------ACTCT--------CCC------------------G-GCCAATCGTGGCATCTTAATGC---GGCC----CTGACATTTAAATAGATGCTAATTC---C--CATCATAACTGACT--------------CGAGA----------------------CTCCGGTCCCGTTT-CC----------------------------------TTTC--------AA--CTGAACTA--ATGAATT------------------TGAACCC-----GCCAGTCGATTACTGGGGCT------GCT--CGA-TT------------GAGA-----CAGA----------------------CTC--ACGA-----CGAC----------CCGACT-----T----------GAATCTCT------------------------------------ACTTCCTG---------CTGGCCGCTTTCTTT-GCGCGTGAATCCGTGTAACCGCAAC---------------------CC----------------------------GCACAGAA--G---AAAAA------------GACACAAAACTGTGATTTGCCCAAA---AACAG-AAAGCC-------GGCAAGAAAGCCAT-------------------------GCTTTGCGGATATAAACGCT-TTAAAA------CTCCATA--TTGC-------GGCC-----------TGGCCCGGATGCGA---------------------------------------CGACAATTGTGAA---GA----CCAGACC-AAAT---------------------GGCCA-AAC------TG------CG-----ACTCCGAGT-------TTAGCT-------------------GGCAAA--TGTCTACGCAGTGTTGTC---GCTTCTCCT----GCTTTTGTTGC---CTCTGCTCAACT------GA------------tg---------------tggttgttg--gctgtt-ggt-------tgt-tggttgt--tcgcttgttgC------------------CGCTTCGTGTCAACT-------GACTGGGGGCCTT--------------------------------------------------AGTTTTC--------------GGCTTTTGTTTTCACA-----AGCCAAGCCGCCCCATTTTGCTTAGCC------------A-----GGCA-----GCAAGTTGGCCAG-----------------AGCCAT---------------CCCATAACATTTGCCTCAACGTTTCCTGT s droFic2.KB457177 94585 751 + 995874 ---CGTTAAGTGCTTA----------------AGCAGCAGGTTA--CCC----------CTCG-----------CAA--------------TTT-G------GCCAAATAATTGGT-AACCGA-AAACAATAAG-----------------CTC-----------GTTTCT--------CGT----------------ACTCT--------CCC------------------G-GCCAATCGTGGCATCTTAATGC---GGCC----CTGACATTTAAATAGATGCTAATTC---C--CATCATAACTGACT--------------CTGGC------------------GTTCTGGAGTTCCCGTTTCGC--------------------------------GGGT--------------CTGAACTA--ATGAATT------------------TGAACCC-----GCC-----------------------ACT--CGA-TT------------GAGGCGGCCCAGA----------------------CTC--ACGA-----CGAC----------CCGACTGCCAAC----------GGCTGCCA------------------------------------ACTTCCTG---------CTGGCCGCTTTCTTT-GCGCGTGAATCCGTGTAACCGCAGC---------------------CC----------------------------GCAGCCGA--A---GAAAA------------GACACAAAACTGTGATTTGCCCAAA---AACAG-AAAGCC-------GGCAAGAAAGCTTCGCctcgctttgctttgcttt-----gctttgcgGATATAAACGCT-TTAAAA------CTCCATA--TTGC-------GGCC-----------TGGCCCGGATGCGA---------------------------------------CGACAATTGTGAA---GA----C--GACC-AAAT---------------------GGCCA-AA-----------------------CTCCCAGT-------TTAGCT-------------------GGCAAA--TGTCTACGCAGTGTTGTC---GCTTCTGCC----GCTTTTG-TGC---T----CTCCACT------GA-Gctgatgtggttgttgct----------tgttggttg--gttgtttggctgctggttgc-tggttgt--tcgcttgttgc------------------CGCTCCGTGTCAACT-------GACT-GGGGCCTt--------------------------------------------------agctttcggctttcggcttcTGGCTTTTGTTTCCACA-----AGCCGGGCCGCCCCATTTTGCTTAGCC------------A------------------GTTGGCCAG-----------------AGCCAT---------------CCCATAACATTTGCCTCAACGTTTCCTGT s droPse3.chr3 1364372 795 - 19787792 ----------------------------------------------------------GAGTG-----------CAA--------------TTTCG------GGCAAATAATTGCCAAACGGA-AAACAATaag-----------------ccctggccct----ggctct--------ggc----------------c--ct--------ggccg---------------ag-GGCAATCGTGGCATCTTAATGC---GCCCCTGACTGACATTTAAATAGATGCTAATTC---C--CATCATAACTGA--------------------A---------------------------GCCCCGACT-CT--------------------------------G-----------------CCCAACTA--ATGAATT------------------TGAACTCTCT--CCC-----------------------ACT--CGA-TT------------Gctc-----cctatctctctttctctctctctccactc--aCGACTCAACGAG----------T-GACT-----C----------TCTTcccagtacgagtacgagtacgagtcgaGT-----------ACTTCCTG---------CTGGCCGCTTTCTTT-GCGCGTGAATCCGTGTAACCGCAGC---------------------ACAGCGCTTACCAATCCCAGAAATGGCGGGGAAgcggc--a---aacag------------aaaacaaaactgtgATTTgaccaaa---aacag-aaagcc-------GGCCAGAAA------------------------------GCTTGGCGGATATAAACGCT-TTAAGA------CTCCATA--TTGTGGTGGCAGGCC-----------CGGCCCGGATGCGA--------------CTACAACGA----------------CGACAATTGTGGA---AG----A--GACC-AAAT---------------------GGCCA-AACC----atccaccaacagcagcaccaccagcggcagcaccagctcT---------------TCAGCAAA--TTTCTACGCAGTGGAGGA---GGTTGTG--------------TGT---C----TTCCTct------gc-----------------------------tgtttgttg--gttgtt-----------gtt-tggttgt--ttggttgttgctgctgtgctgtgctgtgctgtttcGTGTCAACT-------gact-ttggctct--------------------------------------------------ggctttcggctttct------ggcttttgttttcaca----------AGCCGCCCCATTTTGCTTGCCT------------C------------------ATActcca------------------tgccacatgcccatgcccaggcccatgccaTTTGCCCCAACGTTTCCTGT s droPer1.super_34 553234 784 - 916997 ----------------------------------------------------------GAGTG-----------CAA--------------TTTCG------GGCAAATAATTGCCAAACGGA-AAACAATAAG-----------------CCCTGGCCCT----GGCTCT--------GGC----------------C--CT--------GGCTG---------------AG-GGCAATCGTGGCATCTTAATGC---GCCCCTGACTGACATTTAAATAGATGCTAATTC---C--CATCATAACTGA--------------------A---------------------------GCCGCGACT-CT--------------------------------G-----------------CCCAACTA--ATGAATT------------------TGAACTCTCT--CCC-----------------------ACT--CGA-TT------------Gctc-----tctatctctctttctctctctctcCACTC--ACGACTCAACGAG----------T-GACT-----C----------TCTTCCCAGTACGAGTACGAGTACGAGTCGAGT-----------ACTTCCTG---------CTGGCCGCTTTCTTT-GCGCGTGAATCCGTGTAACCGCAGC---------------------ACAGCGCTTACCAATCCCAGAAATGGCGGGGAAGCGGC--A---AACAG------------AAAACAAAACTGTGATTTGACCAAA---AACAG-AAAGCC-------GGCCAGAAA------------------------------GCTTGGCGGATATAAACGCT-TTAAGA------CTCCATA--TTGTGGTGGCAGGCC-----------CGGCCCGGATGCGA--------------CTACAACGA----------------CGACAATTGTGGA---AG----A--GACC-AAAT---------------------GGCCA-AACC----ATC------CAGCAGCACCACCAGCAGCAGCACCAGCTCT---------------TCAGCAAA--TTTCTACGCAGTGGAGGA---GGTTGTG--------------TGT---C----TTCCTCT------GC-----------------------------TGTTTGTTG--GTTGTT-----------GTT-TGGTTGT--TTGGTTGTTGC-----TGCTGTGCTGTGCTGTTTCGTGTCAACT-------GACT-TTGGCTCT--------------------------------------------------GGCTTTCGGCTTTCT------GGCTTTTGTTTTCACA----------AGCCGCCCCATTTTGCTTGCCC------------C------------------ATACTCCA------------------TGCCACATGCCCATGCCCAGGCCGATGCCATTTGCCCCAACGTTTCCTGT s droMir2.chr3 1405453 769 - 20862834 ----------------------------------------------------------GAGTG-----------CAA--------------TTCCG------GGCAAATAATTGCCAAACGGA-AAACAATAA------------------------------------CT--------GA--------------------CT--------GGCCG---------------AG-GGCAATCGTGGCATCTTAATGC---GCCCCTGACTGACATTTAAATAGATGCTAATTC---C--CATCATAACTGA--------------------A---------------------------GCCCCGACT-CT--------------------------------G-----------------CCCAACTA--ATGAATT------------------TGAActctct--ccc-----------------------gct--cga-tt------------gctc-----tctatctctctatctctctctctccactc--aCGACTCAACGAG----------T-GACT-----C----------TCTTcccagtacgagtacgagta-----cgagt-----------acttccTG---------CTGGCCGCTTTCTTT-GCGCGTGAATCCGTGTAACCGCAGC---------------------ACAGCGCTTACCAATCCCAGAAATGGCGGGGAAgcggc--a---aacag------------aaaacaaaactgtgatttgaccaaa---aacag-aaagcc-------GGCCAGAAA------------------------------GCTTGGCGGATATAAACGCT-TTAAGA------CTCCATA--TTGTGGTGGCAGGCC-----------CGGCCCGGatgcga--------------cgacaacga----------------cgacaattGTGGA---AG----A--GACC-AAAT---------------------GGCCA-AAcc----atc------cagcagcaccaccagcagcagcaccagctct---------------tCAGCAAA--TTTCTACGCAGTGGAGGA---GGTTGTG--------------TGT---C----TTcctct------gc-----------------------------tgtttgttg--gttgtt-----------gtt-tggttgt--ttggttgttgc-----tgctgtgctgtgctgtttcGTGTCAACt-------gact-ttggctctggctttc-------------------------------------------ggctttcggctttct------ggcttttgttttcaca----------Agccgccccattttgcttgccc------------c------------------atactcca------------------tgccacatgcccatgcccaggcccatgccatttgccccaACGTTTCCTGT s droWil2.CH963894 1332075 729 + 2843958 -----------------------------------------------------------GGCT-----------CAA--------------ACT-GAGAACAGGCAAATAATTGCT-TATTGGCAAACAATAAGGCAA-------------CTC-----------GATATC--------GTT----------------A--CT--------GCTTCTTCGATTCTATGGTTAG-GCCAATCGTGGCATCTTAATGC---CCTG----ATGACATTTAAATAGATGCTAATTC---CCTCATCATAACTG-CA--------------GTAAA-------------------------------------CA--------------------------------GT----------------TTGAACTA--ATGAATT------------------TGAACTC-----ACC-----------------------------GA-TT---------------------TA--------------------------------------CGAT----------TCAACT-----T-----------CCTGTTG------------------------------------GCTTGCTG---------CT---CGCTTTCTTT-GCGCGTGAATCCGTGTAACcgcaaa---------------------ga--------------------------------------a---agaaa------------aaccgaAAACTGTGATTTGACCAAAACGAGAAG-AAAGCC-------AGCCAGCAA------------------------------GCTT-GCGGATATAAACGCT-TTCGGAAAATACCTCCATA--TTGT-------GGTC-GGTCGTCTCGTCGCCCGGATGCGACacaacggcaatggcaacagcaacagcaaacgaTGACGGCGACAACTTTTCT---GA----A--GACC-AAAT---------------------GGcca-aactccaactc------ca-----actccaact-------ttagctccaacttcaacttccaactGGCAAA--TGTCTACGCAACTTGGTT---TTCTCCTCCCTCagcaattgttgt---t----gat-gtt------gttttcggtattgctgctgtt---------gctgttgttgttgttgtt--gc-------tgt-tgttcattctcgattgctgc------------------tgttttgtgtcaact-------ggct-ttggcttt----ttggg-----------------------------------------ggctttt--------------ggcttttgtttgctgA---------AAGCCGCCCCATTTTGCCTG--C------------T----------------------GCT-------------------GGCCAT--------------------AACATTTGCTTAACCGTTTCctgt s droVir3.scaffold_12875 7370690 681 + 20611582 --------------------------------CTCTGCAGGTTG--CCT----------ATCGA--GCCCCATACAA--------------TTT-G------GCCAAATAATTGCT-GGCTGA-GAACAATAAGCCAG-----AGCCGAAGCTC-----------GTTGCT--------CTT------------CGCGG--CA--------GCG------------------G-CCCAATCGTGGCATCTTAATGC---GCGC----CAGACATTTAAATAGATGCTAATTC---T--CATCATAACTGCAA--------------CAAGA--------------------CTTAAGACTTAAGACT-TA--------------------------------AGTCCAGCTCTTCAAG--TTGGCCTA--ATAAATGTTTTTGTCGGTTTTGTGCCGCTCAC-----GAT-----------------------GTG--CAC-TTTCTTG-------TTGG-----CATC----------------------TTT--GGAG-----CTAT----------TGGAG------C------------------------------------------------------ACTTCCTG---------CTGCCCGCTTTCTTT-GCGCGTGAATCCGTGTAACCGCAAA---------------------CT--------------------------------------G--------------------------------TGATTTGACCAAA---AACAG-AAAGCC-------GCCG---AG------------------------------GCTT-GCGGATATAAACGCT-TTAAAG-------TGCATG--TTGT----------------------TGGCCCGGATGCGA--------------C------------------------CGA-----ACGAAACCCA----C--AACCAAACC---------------------AACCA-AAC------TC------CG-----ACTCTGACA-------ATGTC----------------------------TCTCTACGCAGTGTTGCC------TCTGTC---------TACTGA---t----tgttgtt------cttcttgttgttgtcgctgta---------gttgttgttg--ttgttg-----------ttg-ttgttgt--t--gttgctgc------------------tgttTCGTGTCAACT-------GGCT-CTGGCTTT--------------------------------------------------GGCTTTG------------------------TTTGCC----------AGCCGCCCCATTTTGACCAGCC------------CGATTCAGCC--CCGGCGGCTTGGCCT------------------GGCCTG---------------GCCATAACATTTG-CTTAACGTTTCCTGT s droMoj3.scaffold_6496 26165595 671 + 26866924 -----------GGCTGTG--------------CTCTGCAGGTTG--CCT----------ATCG---GCCCCTTACAA--------------TTT-G------GCCAAATAATTGCT-GACTGA-GAACAATAAGCCAG-----GAGGCGCGCTC-----------GTTGCT--------CTT----------------G--TG--------AAT------------------G-GCCAATCGTGGCATCTTAATGC---GCGC----CTGACATATAAATAGATGCTAATTC---C--CATCATAACTGCAA--------------CAACT--------------------GCT--------GGACT-TC--------------------------------TAGTCAGCTCTTC-AG--TTGGCCCAATATAAATG--------------GAAACGCTCAC-----GAT-----------------------GTGCTCAC-TTTCTTG-------TTGG-----CATC----------------------TTT--GGAG-----CTGC----------TGGAG------C------------------------------------------------------ACTTCCTG---------CTGGCCGCTTTCTTT-GCGCGTGAATCCGTGTAACCGCAAA---------------------CT--------------------------------------G--------------------------------TGATTTGACCAAA---AACAG-AAAGCC-------GCCG---CG------------------------------GCTT-GCGGATATAAACGCT-TTAAAG-------TGCACG--TTGT----------------------TCGCCCGGATGCAA--------------C------------------------CGA-----ACGAAACCCA----C--AGCCGAACC---------------------AGCCA-AAC------TC------CA-----ACTCTGACA-------ATGTC----------------------------CCTCTACGCAgtgttgtc------tctgtc---------tgctgaatgt----tgttgtt------gttttagttgttgttgctacatctgctgctgctgctgttg--ctgttt-----------ctg-ttgctgt--t--gttactgc------------------tgTTTCGTGTCAA--------------CTGACTTT--------------------------------------------------GGCTTTG------------------------TTTGCC----------AGCCGCCCCATTTCGACCAGCC------------CCA-GCAGCTTACGCGCGCCTTGCCCT------------------GGCCTG---------------GCCATAACATTTG-CTTAACGTTTCCTGC s droAlb1.JH854640 327411 705 + 406291 -----------GCCTTAGTCTCTAGGATCTGCGTTTGCAGGTTGTTCCT----------CTGGATCGGGCCATTCAA--------------TTT-A------ACCAAATAATTGCT-AACTTC-GAACAATAAGCTAGCATCAGAGCTGAGATC-----------GTTGTT--------CTCAGACCTGAACCTTGCCG--TG-------CCCA------------------G-GCCAATCGTGGCATGTTAATAT---GCTC---GCTGGCATTTAAATAGATGATAATTC---T--CAtcataacagcag--------------caac--------------------------------aaagt-ta--------------------------------AG------------AA--TTAGACTT-TGCGAATT-------TCGTATTGAGCTGCTCAC-----GTC-----------------------GTG--AGC-TTTCTTG-------AGCT-----CATT----------------------TTTGGGGAG-----CTAT----------TGGAG------C------------------------------------------------------ACTTCCTGCTCTCTCGCCTGTTCGCTTTCTTT-GCGCGTGAATCCGTGTAACCGCAAA---------------------CT--------------------------------------G--------------------------------TGATTTGACCAAA---AACAG-AAAGTCAGTCGTTGCCGGTCAG------------------------------GCTT-GCGGATATAAACGCT-TTAAAG-------TGCATA--TTGT----------------------TGGCCCGGATGCGA--------------CGA----------------------CGA-----GCGAA--CCA----A--AATC-CACC---------------------AGCgacaac------tc------ca-----actccaaca-------actacagcaac--------------agcaacaatgtctACGCAGtgttgtc------tctgtc------------------t----tgttgtt------------------------------------gttgttggtg--ttgtct-----------ctg-ttgttgt--t--attgctgt------------------tgtttcatGTCAATTCTCTTTCGGCT-CTGAC-TT--------------------------------------------------GGCTTTG------------------------TTCGCC----------AGCCGCCCCATTTTG-Cctgct------------gtgtgttgtt-----gttgcccgtcTT------------------GGCCTG---------------GCCACAACATTTG-CTTAACGTTTCCTGT s droGri2.scaffold_15245 921260 690 + 18325388 -----------GGCCTAGTCTCT---------AGTTGCAGGTTG---CT----------ATCGGGGCAGCCATACAA--------------TTT-G------GCCAAATAATTGCT-GGCCGA-GAACAATAAGGCAA-----GGAGGCAGCCCAGGCAACCCAGGCAGTT--------CGC----------------G--GGCCAAGCTCGTT------------------G-CCCAATCGTGGCATCTTAATGCTGTGCGA----CTGACATTTAAATAGATGCTAATTCTCAT--CATCATAACTGTAAGGAACTGGAAGAGTTAAGA--------------------GTTACGAGTTACGAGT-TA--------------------------------AGACTTAGTCAGCGAG--TTGGTCTA--ATAAATG--------GATTTT----CGCTCAC-----GAT-----------------------GTG--CAC-TTTCTTGGC-----TGGG-----AAGC---------------------------GCAA-----CTAT----------TTGAGC-----C------------------------------------------------------ACTTCCCG---------CTGGCCGCTTTCTTCGGCGCGTGAATCCGTGTAACCGCAAA---------------------CT--------------------------------------G--------------------------------TGATTTAACCAAA---AACAG-AAAGCC-GACGCCGACGACCAG------------------------------GCTT-GCGGATATAAACGCTATCAAAG-------TGCATGTTTTGC----------------------TCGCCCGGATGCGA--------------C------------------------CGAC--TGACAAACCCCA----c--aaaccaaccaaaccaaaccaaaccgaaccgaacca-aaccgaa--cc------aa-----acTCCAACT-------CCAACTCTGAC--------------AATGTC--TCTTTACGCAGTGT----------------------------------t----t------------------------------------------gttgttgttg--ttattg-----------ttg-ctgttgt--t--gcttttgc------------------tgttTCGTGTCAACT-------GGCT-TTGGCTTT--------------------------------------------------GGCTTTG------------------------TTCGCC----------AGCCGCCCC---------------------------------------------------T------------------GGCCTG---------------GCCATAACATTTG-CTTAACGTTTCCTGT a score=252281.000000 s dm6.chr2R 24372035 41 + 25286936 TCACAATGTG------------------------GCC----A--CTGTCC-----------------------TGTGGTTCTGATTGTG--TGATT s droSim1.chr2R 18710760 41 + 19596830 TCACAATGTG------------------------GCC----G--CTGTCC-----------------------TGTGGTTCTGATTGTG--TGATT s droSec1.super_23 130094 41 + 989336 TCACAATGTG------------------------GCC----G--CTGTCC-----------------------TGTGGTTCTGATTGTG--TGATT s droYak3.chr2R 20220206 41 + 21139217 TCAAAATGTG------------------------GCC----A--CTGTCC-----------------------TGCGGTTCTGATTGTG--TGATT s droEre2.scaffold_4845 21617749 40 + 22589142 TCAAAATGTT------------------------GCC----G--CTGTCC-----------------------TGCGGTTCTGATTGTG---GATT s droBia2.KB462602 812702 42 + 3129309 TCAGAATGTTC-----------------------GCC----G--CTGTCC-----------------------TGTGGTTGTGATTGTG--TGATT s droSuz1.KI419649 12059073 42 - 14502029 TCAGAATGTTC-----------------------GCC----G--CTGTCC-----------------------TGTGGTTGTGATTGTG--TGATT s droAna3.scaffold_13266 5722587 42 - 19884421 TGAGAATGCTT-----------------------GCC----G--CTGTCC-----------------------TGTGGTTCTGATTGTG--TAATT s droBip2.KB464407 1972505 42 + 2915140 TGAGAATGCTT-----------------------GCC----G--CTGTCC-----------------------TGTGGTTCTGATTGTG--TAATT s droEug2.KB465067 615220 42 + 1515531 TCAGAATGCTC-----------------------TCC----C--CTGTCC-----------------------TGTGGTTGTGATTGTG--TGATT s droEle2.KB458573 538866 39 - 5320397 TCAGAATGTTT-----------------------GCC----A--CAGGAC-----------------------GGTAG---TGATTGTG--TGATT s droKik2.KB459527 292015 65 - 1234237 TCAGAATGTTG-----------------------CCC----g--ctgtcctgtcctgtccccTTGGTTGTGATTGTGACTCTGACTGTG--TGATT s droTak2.KB461535 158284 42 - 669855 TCAGAATGTTC-----------------------GCC----G--CTGTCC-----------------------TGTGGTTGTGATTGTG--TGATT s droRho2.KB449310 53329 42 - 65043 TCAGAATGTTC-----------------------GCC----G--CTGTCC-----------------------TGTGGTTGTGATTGTG--TGATT s droFic2.KB457177 95336 42 + 995874 TCAGAATGTTT-----------------------GCC----G--CTGTCC-----------------------TGTGGTTGTGATTGTG--TGAAT s droPse3.chr3 1365167 57 - 19787792 TGAGAATTTGCAGAGCCCcg-----ctgt-----cct----gtcctgtcc-----------------------tgtggTTGTGATTGTG--TGATT s droPer1.super_34 554018 62 - 916997 TGAGAATTTGCAGAGCCCCGctgtcctgt-----cct----gtcctgtcc-----------------------tgtGGTTGTGATTGTG--TGATT s droMir2.chr3 1406222 67 - 20862834 TGAGAATTTCCAGAGCCCCGCTGTCCTGTCCttccct----gtcctgtcc-----------------------tgtggTTGTGATTGTG--TGATT s droWil2.CH963894 1332804 47 + 2843958 tgaaaattttt-----------------------gccTACAG--TTTGCC-----------------------TG-AGTTGTGATTGTAAATGTTT s droVir3.scaffold_12875 7371393 37 + 20611582 --TTGGCTCGT-----------------------TTC---AG--TTGGGT-----------------------TTGGATTGGT----TT--GGGTT s droAlb1.JH854640 328116 28 + 406291 --TCAACTCTT-----------------------GTC-------TTAAGC-----------------------TTTG-----------T--GGGTT s droGri2.scaffold_15245 921950 40 + 18325388 --TGAACTCAT-----------------------CGC----G--CTGTGC-----------------------CTCACttggcatcgtt--tggtt a score=71407.000000 s dm6.chr2R 24372076 4 + 25286936 CCTC s droSim1.chr2R 18710801 4 + 19596830 CCTC s droSec1.super_23 130135 4 + 989336 CCTC s droYak3.chr2R 20220247 4 + 21139217 CCTC s droEre2.scaffold_4845 21617789 4 + 22589142 CCTC s droBia2.KB462602 812744 4 + 3129309 CCTC s droSuz1.KI419649 12059115 4 - 14502029 CCTC s droAna3.scaffold_13266 5722629 4 - 19884421 CCTC s droBip2.KB464407 1972547 4 + 2915140 CCTC s droEug2.KB465067 615262 4 + 1515531 CCTC s droEle2.KB458573 538905 4 - 5320397 CCTC s droKik2.KB459527 292080 4 - 1234237 CCTC s droTak2.KB461535 158326 4 - 669855 CCTC s droRho2.KB449310 53371 4 - 65043 CCTC s droFic2.KB457177 95378 4 + 995874 CCTC s droPse3.chr3 1365224 4 - 19787792 CCTC s droPer1.super_34 554080 4 - 916997 CCTC s droMir2.chr3 1406289 4 - 20862834 CCTC s droWil2.CH963894 1332851 4 + 2843958 CTTC s droVir3.scaffold_12875 7371436 4 + 20611582 CCGC s droAlb1.JH854640 328150 4 + 406291 CCAC a score=199101.000000 s dm6.chr2R 24372080 23 + 25286936 CTACAAAAT--CAA--GGGACAGTGGT s droSim1.chr2R 18710805 22 + 19596830 CTACAAAAT--CGA---GGACAGTGGT s droSec1.super_23 130139 22 + 989336 CTACAAAAT--CGA---GGACAGTGGT s droYak3.chr2R 20220251 23 + 21139217 CTACGAAAT--CGA--GGGACAGTGGT s droEre2.scaffold_4845 21617793 23 + 22589142 CTACGAAAT--CGA--GGGACAGTGGT s droBia2.KB462602 812748 23 + 3129309 CTACAAAAG--CAA--GGGACAGTGGT s droSuz1.KI419649 12059119 23 - 14502029 CTACAAAAT--CGA--GGGACAGTGGT s droAna3.scaffold_13266 5722633 25 - 19884421 CTACAAAATGCTTA--GCCACAGTGCC s droBip2.KB464407 1972551 25 + 2915140 CTACAAAATGCTCA--GCAACAGTGGC s droEug2.KB465067 615266 23 + 1515531 CTACAAAAT--CAA--GGGACAGTGGT s droEle2.KB458573 538909 23 - 5320397 CTACAAAAT--TGA--GGAACAGTGGT s droKik2.KB459527 292084 25 - 1234237 CTACAAAAT--TTAGGGGGACAGTGGT s droTak2.KB461535 158330 23 - 669855 CTACGAAGT--CGA--GGGACAGTGGT s droRho2.KB449310 53375 23 - 65043 CTACAAAAT--TGA--GCAACAGTGGT s droFic2.KB457177 95382 23 + 995874 CTACGAAAT--CGA--GGAACAGTGGT s droPse3.chr3 1365228 23 - 19787792 CTACAAAAT--CAG--GGAACAGTGGT s droPer1.super_34 554084 23 - 916997 CTACAAAAT--CAA--GGAACAGTGGT s droMir2.chr3 1406293 23 - 20862834 CTACAAAAT--CAA--GCAACAGTGGT s droVir3.scaffold_12875 7371440 20 + 20611582 CTACCCACA--CAC-----ACAGTGGT s droAlb1.JH854640 328154 5 + 406291 CTACC---------------------- a score=-76926.000000 s dm6.chr2R 24372103 13 + 25286936 T--------------------------------------------------------------------------------CACAAT---GATGTC-------- s droSim1.chr2R 18710827 13 + 19596830 T--------------------------------------------------------------------------------CACGAA---GATGTC-------- s droSec1.super_23 130161 13 + 989336 T--------------------------------------------------------------------------------CACGAA---GATGTC-------- s droYak3.chr2R 20220274 13 + 21139217 T--------------------------------------------------------------------------------CGCAAA---GATGTC-------- s droEre2.scaffold_4845 21617816 13 + 22589142 C--------------------------------------------------------------------------------CACAGA---GATGGC-------- s droBia2.KB462602 812771 16 + 3129309 C--------------------------------------------------------------------------------CATTCATTTAGTGtc-------- s droSuz1.KI419649 12059142 13 - 14502029 T--------------------------------------------------------------------------------CAGGGA---GATgtc-------- s droAna3.scaffold_13266 5722658 16 - 19884421 T--------------------------------------------------------------------------------CAGATATTTGTAGTT-------- s droBip2.KB464407 1972576 16 + 2915140 T--------------------------------------------------------------------------------CAAATTCGAGATGTT-------- s droEug2.KB465067 615289 13 + 1515531 T--------------------------------------------------------------------------------CAGGAA---AATGTC-------- s droEle2.KB458573 538932 93 - 5320397 TAaggaacttaaaataatttttattttaaaactgctTAATAGtctaaatcaaatataaagtgttacaaaaaaactacttaacagaaa---aatgtc-------- s droKik2.KB459527 292109 13 - 1234237 T--------------------------------------------------------------------------------CAGGAA---AGGGTT-------- s droTak2.KB461535 158353 13 - 669855 T--------------------------------------------------------------------------------CAGGGA---GATgcc-------- s droRho2.KB449310 53398 13 - 65043 T--------------------------------------------------------------------------------GAAAAA---GATATT-------- s droFic2.KB457177 95405 13 + 995874 T--------------------------------------------------------------------------------CGGGGA---GGTGTC-------- s droPse3.chr3 1365252 15 - 19787792 T--------------------------------------------------------------------------------CGGATACT-GATTTC-------- s droMir2.chr3 1406317 15 - 20862834 T--------------------------------------------------------------------------------CGGATACT-GATTTC-------- s droVir3.scaffold_12875 7371460 13 + 20611582 -------------------------------------------------------------------------------------------CCTTCAAATTCTC s droAlb1.JH854640 328159 8 + 406291 ----------------------------------------------------------------------------------------------TTAAATTC-- a score=-153910.000000 s dm6.chr2R 24372116 30 + 25286936 TT----ACTTGTAATGCAGAGATGTC-----------ACAATGAA s droSim1.chr2R 18710840 30 + 19596830 TT----ACTTGAAACGAAGAGATGTC-----------ACAATGAA s droSec1.super_23 130174 30 + 989336 TT----ACTTGAAATGCAGAGATGTC-----------ACAATGAA s droYak3.chr2R 20220287 30 + 21139217 TC----ACTTGAACTGCAGAGATGTC-----------ACAATGAA s droEre2.scaffold_4845 21617829 34 + 22589142 TT----ACTTGAAATGAAATACTTACTTG-------AAGTAAGAA s droBia2.KB462602 812787 31 + 3129309 ttc---attttaaaaacaaagtcttc-----------cctttcaa s droSuz1.KI419649 12059155 31 - 14502029 ttc---atttaaaaatcaaagatttc-----------cccattaa s droAna3.scaffold_13266 5722674 17 - 19884421 TT----TATTT-----AAGGTTT-------------------TAA s droBip2.KB464407 1972592 28 + 2915140 TT----TCTTC--CCAAAGAATCTTC-----------CCAAATAA s droEug2.KB465067 615302 27 + 1515531 TTT---ACTTAGTATACAGAGT---------------ACAAGAAA s droEle2.KB458573 539036 32 - 5320397 at----tcttaagaAGCAAAGTCTTCCA---------AAAATGAG s droKik2.KB459527 292122 27 - 1234237 TT-------TGAGATAGGTAAAGGTT-----------ACTTATAT s droTak2.KB461535 158366 36 - 669855 tt----aatttaaatactggattttttttcc-----aataattaa s droRho2.KB449310 53712 30 - 65043 TT----ACATTCAGTGTAAAATGCTT-----------TTTAGAAG s droFic2.KB457177 95418 40 + 995874 --TTggatttgtaaaataatatttacaatacTG---TTTTAGGAA s droPse3.chr3 1365267 26 - 19787792 --------CCATAGCTCTGAAAGATG-----------GCAAAGAA s droMir2.chr3 1406332 26 - 20862834 --------CCATAGCTCTGAAAGATG-----------GCAAAGAA s droVir3.scaffold_12875 7371473 26 + 20611582 -------------------AAATATCAAATGTAAAAAGCATTCAG s droAlb1.JH854640 328167 9 + 406291 ------------------------------------AACAGTGGG a score=-297941.000000 s dm6.chr2R 24372146 44 + 25286936 TAGTT-------------------------------C----TTTAT-----AT-GTTATGA-------ATATTTATG--------------------TCAGCCAATAAATAT s droSim1.chr2R 18710870 44 + 19596830 CAGTT-------------------------------C----TTTAT-----TT-GTTATAA-------TTATTTATG--------------------TCAGGCAATAAATAC s droSec1.super_23 130204 44 + 989336 CAGTT-------------------------------C----TTTAT-----TT-GTTATGA-------ATATTTATG--------------------TAAGGCAATGAATAC s droYak3.chr2R 20220317 27 + 21139217 TGGTT------------------------------------ATTAT-----AT-GTTTTGA-------ATATTCA------------------------------------C s droEre2.scaffold_4845 21617863 26 + 22589142 TATTT------------------------------------TCTAT-----AT-TTTCTGC-------ATAGTTA------------------------------------- s droBia2.KB462602 812818 37 + 3129309 -----------------------------------------tttat-----ttaggTTTCA-------AGAACCA----------------------ttcgcaaataaaaat s droSuz1.KI419649 12059186 37 - 14502029 t----------------------------------------tttat-----taaattttga-------agaACCA----------------------TTGgc-tttaaaaac s droAna3.scaffold_13266 5722691 17 - 19884421 GA---------------------------------------GTTAA-----AG-TAGCGGA-------G------------------------------------------- s droBip2.KB464407 1972620 30 + 2915140 GA---------------------------------------TATAA-----GA-TATAGGT-------GTATTGA------------------------------TAAATAC s droEug2.KB465067 615329 40 + 1515531 GAGC-------------------------------------ATTGC-----TT-AGAATGA-------ATACTGT----------------------ACATGATACTAAAAC s droEle2.KB458573 539068 65 - 5320397 TGccttgtt--------------taaat--------t----tttga-----tt-gtcTTGCTGTAGTTATAGTTATATA---------------ACTTTGTAgaacaaaaac s droKik2.KB459527 292149 39 - 1234237 TAAttcaataatat------aaatgtat--------a----attag-----at-gatttag-------at------------------------------------------ s droTak2.KB461535 158402 82 - 669855 atattttactttaa------atatcttt-------gg----ttttt-----at-atttgaa-------ttatCAATCTATAATGTTTTCTTAACAAAATGGTTAatacatac s droRho2.KB449310 53742 31 - 65043 AAG--------------------------------------aatag-----tt-aatataa-------atattta----------------------------agtacat-- s droFic2.KB457177 95458 71 + 995874 TTGTTCAATGGTTTCAAACCAAATCCCTTATCTC-AC----TATGT-----AA-AATATGA-------AGATCAA----------------------ACATTCGGtctaaa- s droVir3.scaffold_12875 7371499 28 + 20611582 ----------------------------TAGTTCAACAAATTCTAC-----TA-ATTAAAA-------A------------------------------------------- s droAlb1.JH854640 328176 29 + 406291 ----------------------------CAGTTCTGC----TCTTCGcaggca-attaaaa-------t------------------------------------------- a score=4713.000000 s dm6.chr2R 24372190 3 + 25286936 CAT s droSim1.chr2R 18710914 3 + 19596830 CAT s droSec1.super_23 130248 3 + 989336 CAT s droYak3.chr2R 20220344 3 + 21139217 TAT s droBia2.KB462602 812855 3 + 3129309 aat s droSuz1.KI419649 12059223 3 - 14502029 tat s droBip2.KB464407 1972650 3 + 2915140 TAT s droEug2.KB465067 615369 3 + 1515531 TAT s droEle2.KB458573 539133 3 - 5320397 ctt s droTak2.KB461535 158484 3 - 669855 aat s droAlb1.JH854640 328206 3 + 406291 cag a score=-213406.000000 s dm6.chr2R 24372193 35 + 25286936 TCACTTT---TCGATAAT------------------------------------------GTTCC----AAAGTTTAGGTTGTT---- s droSim1.chr2R 18710917 40 + 19596830 TCACTTT---TCGATAATGT----------------------------------AGAAAAGTTGC----AAAGTTTA---TGTT---- s droSec1.super_23 130251 40 + 989336 TCACTTT---TCGATAATGT----------------------------------AGAAAAGTTGC----AAAGTTTA---TGTT---- s droYak3.chr2R 20220347 40 + 21139217 TCACATT---TAGATTATTC----------------------------------ACAAGAGGTCC----CACGTTAA---Ggtt---- s droEre2.scaffold_4845 21617889 31 + 22589142 ----------------AGGA----------------------------------AGAAGAAATACCATTCACTATTG---GGTT---- s droBia2.KB462602 812858 32 + 3129309 gta---t---ctAATTGTTT---------------------------------------TATACC----AGCGGGTA---CGGT---- s droSuz1.KI419649 12059226 61 - 14502029 tta---t---ccAATTGTTTAAATTC-CGCTttcataa-----tatta----ttaaaactattCC----CAAACATT---CTGT---- s droAna3.scaffold_13266 5722708 2 - 19884421 ----------------------------------------------------------------------------------TT---- s droEug2.KB465067 615375 16 + 1515531 -------------------------------------------------------------TTCC----AATCTACA---AGTC---- s droEle2.KB458573 539139 70 - 5320397 tcatattgaattgtaaatgtaaatactCAGGGTTAAAA-----TACTAAC--CTAAAGGAATGCT----CAAtatca---attt---- s droKik2.KB459527 292188 35 - 1234237 -----------------------------------aca-----ttttaaa--gcaaagaaaatgt----tCTATTCG---TGAT---- s droTak2.KB461535 158487 47 - 669855 ------------------------------ttttaaaagaactttttaaaattcaatcaaTGCCC----AAAGttct---tgtt---- s droRho2.KB449310 53773 21 - 65043 --------------------------------------------------------TACGTATTC----AACAAGCC---CGTT---- s droFic2.KB457177 95529 19 + 995874 ----------------------------------------------------------acatttt----atgataTG---CTTT---- s droAlb1.JH854640 328209 30 + 406291 ---------------------------------------------------ACTGTCtgcaatgc----aaataaca---aGTGGAAA a score=-179327.000000 s dm6.chr2R 24372228 109 + 25286936 ATGA-------------AT-------------------AC---------TTTAAATAAACCCAAAC-------------------------------------TTG-----------------------C------AAGCAAGCCACTTTG---GTATCCAATAAACC-------------TAGTATACAT-------------TTTTCATAGAGACTGGGAT------TGTGTTTGTTGATT-------TC-AGTGAT s droSim1.chr2R 18710957 109 + 19596830 ATGA-------------AT-------------------AC---------TTTAAATAAACCCAAAC-------------------------------------TTG-----------------------C------AAGCAAGCCACTTTA---GTATCCAATAAACC-------------TAGTATACAA-------------TTTTCATAGAGACTGGGAT------TGTGTTTGTTGATT-------TC-AATGAT s droSec1.super_23 130291 109 + 989336 ATGA-------------AT-------------------AC---------TTTAAATAAACCCAAAT-------------------------------------CTG-----------------------C------AAGCAAGCCACTTTA---GTATCCAATATACC-------------TAGTATACAT-------------TTTTCATAGAGACTGGGAT------TGTGTTTGTTGATT-------TC-AATGAT s droYak3.chr2R 20220387 104 + 21139217 ataa-------------at-------------------ac---------tttaaagaAGCCCTAAC-------------------------------------TT---------------------------------TCCAGCTACTTTA---GTGTCCAATGAAca--------------tgtatacat-------------tttttatagaGACTGCGAT------TGTGTTTGTTGATT-------TC-AATGAT s droEre2.scaffold_4845 21617920 104 + 22589142 GTAA-------------AG-------------------AC---------TTTAAAGAACCCCAAAC-------------------------------------CT---------------------------------GCCAGCTACTTTA---GTACCCAATGAACA--------------AGTATACAT-------------TTTTTATAGAGACTGGGAT------TGTGTTTGTTGATT-------TC-AATGAT s droBia2.KB462602 812890 174 + 3129309 ATTA-------------GTTTCA--TT-----------TC---------TTCtaataaatctaaatatatAACCCTTATAAAATAACctctttaaaattctttttaggTGTTGAATAAAAATCTCACTTT------CCACAA-CCTTTTTA---AGGTCCAATCATCA--------------TGTATGCTTG------------TTTTTATAGAGACTGGAAT------AGTTTTTATCTATT-------CC-AATGAT s droSuz1.KI419649 12059287 167 - 14502029 CTTATAAATCTCTAAAGATAACA--TTG-ATAAaataacc---------tttttaaaattcaaagt-------tcctttaaaat-atttcaaagaaaatCACGCTA-----------------------T------CTACAAGCCCTTTTA---AGGTTCAATCATCG--------------CGTTTACTCG------------TTGTTATAGAGACTAGAAT------TGTTTTTATCTATT-------TC-AATGAT s droAna3.scaffold_13266 5722710 109 - 19884421 TTTA-------------AT-------------------ACAA----GAATTTGGAGAAAAAGAATT-------------------------------------GTA-------------------------------------TATCCTTA---AGATTGTATATCCATCTTAAA------TGACATACTG--------------TCTTATAGA-ACT---AT------TATCCTTACTACTC-------TCTAATACT s droEug2.KB465067 615391 137 + 1515531 TTCA-------------ATGAAAGGTT-----------ACTGCTTTGCATTTTACCAAGCCCAATC-------------------------------------AGT-----------------------T------Cataaagttcttttt---aaatattgaaaaca---taaatGGGTTCAATAAACATA------------CCTATATAGAGACAAGGGT------GGCTTTTATTGACT-------TC-AATGAT s droEle2.KB458573 539209 134 - 5320397 gtaa-------------aataaataacgtaTTCAACAAGC---------CCTTTCTaagttcaaac-------------------------------------att-----------------------t--taaacaaaaagcattTCTACCGAGGTTTAATAATCA--------------TGTTTACAT-------------TTCTTATGGAGTCTAGgaa------ctcttttattttgt-------ta-aaaatt s droKik2.KB459527 292223 104 - 1234237 TTTA----------------------------------TC---------TTCACAAAAATACATAG-------------------------------------TTG-----------------------AAACAGATTAAAAAGGTtctta---aaatgtgtttaacC-------------TAGTTTATAA-------------TCTTAACA---------TT------GGTCTATTTAGATT-------TC-AATGAT s droTak2.KB461535 158534 103 - 669855 a--a-------------at-------------------at---------ttaaaagaaaagcaCAC-------------------------------------CTA-----------------------C----------AAGCTCTTTCA---AGGCCCAATAAaca--------------tgaatacat-------------tttttatagcgACTAGAATA-----GGTTTTTATCTATC-------TC-AATGAT s droRho2.KB449310 53794 113 - 65043 CTAT-------------GTTCAATCA------------AT---------TTAAAGGAAAAACACTC-------------------------------------CAA-----------------------A--------CCAAACCCTTTCA---AGTTTTAATAAtca--------------tgtttacat-------------tttttatagacACTACGat------ggcttttatttgtt-------tc-aatGAT s droFic2.KB457177 95548 106 + 995874 ATGA-------------GC-------------------AC---------CTAAAGGAGAAATATAC-------------------------------------ATA-----------------------A--------CTATCTCTTTTTC---GGGTTCAATAGact--------------tgtatacat-------------tttttatagagCCTAGAAT------CACCTTCATTTGTT-------TC-AATAAA s droVir3.scaffold_12875 7371584 122 + 20611582 ----------------------------------------------------ATGAATGTTTTGGT-------------------------------------TTA-----------------------A-------TACAACCAATTTTT---GTCATAAATAAAGT--------------AAAACCCAAGGGGATCTCGGGATCTTTACAGAATCTTTGTCATTGGCATTATTTTTTAAATTATAAGAGC-AAAGAT s droAlb1.JH854640 328239 57 + 406291 ----------------------------------------------------ATGCAAACTTTGTT-------------------------------------TCG-----------------------A-----CTTAAAAACAACTct----------aataattt--------------ag-----------------------------------------------------ttaaat-------ac-AAAGAT a score=-64276.000000 s dm6.chr2R 24372337 36 + 25286936 ATG----CCGTTTGGGCAATAAACAC---CG-----GAATT----------------GGAGTAA s droSim1.chr2R 18711066 36 + 19596830 GTG----CCGTTTGGGCAATAAACAC---CG-----GAATT----------------GGAGTAA s droSec1.super_23 130400 36 + 989336 GTG----CCGTTTGGGCAATAAACAC---CG-----GAATT----------------GGAGTAA s droYak3.chr2R 20220491 36 + 21139217 GTG----CCGTTTGGGCAATAAACAC---AA-----GAATC----------------GGAGCAA s droEre2.scaffold_4845 21618024 36 + 22589142 GTG----TCGTTTGGGCAATAAACAC---CG-----GAATT----------------GGAGTAA s droBia2.KB462602 813064 30 + 3129309 ---------GTTCGGGCCATAAATAC---CG-----GACC-----------------CTCCTAA s droSuz1.KI419649 12059454 31 - 14502029 ---------GTTCGGGCAATAAATTC---CG-----GACCT----------------TTCCTAA s droAna3.scaffold_13266 5722819 21 - 19884421 AAGT---CCCTCTTAGAAATCACC---------------------------------------- s droEug2.KB465067 615528 40 + 1515531 GTACAAAAAGTATGAGCAATGAAAAC---AA-----TATTG----------------ACCCTAG s droEle2.KB458573 539343 49 - 5320397 -------atgtatgtgCCATAAAAGC---CA-----TTTCTCCCACACCCAAAACAGCACACAA s droTak2.KB461535 158637 34 - 669855 ---------GTTTGGGCAATAAATACCTACA-----GACCT----------------TTCCCAA s droRho2.KB449310 53907 31 - 65043 ---------GTATGTGCAATAAATGC---CT-----CAGTT----------------TCCACAA s droFic2.KB457177 95654 28 + 995874 ---------GTGTGTAAAAGGAACAC----------ACACT----------------CCCACA- s droVir3.scaffold_12875 7371706 31 + 20611582 --------CGCTTCATAATACAGCAT---GAAAAGTGACTA----------------G------ s droAlb1.JH854640 328296 17 + 406291 --------TGCTTC---------CAT---TA-----GCTTA----------------G------ a score=26182.000000 s dm6.chr2R 24372373 10 + 25286936 CCCAAAG-----CCA s droSim1.chr2R 18711102 10 + 19596830 CCCAAAG-----CCA s droSec1.super_23 130436 10 + 989336 CCCAAAA-----CCA s droYak3.chr2R 20220527 10 + 21139217 CCCAAAG-----CCA s droEre2.scaffold_4845 21618060 10 + 22589142 CCCAAAA-----CCA s droBia2.KB462602 813094 11 + 3129309 CCCAAAA----GCCA s droSuz1.KI419649 12059485 11 - 14502029 ACCAAAA----CCCA s droAna3.scaffold_13266 5722840 3 - 19884421 ------------ACT s droEug2.KB465067 615568 11 + 1515531 CCCAACT----GCCA s droEle2.KB458573 539392 10 - 5320397 ACTAAAC-----CCA s droKik2.KB459527 292604 10 - 1234237 CCCAAAT-----CAA s droTak2.KB461535 158671 11 - 669855 CCCGAAA----CCCA s droRho2.KB449310 53939 10 - 65043 CCCAAAA-----CCA s droFic2.KB457177 95682 10 + 995874 -CCAAAA----TCCA s droVir3.scaffold_12875 7371763 10 + 20611582 CACAGAG-----TCG s droMoj3.scaffold_6496 26166827 10 + 26866924 CTCAACA-----CCA s droAlb1.JH854640 328313 13 + 406291 --caaagtattttca a score=96237.000000 s dm6.chr2R 24372383 22 + 25286936 TTTCATCT--------TGTATGC-AAGCCCC s droSim1.chr2R 18711112 22 + 19596830 TTTCATCT--------TGTATGC-AAACCCC s droSec1.super_23 130446 22 + 989336 TTTCATCT--------TGTATGC-AAACCCC s droYak3.chr2R 20220537 22 + 21139217 TTTCATCT--------CGTATGC-AAACCCC s droEre2.scaffold_4845 21618070 22 + 22589142 TTTCATCT--------CGTATGC-AAACCCC s droBia2.KB462602 813105 22 + 3129309 TTTCATCG--------TGTTTTC-TCACCCT s droSuz1.KI419649 12059496 22 - 14502029 TTTCATCG--------CGTATTC-TCACCCT s droAna3.scaffold_13266 5722843 11 - 19884421 TTTCACCC--------CTT------------ s droEug2.KB465067 615579 22 + 1515531 TTTCATCG--------TATATTC-TCACCCT s droEle2.KB458573 539402 22 - 5320397 TTTCATCT--------TATATTC-TTACCCT s droKik2.KB459527 292621 22 - 1234237 TTTCATGC--------TAAACTC-TCACCCC s droTak2.KB461535 158682 22 - 669855 TTTCATTT--------CGTATTC-TCACCCT s droRho2.KB449310 53949 22 - 65043 TTTCATCT--------TGTATTC-TTACCCT s droFic2.KB457177 95692 22 + 995874 TTTCATCT--------TGTATTC-CTACCCT s droPse3.chr3 1365324 22 - 19787792 TTTCTTCC--------TGTTTTC-GAACCAC s droPer1.super_34 554180 22 - 916997 TTTCTTCC--------TGTTTTC-GAACCAC s droMir2.chr3 1406415 22 - 20862834 TTTCTTCC--------TGTTTTC-GAACCAC s droVir3.scaffold_12875 7371784 28 + 20611582 CTTGATTCGTTCCGATTGTTTTT-GCTTC-- s droMoj3.scaffold_6496 26166848 20 + 26866924 TTTTCTTC--------TGCGTTT-GTGCC-- s droAlb1.JH854640 328337 21 + 406291 TTTCATTA--------AGCTTTCAGCACC-- s droGri2.scaffold_15245 922703 16 + 18325388 TTTGATTT--------TGT-----GCACC-- a score=-13341.000000 s dm6.chr2R 24372405 12 + 25286936 TT---------TGTGCCACGG------- s droSim1.chr2R 18711134 12 + 19596830 TT---------TGTGCCACGG------- s droSec1.super_23 130468 12 + 989336 TT---------TGTGCCACGG------- s droYak3.chr2R 20220559 12 + 21139217 TT---------TGTGCCACTG------- s droEre2.scaffold_4845 21618092 12 + 22589142 TT---------TGTGCCACTG------- s droBia2.KB462602 813127 12 + 3129309 TT---------TGAGCCACTG------- s droSuz1.KI419649 12059518 12 - 14502029 TT---------TGTGCCACTG------- s droAna3.scaffold_13266 5722854 12 - 19884421 TT---------CGTGCCACTG------- s droBip2.KB464407 1972720 12 + 2915140 TT---------CATACCACTG------- s droEug2.KB465067 615601 12 + 1515531 TT---------TGGACCACAG------- s droEle2.KB458573 539424 12 - 5320397 TT---------TGCGCCACTG------- s droKik2.KB459527 292644 12 - 1234237 TT---------TGCTCCACTG------- s droTak2.KB461535 158704 12 - 669855 TT---------TGCGCCACTG------- s droRho2.KB449310 53971 12 - 65043 TT---------TGGGCCACTG------- s droFic2.KB457177 95714 12 + 995874 TT---------TGCGCCactg------- s droPse3.chr3 1365354 19 - 19787792 CCCATCCcacacatcccac--------- s droPer1.super_34 554210 10 - 916997 CC---------CATCCCAC--------- s droMir2.chr3 1406445 10 - 20862834 CC---------CAtcccac--------- s droVir3.scaffold_12875 7371812 10 + 20611582 -----------------ACTGTGG-TGG s droMoj3.scaffold_6496 26166868 10 + 26866924 -----------------ACTGTGC-CGG s droAlb1.JH854640 328358 5 + 406291 -----------------ACAGT------ s droGri2.scaffold_15245 922719 11 + 18325388 -----------------ACTGTGGATGA a score=1126984.000000 s dm6.chr2R 24372417 76 + 25286936 TTATCC-TTT---GGCC------------------TGTTCC--CTGG-GCAATTGTGCGTTAGATTTAAGTGCTTTCGTTTGCCAGGCTTAATTTGCATTT s droSim1.chr2R 18711146 76 + 19596830 TTATCC-TTT---GGCC------------------TGTTCC--CTGG-GCAATTGTGCGTTAGATTTAAGTGCTTTCGTTTGCCAGGCTTAATTTGCATTT s droSec1.super_23 130480 76 + 989336 TTATCC-TTT---GGCC------------------TGTTCC--CTGG-GCAATTGTGCGTTAGATTTAAGTGCTTTCGTTTGCCAGGCTTAATTTGCATTT s droYak3.chr2R 20220571 76 + 21139217 TTATCC-TTT---GGCC------------------TGTTCC--CTGG-GCAATTGTGCGTTAGATTTAAGTGCTTTCGTTTGCCAGgcttaatttgcattt s droEre2.scaffold_4845 21618104 76 + 22589142 TTATCC-TTT---GGCC------------------TGTTCC--CTGG-GCAATTGTGCGTTAGATTTAAGTGCTTTCGTTTGCCAGGCTTAATTTGCATTT s droBia2.KB462602 813139 76 + 3129309 TTATCC-TTT---GGCC------------------CGTTCC--CTGG-GCAATTGTGCGTTAGATTTAAGTGCTTTCGTTTGCCAGgcttaatttgcattt s droSuz1.KI419649 12059530 77 - 14502029 TTATCCTTTT---GGCC------------------CGTTCC--CTGG-GCAATTGTGCGTTAGATTTAAGTGCTTTCGTTTGCCAGgcttaatttgcattt s droAna3.scaffold_13266 5722866 75 - 19884421 TCATTC--CT---GCCC------------------CATTCC--CTGG-GCAATTGTGCGTTAGATTTAAGTGCTTTCGTTTGCCAGGCTTAATTTGCATTT s droBip2.KB464407 1972732 75 + 2915140 TTATGC--CT---GCCC------------------CATTCC--CTGG-GCAATTGTGCGTTAGATTTAAGTGCTTTCGTTTGCCAGgcttaatttgcattt s droEug2.KB465067 615613 76 + 1515531 TTGTGT-CTT---GGCC------------------CGTTCC--CTGG-GCAATTGTGCGTTAGATTTAAGTGCTTTCGTTTGCCAGccttaatttgcattt s droEle2.KB458573 539436 76 - 5320397 TTATCC-TTT---AGCT------------------TGTTCC--CTGG-GCAATTGTGCGTTAGATTTAAGTGCTTTCGTTTGCCAggcttaatttgcattt s droKik2.KB459527 292656 79 - 1234237 TTATCC-TTTTCGGCAC------------------CGTTCC--CTGG-GCAATTGTGCGTTAGATTTAAGTGCTTTCGTTTGCCAggcttaatttgcattt s droTak2.KB461535 158716 77 - 669855 TTATCCTTTT---GGCC------------------CGTTCC--CTGG-GCAATTGTGCGTTAGATTTAAGTGCTTTCGTTTGCCAGgcttaatttgcattt s droRho2.KB449310 53983 77 - 65043 TTATCCTTTT---GGCC------------------CGTTCC--CTGG-GCAATTGTGCGTTAGATTTAAGTGCTTTCGTTTGCCAGgcttaatttgcattt s droFic2.KB457177 95726 77 + 995874 ttttcctttt---ggcc------------------cgTTCC--CTGG-GCAATTGTGCGTTAGATTTAAGTGCTTTCGTTTGCCAGgcttaatttgcattt s droPse3.chr3 1365373 73 - 19787792 --atcc--cc---atcc------------------cgtTCC--CTGG-GCAATTGTGCGTTAGATTTAAGTGCTTTCGTTTGCCAGgcttaatttgcattt s droPer1.super_34 554220 73 - 916997 --ATCC--CC---ATCC------------------CGTTCC--CTGG-GCAATTGTGCGTTAGATTTAAGTGCTTTCGTTTGCCAGGCTTAATTTGCATTT s droMir2.chr3 1406455 73 - 20862834 --atcc--cc---atcc------------------cgtTCC--CTGG-GCAATTGTGCGTTAGATTTAAGTGCTTTCGTTTGCCAGgcttaatttgcattt s droWil2.CH963894 1334116 88 + 2843958 TTAGGC-CTT---GGCCGG-----GCTGCCAG---TGCTCCTTCCTG-GCAATTGTGCGTTAGATTTAAGTGCTTTCGTTGCCAAGgcttaatttgcattt s droVir3.scaffold_12875 7371822 77 + 20611582 -----------------TAG----GCTGCCGTGGTTTTGCA--CTCGTGGAATTGTGCGTTAGATTTAAGTGCTTTCGTT-GTGGGGCTTAATTTGCATTT s droMoj3.scaffold_6496 26166878 80 + 26866924 -----------------TCGGTGTGTTGCCGTGG-TTTGCA--CTCGCGGAATTGTGCGTTAGATTTAAATGCTTTCGTT-ATGGGGCTTAATTTGCATTT s droAlb1.JH854640 328363 58 + 406291 ----------------------------------------A--TTCGTACAATTGTGCGTTAGATTTAAGTGCTTTCGTT-GTGGgacttcatttgcattt s droGri2.scaffold_15245 922730 78 + 18325388 -----------------TGGGTTTGCTGTTGT---TTTGCA--CTGTTGGAATTGTGCGTTAGATTTAAGTGCTTTCGTT-GTGGGGCTTAATTTGCATTT a score=2380818.000000 s dm6.chr2R 24372493 209 + 25286936 TTATTTTTATGTTTTCATTGAAAGCGCCAGCATCAATGGAGCCCGCT---------GCCTTCGG-------------------------AGGCTTTGG----AGGC------------------------------------------------TCCGGAGGAGAGCACA-TTTGGCTATTC-------CTTTGTTTT--------------------CGG-C-TTAAAGTTATCAGTGTCGGTAGATGTACACGGCATCAACG---------GT------AGCAG---------------------------------------------------------------------------------------CAACATGCAAAATGCAAATGTTTATTGGCC-AAATGCTG--AACGATCT-----------------C--GGCC-AG-C---- s droSim1.chr2R 18711222 225 + 19596830 TTATTTTTATGTTTTCATTGAAAGCGCCAGCATCAATGGAGCCCGCT---------GGCTGCGG-------------------------AGGCTTCAG----AGGC------------------CGGAGACTTTGGAGGC--------------TCCGGAGGAGAGCACA-TTTGGCTATTC-------CTTTGTTTT--------------------CGG-C-TTAAAGTTATCAGTGTCGGTAGATGTACACGGCATCAACG---------GT------AGCAG---------------------------------------------------------------------------------------CAACATGCAAAATGCAAATGTTTATTGGCC-AAATGCTG--AACGATCT-----------------C--GGCC-AG-C---- s droSec1.super_23 130556 233 + 989336 TTATTTTTATGTTTTCATTGAAAGCGCCAGCATCAATGGAGCCCGCT---------GGCTGCGg-------------------------aggcttcag----aggct-------tcggaggcttcataggcttTGGTGGC--------------TCCGGAGGAGAGCACA-TTTGGCTATTC-------CTTTGTTTT--------------------CGG-C-TTAAAGTTATCAGTGTCGGTAGATGTACACGGCATCAACG------------------GCAG---------------------------------------------------------------------------------------CAACATGCAAAATGCAAATGTTTATTGGCC-AAATGCTG--AACGATCT-----------------C--GGCC-AG-C---- s droYak3.chr2R 20220647 227 + 21139217 ttatttttatgttttcattgAAAGCGCCAGCATCAATGGAGCCCGCTGGCTTCCGAGGCTTCCG-------------------------AGGCTTTGG----AGGC-------------------------TTTGGTGGC--------------TTCGGAGGAGAGCACA-TTTGGCTATTC-------CTTTGTTTT--------------------GGG-C-TCAAAGTTATCAGTGTCGGTAGATGTACACGGCATCAACG---------GT------AGCAG---------------------------------------------------------------------------------------CaacatgcaaaatgcaaatgtttattGGCC-AAATGCTG--AACGATCT-----------------C--GGCC-AG-C---- s droEre2.scaffold_4845 21618180 218 + 22589142 TTATTTTTATGTTTTCATTGAAAGCGCCAGCATCAATGGAGCCCGCT---------GGCCTCGG-------------------------AGGCTTTGG----AGGC-------------------------TTGTGAGGC--------------TTCGGAGGAGAGCACA-TTTGGCTATTC-------CTTTGTTTT--------------------CGG-C-TTAAAGTTATCAGAGTCGGTAGATGTACACGGCATCAACG---------GT------AGCAG---------------------------------------------------------------------------------------CAACATGCAAAATGCAAATGTTTATTGGCC-AAATGCTG--AACGATCT-----------------C--GGCC-AG-C---- s droBia2.KB462602 813215 197 + 3129309 ttatttttatgttttcattgaAAGCGCCAGCATCAATGGAGCCCGCT---------GGCTTC----------------------------------------AGTC-------------------------------------------------------GGGAGCACA-TTTGGCTATTC-------CTTTGTTTT--------------------CGG-C-TTAAAGTTATCAGTGTCGGTAGATGTACACGGCATCAAcg---------gtagcagcagcag---------------------------------------------------------------------------------------caacatgcaaaatgcaaatgtttatTGGCC-AAAAGCTG--AACGATCT-----------------C--AGCC-GG-C---- s droSuz1.KI419649 12062545 194 - 14502029 ttatttttatgttttcattgAAAGCGCCAGCATCAATGGAGCCCGCT---------GGCTTC----------------------------------------AGTC-------------------------------------------------------GAGAGCACA-TTTGGCTATTC-------CTTTGTTTT--------------------CGG-C-TTAAAGTTATCAGTGTCGGTAGATGTACACGGCATCAACg---------gt---agcagcag---------------------------------------------------------------------------------------caacatgcaaaatgcaaatgtttatTGGCC-AAATGCTG--AACGATCT-----------------C--AGCC-AG-C---- s droAna3.scaffold_13266 5722941 247 - 19884421 TTATTTTTATGTTTTCATTGAAAGCGCCAGCATCAATGGAGCCCGC----------TGCT-CGG-------------------------CGG-----------------------------------------------------------------AGAGTTGGGCGCATTTTGGCTATTC-------CTTTGTTTT--------------------CGG-C-TTTAAGTTATCAGTGTCGGTAGATGTACACGGAATcaccg---------gt------agcaggaaaagcagtagcagtagcagcaacagct--------------------acagc--CAAAAA-------CA---ACT-----GAGAACAACATGCAAAATGCAAATGTTTATTGGCC-AAATACTG--AACGATCA-----------------C--AGCCGGGTC---- s droBip2.KB464407 1972807 253 + 2915140 ttatttttatgttttcattGAAAGCGCCAGCATCAATGGAGCCCGCT---------TGCT-CGC-------------------------TGGCT---------GGC-------------------------------------------------CTGGAGTTGGGCGCA-TTTGGCTATTC-------CTTTGTTTT--------------------CGG-C-TTTAAGTTATCAGTGTCGGTAGATGTACACGGAATCACCG---------GT------AGCAGGAACAGCCAaagcagcagtagcaacagca--------------------acagc--caaaAA-------CA---ACT-----GAGAACAacatgcaaaatgcaaatgtttATTGGCC-AAATACTG--AACGATCA-----------------C--AGCC-GGTC---- s droEug2.KB465067 615689 239 + 1515531 ttatttttatgttttcattgAAAGCGCCAGCATCAATGGAGCCCGCT---------GGCTTC----------------------------------------AGTC-------------------------------------------------------GAGAGCACA-TTTGGCTATTC-------CTTTGTTTT--------------------CGG-C-TTAAAGTTATCAGTGTCGGTAGATGTACACGGCATCAAcg---------gt------agcag------caacagcagcggcagcagcagca--------------------gcagcaacaataa-------caac-aca-----GAGAACaacatgcaaaatgcaaatgtttatTGGCC-AAATGCTG--AACGATCT-----------------C--AGCC-GG-C---- s droEle2.KB458573 539512 237 - 5320397 ttatttttatgttttcattgAAAGCGCCAGCATCAATGGAGCCCGCT---------GGCTTC----------------------------------------AGTA-------------------------------------------------------GAGAGCACA-TTTGGCTATTC-------CTTTGTTTT--------------------CGG-C-TTAAAGTTATCAGTGTCGGTAGATGTACACGGCATCAACG---------GT------AGCAG------CCGccacagaaacaacaacagca--------------------acagtagcaacaa-------ca---aca-----gagaataacatgcaaaatgcaaatgtttatTGGCC-AAATGCTG--AACGATCT-----------------C--AGCC-AG-C---- s droKik2.KB459527 292735 217 - 1234237 ttatttttatgttttcattgaaaGCGCCAGCATCAATGGAGCCCGCTGCT------GGCTGC--------------------------------TCGT----TCGC-------------------------------------------------------TGGAGCACA-TTTGGCTATTC-------CTTTGTTTT--------------------CGG-C-TTAAAGTTATCAGTGTCGGTAGATGTACACGGCATCAacg---------gt------agcag--------------------------------------------------------cagcag-------caacaaca-----gagaacaacatgcaaaatgcaaatgtttaTTGGCC-AAATGCTG--AACGATCT-----------------C--AGCC-GG-C---- s droTak2.KB461535 158793 216 - 669855 ttatttttatgttttcattGAAAGCGCCAGCATCAATGGAGCCCGCT---------GGCTTT---------------------------CGGCTTC------AGTC-------------------------------------------------------GAGAGCACA-TTTGGCTATTC-------CTTTGTTTT--------------------CGGCC-TTAAAGTTATCAGTGTCGGTAGATGTACACGGCATCAACG---------gt------agcag------cagccgcagcagtag------------------------------------------------------------------caacatgcaaaatgcaaatgtttATTGGCC-AAATGCTG--AACGATCT-----------------CAGAGCC-AG-C---- s droRho2.KB449310 54060 234 - 65043 ttatttttatgttttcattgAAAGCGCCAGCATCAATGGAGCCCGCT---------GGCTTC----------------------------------------AGTC-------------------------------------------------------GAGAGCACA-TTTGGCTATTC-------CTTTGTTTT--------------------CGG-C-TTAAAGTTATCAGTGTCGGTAGATGTACACGGCATCAACG---------GT------AGCAG------------Ccgcaatagcaacaaca--------------------acaacagcaacaa-------caacaaca-----gagaacaacatgcaaaatgcaaatgtttattggcc-aaatgctG--AACGATCT-----------------C--AGCC-AG-C---- s droFic2.KB457177 95803 221 + 995874 ttatttttatgttttcattgAAAGCGCCAGCATCAATGGAGCCCGCT---------GGCTTC----------------------------GGCTTCAGCTTCAGTC-------------------------------------------------------GAGAGCACA-TTTGGCTATTC-------CTTTG-TTT--------------------CGG-C-CCAAAGTTATCAGTGTCGGTAGATGTACACGGCATCAACG---------gt------agcag--------------------------------------------------------cggcaa-------caacagcg-----gAGAACaacatgcaaaatgcaaatgtttattGGCC-AAATGCTG--TACGATCT-----------------C--AGCC-AG-C---- s droPse3.chr3 1365446 332 - 19787792 ttatttttatgttttcattGAAAGCGCCAGCATCAATGGAGCCCGCT---------GACTTCAG-------------------------CAGATCCG-----AGCCGAGTGGCACCGAGTGGATctgagagtggagtggaagctgagagctgagagctgagGCGAGCACA-TTTGGCTATTC-------CTTTGTTTT--------------------CGG-C-CTTAAGTTATCAGCGGCGGTAGATGTACACGGCATCAACggtagcagcagt------agcag------cagtagcagcagtagcaacagcaacagtggtagcagcagca--gcagcagcagcag-------cagcagca-----acatgcaacatgcaaaatgcaaatgtttatTGGCC-AAATGCTG--AACGATCT-----------------C--AACG-AG-C---- s droPer1.super_34 554293 302 - 916997 TTATTTTTATGTTTTCATTGAAAGCGCCAGCATCAATGGAGCCCGCT---------GACTTCAG-------------------------CAGATCCG-----AGCCGAGTGGCACCGAGTGGATCTGAGAGTGGAGTGGAAGCTGAGAGCTGAGAGCTGAGGCTAGCACA-TTTGGCTATTC-------CTTTGTTTT--------------------CGG-C-CTTAAGTTATCAGCGGCGGTAGATGTACACGGCTTcaacg---------gt------agcag------cagtagcagcagtagcaacagcaacagtggt-----------------------ag-------caacagca-----acatgcaacatgcaaaatgcaaatGTTTATTGGCC-AAATGCTG--AACGATCT-----------------C--AACG-AG-C---- s droMir2.chr3 1406528 307 - 20862834 ttatttttatgttttcattGAAAGCGCCAGCATCAATGGAGCCCGCT---------GACTTCAG-------------------------CAGATCCG-----AGCCGAGTGGCACCGAGTGGATctgagagtggagtgga-------agctGAGAGCTGAGGCGAGCACA-TTTGGCTATTC-------CTTTGTTTT--------------------CGG-C-CTTAAGTTATCAGCGGCGGTAGATGTACACGGCATCAACG---------gt------agcag------caaaagcagcagtagcaacagcaacagtgg-----------tagcaacagcagcag-------ccacagca-----acatgcaacatgcaaaatgcaaatgtttattGGCC-AAATGCTG--AACGATCT-----------------C--AACG-AG-C---- s droWil2.CH963894 1334204 253 + 2843958 ttatttttatgttttcatcGAGAGCGCCAGCATCAATGGAGCCCGCT---------TCCATT----------------------------------------TGGC--------------------------------------TAttcctttgttttgtttcgtttggt-ttttggtattctttttgtttttatttt--------------------tgg-cttttgctttATCAGTAGCGGTAGATGCAcacggcaacaaca---------ac------tacaa------caataacaataagaa----------------------------gcaactgcaaaaa-------caacaactacaacaagaataacatgc-aaatgcaaatgtttatTGGCC-AAAT---------Ggctt-----------------a--agaa-aa------ s droVir3.scaffold_12875 7371899 219 + 20611582 TTATTTTTATGTTTTCATTGAAAGCGCCAGCATCAATGGAGCCCGCA---------A-------------------------------------CTGG----GCGC---------------------------------------------------------ACACACA-TTTGGCTATTC-------CTTTGTTTT----------------GCGGCGG-C-TC----CTATCAGTGTCGGTAGATGCACACGCcatcaacg---------gt------agcgg------caacagcagcag---------ca--------------------acaataacaacga-------caacaaca-----g----caacaTGC-AAATGCAAATGTTTATTGCCCAAAATGCTG---------------------------A--AGGG-Gg-cagc- s droMoj3.scaffold_6496 26166958 219 + 26866924 TTATTTTTATGTTTTCATTGAAAGCGCCAGCATCAATGGAGCCCGCA---------A-------------------------------------CAGG----GAGC---------------------------------------------------------ACTCACA-TTTGGCTATTC-------CTTTGTTTC----------------GCGGCGG-C-TC----CTATCAGTGTCGGTAGATGCACACGCCATCAGCG---------GA------AGGAG------Aaacaacaacag---------aa--------------------acagcagcaacaa-------cagcaatg-----g----caacaTGC-AAATGCAAATGAATGTTGGCCAAAATGCTG---------------------------G--AGGA-GG-Caaa- s droAlb1.JH854640 328421 298 + 406291 ttatttttatgttttcattgaAAGCGCCAGCATCAATGGAGCCCGCA---------AACTG--------GGCAATTGGTGGCCAAAGG-GTGCCCAGG----GGGC----------------------------------GGGGAGGCGGCCAAAAGAGAGCTGCACACA-TTTGGCTATTC-------CTTTGTTCAAcgcgacggc-----ggcggcgg-c-tc----GTATCAGTGTCGGTAGATGCACACGGCATCAAcg---------gt------agcag------caacaacaatagtacaagtaata--------------------acaacaacaatga-------caacaaca-----g----taacatgc-aaatgcaaatgtttattgCCCAAAATGCTGCACACGA--------------------G--AGCT-GG-CCAAA s droGri2.scaffold_15245 922808 339 + 18325388 TTATTTTTATGTTTTCATTGAAAGCGCCAGCATCAATGGAGCCCGCT---------AACTGCAAACGCAAACAAGGGGCGCATGGAGACGGGTTGAGA----GGGC----------------------------------GACAGGGAGACGGGGAGACGGACCCACACA-TTTGGCTATTC-------CTTTGTTGTTTTTTGTTTCCTTTTAGCGGCGG-C-TC----CTATCAGTGTCGGTAGATGCACACGCCATCAACG---------GT------agcag------caacaacagcaacaacagcagca--------------------gcagcagcaacaacaAGAGGCAACAACA-----G----AAACATGC-AAATGCAAATGTTTATTGCCCAAAATGCTGTGAGAGAGGTAGATGGGAAGTGGAGGGA--AGGG-GG-TCAAA a score=-329753.000000 s dm6.chr2R 24372702 32 + 25286936 TG-AGCTGAG---AACAC-------------GGTCC---------------------------------------TTCTGGCTTC------------------------------------------------------------GCC s droSim1.chr2R 18711447 30 + 19596830 TG-AACTGAG---A--AC-------------GGTCC---------------------------------------TTCTGGCTTC------------------------------------------------------------GCC s droSec1.super_23 130789 30 + 989336 TG-AACTGAG---A--AC-------------GGTCC---------------------------------------TTCTGGCTTC------------------------------------------------------------GCC s droYak3.chr2R 20220874 41 + 21139217 TG-AACTGAGAACA--AC-------------GGTCC---------------------------------------TTCTGGCTTCTC-----------------------------GCCTCC-----------------------GTC s droEre2.scaffold_4845 21618398 48 + 22589142 TG-AACTGAG---A--AC-------------GGTCC---------------------------------------TTCTGTTGCCGG-----------------------------GCCTCCGAGTTGCCAA-------------GTT s droBia2.KB462602 813412 53 + 3129309 TA-AACTGAG---A--ATG------------GGtcc---------------------------------------ttctgttttttt-------------------t------ctcgtttgtgttttttcct-------------gtt s droSuz1.KI419649 12062739 56 - 14502029 TA-AACTGAG---A--ATG------------GGTCc---------------------------------------ttcggttttttt-------------ttc---t------ttcgtttttgtttttttgt-------------att s droAna3.scaffold_13266 5723188 100 - 19884421 TA-AACTGAG---A--AT-------------GGGCCAACACTGTTTTGTTGTTTTGTTTTTTTTTTTTCCATTGATGTTGCTGCTGC-------------TGC---T------GTTGATTTTGTGGCAAGCT----TGAGCG---GCT s droBip2.KB464407 1973060 77 + 2915140 TA-AACTGAG---A--AT-------------GGGCCAACACGgat------------------------------tgctgttgccgc-------------tgc---t------gttgATTTTGTTGCAAGCTGAGCtgtgcggctgct s droEug2.KB465067 615928 34 + 1515531 TGAAACTGAG---A--ATG------------GGtcc---------------------------------------ttctgtttttgt----------------------------------------------------------ttt s droEle2.KB458573 539749 80 - 5320397 TA-AACTGAG---A--ATGGGCTA--ACACTGGTCC---------------------------------------TTCTGTCTTTCTGCATCCAACCCCctgct--t------tttggcttttggcttttgt-------------ttt s droKik2.KB459527 292952 71 - 1234237 TA-AACTGAG---A--AT-------------GGGCTAACACTGTTTGGGGGCCCCTTagatat------------tgctgctgctgc-------------tcca--t------aCTGCCG-------------------------GCT s droTak2.KB461535 159009 48 - 669855 TA-AACTGAG---A--ATG------------GGttc---------------------------------------tttttctccttt------------------------------tttctgtattgtttt-------------ttt s droRho2.KB449310 54294 58 - 65043 TA-AACTGAG---A--ACGGGCTAACACACTGGtcc---------------------------------------ttctgttttttt-------------------tg-----gttccccttgt---------------------ttt s droFic2.KB457177 96024 64 + 995874 TA-AACTGAG---A--AT-------------GGGCTAACAC----------------------------------TGCTGGTCCTTC-------------Tcgg--tg----ttttgtttttgctgcttgGCG------------TTT s droPse3.chr3 1365778 88 - 19787792 TA-AACTGAG---A--AT-------------GGGCTAACActgttttagctgtt---------------------tgctgtggctgc-------tgctgttgctgttgctgttgctgttttagATGCGGCCT-------------GTT s droPer1.super_34 554595 82 - 916997 TA-AACTGAG---A--AT-------------GGGCTAACACTGTTTTAGCTGTT---------------------TGCTGTGGCTGC-------------TGCTGTTGCTGTTGCTGTTTTAGATGCGGCCT-------------GTT s droMir2.chr3 1406835 76 - 20862834 TA-AACTGAG---A--AT-------------GGGTTAACACTGTTTTAgctgtt---------------------tgctgtggctgc-------------------tgctgttgctgttttagATGCGGCCT-------------GTT s droWil2.CH963894 1334457 49 + 2843958 -a-aacaaaa---a--ac-------------tggcCAAC------------------------------------TGATACGTCTGT-------------------CGTACTGACTGACTA------------------------AAT s droMoj3.scaffold_6496 26167223 24 + 26866924 CA-AACTGAA---A--AT-------------TT---AAG------------------------------------TTTTGAA------------------------------------------------------------------ s droAlb1.JH854640 328801 27 + 406291 ca-tcttggc---a--ac-------------ttggcaac------------------------------------tgTTGTC------------------------------------------------------------------ s droGri2.scaffold_15245 923181 27 + 18325388 TG-AAGTTGA---A--GT-------------TAAGCGGG------------------------------------TGCTGAC------------------------------------------------------------------ a score=208448.000000 s dm6.chr2R 24372734 43 + 25286936 ----------TCCG-----------AGCGGCC--------GGGCGATTGGA------------GCGGGT--------------GC--TG---ACTGCCACAAA s droSim1.chr2R 18711477 43 + 19596830 ----------TCCG-----------AGTGGCC--------GGGCGATTGGA------------GCGGGT--------------GC--TG---ACTGCCACAAA s droSec1.super_23 130819 43 + 989336 ----------TCCG-----------AGTGGCC--------GGGCGATTGGA------------GCGGGT--------------GC--TG---ACTGCCACAAA s droYak3.chr2R 20220915 55 + 21139217 ----------TCCG-----------AGTTGCC--------TGGCGATTGGAGCGATTGGAGCGGCGGGT--------------GC--TG---ACTGCCACAAA s droEre2.scaffold_4845 21618446 43 + 22589142 ----------GCCG-----------AGTTGCC--------GGGCGATTGGA------------GCGGGT--------------GC--TG---ACTGCCACAAA s droBia2.KB462602 813465 37 + 3129309 ----------tttt-----------ctGAGCT--------------TTGAA------------GCGGGT--------------GC--TG---ACTGCCACAAA s droSuz1.KI419649 12062795 51 - 14502029 ----------tttt-----------ttttgcttagcTTTGAAGCGATTGAA------------GCGGGT--------------GC--TG---ACTGCCACAAA s droAna3.scaffold_13266 5723288 48 - 19884421 ----------GCTG-----------TTCCTTC---TTTTGAAGCGATTGAA------------GCGGGT--------------GC--TG---ACTGCCACAAA s droBip2.KB464407 1973137 49 + 2915140 ----------gctg-----------ttccttC--TTTTTGAAGCGATGGAA------------GCGGGT--------------GC--TG---ACTGCCACAAA s droEug2.KB465067 615962 43 + 1515531 ----------ttct-----------ggcTTTC--------AAGCGATTGAA------------GCGGGT--------------GC--TG---ACTGCCACAAA s droEle2.KB458573 539829 43 - 5320397 ----------tgta-----------agccTTC--------AAGCGATTGAA------------GCGGGT--------------GC--TG---ACTGCCACAAA s droKik2.KB459527 293023 43 - 1234237 ----------GTTG-----------CCTCTTT--------CGGGCCTTGCA------------GCGGGT--------------GC--TG---ACTGCCACAAA s droTak2.KB461535 159057 43 - 669855 ----------tttg-----------tggcttc--------aAACGATTGAA------------GCGGGT--------------GC--TG---ACTGCCACAAA s droRho2.KB449310 54352 43 - 65043 ----------ttta-----------agctttc--------AAGCAATTGAA------------GCGGGT--------------GC--TG---ACTGCCACAAA s droFic2.KB457177 96088 43 + 995874 ----------TTTA-----------AGCCTTC--------AAACGGTTGAA------------GCGGGT--------------GC--TG---ACTGCCACAAA s droPse3.chr3 1365866 41 - 19787792 ----------CCT-------------TCTTTC--------ATTGGCTCGAA------------GCGGGT--------------GC--TG---ACTGCCACACA s droPer1.super_34 554677 41 - 916997 ----------CCT-------------TCTTTC--------ATTGGCTCGAA------------GCGGGT--------------GC--TG---ACTGCCACACA s droMir2.chr3 1406911 41 - 20862834 ----------CCT-------------TCTTTC--------ATTGGCTCGAA------------GCGGGT--------------GC--TG---ACTGCCACACA s droWil2.CH963894 1334506 46 + 2843958 ----------GGCC-----------GTCGGCT--------GAACATTCCTA------------GCGGGT--------------GC--TGACTACTGCCACAAG s droVir3.scaffold_12875 7372164 43 + 20611582 ----------TTGG-----------AGCTGAA--------GTTGAAGTTAA------------GCGGGT--------------GC--TG---ACTGTCAACAG s droMoj3.scaffold_6496 26167248 40 + 26866924 ----------CTGA-----------AGTTGAG--------ATT---GTTAA------------GCGGGT--------------GC--TG---ACTGTCAACGG s droAlb1.JH854640 328834 59 + 406291 ----------TTGG-----------CTTTTGG--------CATCAGATTCG------------GCGCGTCaggcatcgccatcgccatc---gctgtCAGCAG s droGri2.scaffold_15245 923215 70 + 18325388 AGCGAGGCAGCTGGTCAACGTGCAACATGCAA--------CATGGGggcag------------gcaagctggcaa--------gc--ag---gcaggcagCCA a score=1816620.000000 s dm6.chr2R 24372777 128 + 25286936 GTTGTCG---------------------CCTTT---------------------------------------------------------------------------------TG--TTGTGGCAGCAACCATTTTGGTAAAAACAACTAATCAATT----GGCAAATGTGCCATCCGTCAATCACGC------AGTCAGT-----------------TGGCGGTGGTGTAGGTCACACGACACCA-CACG-GTGGCTGC s droSim1.chr2R 18711520 128 + 19596830 GTTGTCG---------------------CCTTT---------------------------------------------------------------------------------TG--TTGTGGCAGCAACCATTTTGGTAAAAACAACTAATCAATT----GGCAAATGTGCCATCCGTCAATCACGC------AGTCAGT-----------------TGGCGGTGGTGTAGGTCACACGACACCA-CACG-GTGGCTGC s droSec1.super_23 130862 128 + 989336 GTTGTCG---------------------CCTTT---------------------------------------------------------------------------------TG--TTGTGGCAGCAACCATTTTGGTAAAAACAACTAATCAATT----GGCAAATGTGCCATCCGTCAATCACGC------AGTCAGT-----------------TGGCGGTGGTGTAGGTCACACGACACCA-CACG-GTGGCTGC s droYak3.chr2R 20220970 125 + 21139217 GTTGTCG---------------------CCTTT---------------------------------------------------------------------------------TG--TTGTGGCAGCAACCATTTTGGTAAAAACAACTAATCAATT----GGCAAATGTGCCATCCGTCAATCACGC------AGTCAGT-----------------TGGCGGTGGTGTAGGTCACACGACACCA-CTC--GCGGTT-- s droEre2.scaffold_4845 21618489 128 + 22589142 GTTGTCG---------------------CCTTT---------------------------------------------------------------------------------TG--TTGTGGCAGCAACCATTTTGGTAAAAACAACTAATCAATT----GGCAAATGTGCCATCCGTCAATCACGC------AGTCAGT-----------------TGGCGGTGGTGTAGGTCACACGACACCA-CTCG-GCGGCTGC s droBia2.KB462602 813502 126 + 3129309 GTTGTCG---------------------CCTTT---------------------------------------------------------------------------------TG--TTGTGGCAGCAACCATTTTGGTAAGAACAACTAATCAATT----GGCAAATGTGCCATCCGTCAATCAGCC------AGTCAGT-----------------CGGCGGTGGTGTAGGTCACACGACACCA-CA---GTGGCTGC s droSuz1.KI419649 12062846 126 - 14502029 GTTGTCG---------------------CCTTT---------------------------------------------------------------------------------TG--TTGTGGCAGCAACCATTTTGGTAAGAACAACTAATCAATT----GGCAAATGTGCCATCCGTCAATCAGCC------AGTCAGT-----------------TGGCGGTGGTGTAGGTCACACGACACCA-CA---GTGGTTGT s droAna3.scaffold_13266 5723336 127 - 19884421 GTTGTCG---------------------CCTTT---------------------------------------------------------------------------------TGTTTTGTGGCAGCAACCATTTTGGTAAAAACAACTAATCAATT----GGCAAATGTGCCATCCGTCAATCACTT----G-AGTCAGT-----------------CGTCGGTGGTGTAGGTCACACGACACCA-CACG---AGTT-- s droBip2.KB464407 1973186 131 + 2915140 GTTGTCg---------------------ccttt---------------------------------------------------------------------------------tgttttgtggcAGCAACCATTTTGGTAAAAACAACTAATCAATT----GGCAAATGTGCCATCCGTCAATCACTTG---G-AGTCAGTT--------------GGCGGTGGTGGTGTAGGTCATACGACACCA-CACG---AGTT-- s droEug2.KB465067 616005 133 + 1515531 GTTGTCG---------------------CCTTT---------------------------------------------------------------------------------TG--TTGTGGCAGCAACCATTTTGGTAAAAACAACTAATCAATT----GGCAAATGTGCCATCCGTCAATCACCGAGCCG-AGTCAGT-----------------TGGCGGTGGTGTAGGTCACACGACACCA-CACG-ATCGGTGG s droEle2.KB458573 539872 128 - 5320397 GTTGTCG---------------------CCTTT---------------------------------------------------------------------------------TG--TTGTGGCTGCAACCATTTTGGTAAAAACAACTAATCAATT----GGCAAATGTGCCATCCGTCAATCACTG------AGTCAGT-----------------TGGCGGTGGTGTAGGTCACACGACACCA-CACG-AGCGCTGG s droKik2.KB459527 293066 147 - 1234237 GTTGTCG---------------------CCTTT---------------------------------------------------------------------------------TG--TTGTGGCAGCAACCATTTTGGTAAGAACAACTAATCAATT----GGCAAATGTGCCATCCGTCAATCAATT----GAAGTCTGTCCA-GATCGGCGCGGCGCGGCGGTGGTGTAGGTCACACGACACCA-CACGAGTTGATGC s droTak2.KB461535 159100 122 - 669855 GTTGTCG---------------------CCTTT---------------------------------------------------------------------------------TG--TTGTGGCAGCAACCATTTTGGTAAAAACAACTAATCAATT----GGCAAATGTGCCATCCGTCAATCACCC------AGTCAGT-----------------TGGCGGTGGTGTAGGTCACACGACACCA-CACA-GT------ s droRho2.KB449310 54395 128 - 65043 GTTGTCG---------------------CCTTT---------------------------------------------------------------------------------TG--TTGTGGCAGCAACCATTTTGGTAAAAACAACTAATCAATT----GGCAAATGTGCCATCCGTCAATCACTG------AGTCAGT-----------------TGGCGGTGGTGTAGGTCACACGACACCA-CAcg-agtggtgg s droFic2.KB457177 96131 128 + 995874 GTTGTCG---------------------CCTTT---------------------------------------------------------------------------------TG--TTGTGGCAGCAACCATTTTGGTAAAAACAACTAATCAATT----GGCAAATGTGCCATCCGTCAATCACCG------AGTCAGT-----------------TGGCGGTGGTGTAGGTCACACGACACCA-CACG-ATCGGTGG s droPse3.chr3 1365907 130 - 19787792 GTTGTCG---------------------CCTTT---------------------------------------------------------------------------------TG--TTGTGGCAACAACCATTTTGGTAAAAACAACTAATCAATT----GGCAAATGTGCCATCCGTCAATCATTG------AGTCAGT---------------CGCGCTGGTGGTGTAGGTCACACGACACCA-CAcg-agcggcgg s droPer1.super_34 554718 130 - 916997 GTTGTCG---------------------CCTTT---------------------------------------------------------------------------------TG--TTGTGGCAACAACCATTTTGGTAAAAACAACTAATCAATT----GGCAAATGTGCCATCCGTCAATCATTG------AGTCAGT---------------CGCGCTGGTGGTGTAGGTCACACGACACCA-CACG-Agcggcgg s droMir2.chr3 1406952 130 - 20862834 GTTGTCG---------------------CCTTT---------------------------------------------------------------------------------TG--TTGTGGCAACAACCATTTTGGTAAAAACAACTAATCAATT----GGCAAATGTGCCATCCGTCAATCATTG------AGTCAGT---------------CGCGCTGGTGGTGTAGGTCACACGACACCA-CAcg-agcggcgg s droWil2.CH963894 1334552 223 + 2843958 TTTGTCG---------------------CCTTTGTTGCCTGCCATATAtctctctcccccttcccccactccactaacttctctctctctccctcttgcGATCGTTTGATCCCATG--CCTTTGTGACAACCATTTTGGTAAAAACAACTAATCAATC----GGCAAATGTGCCATCCGTCAATCATGGTGgtt-ggtcggttggttggCCTGGCTACTTGACTGTGGTGTAGGTCACACGAcacca-acca--------- s droVir3.scaffold_12875 7372256 129 + 20611582 GCCATCGCCATCACCGTCGCCGTCGCCATCGTG---------------------------------------------------------------------------------TGGCATATCGAAGTGGCCATTTTGGTAAAAACAACTAATCAATC----CGCAAATGTGCCATCCGTCAATCATTG-----------GC-----------------T-----TGGTGTAGGTCACACGACACCA-------------- s droMoj3.scaffold_6496 26167400 112 + 26866924 GCCATCG---------------------TCGTG---------------------------------------------------------------------------------TGGCATAGCCGAGAGGCCATTTTGGT-AAAACAACTAATCAATC----CACAAATGTGCCATCCGTCAATCATTG-----------GC-----------------C-----TGGTGTAGGTCACACGACACCATCAGC--------- s droAlb1.JH854640 328901 112 + 406291 GCTGTTG---------------------CC--G---------------------------------------------------------------------------------TGGCATATCGCTGTGGCCATTTTGGTAATAACAACTAATCAATCGAAAAGCAAATGTGCCATCCGTCAATCATTC-----------GC-----------------------TGGTGTAGGTCACACGACACCA--AGC--------- s droGri2.scaffold_15245 923292 107 + 18325388 GTTGTCG---------------------CC----------------------------------------------------------------------------------------ATATCCAAGTGGCCATTTTGGTAAAAACAACTAATCAATC----GGCAAATGTGCCATCCGTCAATCATTG-----------GC-----------------T---TGTGGTGTAGGTCACACGACACCA-CAGA--------- a score=-238143.000000 s dm6.chr2R 24372905 60 + 25286936 T----GCGGC-------------------gcaac------------------------tt--cggttgcaactt--gagct----gcaa-ctgcaac---------------------------tgcagc--------------------ggccacCGAATTG s droSim1.chr2R 18711648 60 + 19596830 T----GCGGT-------------------GCAAC------------------------TT--CGCTTGCAACTT--GAGCT----GCAA-CTGCAAC---------------------------TGCAGC--------------------GGCCACCGAATTG s droSec1.super_23 130990 54 + 989336 T----GCGGT-------------------GCAAC------------------------TT--CGCTTGCAACTT--GAG-----------CTGCAAC---------------------------TGCAGC--------------------AGCCACCGAATTG s droYak3.chr2R 20221095 60 + 21139217 ------TGGTt------------------gcaac------------------------ttg-aagctgcaactt--gagct----gcaa-ctgcaac---------------------------tgcagc--------------------ggcCGCCGAATTG s droEre2.scaffold_4845 21618617 61 + 22589142 G----GCAGCG------------------GCAAC------------------------TT--CGGTTGCAACTT--GAGTT----GCAA-CTGCAAC---------------------------TGCAGC--------------------GGCCACCGAATTG s droBia2.KB462602 813628 51 + 3129309 T----------------------------GCAGC------------------------TT--TAGCTGCAACTT--CAgtt----------tgcaac---------------------------tgcaaca-------------------ggcCACCGAATTG s droSuz1.KI419649 12062972 51 - 14502029 T----------------------------GCAAC------------------------TT--TAGCTGCAACTT--CGgtt----------tgcaac---------------------------tgcaaca-------------------ggcCACCGAATTG s droAna3.scaffold_13266 5723463 67 - 19884421 -----------------------------GCAGC--------TTGCTGGGTTGTTGGTTTGCTGGTTGCAGCTT--GGAGT----------TGCTAC---------------------------TGTGGC--------------------AGCCACCGAATTG s droBip2.KB464407 1973317 51 + 2915140 -----------------------------GCAGC------------------------TTGCTGGTTGCAGCTT--GCTGG----------CTACTC---------------------------TGTGGC--------------------AGCCACCGAATTC s droEug2.KB465067 616138 55 + 1515531 T----------------------------GCAGC------------------------GG--CGGCTGCAGCTT--tagtt----gcaa-ctgcaac---------------------------agcaac--------------------ggccACCGAATTG s droEle2.KB458573 540000 77 - 5320397 T------GGT-------------------GCAGC------------------------GG--TGGTTGCAACTA--CTGCTgtttgcaa-ctgcaac---------------------------tgcaacagcagcagcag----cagc-ggccacCGAATTG s droKik2.KB459527 293213 21 - 1234237 T----G-----------------------GCAGC------------------------TT-------------------------------------------------------------------------------------------GCTGCAGAATTG s droTak2.KB461535 159222 57 - 669855 -----------------------------GCTGC------------------------AG--TGGCTGCAGCTTTAaagtt----gcaa-ctgcaac---------------------------agcaaca-------------------ggccGCCGAATTG s droRho2.KB449310 54523 64 - 65043 t------ggt-------------------gcagc------------------------tcggtggttgcagttg--caaca----gcagtttgcaac---------------------------tgcaacagc-----------------ggCCACCGAATTG s droFic2.KB457177 96259 100 + 995874 t----gcagtggttgctgctgctacttatgttgc------------------------tg--ctgctgcgactg--cagtt----gcaagttgcaac---------------------------tgctgcagcggcaacagctAACAGCAAGCCACCGAATTG s droPse3.chr3 1366037 93 - 19787792 t------ggcg------------------gcggc---------------ggcgtag--tg--gagttgcagttg--cagtt----ggac-ATGCATCcagtggatgcagtggatgcagtggatgtgtggc--------------------agccaccgaATTG s droPer1.super_34 554848 99 - 916997 tggcggcggcg------------------gcggc---------------ggcgTAG--TG--GAGTTGCAGTTG--CAGTT----GGAC-ATGCATCCAGTGGATTCAGTGGATACAGTGGATGTGTGGC--------------------AGCCACCGAATTG s droMir2.chr3 1407082 105 - 20862834 tggcggcggtg------------------gcggcggcggcagtggcggtggcgtag--tg--gagttgcagttg--cagtt----ggac-ATGCATC---------CAGTGGATGCAGTGgatgtgtggc--------------------agccaccgaaTTG s droWil2.CH963894 1334775 40 + 2843958 -----------------------------ccacc------------------------ac--caccagcaggCC--AGAGT---------CACCAAA---------------------------T------------------------------TCGAATTG s droVir3.scaffold_12875 7372385 13 + 20611582 ------------------------------------------------------------------------------------------------------------------------------------------------------GCGAATTGAATTG s droAlb1.JH854640 329013 19 + 406291 ------------------------------------------------------------------------------------------------------------------------------Cagcaa------------------atgaattcaattg s droGri2.scaffold_15245 923401 7 + 18325388 ------------------------------------------------------------------------------------------------------------------------------------------------------------TGAATTG a score=1511095.000000 s dm6.chr2R 24372965 80 + 25286936 ACTCGCATTCACTTTTGGGG---CA--------------------------------CAT---AAAATGCCACCTTGGTTG--TGAATGTCAGTTAGCCAATTT-------GAAA-----ATTCATTCATTC s droSim1.chr2R 18711708 80 + 19596830 ACTCGCATTCACTTTTGGGG---CA--------------------------------CAT---AAAATGCCACCTTGGTTG--TGAATGTCAGTTAGCCAATTT-------GAAA-----ATTCATTCATTC s droSec1.super_23 131044 80 + 989336 ACTCGCATTCACTTTTGGGG---CA--------------------------------CAT---AAAATGCCACCTTGGTTG--TGAATGTCAGTTAGCCAATTT-------GAAA-----ATTCATTCATTC s droYak3.chr2R 20221155 80 + 21139217 ACTCGCATTCACTTTTGGGG---CA--------------------------------CAT---AAAATGCCACCTTGGTTG--TGAATGTCAGTTAGCCAATTT-------Gaaa-----attcattcattc s droEre2.scaffold_4845 21618678 80 + 22589142 ACTCGCATTCACTTTTGGGG---CA--------------------------------CAT---AAAATGCCACCTTGGTTG--TGAATGTCAGTTAGCCAATTT-------GAAA-----ATTCATTCATTC s droBia2.KB462602 813679 80 + 3129309 ACTCGCATTCACTTTTGggg---ca--------------------------------aat---aaaatgccaCCTTGGTTG--TGAATGTCAGTTAgccaattt-------gaaa-----attcattcattc s droSuz1.KI419649 12063023 80 - 14502029 ACTCGCATTCACTTTTGGGG---CA--------------------------------AAT---AAAATGCCACCTTGGTTG--TGAATGTCAGTTAgccaattt-------gaaa-----attcattcATTC s droAna3.scaffold_13266 5723530 80 - 19884421 ACTCGCATTCACTTTTGGGG---CA--------------------------------CAT---AAAATGCCACCTTGGTTG--TGAATGTCAGTTAGCCAATTT-------GAAA-----ATTCATTCATTC s droBip2.KB464407 1973368 80 + 2915140 ACTCGCATTCACTTTTGGGG---CA--------------------------------CAT---AAAATGCCACCTTGGTTG--TGAATGTCAGTTAGCcaattt-------gaaa-----attcattcattc s droEug2.KB465067 616193 80 + 1515531 ACTCGCATTCACTTTTGGGG---CA--------------------------------AAT---AAAATGCCACCTTGGTTG--TGAATGTCAGTTAGCCAATTT-------gaaa-----attcattcattc s droEle2.KB458573 540083 80 - 5320397 ACTCGCATTCACTTTTGggg---ca--------------------------------aat---aaaatgccacCTTGGTTG--TGAATGTCAGTTAGccaattt-------gaaa-----attcattcattc s droKik2.KB459527 293234 80 - 1234237 ACTCGCATTCACTTTTGGGG---CA--------------------------------AAT---AAAATGCCACCTTGGTTG--TGAATGTCAGTTGGccaattt-------gaaa-----attcattcattc s droTak2.KB461535 159279 80 - 669855 ACTCGCATTCACTTTTGGGG---CA--------------------------------AAT---AAAATGCCACCTTGGTTG--TGAATGTCAGTTAGccaattt-------gaaa-----attcattcattc s droRho2.KB449310 54587 80 - 65043 ACTCGCATTCACTTTTGGGG---CA--------------------------------AAT---AAAATGCCACCTTGGTTG--TGAATGTCAGTTAGCcaattt-------gaaa-----attcattcattc s droFic2.KB457177 96359 80 + 995874 ACTCGCATTCACTTTTGGGG---CA--------------------------------CAT---AAAATGCCACCTTGGTTG--TGAATGTCAGTTAGCCAATTT-------GAAA-----ATTCATTCATTC s droPse3.chr3 1366130 80 - 19787792 ACTCGCATTCACTTTTGggg---ca--------------------------------aat---aaaatgccacCTTGGTTG--TGAATGTCAGTTAGCCAAttt-------gaaa-----attcattcattc s droPer1.super_34 554947 80 - 916997 ACTCGCATTCACTTTTGGGG---CA--------------------------------AAT---AAAATGCCACCTTGGTTG--TGAATGTCAGTTAGCCAATTT-------GAAA-----ATTCATTCATTC s droMir2.chr3 1407187 80 - 20862834 ACTCGCATTCACTTTTGggg---ca--------------------------------aat---aaaatgccacCTTGGTTG--TGAATGTCAGTTAGCcaattt-------gaaa-----attcattcattc s droWil2.CH963894 1334815 109 + 2843958 ACTCGCATTCACTTT---GG---CAAACAGAAAACTGccaatacaaacaaataaaataac---aaaatgccACCTTGGTTG--TGAATGTCAGTTGgccaattt-------gaaa-----attcattCATAC s droVir3.scaffold_12875 7372398 90 + 20611582 AATCGCATTCACTTTGGCTCCA-AA--------------------------------AACAACAAAATGCCACCTTGGCTG--TGAATGTCAGTTGGCCAATTTGGTTG--CAGC-----ATTCATTCATTC s droMoj3.scaffold_6496 26167523 91 + 26866924 AATCGCATTCACTTTGCCTCCA-AA--------------------------------AACAACAAAATGCCACCTTGGCTG--TGAATGTCAGTTGGCCAATTTGGTAGC-CAGC-----GTTCGTTCATTC s droAlb1.JH854640 329032 88 + 406291 aatcgCATTCACTTTGGACC---AA--------------------------------AGC----AAATGCCACCTTGGCTGGATGAATGTCAGTTGGCCAATTTGGAAAAGGAGA-----ATTCATTCATAC s droGri2.scaffold_15245 923408 93 + 18325388 AATCGCATTCACTTTGGCTCTACCA--------------------------------AAC---AAAATGCCACCTTGGCTG--TGAATGTCAGTTGGCCAATTTGGTTG--CAGCTAGGTAGCCATGCAGCC a score=4723053.000000 s dm6.chr2R 24373045 440 + 25286936 --------------------------------------------------------------------------------------------------------------------------------------------------AGTG----------C-TT------TGAC------------GA------------------------------------------------------CTCGC-------------TGA-----------------C-----------TGAC-TA-TTGCCA-ACATTTATTATTAGCCTTTCCCAAACTGACTATTTTTGGAGCTGCCGATGGCCA------CA-------cag---cagca-----------------------------------------------------------gc-agccgcagcaacaacaacatgccgcaCATATCACAGCAAGACAAATTTCTATATAATTGCA-TTTGTCGCAGGCTC------T----CCG----------------------------------------------AGCCTCGAAG---T-TCGA--------------------------------------TACCACTGGC-------------------------------------GA---------GGCCAGATCGG-C---------CA-------------GACAAT--------------------GCCAGGCATTAT-----TTTTATA---TAAATTGCATGCCATTGGCCCGGCCAGTTGGCATTCCA----------------TCC---AGC----------C--AATTGTCGGTGGG--------------------------GA----------------GTTGTGGC-------TCG-----AGAGT--------CGGG---------------------------CGGGACAGGG-TT--------TTCGC----TCCGAT-T-------------GT----------GTTTTTG---------------------------------C--------------C-----TCGCTT-------------T---------TAG-CCAG---------------------GCTCAAACTCTAATTGTCATTTAATGAGACACGCTCGGCATTTGCGCACGACACAC----GACTATCAAT s droSim1.chr2R 18711788 461 + 19596830 --------------------------------------------------------------------------------------------------------------------------------------------------AGTG----------C-TT------TGAC------------GA------------------------------------------------------CTCGC-------------TGA-----------------C-----------TGAC-TA-TTGCCA-ACATTTATTATTAGCCTTTCCCAAACTGACTATTTTTGGAGCTGCCGATGGCCA------CA-------cag---cagcagcagcagca------------ggcgcagcag--------------------------cggc-agccgcagcaacaacaacaTGCCGCACATATCACAGCAAGACAAATTTCTATATAATTGCA-TTTGTCGCAGGCTC------T----CCG----------------------------------------------AGCCTCTAAG---T-TCGA--------------------------------------TACCACTGGC-------------------------------------GA---------GGCCAGATCGG-C---------CA-------------GACAAT--------------------GCCAGGCATTAT-----TTTTATA---TAAATTGCATGCCATTGGCCCGGCCAGTTGGCATTCCA----------------TCC---AGC----------C--AATTGTCGGTGGG--------------------------GA----------------GTTGTGGC-------TCG-----AGAGT--------CGGG---------------------------CGGGCCAGGG-TT--------TTCGC----TCCGAT-T-------------GT----------GTTTTTG---------------------------------C--------------C-----TCGCTT-------------T---------TAG-CCAG---------------------GCTCAAACTCTAATTGTCATTTAATGAGACACGCTCGGCATTTGCGCACGACACAC----GACTATCAAT s droSec1.super_23 131124 461 + 989336 --------------------------------------------------------------------------------------------------------------------------------------------------AGTG----------C-TT------TGAC------------GA------------------------------------------------------CTCGC-------------TGA-----------------C-----------TGAC-TA-TTGCCA-ACATTTATTATTAGCCTTTCCCAAACTGACTATTTTTGGAGCTGCCGATGGCCA------CA-------cag---cagcagcagcagca------------ggcgcagcag--------------------------cggc-agccgcagcaacaacaacaTGCCGCACATATCACAGCAAGACAAATTTCTATATAATTGCA-TTTGTCGCAGGCTC------T----CCG----------------------------------------------AGCCTCGAAG---T-TCGA--------------------------------------TACCACTGGC-------------------------------------GA---------GGCCAGATCGG-C---------CA-------------GACAAT--------------------GCCAGGCATTAT-----TTTTATA---TAAATTGCATGCCATTGGCCCGGCCAGTTGGCATTCCA----------------TCC---AGC----------C--AATTGTCAGTGGG--------------------------GA----------------GTTGTGGC-------TCG-----AGAGT--------CGGG---------------------------CGGGCCAGGG-TT--------TTCGC----TCCGAT-T-------------GT----------GTTTTTG---------------------------------C--------------C-----TCGCTT-------------T---------TAG-CCAG---------------------GCTCAAACTCTAATTGTCATTTAATGAGACACGCTCGGCATTTGCGCACGACACAC----GACTATCAAT s droYak3.chr2R 20221235 448 + 21139217 --------------------------------------------------------------------------------------------------------------------------------------------------agtG----------C-TT------TGAC------------GA------------------------------------------------------CTCGC-------------TGA-----------------C-----------TGAC-TA-TTGCCA-ACATTTATTATTAGCCTTTCCCAAACTGACTATTTTTGGAGCTGCCGATGGCCA------CA-------CAG---CAGTAGTTGCAGtc---------------------g--------------------------cagc-agttgcagcaacaacaacatgccGCACATATCACAGCAAGACAAATTTCTATATAATTGCA-TTTGTCGCAGGCTC------T----CCG----------------------------------------------AGCCTCGAAG---T-TCGA--------------------------------------TACCACTGGC-------------------------------------GA---------GGCCAGATCGG-C---------CA-------------GACAAT--------------------GCCAggcattat-----ttttata---taaattgcatgCCATTGGCCCGGCCAGTTGGCATTCCA----------------TCC---AGC----------C--AATTGTCGTCGGA--------------------------GA----------------GTTGAGGC-------TCG-----AGAGT---------------------------------------CGGGGCAGGG-TT--------TTCGC----TCCGAT-T-------------GT----------GTTTTTG---------------------------------C--------------C-----TCGCTT-------------T---------TAG-CCTG---------------------GCTCAAACTCTAATTGTCATTTAATGAGACACGCTCGGCATTTGCGCACGACACAC----GACTATCAAT s droEre2.scaffold_4845 21618758 458 + 22589142 --------------------------------------------------------------------------------------------------------------------------------------------------AGTG----------C-TT------TGAC------------GA------------------------------------------------------CTCGC-------------TGA-----------------C-----------TGAC-TA-TTGCCA-ACATTTATTATTAGCCTTTCCCAAACTGACTATTTTTGGAGCTGCCGATGGCCA------CA-------cag---cagcagccgcagcc------------------gcag--------------------------cagc-agccgcagcaacaacaacaTGCCGCACATATCACAGCAAGACAAATTTCTATATAATTGCA-TTTGTTGCAGGCTC------T----CCA----------------------------------------------AGCCTCGAAG---T-TCGA--------------------------------------TACCACTGGC-------------------------------------GA---------GGCCAGATCGG-C---------CA-------------GACAAT--------------------GCCAGGCATTAT-----TTTTATA---TAAATTGCATGCCATTGGCCCGGCCAGTTGGCATTCCA----------------TCC---AGC----------C--AATTGTCGGTGGA--------------------------GG----------------GTTGAGGCTCGAGAGTCG-----AGAGT---------------------------------------CGGGGCAGGG-TT--------TTCGC----TCCGAT-T-------------GT----------GTTTTTG---------------------------------C--------------C-----TCGCTT-------------T---------TAG-CCAG---------------------GCTCAAACTCTAATTGTCATTTAATGAGACACGCTCGGCATTTGCGCACGACACAC----GACTATCAAT s droBia2.KB462602 813759 459 + 3129309 --------------------------------------------------------------------------------------------------------------------------------------------------aaTG----------C-TT------TGAC------------GA------------------------------------------------------CTCGC-------------TGA-----------------C-----------TGAC-TA-TTGCCA-GCATTTATTATTAGCCTTTCCCAAACTGACTATTTTTGGAGCTGCCGATGGCCA------CA-------CAA---cagtggcaacagca------------------gcag--------------------------cagc-agcagcagcaacaacaacatgccGCACATATCACAGCAAGACAAATTTCTATATAATTGCA-TTTGTCGCAGGCTC------C----CCA----------------------------------------------AGCCTCGAAG---T-TCGA--------------------------------------TACCACTGGC-------------------------------------GA---------GGCCAGATCGG-C---------CA-------------GACAAT--------------------GCCaggcattatttttattttata---taaattgcaTGCCATTGGCCCGGCCAG-TGGCATTCCA----------------TCC---AGC----------C--AATTGCCAGTTGA--------------------------GA----------------GTTGAGAC-----------------------------------------------------------CCGGGCTGGG-TT--------TTCGC----TCCgat-t-------------gtttgtg-----ttttttg---------------------------------c--------------c-----tCGCTT--TCAGCTC----T---------TAG-CCAG---------------------GCTCAAACTCTAATTGTCATTTAATGAGACACGCTCGGCATTTGCGCACGACACAC----GACTATCAAT s droSuz1.KI419649 12063103 444 - 14502029 --------------------------------------------------------------------------------------------------------------------------------------------------AATG----------C-TT------TGAC------------GA------------------------------------------------------CTCGC-------------TGA-----------------C-----------TGAC-TA-TTGCCA-ACATTTATTATTAGCCTTTCCCAAACTGACTATTTTTGGAGCTACCGATGGCCA------CA-------CAA---Cagtggcaa--------------------------------------------------------c-agcagcagcaacaacaacatgccGCACATATCACAGCAAGACAAATTTCTATATAATTGCA-TTTGTCGCAGGCTC------C----CCA----------------------------------------------AGCCTCGAAG---T-TCGA--------------------------------------TACCACTGGC-------------------------------------GA---------GGCCAGATCGG-C---------CA-------------GACAAT--------------------GCCAggcattat-----ttttata---taaattgcaTGCCATTGGCCCGGCCAGTTGGCATTCCA----------------TCC---AGC----------C--AATTGCCAGTTGA--------------------------GA----------------GTTGAGAC-----------------------------------------------------------TCGGGCTGGG-TT--------TTCGC----TCcgat-t-------------gtttgta---ttttttttg---------------------------------c--------------c-----tcGCTT--TCAGCTT----T---------TAG-CCAG---------------------GCTCAAACTCTAA-TGTCATTTAATGAGACACGCTCGGCATTTGCGCACGACACAC----GACTATCAAT s droAna3.scaffold_13266 5723610 503 - 19884421 --------------------------------------------------------------------------------------------------------------------------------------------------AATG----------C-TT------TGAC------------GA------------------------------------------------------CTCGC-------------TGA-----------------C-----------TGAC-TA-TTGCCA-ACATTTATTATTAGCCTTTCCCAAACTGCCTATTTTTGGAGCTACCGATGgcca------cagc-----cag---tagctgctgcaact------------gcaacaacac--------------------------catc-agcagtagcaacaacaacatgccgcacatatcacagcaaGACAAATTTCTATATAATTGCA-TTTATCGCAGGCTC-------------------------------------------------------------TACTGCAAAACCC-CCAG--------------------------------------CCTGCTCGAC-------------------------------------GA---------AGCCTCCGAGG-C---------CG-------------GACAAT--------------------GCCAGGCATTAT-----TTTTATA---TAAATTGCATGCCATTGGCCTGGCCAG-TGGCATTCCA----------------TCC---AGC----------C--AATTGCCAACAGTATCTGCGGGCGGATGGGCGGATGGCAGG----------------GGGAGGGT-------TCA-----AGGA----------------------------------------GGGTTCTCGC-TT--------TTCGC----TCCGAT-TCGATTCGAT----TG----------TTTTTTT---------------------------------T--------------T-----TTgccaagccagaccagacc---------agg-ccag---------------------gcTCAAACTCTAATTGTCATTTAATGAGACACGCTCGGCATTTGCGCACGACACAC----GACTATCAAT s droBip2.KB464407 1973448 477 + 2915140 --------------------------------------------------------------------------------------------------------------------------------------------------aatG----------C-TT------TGAC------------GA------------------------------------------------------CTCGC-------------TGA-----------------C-----------TGAC-TA-TTGCCA-ACATTTATTATTAGCCTTTCCCAAACTGACTATTTTTGGAGCTACCGATGGCCa------cagcagcagtag---tagctgctgcaact------------gcaactgcaa--------------------------cagc-agcaacaacaacaacaacatgccGCACATATCACAGCAAGACAAATTTCTATATAATTGCA-TTTATCGCAGGCTC------T-----------------------------------------------------ATACTCCAAA---C-CCAG--------------------------------------CCTCTGCGAC-------------------------------------GA---------AACCTCCGAGG-C---------CG-------------GACAAT--------------------GCCaggcattat-----ttttata---taaattgcaTGCCATTGGCCCGGCCAG-TGGCATTCCA----------------TCC---AGC----------C--AATTGCCAACTGTATCTGC--------------------GG----------------GGGAAGGG-------TCA-----AGGA----------------------------------------GGGTTCTCGC-TT--------TTCGC----tccgat-tcgattcgattcgatt----------gtttttt---------------------------------t--------------t-----ttgtta-------------c---------ttg-cCAG---------------------GCTC-AACTCTAATTGTCATTTAATGAGACACGCTCGGCATTTGCGCACGACACAC----GACTATCAAT s droEug2.KB465067 616273 466 + 1515531 --------------------------------------------------------------------------------------------------------------------------------------------------aatG----------C-TT------TGAC------------GA------------------------------------------------------CTCGC-------------TGA-----------------C-----------TGAC-TA-TTGCCA-ACATTTATTATTAGCCTTTCCCAAACTGACTATTTTTGGAGCTACCGATGGCCa------ca-------caa---cagtagcaacaacaac------agcggcggcagcaa--------------------------cagc-agtagaggcaacaacaacatgccGCACATATCACAGCAAGAcaaatttctatataattgCA-TTTGTCGCAGGCTC------T----CCA----------------------------------------------AGCCTCGAAG---T-TCGA-CTCCGAAGC----------------------------CACCACTGGC-------------------------------------GA---------GGCCAGATCGG-C---------CA-------------GACAAT--------------------GCCAggcattat-----ttttata---taaattgcaTGCCATTGGCCCGGCCAGTTGGCATTCCA----------------TCC---AGC----------C--AATTGCCAGTTGA--------------------------GA----------------GTTGAGAG-------T---------------------------------------------------CGGGGCAGGG-TT--------TTCGC----TCCGAT-T-------------GTG---------TTTTTTG---------------------------------C--------------C-----TTGCTT-------------T---------TAG-CCAG---------------------GCTCAAACTCTAATTGTCATTTAATGAGACACGCTCGGCATTTGCGCACGACACAC----GACTATCAAT s droEle2.KB458573 540163 476 - 5320397 --------------------------------------------------------------------------------------------------------------------------------------------------aatG----------C-TT------TGAC------------GA------------------------------------------------------CTCGC-------------TGA-----------------C-----------TGAC-TA-TTGCCA-ACATTTATTATTAGCCTTTCCCAAACTGACTATTTTTGGAGCTACCGATGGcca------ca-------cag---cagcaacaacaaca------------acaacaacaa--------------------------caaa-gcaagcagcaacaacaacatgccGCACATATCACAGCAAGAcaaatttctatataattgCA-TTTGTCGCAGGCTCCAAGCTT----CCA----------------------------------------------AACCCCGAAG---T-TCGAACTTCGAAGC----------------------------CACCACTGGC-------------------------------------Gaggccagatcggccagatcgg-c---------ca-------------gacaatgccaggccaggccaggccgggccaggcattat-----ttttata---taaattgcatGCCATTGGCCCGGCCAGTTGGCATTCCA----------------TCC---AGC----------C--AATTGCCAA------------------------------GA----------------GT-----C----------------------------------------------------------------------TC--------TCCGC----TCCGAT-T-------------GTA---------TTTTTTG---------------------------------C--------------C-----TTGCTT-------------T---------TAG-CCAG---------------------GCTCAAACTCTAATTGTCATTTAATGAGACACGCTCGGCATTTGCGCACGACACAC----GACTATCAAT s droKik2.KB459527 293314 494 - 1234237 --------------------------------------------------------------------------------------------------------------------------------------------------aatATGTGTGCTCTC-TG------TGAC------------GA------------------------------------------------------CTGGC-------------TGACTGGGCTGACTGACTGCC-----------TGAC-TA-TTGCCA-ACATTTATTATTAGCCTTTCCCAAACTGCCTATTTTTGGAGCTACCGATGGCCA------ca-------cag---cagtggcagcagcaac------aactccAGTGGCAG--------------------------TAGC-tttagcagcaacaacaacatgccGCACATATCACAGCAAGacaaatttctatataattgcA-TTTGTCGCAGGCTC--AGCAG----CAA----------------------------------------------AACCTCAAAG---C-T-------------------------------------------------GC-------------------------------------GA---------ACCCAGATCGG-C---------CAT----------CGGACAAT--------------------GCCaggcattat-----ttttata---taaattgcatGCCATTGGCCCGGCCCGGTGGCATTCCA----------------TCC---GGC----------C--AATTGAAAGCCCA--------------------------AA----------------GCCAAGAG-------CCG-----GGGCT---GGGTTCGCT---------------------------CGCTACTCGC-TT--------CTCGC----TCcgat-t-------------g-----------tttttgc---------------------------------t--------------t-----ttgctt-------------t---------tag-cCAG---------------------GCTCAAACTCTAATTGTCATTTAATGAGACACGCTCGGCATTTGCGCACGACACAC----GACTATCAAT s droTak2.KB461535 159359 455 - 669855 --------------------------------------------------------------------------------------------------------------------------------------------------aatg----------c-TT------TGAC------------GA------------------------------------------------------CTCGC-------------TGA-----------------C-----------TGAC-TA-TTGCCA-ACATTTATTATTAGCCTTTCCCAAACTGACTATTTTTGGAGCTACCGATGGCCA------CA-------CAA---Cagtagcaacagca---------------------a--------------------------aagc-aacagcagcaacaacatcatgCCGCACATATCACAGCAAGACAAATTTCTATATAATTGCA-TTTGTCGCAGGCTC------T----CCA----------------------------------------------AGCCTCGAAG---T-TCGA--------------------------------------TACCACTGGC-------------------------------------GA---------GGCCAGATCGG-C---------CA-------------GACAAT--------------------GCCAggcattat-----ttttata---taaattgcatGCCATTGGCCCGGCCAGTTGGCATTCCA----------------TCC---AGC----------C--AATTGCCAGTTGA--------------------------GA----------------GTTGAGTT-------CAGT----TTAGC---------------------------------------CGGGGCAGGGTTT--------TTCGC----TCCGAT-T-------------GTTTGCG-----TTTTTTG---------------------------------C--------------C-----TTGCTT-------------T---------TAG-CCAG---------------------GCTCAAACTCTAATTGTCATTTAATGAGACACGCTCGGCATTTGCGCACGACACAC----GACTATCAAT s droRho2.KB449310 54667 451 - 65043 --------------------------------------------------------------------------------------------------------------------------------------------------aatG----------C-TT------TGAC------------GA------------------------------------------------------CTCGC-------------TGA-----------------C-----------TGAC-TA-TTGCCA-ACATTTATTATTAGCCTTTCCCAAACTGACTATTTTTGGAGCTACCGATGGcca------ca-------cag---cagcaacaacaaca------------------gtag--------------------------caaa-aacagtaacaacaacaacatgccGCACATATCACAGCAAGACAAATTTCTATATAATTGCA-TTTGTCGCAGGCTC------------CA----------------------------------------------AGCCTCGAAG---T-TCGAACTTCGAAGC----------------------------CACCACTGGC-------------------------------------GA---------GGCCAGATCGG-C---------CA-------------GACAAT--------------------GCCaggcattat-----ttttata---taaattgcatGCCATTGGCCCGGCCAGTTGGCATTCCA----------------TCC---AGC----------C--AATTGCCAACCGA--------------------------GA----------------G-----AC-------TCT-------------------------------------------------CGGGGCAGGGTTC--------TCCGC----TCCGAT-T-------------GTA---------TTTTTTG---------------------------------C--------------C-----TTGCTT-------------T---------TAG-CCAG---------------------GCTCAAACTCTAATTGTCATTTAATGAGACACGCTCGGCATTTGCGCACGACACAC----GACTATCAAT s droFic2.KB457177 96439 439 + 995874 --------------------------------------------------------------------------------------------------------------------------------------------------GATG----------C-TT------TGAC------------GA------------------------------------------------------CTCGC-------------TGA-----------------C-----------TGAC-TA-TTGCCA-ACATTTATTATTAGCCTTTCCCAAACTGACTATTTTTGGAGCTACCGATGGcca------ca-------cag---cagcaacaacaacg---------------------------------------------------------ccagcaacaacaacatgccgcacatatcacagcaagacaaATTTCTATATAATTGCA-TTTGTCGCAGGCTC------------CG----------------------------------------------AGCCTCGAGG---T-TCGAACTTCGCAGC----------------------------CACCACTGGC-------------------------------------GA---------GGCCAGATCGG-C---------CA-------------GACAAT--------------------GCCaggcattat-----ttttata---taaattgcatGCCATTGGCCCGGCCAGTTGGCATTCCA----------------TCC---AGC----------C--AATTGCCAGCCAA-----------------------------------------------------------CCG-----AGAGC---------------------------------------CGGGGCAGGGTTT--------TTCGC----TCCGAT-T-------------GTA---------TTTTTTG---------------------------------C--------------C-----TCGCTT-------------T---------TAG-CCGG---------------------GCTCAAACTCTAATTGTCATTTAATGAGACACGCTCGGCATTTGCGCACGACACAC----GACTATCAAT s droPse3.chr3 1366210 527 - 19787792 --------------------------------------------------------------------------------------------------------------------------------------------------aatg----------cTTT------tgac----gactgactga------------------------------------------------------ctgac-------------tga-----------------cgggcggactgacgac-tA-TTGCCA-ACATTTATTATTAGCCTTTCCCAAATTGCCTATTTTTGGAGCTGCTGAtggcca------ca-------cag---ccacagcggcagtagcagcagtagcagcagtggcag--------------------------cagc-agcaaccacaacaacaacatgccGCACATATCACAGCAAGACAAATTTCTATATAATTGCA-TTTGTCGCAGGCTC----TCT----CGA----------------------------------------------AGCC----AG---C-CCGA--------------------------------------TA--GCCAGC-------------------------------------GA---------GGCCAGATCGGAC---------CA-------------GACAAT--------------------GCCCGGCATTAT-----TTCGATA---TAAATTGCATGCCATTGGCCCGACCAG-TGGCATTCCA----------------TCC---AAC----------C--AATTGCCAACTCC--------------------------gg----------------gttcgggg-------ttc-----ggggtCCGGAGTCCGATTCCGATACCGAGTCGAAGCCCCCAACCAGGGGCAGGG-TT--------TCCCCGACTCCCGct-c-------------ct----------gtctctg---------------------------------c--------------c-----tctcaa-------------a---------tct-cagc---------------------tctc-agctctAATTGTCATTTAATGAGACACGCTCGGCATTTGCGCACGACACAC----GACTATCAAT s droPer1.super_34 555027 536 - 916997 --------------------------------------------------------------------------------------------------------------------------------------------------AATG----------CTTT------tgacgactgactgactga------------------------------------------------------ctgac-------------tga-----------------cggacggactgacgac-tA-TTGCCA-ACATTTATTATTAGCCTTTCCCAAATTGCCTATTTTTGGAGCTGCTGATGGCCACACAGCCA-------CAG---CCAcagcggcagtagcagcagtagcagcagtggcag--------------------------cagc-agcaACCACAACAACAACATGCCGCACATATCACAGCAAGACAAATTTCTATATAATTGCA-TTTGTCGCAGGCTC----TCT----CGA----------------------------------------------AGCC----AG---C-CCGA--------------------------------------TA--GCCAGC-------------------------------------GA---------GGCCAGATCGGAC---------CA-------------GACAAT--------------------GCCCGGCATTAT-----TTCGATA---TAAATTGCATGCCATTGGCCCGACCAG-TGGCATTCCA----------------TCC---AAC----------C--AATTGCCAACTCC--------------------------GG----------------GTTCGGGG-------TTC-----GGGGTCCGGAGTCCGATTCCGATACCGAGTCGAAG-CCCCAACCAGGGGCAGGG-TT--------TCCCCGACTCCCGCT-C-------------CT----------GTCTCTG---------------------------------C--------------C-----TCTCAT-------------C---------TCT-CAGC---------------------TCTC-AGCTCTAATTGTCATTTAATGAGACACGCTCGGCATTTGCGCACGACACAC----GACTATCAAT s droMir2.chr3 1407267 509 - 20862834 --------------------------------------------------------------------------------------------------------------------------------------------------aatg----------cTTT------TGac------------ga------------------------------------------------------ctgac-------------tga-----------------cggacggACTGACGAC-TA-TTGCCA-ACATTTATTATTAGCCTTTCCCAAATTGCCTATTTTTGGAGCTGCTGAtggcca------ca-------cag---ccacagc------------------------ggcag--------------------------cagc-agcaaccacaacaacaacatgccGCACATATCACAGCAAGAcaaatttctatataattGCA-TTTGTCGCAGGCTC----TCT----CGA----------------------------------------------AGCC----AG---C-CCGA--------------------------------------TA--GCCAGC-------------------------------------GA---------GGCCAGATCGGAC---------CA-------------GACAAT--------------------GCCCGGCATTAT-----TTCGATA---TAAATTGCATGCCATTGGCCCGACCAG-TGGCATTCCA----------------TCC---AAC----------C--AATTGCCAACTCc--------------------------gg----------------gttcgggg-------ttc-----ggggtccggagtccgagtccgataCAGAGTCGAAGCCCCCAACCAGGGGCAGGG-TT--------TCCCCGACTCCCGCT-C-------------CT----------GTCCCCG---------------------------------Cctcttagctctcagc-----tctcat-------------c---------tct-cagc---------------------tctc-agctctAATTGTCATTTAATGAGACACGCTCGGCATTTGCGCACGACACAC----GACTATCAAT s droWil2.CH963894 1335840 579 + 2843958 --------------------------------------------------------------------------------------------------------------------------------------------------actg----------c-ct------gaac-----------tga------------------------------------------------------ctgac-------------tgg-----------------c-----------tgac-tgttTGCTA-GCATTTATTATTAGCCTTTCCCAAATTGCCTATTTTTGGAGCTGCTGATGGCCA------ca-------cag---cagcagtagcagca------------------gcaa--------------------------caatgagcagttgcaacaacaacatgccGCACATATCACAGCAAGacaaatttctatataattgcattttgtgGCAGGctc------t----ccaccaccaccaccaccaccaccaccaccaccaccaccagcaccagcaccacctccaac---caccaa--------------------------------------ccccaccgcc-------------------------------------aa---------gcccaGGCAGC-T---------TACAGCGAGGCCGCTGACAAT--------------------GCCTggcattat-----ttttata---taaattgcatGCCATTGGCCTGGCCAG---GCATTCCAATTGTTGTATGCCTCCTCC---AGT----------TTGACTTGAGGATTGAGTT-----------------------GG----------------GCTGAGCT-------GCT-----GGAC----------------------------------------TGGGGCAGGG-TTCGTTGCAATTCGC----ATTGCT-C-------------TTggtcacttttgtttttg---------------------------------t--------------tgtttgttgctg-------------c---------tgg-ctgctgttgcatttgtttggtttttgctc-aactctaattgtcatttaatgaGACACGCTCGGCATTTAAGCACGACACACGACTGACTATCAAT s droVir3.scaffold_12875 7372488 574 + 20611582 a------------------------------------------------tatata---------------------------------------tatagtatatatatatatatatatgtatatataCACTCGATCCGAGTACTCATTTG----------C-TG---GTTTGAC------------GAACTGACTCGCC----------------------------------------TCTGTGAC-------------TGA-----------------C-----------AGAC-GA-CGGATC-GCATTTATTATTAGCCTTTCCCAAATTGACTATTTTTGGCGCTGCCGATGGCCA------CA-------CAA-----------------------------------------------------------------CTGC-TGCAACTGCAACTGCAACATGCCGCACATATCACAGCAAGACAAATTTCTATATAATTGCG-TTTGTTGCAGGCTC----CAG----TCG----------------------------------------------AGGCCAGCGG---C-CCGA-----GAAATCCAAAACaacaacaacaacaacaaaaagaaaaactatataaaaatacaataaaataaaaataaaa-------acaaa---------agcaaaCAAAA-C-------ACAA-------------TACAAT--------------------GCT--GCATTAT-----TTTTATA---TAAATTGCATGCCACTGGCC--GC------GCATTCCA----------------CGC---TGCTGCTGCCAGCT--ACTTGCCACTCGC--------------------------CT-----CTCTGGGCCTGGCCGGGAC-------T-------GGG-------------G---------------------------CTGGGCTGGG-CT--------CGTTG-----------C-------------GC----------TGTCCGG---------------------------------C--------------T-----TCAAGT-------------T-------------CCAA---------------------GCTC-AACTCTAATTGTCATTTAATGAGACACGCTCGGCATTTGCGCACGACACAC----GACTATCAAT s droMoj3.scaffold_6496 26167614 670 + 26866924 a------------------------------------------------tgtatatcgagtagatatgtagatatgtgtttgtgtatgtgtatgta---------------------tgtatata--------ATCGGAGTATTCATTTG----------C-CGACTGGTTGAC------------GAACTGCCTCGCCTGCATAtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtTTGAC-------------TGA-----------------C-----------AGGC-GA-CGGATC-GCATTTATTATTAGCCTTTCCCAAATTGACTATTTTTGGCACAGTCGATGgcca------ca-------caaactctgcagtagcagcagcaatagcagtagcagtagcagtagcagcaacagcaacagcaacagcgcaac-tgcaacagcaactgcaacaTGCCGCACATATCACAGCAAGACAAATTTCTATATAATTGCA-TTTGTTGCAGGCTC----GAG----TCG----------------------------------------------AGGCCAGCAG---C-CGCA-----GAAAT----------------------------AAAAACTGAA------TGCAATAAAACACAAAT-------------AAA---------AGCAAACTAAA-C-------ACAA-------------TACAAT--------------------GCT--GCATTAT-----TTTTATA---TAAATTGCCAGCTACTGGCC--GC------GCATTCCT----------------CGC---TGC--CTATctgcc--tcctgcctcctgc--------------------------ctcctgcctccAATCTTGGTTGGGGT-------T-------TGAGC--------TGCG---------------------------CTGGGCTGGG-CT--------AGTCG-------GCTCT-------------GC----------TCTCTGGT--------------------------------C--------------T-----TCAGGT-------------TG--------GAGCTCAA---------------------GCTC-AACTCTAATTGTCATTTAATGAGACACGCTCGGCATTTGCGCACGACACAC----GACTATCAAT s droAlb1.JH854640 329120 643 + 406291 T------------------------------------------------CATGCG---------------AGTACTTGTAATCGCACTCGTACTTG---------------------TACTCACA----------------ATTCATTTG----------T-TG------TGCT------------gagctgttt-------------------------------------gtgtttgtcacTGACGAACTGACTGAagtga-----------------c-----------agacaga-caaacc-gCATTTATTATTAGCCTTTCCCAAATTGACTATTTTTGGCACAGCCGATGGCca------ca-------caa---ctgcaactgcaactgcaacagcagcagcagcagtagcaacag--------------------caac-agcagcggcagcagcaacatgccgCACATATCACAGCAAGACAAATTTCtatataattgca-tttgttgcagGCTC----CAGCAGTCCG----------------------------------------------AGGCCAGCAG---C-CCCA--ATCGGCATC---------------------------GAGTGCTGCG-----GTGTCGTGTGGTATCGAC------------CGCT---------TGCTACCTTAA-----------AA-------------AACAAT--------------------gct--acattat-----ttttatatagtaaattgcATGCCACTGACC--GC------GCATTCCA----------------CGCAAATGCGCAAATACGAC--CATTGCATCTTGC--------------------------AG-TCACTTCCA---ttgggttgggc-------tccttcactgggt--------tggg---------------------------ttgggttggg-tt--------ttttc-------gtt-t-------------gg----------tttccaatgggttATGCCTCCAACCATCCTTCAGTCACAAC--------------T-----CCAAat-------------c---------aagctcaa---------------------gctc-aactCTAATTGTCACTTAATGAGACATGCTCGGCATTTGCGCCAGACACAC----GACTATCAAT s droGri2.scaffold_15245 923501 610 + 18325388 AAAGcaggcaggccaggccaggccagctagccaggccaggccaggcaggcattca---------------ggcattcattcaggcactcattcatt---------------------cagtcata------------------tca--tA----------C-CGACTAC-TGAC------------GAACTGACTCGCG-------------------------------------------CTGAC-------------TGA-----------------C-----------TGAGTGA-CGGATCGGCATTTATTATTAGCCTTTCCCAAATTGACTATTTTTGGCACTGTCGATGGCCA------Ca-------caa---caacaattacaattgcaactgcagcagcaactg-----------------------------cagc-agcaactgcatcagcaacaTGCCGCACATATCACAGCAAGACAAATTTCTATATAATTGCA-TTTGTTGCAGGCTC----CAC----TCG----------------------------------------------AGGCCAGCGG---C-CCCA-----ACaat----------------------------aaaatacaaatacaaatacaaataaaaataagtaaaataaaaaGCAAAA---------CGCAAACAAAA-CACACAATACAA-------------AACAAT--------------------GCT--GCATTAT-----TTTTA-----TAAATTGCATGCCACTGGCC--GCT-----GCATTCCA----------------CGC---AGCTACTACTTGCC--ACACTCGTCTCAC--------------------------AT------------------------------------------------------------------------------------TGGGTTGGG-TC--------CGCTC-----------A-------------GC------------TCcag---------------------------------c--------------t-----ccacgc-------------agctccacgcagctccaA---------------------GCTC-AACTCTAATTGTCATTTAATGAGACACGCTCGGCATTTGCGCACGACACAC----GACTATCAAT a score=102747.000000 s dm6.chr2R 24373485 17 + 25286936 TTGGCAA------GTTG------CAGTT---G--- s droSim1.chr2R 18712249 20 + 19596830 TTGGCAA------GTTG------CAGTTGCAG--- s droSec1.super_23 131585 20 + 989336 TTGGCAA------GTTG------CAGTTGCAG--- s droYak3.chr2R 20221683 17 + 21139217 TTGGCAA------GTTG------CAGTT---G--- s droEre2.scaffold_4845 21619216 17 + 22589142 TTGGCAA------GTTG------CAGTT---G--- s droBia2.KB462602 814218 17 + 3129309 TTGGcaa------gttg------cagtt---g--- s droSuz1.KI419649 12063547 17 - 14502029 TTGGCAA------GTTG------CAGTT---G--- s droAna3.scaffold_13266 5724113 16 - 19884421 TTGGCAA------GTTG------CAGCT------- s droBip2.KB464407 1973925 16 + 2915140 TTGGCAA------GTTG------GAGCT------- s droEug2.KB465067 616739 17 + 1515531 Ttggcaa------gttg------cagtt---g--- s droEle2.KB458573 540639 17 - 5320397 TTGGCAA------GTTG------CAGTT---g--- s droKik2.KB459527 293808 12 - 1234237 TTGGCAA-----------------AGTT---G--- s droTak2.KB461535 159814 17 - 669855 TTGGCAA------GTTG------CAGTt---g--- s droRho2.KB449310 55118 17 - 65043 TTGGCAA------GTTG------CAGTt---g--- s droFic2.KB457177 96878 17 + 995874 TTGGCAA------GTTG------CAGTT---G--- s droPse3.chr3 1366737 23 - 19787792 TTGGCAG------GCAGCATCACCAGTT---G--- s droPer1.super_34 555563 23 - 916997 TTGGCAG------GCAGCATCACCAGTT---G--- s droMir2.chr3 1407776 23 - 20862834 TTGGCAG------GCAGCATCACCAGTT---G--- s droWil2.CH963894 1336419 17 + 2843958 TTAAAAT------GGAG------AAGCT---A--- s droVir3.scaffold_12875 7373062 17 + 20611582 TTGGCGA---------G------CTCCG---CTCG s droMoj3.scaffold_6496 26168284 26 + 26866924 TCGACAACAATTCGATT------CTCCT---CTTG s droGri2.scaffold_15245 924111 17 + 18325388 TTGGCGA------GCAG------CTCCT---C--- a score=-127662.000000 s dm6.chr2R 24373502 30 + 25286936 GCAGC---GGC----AGT------AGCTT--------CAGATTCA------GAATCG s droSim1.chr2R 18712269 30 + 19596830 GCAGC---GGC----AGT------AGCAT--------CAGATTCA------GAATCG s droSec1.super_23 131605 30 + 989336 GCAGC---GGC----AGT------AGCAT--------CAGATTCA------GAATCG s droYak3.chr2R 20221710 30 + 21139217 gcagt---agc----atc------agcat--------cagaatca------gaatcg s droEre2.scaffold_4845 21619233 30 + 22589142 GCAGC---GAC----AGT------AGCAT--------CAGAATCC------AAATCC s droBia2.KB462602 814235 31 + 3129309 cagtt---ggcCGAAGGA------AGCAG--------CGGAATCA------GAA--- s droSuz1.KI419649 12063564 27 - 14502029 GCATC---GGC----AGG------AGCAG--------CGGAATCA------GAA--- s droAna3.scaffold_13266 5724129 10 - 19884421 CCACT---GGA----AG---------------------------------------- s droBip2.KB464407 1973941 10 + 2915140 CCAGT---GGA----AG---------------------------------------- s droEug2.KB465067 616756 24 + 1515531 ccATc---agc----aga------gccag--------cagaatca------------ s droEle2.KB458573 540656 36 - 5320397 gcatc---aac----agc------agcag--------cagcagcagccgtaGAATCA s droKik2.KB459527 293823 27 - 1234237 GCAGT---GCC----ATC------GGTat--------tggaatcg------gaa--- s droTak2.KB461535 159831 30 - 669855 gcagcagaagc----aga------agcag--------cagaatCG------GTA--- s droRho2.KB449310 55135 24 - 65043 gcatc---agc----agc------agcag--------cagaatca------------ s droFic2.KB457177 96895 24 + 995874 GCatc---agc----aga------agcag--------cag---cg------gaA--- s droPse3.chr3 1366760 28 - 19787792 GGAAT---g------ggt------agggg--------gaggggta------gAGGGG s droPer1.super_34 555586 36 - 916997 GGAAT---G------GGA------AGGGGGAGGGGTAGAGGGGTA------GAGGGG s droMir2.chr3 1407799 28 - 20862834 GGAAT---g------ggt------agggg--------gaggggta------gAGGGG s droWil2.CH963894 1336436 29 + 2843958 TCGAT---Ga-----act------gattt--------tgaaatca------ctGCTT s droMoj3.scaffold_6496 26168316 21 + 26866924 --ACA---GAG----GAC-------GGAG--------CAGAAACG------------ s droGri2.scaffold_15245 924128 30 + 18325388 GTATC---GAT----GGCTCTTTTTGCTG--------CTGGATCG------------ a score=-59172.000000 s dm6.chr2R 24373532 23 + 25286936 GAA------------------TCAGCAGTAGAAGAA---------GCCAC----- s droSim1.chr2R 18712299 23 + 19596830 GAA------------------TCAGCAGTAGAAGAA---------GCCAC----- s droSec1.super_23 131635 23 + 989336 GAA------------------TCAGCAGTAGAAGAA---------GCCAC----- s droYak3.chr2R 20221740 41 + 21139217 caatcagaatcagagtcagaatcagcagtagaagaa---------GCCAC----- s droEre2.scaffold_4845 21619263 35 + 22589142 AAATCCGAATCAGAG------TCAGCAGTAGAAGAA---------GCCAC----- s droBia2.KB462602 814266 17 + 3129309 ---------------------TCGGCCGT---AGGA---------GCCAT----- s droSuz1.KI419649 12063591 17 - 14502029 ---------------------TCTGCCGT---AGAA---------GCCAT----- s droAna3.scaffold_13266 5724139 7 - 19884421 ---------------------CCA----------------------TCTT----- s droBip2.KB464407 1973951 7 + 2915140 ---------------------CCA----------------------TCTT----- s droEug2.KB465067 616780 20 + 1515531 ---------------------gcagcagtatcagca---------gcCAT----- s droEle2.KB458573 540692 20 - 5320397 GAA------------------TCAGCAGT---ATAA---------GCCAT----- s droKik2.KB459527 293850 10 - 1234237 ---------------------tc----------gaa---------gtCAC----- s droTak2.KB461535 159861 20 - 669855 GAA------------------TCAGCCGT---CGAA---------GCCAT----- s droRho2.KB449310 55159 14 - 65043 ---------------------ACAGT------AGAA---------GCCAT----- s droFic2.KB457177 96919 17 + 995874 ---------------------TCAGCAGT---GGAA---------GCCAT----- s droPse3.chr3 1366788 19 - 19787792 TA-------------------CCACAAGC---AGGA---------GCTAT----- s droPer1.super_34 555622 28 - 916997 TA-------------------CCACAAGC---AGGAGCTATGGATGCTAT----- s droMir2.chr3 1407827 19 - 20862834 TA-------------------CCACAAGC---AGGA---------GCTAT----- s droWil2.CH963894 1336465 17 + 2843958 AAC------------------TCAAA------AGGA---------GTTCT----- s droMoj3.scaffold_6496 26168337 11 + 26866924 --------------------------------------------TGTCCTTCCAC a score=49328.000000 s dm6.chr2R 24373555 41 + 25286936 C-----------GATGAATC----TGTTCGATTCGCTG-ACAA--------CCCCAACTTGTC----------------------------------------GC s droSim1.chr2R 18712322 41 + 19596830 C-----------GATGAATC----TGTTCGATTCGCTG-ACAA--------CCCCAACTTGTC----------------------------------------GC s droSec1.super_23 131658 41 + 989336 C-----------GATGAATC----TGTTCGATTCGCTG-ACAA--------CCCCAACTTGTC----------------------------------------GC s droYak3.chr2R 20221781 56 + 21139217 C-----------GATGAATC----TGTTCGATTCGCTG-ACAA---------CCCAACTTGTCG--------CACTGCGTCGATT----------------CTGC s droEre2.scaffold_4845 21619298 57 + 22589142 C-----------GATGAATC----TGTTTGATTCGCTG-ACAA--------CCCCAACTTGTCG--------CACTGCATCGGTT----------------CTGC s droBia2.KB462602 814283 57 + 3129309 C-----------GATGAAAA----TGTTCAAATCGCAC-AAAA--------CGCCAGCTTGTCG--------TCCTGCATCGATT----------------CAGG s droSuz1.KI419649 12063608 57 - 14502029 C-----------GATGAAAA----TGTTCGAATCGAAG-AAAA--------ATCCAACTTGTCG--------TCCTGCATCGATT----------------CTGC s droAna3.scaffold_13266 5724146 41 - 19884421 C-----------GATGAATC----TCGTCCTGCTGCTG----------------CTCCTCCTTC--------TGCTGC-------------------------TG s droBip2.KB464407 1973958 38 + 2915140 C-----------GATGAATC----TGTTGGAGCTGCTA----------------CTGCTCCTGG--------TTCTG---------------------------- s droEug2.KB465067 616800 58 + 1515531 C-----------GATGAAAC----TGTTTGAACtgttggaaaa--------aaacaatttgtcg--------TCCTGCATCTATA----------------CTGG s droEle2.KB458573 540712 58 - 5320397 C-----------GATGAAAC----TGTTCGATTCGCTG-ACAA--------AATCATTCTGTCG--------TCCTGCATCCATT---------------GCTGG s droKik2.KB459527 293860 78 - 1234237 A-----------GATGAATC----TGTTCGATTTTCTG-ACAA---ACTGAACTCAGCATTTCG--------TCCTGCCTTGAGGAGCGTTTTTGCTGCCGTTGG s droTak2.KB461535 159881 57 - 669855 C-----------GATGAAAC----TGTTCGAATCGCTG-ACAA--------ACCCAACTTCTCG--------TCCTGCACCGATT----------------CTGG s droRho2.KB449310 55173 57 - 65043 C-----------GATGAATC----TGTTCGATTCGCTG-ACAA--------ACCCATCTTGTCG--------TCCTGCCTCGCTA----------------ctgg s droFic2.KB457177 96936 57 + 995874 C-----------GATGAAAC----TGTTCGATTCGCTG-ACAA--------ACACAACTTGTCG--------TCCTGCCTCGCTT----------------CTGG s droPse3.chr3 1366807 41 - 19787792 C-----------GATGGAAC----TGTTCGAATCGCTG-ACAA--------AACTAACTTGTCG--------T-------------------------------- s droPer1.super_34 555650 41 - 916997 C-----------GATGGAAC----TGTTCGAATCGCTG-ACAA--------AACTAACTTGTCG--------T-------------------------------- s droMir2.chr3 1407846 41 - 20862834 C-----------GATGGAAC----TGTTCGAATCGCTG-ACAA--------AACTAACTTGTCG--------T-------------------------------- s droWil2.CH963894 1336482 79 + 2843958 CCGCTTGGCTAAAAGGAATT----TCAtggaatttcac-aaaattaaataaaatcaacttgCAAAATTGAATTACTGCAATTGC--------------------- s droMoj3.scaffold_6496 26168348 35 + 26866924 ------------------------TCTCGGCATCCTTC-TGTG--------CTCTGACTGACTG--------TCTT----------------------------- s droGri2.scaffold_15245 924188 47 + 18325388 C-----------GCTGAAGCGTGTCCTTCTCCTCCTCC-T-TG--------TCCCGGCTCCTAC--------TCTC----------------------------- a score=24436.000000 s dm6.chr2R 24373596 14 + 25286936 AAGTTAAATGCGAT s droSim1.chr2R 18712363 14 + 19596830 AAGTTAAATGCGAT s droSec1.super_23 131699 14 + 989336 AAGTTAAATGCGAT s droYak3.chr2R 20221837 8 + 21139217 AGGCTAAA------ s droEre2.scaffold_4845 21619355 14 + 22589142 AAGTTAAATGCGAT s droBia2.KB462602 814340 14 + 3129309 AAACTAAATGCGAT s droSuz1.KI419649 12063665 14 - 14502029 AAATTAAATGCGAT s droAna3.scaffold_13266 5724187 14 - 19884421 AAATTTAATCAAAA s droBip2.KB464407 1973996 7 + 2915140 -------ATTTAAA s droEug2.KB465067 616858 14 + 1515531 AAATTTAATGCAAT s droEle2.KB458573 540770 14 - 5320397 GAACTTAATTCCAT s droKik2.KB459527 293938 14 - 1234237 AAGCTTAATTCAAT s droTak2.KB461535 159938 14 - 669855 AAACTTAATGCGAT s droRho2.KB449310 55230 14 - 65043 aaattaaattcaat s droFic2.KB457177 96993 14 + 995874 AAACGTAAtgcgaa s droPse3.chr3 1366899 14 - 19787792 AGGCAGTGTGCAGT s droPer1.super_34 555742 14 - 916997 AGGCAGTGTGCAGT s droWil2.CH963894 1336561 11 + 2843958 AAGTT---TGCCTC s droMoj3.scaffold_6496 26168383 11 + 26866924 ---GTGTAAATTGA s droGri2.scaffold_15245 924235 5 + 18325388 ---------ATCAT a score=22289.000000 s dm6.chr2R 24373610 28 + 25286936 ATTG---------AT--GAAGCGCAAGTTAAA------ATGGC----------AT s droSim1.chr2R 18712377 28 + 19596830 ATTG---------AT--GAAGCGCAAGTTGAA------ATGGC----------AT s droSec1.super_23 131713 28 + 989336 ATTG---------AT--GAAGCGCAAGTTGAA------ATGGC----------AT s droYak3.chr2R 20221845 5 + 21139217 ----------------------------------------TGC----------AT s droEre2.scaffold_4845 21619369 28 + 22589142 ATTG---------AT--GAAGCGCCAGCTGGA------ATTGC----------AT s droBia2.KB462602 814354 38 + 3129309 ATTA---------AT--GGagcgcaaattgaa------aatgcaagGCTCTCAAT s droSuz1.KI419649 12063679 38 - 14502029 ATTG---------AT--GGAGCGCAAATTGAA------ATGGCAGGGCTTTCAAT s droAna3.scaffold_13266 5724201 34 - 19884421 ATTG---------AT--AAAGTACAAATTGAAAATGGCACTGC----------AT s droBip2.KB464407 1974003 34 + 2915140 ATTG---------AT--GAagaacaaattgaaaatggcaCTGC----------AA s droEug2.KB465067 616872 38 + 1515531 ATTG---------AT--GAAGCGCAAAGCCCA------ACTGCAAGGCTCTTCAT s droEle2.KB458573 540784 38 - 5320397 ATTG---------AT--GGagggcaaattgaa------attgcaagGCTCTTCAT s droKik2.KB459527 293952 28 - 1234237 GTTG---------AT--GAAGCGTAAATTGGA------ATGGC----------AT s droTak2.KB461535 159952 28 - 669855 ATTG---------AT--GAAGCACAAATTGAA------ACTGC----------AA s droRho2.KB449310 55244 28 - 65043 attg---------aT--GAGGCGCAGATTGAA------ATTGC----------AG s droFic2.KB457177 97007 16 + 995874 ataa---------at--gaa------------------atagc----------AT s droPse3.chr3 1366913 37 - 19787792 Gctgtgcttttgttt--gtgaagcaaattcaa------attgc----------at s droPer1.super_34 555756 37 - 916997 GCTGTGCTTTTGTTT--GTGAAGCAAATTCAA------ATTGC----------AT s droWil2.CH963894 1336572 27 + 2843958 CTTT---------AT--GTCACCCAAAGTATa------gttt-----------at s droMoj3.scaffold_6496 26168394 33 + 26866924 TTTG---------TTCAGCAAAAGCAGTAGGA------ATGCC-------CCAGT s droGri2.scaffold_15245 924240 26 + 18325388 GCTG---------TT--GCCGTTGCATTTGGA------GTG------------AT s apiMel4.GL630491 11565 28 + 65118 attt---------at--ataatataatttata------atcag----------aa a score=-85080.000000 s dm6.chr2R 24373638 18 + 25286936 TTAG------CATCTAAACCAGAA s droSim1.chr2R 18712405 18 + 19596830 TTAG------CATCTGAACCAGAT s droSec1.super_23 131741 18 + 989336 TTAG------CATCTGAACCAGAA s droYak3.chr2R 20221850 14 + 21139217 CTAC------CATCT---TCAGA- s droEre2.scaffold_4845 21619397 18 + 22589142 TTAG------CAACTGAAGCAGAT s droBia2.KB462602 814392 23 + 3129309 TTAG-AGCAACATCCGAGTCACTA s droSuz1.KI419649 12063717 23 - 14502029 TTAG-CTTAACATTTGAGtcacta s droAna3.scaffold_13266 5724235 16 - 19884421 TT--------TGGCCAAGTCAGTA s droBip2.KB464407 1974037 16 + 2915140 TT--------CGGCAAAGtcagtt s droEug2.KB465067 616910 24 + 1515531 TGAAACATATCATCTAAGCCACTT s droEle2.KB458573 540822 23 - 5320397 TTGG-AATACCATCTgagaaacta s droTak2.KB461535 159995 18 - 669855 TTAT------CATCTGAGTCACTA s droRho2.KB449310 55281 24 - 65043 TTAGGAGCACCATCTGAGTcacca s droFic2.KB457177 97028 17 + 995874 TTAA-CATATCATTCGAG------ s droPse3.chr3 1366950 12 - 19787792 ------------tttgggtTGATG s droPer1.super_34 555793 12 - 916997 ------------TTTGGGTTGATG s droWil2.CH963894 1336599 18 + 2843958 ------ttacattttatggCATCA s droMoj3.scaffold_6496 26168429 9 + 26866924 ---------------AAATAAATA s droGri2.scaffold_15245 924268 9 + 18325388 ---------------TTATAAATT s apiMel4.GL630491 11593 17 + 65118 ------ttacgatataacaaaaa- a score=-274043.000000 s dm6.chr2R 24373656 15 + 25286936 GA-----------------------------TAAACTA----------TTT-----------------------------------AAC s droSim1.chr2R 18712423 15 + 19596830 GA-----------------------------TAAACTA----------TTT-----------------------------------AAC s droSec1.super_23 131759 15 + 989336 GA-----------------------------TAAGCTA----------CTT-----------------------------------AAC s droYak3.chr2R 20221864 13 + 21139217 -------------------------------TACGCCA----------TTT-----------------------------------AAA s droEre2.scaffold_4845 21619415 34 + 22589142 ATT-------------------GGCATATC-TACACTAAAGTATCTTCTTC-----------------------------------GAG s droBia2.KB462602 814415 37 + 3129309 CA-----------------------------TAAAATG----------TTTCAGCGTTATGAGGAGAATGAAC-------------taa s droSuz1.KI419649 12063740 49 - 14502029 aa-----------------------------taaaata----------ttattaagttatATAAAACATCAAA-TTCTGATAGGGGTAA s droAna3.scaffold_13266 5724251 15 - 19884421 TA-----------------------------TAGAAAA----------GGG-----------------------------------AAT s droBip2.KB464407 1974053 15 + 2915140 ta-----------------------------taaaaaa----------ttg-----------------------------------aat s droEug2.KB465067 616934 32 + 1515531 AATAA------------GACTCAACGTACCATAAGTCA----------CTC-----------------------------------AAA s droEle2.KB458573 540845 46 - 5320397 aa-----------------------------taaaatt----------taataaagtgaCAGGCACCTTATGTGCTAGGACA----AAC s droKik2.KB459527 294411 15 - 1234237 -------------------------GT----TGAACTT----------TTT-----------------------------------AGC s droTak2.KB461535 160013 41 - 669855 ---AATGAAATGGGATGAAGTGGTAGTCCcattaaata----------tgc-----------------------------------aaa s droRho2.KB449310 55305 13 - 65043 -------------------------------aataaaa----------ttt-----------------------------------aat s droFic2.KB457177 97045 15 + 995874 -----------------------------AAGGcacta----------tat-----------------------------------aaa s droPse3.chr3 1366963 2 - 19787792 ----------------------------------GC----------------------------------------------------- s droPer1.super_34 555806 2 - 916997 ----------------------------------GC----------------------------------------------------- s droWil2.CH963894 1336617 15 + 2843958 --------------------AGTGaattaaataca------------------------------------------------------ s droMoj3.scaffold_6496 26168440 12 + 26866924 --------------------------------AGAGCA----------TTA-----------------------------------CAC s droGri2.scaffold_15245 924278 7 + 18325388 -------------------------------------A----------TTT-----------------------------------GTT s apiMel4.GL630491 11610 15 + 65118 -----------------------------ggtaaaaaa----------tat-----------------------------------aac a score=-431507.000000 s dm6.chr2R 24373671 39 + 25286936 AGATAAGCTCGAAAGTGCATACGA--------------------------------------------------------TGA----------------------------------------------A---ATT------AA--AACCAC--- s droSim1.chr2R 18712438 27 + 19596830 AGATAAGCT------------CGA--------------------------------------------------------TGA----------------------------------------------A---ATT------AA--AACCAC--- s droSec1.super_23 131774 27 + 989336 AGATAAACT------------CGA--------------------------------------------------------TGA----------------------------------------------A---ATT------AA--AACCAC--- s droYak3.chr2R 20221877 35 + 21139217 AGATAAGCT------------CAAAAGT----------------------------------------AGCT--------CAA----------------------------------------------G---ATT------AT--AAGCAC--- s droEre2.scaffold_4845 21619449 35 + 22589142 AGATAAGCT------------CGAAAGT----------------------------------------AGCT--------CAA----------------------------------------------G---AGT------TT--AACCAC--- s droBia2.KB462602 814452 88 + 3129309 aaatcaaca------------caaaaat-------------------------------CAAGCA--AAGGC--------TGCATATGATACTACgaataattgtttttcattttgtctCAATCTCGTTA---ATT------GC--CACTAT--- s droSuz1.KI419649 12063789 95 - 14502029 Aggtaaata------------aaagaat-------------------------------aaatca--TAGACAGTTGTA-TGAATTAAATACTATGAAtaattgtttcttattttaccTTAAGCTCAAAA---ACT------AC--CACTAT--- s droAna3.scaffold_13266 5724266 16 - 19884421 --AAAAGCT------------TT---------------------------------------------------------GGG----------------------------------------------A---ATT------------------- s droBip2.KB464407 1974073 18 + 2915140 GGATAAACT------------TT---------------------------------------------------------TGC----------------------------------------------A---ATT------------------- s droEug2.KB465067 616966 33 + 1515531 AGATAAGCT------------AGC--------------------------------------------------------AGC----------------------------------------------A---ATCTACTACAA--CACTAT--- s droEle2.KB458573 540891 73 - 5320397 AACTATGTT------------AAGAAATTCAT--------TTCCTTGCCTATGATGAGGTAAACA--AAGGTAGAAgcattaa----------------------------------------------a---tgt------aa--tatttc--- s droKik2.KB459527 294428 29 - 1234237 ATATAATCC------------CCT--------------------------------------------------------TGA--------------------------------------------TTA---ATT------AG--AAACAc--- s droTak2.KB461535 160054 29 - 669855 caattatat------------tta--------------------------------------------------------tgc----------------------------------------------a---aat------acgtaaattt--- s droRho2.KB449310 55545 35 - 65043 AGATAAGgt------------gaaaaatgaat------------------------------------------------tat----------------------------------------------t---act------AT--AACCAT--- s droFic2.KB457177 97063 81 + 995874 taataaagt------------cgAAAAAGCGCCATCtcttttgtttgtctgtttcaATTGAAGCATTAAGTTTCTCGGG-TGA----------------------------------------------A---AAT------A---GACAGT--- s droPse3.chr3 1366965 12 - 19787792 ---------------------------------------------------------------------------------------------------------------------------------A---AAT------GG--AACTGG--- s droPer1.super_34 555808 12 - 916997 ---------------------------------------------------------------------------------------------------------------------------------A---AAT------GG--AACTGG--- s droWil2.CH963894 1336632 32 + 2843958 atataaACA------------CGAGAA-----------------------------------------------------GGA----------------------------------------------A---Tat------agaaaacaga--- s droMoj3.scaffold_6496 26168452 25 + 26866924 --------------------------------------------------------------------------------------------TATGCCAAAATAT------------------------A---ATT------TA--CAGGTC--- s droGri2.scaffold_15245 924285 28 + 18325388 --------------------------------------------------------------------------------------------CATCTGAAAGGGT------------------------ATGCATT------AA--AAAAAT--- s apiMel4.GL630491 11625 36 + 65118 -----------------------------------------------------------------------------------------atatacgtcaaatatttgtac-------------------a---aat------ct--GATCATTTC a score=-447862.000000 s dm6.chr2R 24373710 34 + 25286936 C--TAAATCTTC------------------TAC-AGA--GCTTT----------TT--CATCG------------------------------------------------AGTAA--G s droSim1.chr2R 18712465 34 + 19596830 T--TTAATCTTC------------------TAC-AGA--GCTTG----------TT--CATCG------------------------------------------------AGTAA--G s droSec1.super_23 131801 34 + 989336 T--TTAATCTTC------------------TAC-AGA--GCTTG----------TT--CATCA------------------------------------------------AACAA--G s droYak3.chr2R 20221912 28 + 21139217 T--TAAATCCAT---------------------------GCATG----------TT--CACTG------------------------------------------------AATAA--G s droEre2.scaffold_4845 21619484 36 + 22589142 T--GAAATCTCT------------------TCC-TTATAGCATG----------TT--CATTG------------------------------------------------GATAA--G s droBia2.KB462602 814540 31 + 3129309 A--TTAATCTTC----------------------ACA--CCAAG----------CT--ATTTG------------------------------------------------AATTA--G s droSuz1.KI419649 12063884 31 - 14502029 A--TCAATCTTC----------------------ACA--CCATG----------AT--ATTTG------------------------------------------------AACTA--G s droAna3.scaffold_13266 5724282 2 - 19884421 ---------------------------------------GC------------------------------------------------------------------------------ s droBip2.KB464407 1974091 2 + 2915140 ---------------------------------------GT------------------------------------------------------------------------------ s droEug2.KB465067 616999 31 + 1515531 T--TTGTTCATT----------------------AGA--TCTTA----------AT--TGTCG------------------------------------------------AGTAA--A s droEle2.KB458573 540964 34 - 5320397 a--tttattata------------------tat-ata--atttc----------ct--GGCAA------------------------------------------------GTTAA--A s droKik2.KB459527 294457 60 - 1234237 c--ctaaatatt----------att----attc-att--gGCTG----------Tt--taatg--------------------cttattataata--------tatctaaaaataaatg s droTak2.KB461535 160083 52 - 669855 a--ttaatttactcaATCCGTTATTGTTAATTT-ATA--GCTTT----------AT--AATCA------------------------------------------------ACTCA--A s droRho2.KB449310 55580 33 - 65043 C--ATATTGttc-------------------aa-aac--acttt----------aa--aatta------------------------------------------------aatca--g s droFic2.KB457177 97144 100 + 995874 T--TTAGTGCTTGTCAGAAAACAAGGAACTTCA-GTA--ATGCT----------AT--TATTGGCAGCCGAGATAAGCTAGCACTTATTATTACAATCTTCGCGGCTTGATAATCA--G s droPse3.chr3 1366977 36 - 19787792 CAGTGGGTGTGC------------------CAC-ACA--GCTCC----------AA--GGTCT------------------------------------------------GTCTA--T s droPer1.super_34 555820 36 - 916997 CAGTGGGTGTGC------------------CAC-ACA--GCTCC----------AA--GGTCT------------------------------------------------GTCTA--T s droWil2.CH963894 1336664 33 + 2843958 a--ataatgTCT----------------------GTA--GTTTA----------TTAAAATCT------------------------------------------------ATTAa--g s droMoj3.scaffold_6496 26168477 37 + 26866924 G--GCTAAAATA------------------CAC-AGA--ATGCAGAG-------TT--GATCC------------------------------------------------AAAAA--G s droGri2.scaffold_15245 924313 44 + 18325388 C--GAAATATTT------------------CAT-CAA--ATTTAGCAAACGATTTC--TATAG------------------------------------------------AAAAA--C s musDom2.KB855869 35969 5 - 245279 ----------------------------------------------------------------------------------------------------------------caaa--a s apiMel4.GL630491 11661 35 + 65118 --TCAAGTTTTT------------------TCCAGTA--ATCAC----------TT--CAAGG------------------------------------------------AATAA--T a score=-289968.000000 s dm6.chr2R 24373744 44 + 25286936 CG---------T--------------------------ATTAAATGTTTT------T---------AA-----TAATTTGGTAT-----------------------------T----------T--ATA----------GTT--------------TAAGCTT s droSim1.chr2R 18712499 44 + 19596830 CG---------T--------------------------ATTAAATGTTTT------T---------AA-----TAAGCTGGTAT-----------------------------T----------T--ATA----------GTT--------------TAAAATT s droSec1.super_23 131835 44 + 989336 CG---------T--------------------------ATTAAATGATTT------T---------AA-----TAAGTTGGTAT-----------------------------T----------T--ATA----------GTT--------------TCAATTT s droYak3.chr2R 20221940 44 + 21139217 CG---------T--------------------------ATTAGATGTGTC------T---------AA-----TAAGTATGTAT-----------------------------T----------T--ATA----------GAT--------------TAAATTT s droEre2.scaffold_4845 21619520 43 + 22589142 CG---------T--------------------------ATTATATGTTTC------T----------A-----CGAGTATGTAT-----------------------------T----------T--ATA----------GTT--------------GAAATTT s droBia2.KB462602 814571 44 + 3129309 CC---------T--------------------------CTTTAATGAATC------t---------aa-----taactatttat-----------------------------t----------t--ata----------gct--------------ttaATGT s droSuz1.KI419649 12063915 44 - 14502029 CC---------t--------------------------cttaaatgaatt------t---------aa-----taagtatttat-----------------------------t----------t--ata----------gct--------------taAATTT s droAna3.scaffold_13266 5724284 30 - 19884421 ----------------------------------------------TGTT------C---------AA-----TTATGTTCTTG-----------------------------T----------T--ATA---------------------------TATACTT s droBip2.KB464407 1974093 35 + 2915140 ----------------------------------------------TCTT------T---------AA-----TTATGTTCTGG-----------------------------T----------T--ATA----------TATT------------GTATACTT s droEug2.KB465067 617030 44 + 1515531 AC---------T--------------------------CATAAATCagat------t---------aa-----tttgtatttat-----------------------------t----------a--tta----------gct--------------CAAATAT s droEle2.KB458573 540998 54 - 5320397 GA---------A--------------------------AGATAAGgtcaa------a---------aa-----tgaattattat-----------------------------tgCCAGCAGTAT--GTA----------AAT--------------CAAAACC s droKik2.KB459527 294517 59 - 1234237 tg---------t--------------------------attaaatacctt------t---------aaataattaaatcggcat-----------------------------c----------t--aaaatatGTTCCTATT--------------ATAGTTT s droTak2.KB461535 160135 69 - 669855 TT---------TTCACAATTTAGTAATCCA-AATAGAATCTGAACGATTT------T---------Aa-----taggtatatat-----------------------------t----------t--ata----------gct--------------tAAATTT s droRho2.KB449310 55613 43 - 65043 cc---------t--------------------------tttaaataattt------t----------a-----taagtatGTAT-----------------------------T----------A--ATA----------GCT--------------TTAATTT s droFic2.KB457177 97244 36 + 995874 CC---------T--------------------------TCTAAATGATTT------C---------TA-------------TAT-----------------------------T----------T--ATA----------GCT--------------CAATTTT s droPse3.chr3 1367013 58 - 19787792 CT---------C--------------------------TCGCTGGAAGTT------C---------AC-----TAATGAATGGC-----------------------------T----------T--ACA----------ACCGGAACACTTTAAAGACAATTT s droPer1.super_34 555856 58 - 916997 CC---------C--------------------------TCGCTGGAAGTT------C---------AC-----TAATGAATGGC-----------------------------T----------T--ACA----------ACCGGAACACTTTAAAGACAATTT s droWil2.CH963894 1336697 50 + 2843958 at---------t--------------------------gtaattttttttcgaaaat---------aa-----tAAAGCCACAT-----------------------------T----------G--GAA----------ATT--------------GAAACTT s droMoj3.scaffold_6496 26168514 39 + 26866924 AT---------T--------------------------TCATTCTCACTT------G---------AA-----CAG-----TGT-----------------------------T----------G--AAA----------TAC--------------TAATCAC s droGri2.scaffold_15245 924357 55 + 18325388 ATATATGGTTAT--------------------------TCAATGCCA--T------A---------AA-----TAGATATTTAT-----------------------------T----------G--CTA------TTTTTAC--------------TTGCCAT s musDom2.KB855869 35974 82 - 245279 ta---------t--------------------------tttaaatgtctt------ttcaaatattag-----tagatttttatatgttttcttaggCGATGACATCCGGAGGT----------T--ATA----------ATA--------------CGtgttt s anoGam1.chr2L 21206369 48 - 48795086 -----------------------------------CGAATTAAGTTGTTT------A---------AA---ATTAAAGCAATTT-----------------------------T----------TCAATG----------GTC--------------TGCATTA s apiMel4.GL630491 11696 64 + 65118 ---------------CTTTTCTctattgaagaaagaaaaaaatatatcct------t---------ga-----aatttctttgt-----------------------------g----------a--tcg----------ttt--------------gaaaatt a score=-378021.000000 s dm6.chr2R 24373788 42 + 25286936 -CTTGGCA-GTTGC-ATGCTTAC-----------T-----------CACTC--------------GACAT--TGT----------TGTTTTTG s droSim1.chr2R 18712543 45 + 19596830 -CTTGGCA-GTTGC-ATGCTGAC-----------TCG--------ACATTC--------------GAAAT--TGT----------TGTGTTTG s droSec1.super_23 131879 45 + 989336 -CTTGGCA-GTTGC-ATGCTGAC-----------TCG--------ACATAC--------------GAAAT--TGT----------TGTCTTTG s droYak3.chr2R 20221984 46 + 21139217 -CTTGGCATGCTGC-ATGCTTAC-----------CCG--------GCATAC--------------GAAAT--TGT----------TGTCTTTG s droEre2.scaffold_4845 21619563 31 + 22589142 -CTTGGCA-GATGC-A---------------------------------AC--------------GAAAA--TGC----------TGTCTTTG s droBia2.KB462602 814615 68 + 3129309 -CTTGGCA-GAGGCTAGGCAAAC-----------TCA--------GCATATCCATTAATTACAAAGAAAA--TGTATGA--GAAATGCCTCCG s droSuz1.KI419649 12063959 68 - 14502029 -CTTGGCA-AAGGCTAGGTAAAC-----------TCA--------GCATATCTATTAATTGCAAAGAAAA--TGTATGA--GAAATGCGAATA s droAna3.scaffold_13266 5724314 41 - 19884421 -CCCAGAA-ATAGA-----CAAA-----------AAT--------GTACGA--------------GAACA--TAT----------TATTTTGG s droBip2.KB464407 1974128 29 + 2915140 -CCCAGAA-ATAGA------------------------------------A--------------AAACA--CAT----------TATTTTGG s droEug2.KB465067 617074 26 + 1515531 -CTTGGCA-GGTGC----------------------------------CAC--------------AAATA--CAT----------AAT----- s droEle2.KB458573 541052 66 - 5320397 -TTTGATA-ATCAA-ATTAGaacatttaatgatttta--------atatat--------------aaata--tttatagcttGAATTTCTTGG s droKik2.KB459527 294576 43 - 1234237 -CTTGGCA-TCAAA-AAGGTCAT-----------TT----------TActa--------------taata--aat----------ttcttttc s droTak2.KB461535 160204 68 - 669855 -CTTGGCA-GTGGTCAGGCAAAT-----------GCA--------acgtatttattaattataaagaaCA--TTTATGAGAAA--TGCATATA s droRho2.KB449310 55656 50 - 65043 -CTTGGCA-AAGGTTAGGTAAAC-----------TCA----TGTCGTcaac--------------aaatt--tat----------tcattttc s droFic2.KB457177 97280 49 + 995874 -CTTGGCA-GAGAAACGGTAAAC-----------Aca--------aaatttcta-----------ttaat--tgt----------tttctttg s droPse3.chr3 1367071 45 - 19787792 -TTCAGTG-GGAGT-TACAGAAT-----------TGC--------TTGCAC--------------TAAAT--TAT----------ACTTTAAG s droPer1.super_34 555914 45 - 916997 -TTCAGTG-GGAGT-TACAGAAT-----------TCC--------TTGCAC--------------TAAAT--TAT----------ACTTTAAG s droMoj3.scaffold_6496 26168555 47 + 26866924 --ATGGAA-CTCCC-CCTCCTGC-----------TCC----TCCGTTTGTT--------------GCGAT--AAT----------TGCTATT- s droGri2.scaffold_15245 924418 46 + 18325388 -TATAGTA-ATTTA-GCATTGGC-----------TCC--------TTTGTT--------------AAGGTTCAAT----------TTTAATT- s musDom2.KB855869 36056 52 - 245279 -ttcagca-atttt--tacaaat-----------ttaaatatttattattc--------------aacat--ttt----------caattcca s anoGam1.chr2L 21206425 34 - 48795086 -CTTGTTA-GTGAA-----CAAT-----------CTG--------GTATTG--------------TGAAC--TTT----------T------- s apiMel4.GL630491 11760 39 + 65118 atttag---attta-tgcTTAAC-----------TTT--------ACATGC--------------AAAAG--TCT----------TTG----- a score=-92938.000000 s dm6.chr2R 24373830 5 + 25286936 ----CA-------GAT s droSim1.chr2R 18712588 5 + 19596830 ----CA-------GTT s droSec1.super_23 131924 3 + 989336 ----CA-------G-- s droYak3.chr2R 20222030 5 + 21139217 ----CA-------GAT s droEre2.scaffold_4845 21619594 12 + 22589142 ----CATTGGTATGAT s droBia2.KB462602 814683 3 + 3129309 ----CA-------A-- s droSuz1.KI419649 12064027 3 - 14502029 ----CA-------A-- s droAna3.scaffold_13266 5724355 2 - 19884421 ----CA---------- s droBip2.KB464407 1974157 2 + 2915140 ----CA---------- s droEug2.KB465067 617100 3 + 1515531 ----CA-------A-- s droEle2.KB458573 541118 5 - 5320397 ----CA-------TGT s droKik2.KB459527 294619 3 - 1234237 ----ta-------a-- s droTak2.KB461535 160272 3 - 669855 ----CA-------A-- s droRho2.KB449310 55706 3 - 65043 ----tt-------t-- s droFic2.KB457177 97329 5 + 995874 ----tg-------tgc s droMoj3.scaffold_6496 26168603 1 + 26866924 ----T----------- s droGri2.scaffold_15245 924467 1 + 18325388 ----T----------- s musDom2.KB855869 36111 1 - 245279 ----t----------- s anoGam1.chr2L 21206463 1 - 48795086 ----T----------- s apiMel4.GL630491 11808 5 + 65118 CAATT----------- a score=-21933.000000 s dm6.chr2R 24373835 12 + 25286936 TGGTA-----------------------TATGCAG s droSim1.chr2R 18712593 12 + 19596830 TGGTA-----------------------TATGGTA s droYak3.chr2R 20222035 12 + 21139217 TGCTA-----------------------TGTGCAG s droEre2.scaffold_4845 21619606 12 + 22589142 TGGTA-----------------------TGTGCAG s droEle2.KB458573 541123 28 - 5320397 Cgtcaaca----atttttctttgtcaTTTGTG--- s droFic2.KB457177 97334 24 + 995874 TGCAAGTgtcatatatttatttga----------- s anoGam1.chr2L 21206464 22 - 48795086 -------------TAAAGGCTAGTAATGACTGAAA s apiMel4.GL630491 11813 11 + 65118 TAGTA-----------------------TGAgct- a score=-301274.000000 s dm6.chr2R 24373847 22 + 25286936 CA---AT---------------------------AAA---------ATGACAA-AA-----GAA--TAA- s droSim1.chr2R 18712605 27 + 19596830 TATATATAA-------------------------ATA---------ATGACAA-TA-----GAA--TAA- s droSec1.super_23 131927 22 + 989336 -----ATTA-------------------------AAA---------ATGACAA-GA-----GAA--TAA- s droYak3.chr2R 20222047 22 + 21139217 AA---AT---------------------------GAA---------ATGCCAA-AA-----GAA--TAA- s droEre2.scaffold_4845 21619618 22 + 22589142 AA---AT---------------------------TAA---------ATGCCAA-AA-----GAA--TAA- s droBia2.KB462602 814686 16 + 3129309 -----GT---------------------------CAA---------ATGCCAA-AA-----------TA- s droSuz1.KI419649 12064030 16 - 14502029 -----AT---------------------------caa---------atgccaa-aa-----------aa- s droAna3.scaffold_13266 5724357 18 - 19884421 -----AA---------------------------GAA---------ATGATAG-AC-------A--TAG- s droBip2.KB464407 1974159 18 + 2915140 -----AG---------------------------AAA---------ATAATAG-AC-------A--TAG- s droEug2.KB465067 617103 20 + 1515531 -----GT---------------------------CAA---------ATGCCAA-AA-----GAA--TAC- s droEle2.KB458573 541151 22 - 5320397 -----GC---------------------------ACa---------atgaaaa-at-----tcatttaa- s droKik2.KB459527 294622 20 - 1234237 -----ag---------------------------aaa---------acaacaa-at-----ata--tac- s droTak2.KB461535 160275 20 - 669855 -----AT---------------------------CGA---------GTGCCAA-AA-----TAA--TCA- s droRho2.KB449310 55709 20 - 65043 -----GT---------------------------GTG---------CCACAAA-TA-----GCA--taa- s droFic2.KB457177 97358 20 + 995874 -----at---------------------------caA---------ATGCCAA-AA-----TAA--TCA- s droPer1.super_34 555959 6 - 916997 -------------------------------------------------------------ACA--TCT- s droMir2.chr3 1408115 14 - 20862834 -----------------------------------------------TGGGAG-TT-----ACA--GAA- s droMoj3.scaffold_6496 26168604 21 + 26866924 -------TA-------------------------TAATTTGGAATCATGTGAG----------------- s droGri2.scaffold_15245 924468 39 + 18325388 -------TAGT---TCACCATTTC----CAACACTAATTTTATAGTTTGCTAA----------------- s musDom2.KB855869 36112 30 - 245279 ----------tggtttgacagttcattgtcccagcaa---------ctg--------------------- s anoGam1.chr3L 4067314 22 + 41284009 -----------------------------------CA---------TTAACAA-TACATACGGA--TTA- s apiMel4.GL630491 11824 19 + 65118 -----------------------------------ta---------ataagaataa-----aaa--taag a score=-702623.000000 s dm6.chr2R 24373869 67 + 25286936 T-T----------TCAAATTGTAT-----------------------TGTATATTATA-----AAGTGTTCTTATGACATCAGCCCTT---------AAATAAGA------------TCGTA------------------TTGT------------------------T s droSim1.chr2R 18712632 67 + 19596830 T-T----------TCAAATTAAAT-----------------------TGCACATTATA-----AAGTGTTCCTATGACATCAGCCCTT---------AAATGAGA------------TCATA------------------CTGT------------------------T s droSec1.super_23 131949 67 + 989336 T-T----------TCAAATTAAAT-----------------------TGCACATTATA-----AAGTGTTCTTATGACATCAGCCCTT---------AAATGAGA------------TCATA------------------CTGT------------------------T s droYak3.chr2R 20222069 77 + 21139217 T-T----------tcttattatat----------at---atatatattatatattata-----aagttTTCTGGCGCCATCAATCCCT---------AAATCAGT------------TCATA------------------CTGA------------------------T s droEre2.scaffold_4845 21619640 87 + 22589142 T-T----------TCTAATTATATTAC---CCTAATCTGATCAAGATTGTATATTATA-----AGGTGTTCATGTGACATCAAACCCT---------AAATTAGG------------TCATA------------------CTGT------------------------T s droBia2.KB462602 814702 90 + 3129309 TCT----------TCCTATAATATTGAG--CTAAAACTTTTAAGGAATGTATATTATA-----ACGTTTTATAATAATACGGGCCCCT--------AAAATTATG------------Tcatg------------------tttg------------------------t s droSuz1.KI419649 12064046 88 - 14502029 t-t----------tCGTATTATAAACA---CTTAAACATTTCAAGAATGTAATGTata-----atgttttataataataccAACCCCT--------AAAATTATg------------tcata------------------tttg------------------------t s droAna3.scaffold_13266 5724375 38 - 19884421 T-A----------TGTCATTTTAT-----------------------------------------------TTATAACAAAAGCTGCT--------------AGA------------CCATA----------------------------------------------- s droBip2.KB464407 1974177 48 + 2915140 A-CACCTTCTCATTGACACTTTAT-----------------------------------------------TTATAACAAAAGCTGCT--------------AGC------------ATATA----------------------------------------------- s droEug2.KB465067 617123 102 + 1515531 C-T----------TC---TTATATTCAC--CTGAAACTGCTGAGGAATGTATATTGCA-----ACAC-TTCCTATAATATAACCCCTA---------AAATTAGA------------TTACAATGCATAAGAATAATACCTTCA------------------------T s droEle2.KB458573 541173 87 - 5320397 t-t----------tcgtattATATTTAC--CTTAAACTGCTCAAGaatgtatattata-----aaatttcgtAATAAGATCATGCTTA--C---ATAAAGCGGAG------------GCATA----------------------------------------------- s droKik2.KB459527 294642 72 - 1234237 g-c----------tctcaaaacaa------------caaataaatatggtACATCAAC-----ATGCTCAACAAGAAAAAC-GTCTCT---------ATATTAAC------------TAAGA----------------------------------------------- s droTak2.KB461535 160295 62 - 669855 T-C----------TC-TATTGTATTTac--cttaaa-------------------------------tttataatagtaTCATCCCCT--------TCAATTATG------------tcatg------------------ttta------------------------t s droRho2.KB449310 55729 89 - 65043 t-t----------tcttattatatttac--CTTAAGCTGCTCAAGAATGTatattata-----acattttataatacgATCATACTTATAT---ATAAAGCGAGG------------GCACA----------------------------------------------- s droFic2.KB457177 97378 61 + 995874 T-T----------ACTCAACAAAT-------------------------TATACCAC-----------TTTTGAAAAGATCAACCCCC-------TTAATTTAGT------------TCATC------------------CCtg------------------------t s droPse3.chr3 1367134 81 - 19787792 ------------------ttgtagttttcATTCAATATTTCAAAGAATATAATCTATA-----GAAGTCTATAA-ATTATGATCCTTT-------GCCTTTAAtc------------tcata------------------at--------------------------- s droPer1.super_34 555989 69 - 916997 ------------------------------TTCAACATTTCAAAGAATATAATCTATA-----GAAGTCTATAA-ATTATGATCCTTT-------GCTTTTAATC------------TCATA------------------AT--------------------------- s droMir2.chr3 1408173 80 - 20862834 ------------------tcttaGTTTCCATTCAACATTTCAAAGAATATAATCTATA-----GAAGTCTATAA-ATTATGAT-CTTT-------GCCTTTAATc------------tcata------------------at--------------------------- s droMoj3.scaffold_6496 26168625 69 + 26866924 ------------------------TCTC--TCGTAAATTTATGATCTTGT-------------GCGTGTTGACATGACATTAGAACAA------GTTCATTTAGC------------TCGCC------------------ATTA------------------------- s droGri2.scaffold_15245 924507 112 + 18325388 ------------------------TCTCCTCCGGCAATTTATGGATCTCTA----ACA-----GCTGACTGACACAACATGACAACTA------ATTAATTAAACTTTAAATGTTTATTGCT------------------ATCAGCGACAGCGATTCTTATTTCCTAGt s musDom2.KB855869 36142 58 - 245279 -----------------------------------------------tgtctacctat-----attttctaccatggtatagATATTC--C---AAAATGTCACA------------TTATC------------------TACT------------------------A s anoGam1.chr3L 4067336 67 + 41284009 ---------------------------------------TTTAGAATTGTATTCTATACTGACAGAAGAATCTATGCCGTATACTTTT--C--AACCAAACAATT------------CTATT----------------------------------------------- s apiMel4.GL630491 11843 91 + 65118 -----------tttcataTCATATCGTCAACgagatatttgtaataaaat-tatcata-----atattctatttcgatattatttgta--ttaaaagtttttaaa------------ttgtt----------------------------------------------- a score=-515815.000000 s dm6.chr2R 24373936 105 + 25286936 ATTTGCAGAGCA-------AGAAG----------TGCTTAGTA-----GTTTAATCGGCTGA-TAATGGAT------TTAACCCCCATGA------------TGATGT-----------CGGATGAGAAATC---------TGCA-CAGT--GAG---CAAATAAGGG--TCTT s droSim1.chr2R 18712699 105 + 19596830 ATTTTTAGAGCA-------AGAAG----------TGCTTAATA-----GTTTAATCGGCTGA-TAATGGAT------TCAACCCCCATGA------------TGATGT-----------CAGCTGAGATGTC---------TGCG-CAGT--GAG---CAGATAAGGG--TCTT s droSec1.super_23 132016 107 + 989336 ATTTTTAGAGCA-------AGAAG----------TGCTTAATA-----GTTTAATCGGCTGA-TAATGGAT------TCAACCCCCATGA------------TGATGT-----------CAGTTGAGATATC---------TGCG-CAGT--GAG---CAGATAAGGGTCTCTT s droYak3.chr2R 20222146 107 + 21139217 ATAGGTGAAGCA-------AGTAAA------ACCtgttaaata-----gtttaatcaaCTGA-TAATGGAA------TCA--CCCCAAGA------------TGATGT-----------CATATGAGATAGC---------TGCG-CAGT--GAG---CACATGAGGG--Gttt s droEre2.scaffold_4845 21619727 88 + 22589142 A---------------------------------CTTTAAATA-----G-TTAATCGGCTGA-TAATGGAA------TCAACCCCCGAGA------------TGATTT-----------CAGATGAGAAATC---------TGCG-CAGC--GAG---CACTTAAGGG--GTTT s droBia2.KB462602 814792 114 + 3129309 atttataaagct-------AATAAT------GCTTGCTTATCG-----ACTTAATCAGTTGA-TAATAGAACCCA-AGCAACCCCTAAGA------------TAGTGT-----------CAGTGGAAGTATT---------CGCT-CAGC--GAG---CTCGTCAGGG--CTTT s droSuz1.KI419649 12064134 113 - 14502029 atttataaagcA-------AATAAT------GCTTGCTAAAGG-----TCTTAATCATTTAA-TAATGGAA-CCG-AGCAACCCCTAAGA------------TGGTGT-----------CAGTGGAAATGTT---------TGCT-CAGC--GAG---CACTTGAGGG--CTTT s droAna3.scaffold_13266 5724413 67 - 19884421 ----------------------------------TACTAAGCA-----GTTTATTAATCTAA-TCATATTT-------------------------------------------------AAGGGAAACTAG---------AACG-AAGC--AAG---C-TATGATGG--GCAC s droBip2.KB464407 1974225 67 + 2915140 ----------------------------------TACTAAGCA-----GCTTATTAATCTAA-TCATATCA-------------------------------------------------GGGGGAAACTAG---------AACG-AAAC--AAG---C-TTTGATGG--GCAC s droEug2.KB465067 617225 106 + 1515531 ACCTTCAATGCATTCG--GAATAAT------ACCTTCTGAACG-----ACTTAACCTCTTAA---------------TCAACCCCCAAGA------------TGATGC-----------CAGTGGAAGTATT---------TGCT-GAGC--GAG---CCCTTGAGAG--GTTT s droEle2.KB458573 541260 82 - 5320397 -------------------AAGAAT------ATGCGCTAAATG-----ATTTAATCACATAA-TAATGGAA------TCAACCCCTAAGA------------TGATGT-----------CAGTGGAAATA------------------------------CTTGAGGG--TGTT s droKik2.KB459527 294714 85 - 1234237 ----------------------------------CGCATA----------TTATCcacttaaataattgaa------tCAACCCCTAGAGAT----------TGATGT-----------CGTGGAAAAATTC---------TGC--CAGC--GAG---TAAATGTTGG--GCTC s droTak2.KB461535 160357 115 - 669855 atttataaggcA-------TACAAT------GCCTACTAAACg-----atttaatcatttaa-taatGGAACCAACACCAACCCCTAAGA------------TGATGT-----------CGGGGGAAATACT---------TGCT-CAGC--GAG---CAGTTGAGGG--CCAT s droRho2.KB449310 55818 86 - 65043 -------------------AAGAATAAT-GCGCTTACTAAAAG-----ATTTAATCAGATAA-TAATGGAA------TCAACCCCTAAGA------------TGATGT-----------CAGTGGAAATAT-------------------------------TGAGGA--GATT s droFic2.KB457177 97439 111 + 995874 atttataaaactcaAGAAGAATAA----------TGCTCGGTA-----A-TAGATCTTATTA-TAATGGAA------TCAACCCCTGAGA------------TGATGT-----------CAGTGGGGAGATT---------AGCT-CAGC--AAG---CAGTTGAGGG--ATTT s droPse3.chr3 1367215 93 - 19787792 -------------------aataa----------atatcaaCA-----GAAGAACCATATAA-CA--TGAT------TCAACTCCTAT-A------------TAAACC-----------AAGTGGAAAGCTC---------TCCTCCAACAAAAA---CCCTTAATGG--GGCC s droPer1.super_34 556058 93 - 916997 -------------------AATAA----------ATATCAACA-----GAAGAACCATATAA-CA--TGAT------TCAACTCCTAT-A------------TAAACC-----------AAGTGGAAAGCTC---------TCCTCCAACAAAAA---CCCTTAATGG--GGCC s droMir2.chr3 1408253 93 - 20862834 -------------------aataa----------atttcaaca-----GAAGAACCATATAG-GA--TGAT------TCAGCCCCTAT-A------------TAAGCC-----------AAGTAGAAAGCTC---------TCCTTCAACAAAAG---CCCTTAATGG--GGCC s droMoj3.scaffold_6496 26168694 102 + 26866924 ---------TTT-------ATAGAT---------CTTTCCGCA-----TTTTTATTGGCTAA-TCAGTCGC------CTATCTTACGTTT------------TAGCTT---------TTTCCGTAAAAGAGC---------TTTT-GGCG--AAAAGTCACGGAATGG--CCAT s droGri2.scaffold_15245 924619 137 + 18325388 attatttatttt-------atttatttt-ttG--TTTTTTGCA-----TTTTATTTTGCCAA-TCATTTGC------TTATCATGCTTCTATAA-------ATAGCATCATTTTAAGTTGATGTGAAACAACCCTGTTCATTGTT-CGCC--AAG---CATAAGTTGG--GTGT s musDom2.KB855869 36200 119 - 245279 AACCTCAATGTAAACATGAAACACTGATATTTTCCTCCAATCG-----ACATAATAGTGAGT-TATCCGAG--------AACCTTAATAA------------AAATGA-----------CA----AAGAATT---------TTCA-TAGC--CAAATACAAATAACGC--CATA s anoGam1.chr2L 9211201 107 + 48795086 ----------------------------GATTGTTGTTCGGGATATGTGATGAATCGCTTGA-AAATTCAT------GTCATCATCATGAAGGAGCGCAACATAATCG-----------TAGGTATAAGTAT---------TTAT-AGGT--GCA---CAAGGAACGG------ s apiMel4.GL630491 11934 75 + 65118 ----------------------------tctgtgcgtcaatat-----taatatttttttat-ttttaatt------ttatttcctttaa------------ctatat-----------ataataatatatt---------aata-ta-------------------------- a score=1420132.000000 s dm6.chr2R 24374041 75 + 25286936 TTTTCCCG-GCGAGTTCCAATA---GCCTCCGTGGCGCAATTGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGG s droSim1.chr2R 18712804 75 + 19596830 TTTTCCCG-GCGACTTCCAATA---GCCTCCGTGGCGCAATTGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGG s droSec1.super_23 132123 75 + 989336 TTTTTCCA-GCGAGTTCCAATA---GCCTCCGTGGCGCAATTGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGG s droYak3.chr2R 20222253 75 + 21139217 ttttCCCG-TCGAGTTCCAACT---GCCTCCGTGGCGCAATTGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGG s droEre2.scaffold_4845 21619815 75 + 22589142 TTTCCTCG-GCGAATCTCAATA---GCCTCCGTGGCGCAATTGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGG s droBia2.KB462602 814906 75 + 3129309 ATTTCCGA-GTGAATCTCAACA---GCCTCCGTGGCGCAATTGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGG s droSuz1.KI419649 12064247 75 - 14502029 ATTTCCGA-GACGATTTCAACA---GCCTCCGTGGCGCAATTGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGG s droAna3.scaffold_13266 5724480 75 - 19884421 TTCGCCAG-GGCGCTTCCAAGA---GCCTCCGTGGCGCAATCGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGG s droBip2.KB464407 1974292 75 + 2915140 TTCGCCAG-GGTGCTTCCAAGA---GCCTCCGTGGCGCAATCGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGG s droEug2.KB465067 617331 75 + 1515531 ATTTCCCT-CTGGACTTCAACA---GCCTCCGTGGCGCAATTGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGG s droEle2.KB458573 541342 75 - 5320397 ATTTCTCA-GCGAGTTCCAAGA---GCCTCCGTGGCGCAATTGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGG s droKik2.KB459527 294799 75 - 1234237 GCTGCCCG-ATGGATTCCAAGA---GCCTCCGTGGCGCAATCGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGG s droTak2.KB461535 160472 75 - 669855 TTTTCCCC-GAGAGTTTCAATA---GCCTCCGTGGCGCAATTGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGG s droRho2.KB449310 55904 75 - 65043 GTTTCGCA-ACGAAATCCAAGA---GCCTCCGTGGCGCAATTGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGG s droFic2.KB457177 97550 75 + 995874 ATTTTCCG-GCGACTTCCAAGA---GCCTCCGTGGCGCAATCGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGG s droPse3.chr3 1367308 76 - 19787792 ATTGTCGGTGCGTTTTTCAAGA---GCCTCCGTGGCGCAATTGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGG s droPer1.super_34 556151 76 - 916997 ATTGTCGGTGCGTTTTTCAAGA---GCCTCCGTGGCGCAATTGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGG s droMir2.chr3 1408346 76 - 20862834 ATTGTCGGCGCGTTTTTCAAGA---GCCTCCGTGGCGCAATTGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGG s droVir3.scaffold_12875 7374087 75 + 20611582 TTTGCCGC-TAGATTTTCAACC---GCCTCCGTGGCGCAATCGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGG s droMoj3.scaffold_6496 26168815 75 + 26866924 TTTTCCAC-GCGGCCCTCAGTT---GCCTCCGTGGCGCAATCGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGG s droGri2.scaffold_15245 924757 74 + 18325388 TTTTCGGC-T-GGCCGCCAACT---GCCTCCGTGGCGCAATTGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGG s musDom2.KB855869 36319 74 - 245279 ----CAGA-CACGACGCCAACATCTGCCTCCGTGGCGCAATTGGCTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGG s anoGam1.chr2L 9211308 65 + 48795086 -----------AAATTCATATC---GCCTTCGTGGCGCAATCGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGG s apiMel4.GL630491 12009 68 + 65118 --------cgacAGATCACGCG---GCCTCCGTGGCGCAATCGGCTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGG a score=471424.000000 s dm6.chr2R 24374116 31 + 25286936 TTCGAGTCCACCCGGGGGCGCAT---CTAACTTT s droSim1.chr2R 18712879 31 + 19596830 TTCGAGTCCACCCGGGGGCGCAT---CAAACttt s droSec1.super_23 132198 31 + 989336 TTCGAGTCCACCCGGGGGCGCAT---CAAACTTT s droYak3.chr2R 20222328 34 + 21139217 TTCGagtccacccgggggcgcatcaaagaaattt s droEre2.scaffold_4845 21619890 31 + 22589142 TTCGAGTCCACCCGGGGGCGCat---aaaaactt s droBia2.KB462602 814981 31 + 3129309 TTCGAGTCCACCCGGGGGCgctg---aaaatctt s droSuz1.KI419649 12064322 31 - 14502029 TTCGAGTCCACCCGGGGGCgctt---aaaatctt s droAna3.scaffold_13266 5724555 31 - 19884421 TTCGAGTCCACCCGGGGGCGGTT---CATCTTTT s droBip2.KB464407 1974367 29 + 2915140 TTCgagtccacccgggggcggct---c--ttttt s droEug2.KB465067 617406 31 + 1515531 TTCGAGTCCACCCGGGGGCGaag---caattttt s droEle2.KB458573 541417 31 - 5320397 TTCGAGTCCACCCGGGGGCGgca---caactttt s droKik2.KB459527 294874 31 - 1234237 TTCGAGTCCACCCGGGGGcgtat---caatattt s droTak2.KB461535 160547 31 - 669855 TTCGAGTCCACCCGGGGGCGCtt---caatactt s droRho2.KB449310 55979 31 - 65043 TTCGAGTCCACCCGGGGGcgaaa---caactttt s droFic2.KB457177 97625 31 + 995874 TTCGAGTCCACCCGGGGGcgtat---gatttttt s droPse3.chr3 1367384 31 - 19787792 TTCgagtccacccgggggcgcaT---ATAtctat s droPer1.super_34 556227 31 - 916997 TTCGAGTCCACCCGGGGGCGCAT---ATATCTAT s droMir2.chr3 1408422 31 - 20862834 TTCGAGTCCACCCGGGGGCGCAT---ATCtctat s droVir3.scaffold_12875 7374162 31 + 20611582 TTCGAGTCCACCCGGGGGCGAAT---Gaattttt s droMoj3.scaffold_6496 26168890 31 + 26866924 TTCGAGTCCACCCGGGGGCGAGA---CACttttt s droGri2.scaffold_15245 924831 31 + 18325388 TTCGAGTCCACCCGGGGGCGGAT---TACTTTTT s musDom2.KB855869 36393 31 - 245279 TTCGAGCCCACCCGGGGGCGCAT---TTCccttt s anoGam1.chr3L 4069868 31 + 41284009 TTGGCGTCGTCTAGGAATCGGAC---ATGTTTAT s apiMel4.GL630491 12077 29 + 65118 TTCGATCCCACCTGGGGGCGAAT---CGATTT-- a score=-12230.000000 s dm6.chr2R 24374147 12 + 25286936 T---TT------------TTTTTGTTT s droSim1.chr2R 18712910 12 + 19596830 t---tt------------ttgatttat s droSec1.super_23 132229 12 + 989336 T---TT------------TTGTTTAAT s droYak3.chr2R 20222362 24 + 21139217 t---ttttacttgttttgtttactttt s droEre2.scaffold_4845 21619921 12 + 22589142 t---tt------------tttaatttg s droBia2.KB462602 815012 12 + 3129309 t---tt------------ttctttttt s droSuz1.KI419649 12064353 12 - 14502029 t---tt------------ttctttttt s droAna3.scaffold_13266 5724586 15 - 19884421 T---TT--GCT-------TTTCttttt s droBip2.KB464407 1974396 15 + 2915140 t---tt--aat-------tttcttttt s droEug2.KB465067 617437 12 + 1515531 t---at------------tttttttat s droEle2.KB458573 541448 12 - 5320397 t---ta------------ttttatttt s droKik2.KB459527 294905 12 - 1234237 t---tt------------tcttattac s droTak2.KB461535 160578 12 - 669855 t---tt------------tttttttat s droRho2.KB449310 56010 12 - 65043 t---tt------------ttgtataac s droFic2.KB457177 97656 12 + 995874 t---ct------------tttttattt s droPse3.chr3 1367415 12 - 19787792 t---tt------------tcccatttt s droPer1.super_34 556258 12 - 916997 T---TT------------TCCCATTTT s droMir2.chr3 1408453 12 - 20862834 t---tt------------tcccatttt s droVir3.scaffold_12875 7374193 10 + 20611582 t---tt------------gttaatt-- s droMoj3.scaffold_6496 26168921 10 + 26866924 t---tt------------ttttttt-- s droGri2.scaffold_15245 924862 13 + 18325388 TGCGCT------------TTTATTA-- s musDom2.KB855869 37862 12 - 245279 t---tt------------ttttgttac s anoGam1.chr3L 4069899 12 + 41284009 -------------GTCGATTGATTT-- s apiMel4.GL630491 12106 12 + 65118 T---TT------------Gtacaatat a score=-4585.000000 s dm6.chr2R 24374159 1 + 25286936 A s droSim1.chr2R 18712922 1 + 19596830 t s droSec1.super_23 132241 1 + 989336 T s droYak3.chr2R 20222386 1 + 21139217 a s droEre2.scaffold_4845 21619933 1 + 22589142 a s droBia2.KB462602 815024 1 + 3129309 t s droSuz1.KI419649 12064365 1 - 14502029 t s droAna3.scaffold_13266 5724601 1 - 19884421 a s droBip2.KB464407 1974411 1 + 2915140 a s droEug2.KB465067 617449 1 + 1515531 t s droEle2.KB458573 541460 1 - 5320397 t s droKik2.KB459527 294917 1 - 1234237 t s droTak2.KB461535 160590 1 - 669855 t s droRho2.KB449310 56022 1 - 65043 c s droFic2.KB457177 97668 1 + 995874 a s droPse3.chr3 1367447 1 - 19787792 a s droPer1.super_34 556288 1 - 916997 A s musDom2.KB855869 37879 1 - 245279 A s apiMel4.GL630491 12118 1 + 65118 a a score=-225463.000000 s dm6.chr2R 24374160 15 + 25286936 A--------------------------AT---------------------AAATAGC--TTCTA-- s droSim1.chr2R 18712923 41 + 19596830 aatcaattaattattatatttattattat---------------------aaaCAGC--TTTTA-- s droSec1.super_23 132242 19 + 989336 A----------------------TAATAC---------------------AAGCAGC--TTCTA-- s droYak3.chr2R 20222387 19 + 21139217 a----------------------tttaat---------------------aaatagc--ttccc-- s droEre2.scaffold_4845 21619934 19 + 22589142 a----------------------tttaat---------------------aaataGC--TTCTC-- s droBia2.KB462602 815025 15 + 3129309 t--------------------------tt---------------------aaatggc--tttCT-- s droSuz1.KI419649 12064366 21 - 14502029 t--------------------tctttatt---------------------aaatagc--TTCCT-- s droAna3.scaffold_13266 5724602 27 - 19884421 t--------------ttaattttttattt---------------------taatGGC--TTCCC-- s droBip2.KB464407 1974412 30 + 2915140 t-----------ttattatttttttattt---------------------taatggc--ttCCT-- s droEug2.KB465067 617450 20 + 1515531 t---------------------actaatt---------------------AAATAGC--TTCCT-- s droEle2.KB458573 541461 32 - 5320397 c---------tttttttttatttattatc---------------------taaTAGC--TTCCT-- s droKik2.KB459527 294918 53 - 1234237 a---------tttcattttaaattttctttggtTAATAAGTAAATAGTCAAAATAGC--Ttcct-- s droTak2.KB461535 160591 16 - 669855 a-------------------------att---------------------aaatagc--ttcct-- s droRho2.KB449310 56023 30 - 65043 t-----------tttttttatacaatatt---------------------aaataGC--TTCCT-- s droFic2.KB457177 97669 12 + 995874 c----------------------ctctCT---------------------TAATA----------- s droPse3.chr3 1367454 16 - 19787792 ------------------------------ggc-----------------aaatggct-ttttt-- s droPer1.super_34 556295 16 - 916997 ------------------------------GGC-----------------AAATGGCT-TTTTT-- s droMir2.chr3 1410220 16 - 20862834 ------------------------------ggc-----------------aaatggct-ttttt-- s droVir3.scaffold_12875 7374203 7 + 20611582 ---------------------------------------------------------tattttt-- s droMoj3.scaffold_6496 26168931 7 + 26866924 ---------------------------------------------------------ttttttt-- s droGri2.scaffold_15245 924875 7 + 18325388 ---------------------------------------------------------TATTTTT-- s musDom2.KB855869 37880 27 - 245279 --------------CGTAAATTTTGCAAG---------------------CAGAAAC--TTCAC-- s anoGam1.chr3L 4069912 15 + 41284009 --------------------------AAT---------------------GAAGAGC--TTCAG-- s apiMel4.GL630491 12119 15 + 65118 -------------------------------------------------aaagaaga--tcTCTTA a score=28194.000000 s dm6.chr2R 24374175 27 + 25286936 TA--------------------------ATGTTTTT-AGTTCAT---AAAGCT-TTTG s droSim1.chr2R 18712964 27 + 19596830 TA--------------------------ATGTTTTT-TGTTCAT---AATTCC-TTTG s droSec1.super_23 132261 27 + 989336 TA--------------------------ATGTTTTT-GGTTCAT---AAAGCT-TTTG s droYak3.chr2R 20222406 28 + 21139217 ta--------------------------atgtttttGGGTTCAT---aaagct-ttta s droEre2.scaffold_4845 21619953 26 + 22589142 TA--------------------------ATGTCGTT-GGTTCAT----GAGCT-TTTG s droBia2.KB462602 815040 27 + 3129309 TA--------------------------ATGTTTCG-CGTTagt---aaaact-ttta s droSuz1.KI419649 12064387 27 - 14502029 TA--------------------------ATGTTTTG-Ggttaat---aaaact-ttta s droAna3.scaffold_13266 5724629 25 - 19884421 TA--------------------------GTGTGT---ACTCGAT---TATTGT-TGAA s droBip2.KB464407 1974442 25 + 2915140 TA--------------------------GTGCAC---ACTCAAT---TACTCT-TAAA s droEug2.KB465067 617470 27 + 1515531 TA--------------------------ATGTTTTT-gcttaat---aaaact-ttta s droEle2.KB458573 541493 27 - 5320397 TA--------------------------GTgctttt-tgttaat---aaaact-tata s droKik2.KB459527 294971 27 - 1234237 ta--------------------------atgttttt-tattaat---aaaact-cata s droTak2.KB461535 160607 27 - 669855 ta--------------------------atgttttt-ggttatt---aaaact-ttta s droRho2.KB449310 56053 28 - 65043 TA--------------------------ATGTTTTGCTGttaat---aaaact-tata s droFic2.KB457177 97681 26 + 995874 -A--------------------------GCATTTCT-CGTTAAT---AAAACt-cata s droPse3.chr3 1367470 28 - 19787792 ta--------------------------atgttttc-ttaaaat---atatttatttg s droPer1.super_34 556311 28 - 916997 TA--------------------------ATGTTTTC-TTAAAAT---ATATTTATTTG s droMir2.chr3 1410236 28 - 20862834 ta--------------------------atgttttc-ttaaaat---atatttatttg s droVir3.scaffold_12875 7374210 22 + 20611582 tt--------------------------atGTGCTC------AT---AAATAT-TTTG s droMoj3.scaffold_6496 26168938 48 + 26866924 tttATAAATTGCTTGCAATAAACATTTAAAGTCATC------AT---Gaaatt-ttta s droGri2.scaffold_15245 924882 22 + 18325388 CG--------------------------TAATTATT------AA---ATACAT-TTAA s musDom2.KB855869 37907 29 - 245279 CA--------------------------TCGTATTG-TATATATTCTAAAGCT-TTG- s anoGam1.chr3L 4069927 27 + 41284009 TT--------------------------ATTTGCCT-TTTTCAT---AAAATT-TGTA s apiMel4.Group5 12256257 27 + 14363272 ta--------------------------atgtATTC-TTCCAAT---TAAACG-TCAT a score=112821.000000 s dm6.chr2R 24374202 16 + 25286936 ----CTTATT-GC------TT--TTGTGC s droSim1.chr2R 18712991 16 + 19596830 ----TTTATT-GA------TT--TTGTGT s droSec1.super_23 132288 16 + 989336 ----TTTATT-GA------TT--TTGTGT s droYak3.chr2R 20222434 16 + 21139217 ----tttatt-gc------tt--ttgtGT s droEre2.scaffold_4845 21619979 16 + 22589142 ----TTTATT-GC------TT--TTGTGC s droBia2.KB462602 815067 16 + 3129309 ----tttatt-gc------tt--ttgtGT s droSuz1.KI419649 12064414 16 - 14502029 ----tttatt-gc------tt--ttgTGT s droAna3.scaffold_13266 5724654 16 - 19884421 ----ATTATT-AG------CT--TTGTGT s droBip2.KB464407 1974467 16 + 2915140 ----ATTGGT-AG------TT--TTGTGT s droEug2.KB465067 617497 16 + 1515531 ----tttatt-ac------tt--ttgcGT s droEle2.KB458573 541520 16 - 5320397 ----tttatt-ac------tt--ttgtgt s droKik2.KB459527 294998 17 - 1234237 ----tttattagt------tt--ttgtgt s droTak2.KB461535 160634 16 - 669855 ----tttatt-ac------tt--ttgtgT s droRho2.KB449310 56081 16 - 65043 ----tttatt-ac------cT--TTGTGT s droFic2.KB457177 97707 16 + 995874 ----tttatt-ac------tt--ttgtgt s droPse3.chr3 1367498 18 - 19787792 ----tttatt-cg------tTTATTGTGT s droPer1.super_34 556339 18 - 916997 ----TTTATT-CG------TTTATTGTGT s droMir2.chr3 1410264 18 - 20862834 ----tttatt-cg------tttattgtgt s droMoj3.scaffold_6496 26168991 15 + 26866924 ----tttaat-aa-------t--tattat s droGri2.scaffold_15245 924910 16 + 18325388 ----CTAAGT-GA------CT--CAGCGC s musDom2.KB855869 37936 22 - 245279 ----CTTATC-GCAAAAAgct--ttattt s anoGam1.chr3L 4069958 14 + 41284009 ----CTGAGC-AT------TT--AAGT-- s apiMel4.Group5 12256284 20 + 14363272 ACGATACAAT-ga------tt--atttgc a score=56013.000000 s dm6.chr2R 24374218 6 + 25286936 GACGAA----- s droSim1.chr2R 18713007 6 + 19596830 GGCGAA----- s droSec1.super_23 132304 6 + 989336 GGCGAA----- s droYak3.chr2R 20222450 6 + 21139217 GGCGAA----- s droEre2.scaffold_4845 21619995 6 + 22589142 GGCGAA----- s droBia2.KB462602 815083 6 + 3129309 GGCGAA----- s droSuz1.KI419649 12064430 6 - 14502029 GGCGAA----- s droAna3.scaffold_13266 5724670 6 - 19884421 GTCGAA----- s droBip2.KB464407 1974483 6 + 2915140 GCCgaa----- s droEug2.KB465067 617513 6 + 1515531 CGCGAA----- s droEle2.KB458573 541536 6 - 5320397 ggcgaa----- s droKik2.KB459527 295015 6 - 1234237 TGCGAA----- s droTak2.KB461535 160650 6 - 669855 GGCGAA----- s droRho2.KB449310 56097 6 - 65043 GGCGAA----- s droFic2.KB457177 97723 6 + 995874 tgcgaa----- s droPse3.chr3 1367516 6 - 19787792 AGCGAA----- s droPer1.super_34 556357 6 - 916997 AGCGAA----- s droMir2.chr3 1410282 6 - 20862834 agcgaa----- s musDom2.KB855869 37958 6 - 245279 gaagaa----- s anoGam1.chr3L 4069972 5 + 41284009 -TCGAT----- s apiMel4.Group5 12256304 6 + 14363272 -----atttat a score=20255.000000 s dm6.chr2R 24374224 2 + 25286936 TC- s droSim1.chr2R 18713013 2 + 19596830 TT- s droSec1.super_23 132310 2 + 989336 TT- s droYak3.chr2R 20222456 2 + 21139217 TT- s droEre2.scaffold_4845 21620001 2 + 22589142 TT- s droBia2.KB462602 815089 2 + 3129309 TT- s droSuz1.KI419649 12064436 2 - 14502029 TT- s droAna3.scaffold_13266 5724676 2 - 19884421 TT- s droBip2.KB464407 1974489 2 + 2915140 tt- s droEug2.KB465067 617519 2 + 1515531 TT- s droEle2.KB458573 541542 2 - 5320397 tt- s droKik2.KB459527 295021 2 - 1234237 TT- s droTak2.KB461535 160656 2 - 669855 TT- s droRho2.KB449310 56103 2 - 65043 TT- s droFic2.KB457177 97729 2 + 995874 tt- s droPse3.chr3 1367522 2 - 19787792 TT- s droPer1.super_34 556363 2 - 916997 TT- s droMir2.chr3 1410288 2 - 20862834 tt- s droMoj3.scaffold_6496 26169010 2 + 26866924 tt- s anoGam1.chr3L 4069978 2 + 41284009 CC- s apiMel4.Group5 12256310 2 + 14363272 -ta a score=136133.000000 s dm6.chr2R 24374226 40 + 25286936 T---AAAGTGTGCAATTA-GTGAAGGGAAATCGCACA-CGC---TATG s droSim1.chr2R 18713015 40 + 19596830 T---AAAGTGCGCAATTA-GTGAAGGGAAATCGCACA-CGC---TATG s droSec1.super_23 132312 40 + 989336 T---AAAGTGCGCAATTA-GTGAAGGGAAATCGCACA-CGC---TATG s droYak3.chr2R 20222458 40 + 21139217 C---AAAGTGTGCAATTA-GTAAAAGGAAATTGCACA-CGC---TGCG s droEre2.scaffold_4845 21620003 40 + 22589142 T---AAAGTGTGCAATTA-GTAAAGGGAAATCGCACA-CGC---CATG s droBia2.KB462602 815091 39 + 3129309 T---TAATTGGGAAATTA-CCAAAGGGAAATCGC-CT-CGC---TGTG s droSuz1.KI419649 12064438 40 - 14502029 T---TAATTGTGAAATTA-CTAAAGGGAAATCGCACA-CGT---TGTG s droAna3.scaffold_13266 5724678 37 - 19884421 C---TAATGGCAAA---A-ATTAAGTGAAATCGCTGA-GGT---TGTG s droBip2.KB464407 1974491 37 + 2915140 t---taatggaaaa---a-attaagtGAAATCGCTGA-CAT---TGTG s droEug2.KB465067 617521 40 + 1515531 T---TAATTGTGCAATTA-CTAAGGTGAAATCGCACA-CGC---CTTG s droEle2.KB458573 541544 40 - 5320397 t---taattgtttgatta-cTGAAGTGAAATTGCAAA-CGC---TTTG s droKik2.KB459527 295023 41 - 1234237 T---TAATGGTACAATTA-ACAAAGTGAAATCGCAAATCGC---TTTG s droTak2.KB461535 160658 40 - 669855 T---TAATTGTGCAATTA-CCACAGTGAAATCGCACT-CGC---TCTG s droRho2.KB449310 56105 40 - 65043 T---TAATTGTTCAATTA-CCGAATTGAAATCACACA-CGC---TTTG s droFic2.KB457177 97731 40 + 995874 t---aaattgcataatta-tCGCAGAAGAATCGCAAA-CAT---AATG s droPse3.chr3 1367524 39 - 19787792 T---CAATGATGTGTTTA-ACAAAGTGAAATCGTCTG-TTT---TGT- s droPer1.super_34 556365 39 - 916997 T---TAATGATGTGTTTA-ACAAAGTGAAATCGTCTG-TTT---TGT- s droMir2.chr3 1410290 39 - 20862834 t---taatGATGTGTTTA-ACAAAGTGAAATCGTCTG-TTG---TGT- s droMoj3.scaffold_6496 26169012 38 + 26866924 tgtataaatatGCACTTC-ATAAGGGAA-----CTCA-AGT---CTTC s musDom2.KB854189 397268 44 - 956917 t---taagtgttTAGGTAGGTTTAGGGAAATAATACA-AGGGAATATA s anoGam1.chr3L 4069983 33 + 41284009 T---GTATTGCATTCTTG-C-------AAACATTTTA-CTC---GACT s apiMel4.Group5 12256312 38 + 14363272 t---aaattttataa--a-ttttaacagattCTCATT-CGA---TATG a score=-207181.000000 s dm6.chr2R 24374266 71 + 25286936 GGAGGTCTG-----------CAAATGAATTC---CGTGAAC--A---------CAGAATAT------------------------TTTAGGCACC-TACGTATGT-AGAAAGAACGACG--ACA s droSim1.chr2R 18713055 71 + 19596830 GGAGGTCTG-----------CAAATGAATTC---CGTGAGC--A---------CAGAATAC------------------------ATTAGGCACC-TACATATGT-AGGAAGAACGACG--ACG s droSec1.super_23 132352 71 + 989336 GGAGGTCTG-----------CAAATGAATTC---CGTGAGC--A---------CAGAATAC------------------------ATTAGGCACC-TACACATGT-AGGAAGAACGACG--ACG s droYak3.chr2R 20222498 55 + 21139217 GGAGGTCTG-----------AA------------CACAGAC--A---------CAGCATTT------------------------ATTGGGCAAC---------T-GAAAAGAACGACGA-ACG s droEre2.scaffold_4845 21620043 60 + 22589142 GGAGGTCTG-----------CGAATGTGTTC---CGCGAAC--A---------CAGAATAT------------------------ATTGGGCAAT---------T-AGAGAGAACG-----ACG s droBia2.KB462602 815130 57 + 3129309 GGAGGTCTG----------TTACTTAAGTTC---CGCCAAT--A---------GAAAACGG------------------------ATTAGA-------------T-GGGGGGAAGA-----ACA s droSuz1.KI419649 12064478 57 - 14502029 GGAGGTCTG-----------TAATTAAGTTC---CCTCGAC--A---------AAGAAAAG------------------------ATTAGA-------------TAAGGGGGAAGA-----ACA s droAna3.scaffold_13266 5724715 64 - 19884421 GGAGGTCTG----------TCAATTAAAATC---CCCACACAGAG-----AGTCAGTAGCG------------------------ATTAGATAAG---------T-CGGAAGA--------AGA s droBip2.KB464407 1974528 62 + 2915140 GGAGGTCTG----------TCAATTAAATTC---CCCGCAC--AG-----AGTCAGAGGCG------------------------ATTAGATAAG---------T-CGGAAGA--------AGA s droEug2.KB465067 617561 59 + 1515531 GGAGGTCTG----------CGAAATAAATTC---TGCCAAC--A---------GCAAATAG------------------------ATTAGA-------------T-AAGCAGATAAGC---AGC s droEle2.KB458573 541584 46 - 5320397 GGAGGTCTG----------TAAATTAACTGT---CGTCAAG--A---------AAGAATAG------------------------ATtaga-------------t-a--------------a-- s droKik2.KB459527 295064 46 - 1234237 GGAGGTCTT-----------GAA------------GCTCGT--A---------AAGAATTG------------------------ATTAGATAAG---------T-CGGAaga--------a-- s droTak2.KB461535 160698 37 - 669855 GGAGGTCTT-----------TAAATAAAGTT---CGAACAG--G------------------------------------------------------------T-TCGAA----------ACA s droRho2.KB449310 56145 69 - 65043 GGAGGTCCG----------CAAATTTACTGC---TGTGAGG--AACGAATAGATAGAATAG------------------------ATTAGATAAA---------T-AGGAAGAGT------AGT s droFic2.KB457177 97771 52 + 995874 GGTGGTCCG----------TGTATTTGGTTT---cggcaat--a---------aaaaacag------------------------attAGATAAG---------T-AGG------------A-- s droPse3.chr3 1367563 55 - 19787792 ---GGTCTG-----------TAATTAAATCCGAAAGGTGGT--A---------GGGGCTAG------------------------ATAAGATAAA---------T-AGGAA----------ATA s droPer1.super_34 556404 55 - 916997 ---GGTCTG-----------TAATTAAATCCGAAAGGTGGT--A---------GGGGCTAG------------------------ATAAGATAAA---------T-AGGAA----------ATA s droMir2.chr3 1410329 55 - 20862834 ---GGTCTG-----------TAATTAAATACGAAAGGTGGT--A---------GGGGCTAG------------------------ATAAGATAAA---------T-AGGAA----------ATA s droMoj3.scaffold_6496 26169050 68 + 26866924 TCATATGTG-----------TATATCTCTAA---TATAAAC--A---------TGGAAAAGTATACAATTATCATCTAGACTAAAATAAGACA------------------------------- s musDom2.KB854189 397312 67 - 956917 AAAAGTCTCAGCGGACAGTTCTTATTGATTA---TGTCAag--a---------atggatat------------------------tttaaagaag-aacaa---t-aaaa-------------- s anoGam1.chr3L 4070016 76 + 41284009 CAATATGCG-----------CTCTTAAATCT---CCCAAAC--A---------CATATTAT--------------------CTACCTTATTTAAACTTCAAGTGT-GGCCACACTAACGCTA-- a score=-178.000000 s dm6.chr2R 24374337 2 + 25286936 AA- s droSim1.chr2R 18713126 2 + 19596830 AA- s droSec1.super_23 132423 2 + 989336 AA- s droYak3.chr2R 20222553 2 + 21139217 AA- s droEre2.scaffold_4845 21620103 2 + 22589142 AA- s droBia2.KB462602 815187 2 + 3129309 AG- s droSuz1.KI419649 12064535 2 - 14502029 AG- s droAna3.scaffold_13266 5724779 2 - 19884421 CA- s droBip2.KB464407 1974590 2 + 2915140 CA- s droEug2.KB465067 617620 2 + 1515531 AG- s droTak2.KB461535 160735 2 - 669855 GG- s droRho2.KB449310 56214 2 - 65043 TA- s droPse3.chr3 1367618 2 - 19787792 AA- s droPer1.super_34 556459 2 - 916997 AA- s droMir2.chr3 1410384 2 - 20862834 AA- s musDom2.KB854189 397379 2 - 956917 aa- s anoGam1.chr3L 4070092 2 + 41284009 -AC a score=17588.000000 s dm6.chr2R 24374339 13 + 25286936 CAGACGTATAATT s droSim1.chr2R 18713128 13 + 19596830 CAGACGTATAATT s droSec1.super_23 132425 13 + 989336 CAGACGTATAATT s droYak3.chr2R 20222555 13 + 21139217 CAGGCgtataatt s droEre2.scaffold_4845 21620105 13 + 22589142 CAGTCGTATAATT s droBia2.KB462602 815189 13 + 3129309 CGCAGGTataatt s droSuz1.KI419649 12064537 13 - 14502029 CGCACaaataatt s droAna3.scaffold_13266 5724781 13 - 19884421 TATTCCACTAATT s droBip2.KB464407 1974592 13 + 2915140 TATTCCACTAATT s droEug2.KB465067 617622 12 + 1515531 GGAACATATAGT- s droEle2.KB458573 541630 10 - 5320397 ---acatttaatt s droKik2.KB459527 295110 7 - 1234237 ------tataatt s droTak2.KB461535 160737 13 - 669855 CGAAcatataatt s droRho2.KB449310 56216 13 - 65043 CAAACCAATAATT s droPse3.chr3 1367620 7 - 19787792 C------ATCAAT s droPer1.super_34 556461 7 - 916997 C------ATCAAT s droMir2.chr3 1410386 7 - 20862834 C------ATCAAT s anoGam1.chr3L 4070094 13 + 41284009 AAAACGCATCATT a score=19266.000000 s dm6.chr2R 24374352 48 + 25286936 TGA-TTTTTATTGAGCGAT--------------------------------AGCA---------GAGCCATTA-------CC------AGGAT-TATTTCAAGC s droSim1.chr2R 18713141 48 + 19596830 TGA-TTTTTATTGAGCGAT--------------------------------AGCA---------GAGCCATTA-------CC------AGGAT-TATTTCAAGC s droSec1.super_23 132438 48 + 989336 TGA-TTTTTATTGAGCGAT--------------------------------AGCA---------GAGCCATTA-------CC------AGGAT-TATTTCAAAC s droYak3.chr2R 20222568 48 + 21139217 tga-tttttattgagCGAT--------------------------------AGCA---------GCGCCATTA-------CC------AGGAT-TATTTCAAGC s droEre2.scaffold_4845 21620118 48 + 22589142 TGA-TTTTTATTGAGCGAT--------------------------------AGCA---------GCGCCATTA-------CC------AGGAT-TATTTCAGGC s droBia2.KB462602 815202 48 + 3129309 gga-tttttattgaGCTGT--------------------------------AGCA---------GGGCTATTA-------CG------GGAAT-TATTTCCCGC s droSuz1.KI419649 12064550 48 - 14502029 gga-tttttattgAGCGCT--------------------------------AGCA---------GGGCTATTA-------CC------AGAAT-TATTTCCCTC s droAna3.scaffold_13266 5724794 81 - 19884421 GGA-ATTCGATTGTTTGTTTTTGCAGATAAAAATGATTTGTGGACGGGCCGGACA---------GGGCTCAGA-------CC------AGATCATCTTTATGGC s droBip2.KB464407 1974605 87 + 2915140 GGA-ATTcgattgtttgtttttgcagaTAAAGATGATATATGGACGGGCC-GACA---------GGGCTCTGACTTGGTGCC------AGATCATCTTTATGGC s droEug2.KB465067 617634 44 + 1515531 -----TTTTATTGAGAGAT--------------------------------TGCA---------GGGCTATTA-------CC------AGAAT-TATTTCAAGC s droEle2.KB458573 541640 56 - 5320397 tga-ttattaatggtaaat--------------------------------aaaa-------atgagctATAA-------GCCAATGTAGGTT-TATTTAAGGC s droKik2.KB459527 295117 58 - 1234237 tgattttttataggaAGAT--------------------------------ATAAATGATTTATAGGCTCGGG-------AA------GGCAG-GCAAGCAGGC s droTak2.KB461535 160750 48 - 669855 tga-tttttattgagcGAT--------------------------------AGCA---------GGGCTATAA-------TC------AGGAT-TGCTTCCCGC s droRho2.KB449310 56229 48 - 65043 Agc-tttttattgataaat--------------------------------gaAT-------ATTAGTCATAA-------GC--------TAC-TGTTTAGGGC s droFic2.KB457177 97823 49 + 995874 -GG-TTTTTATCGGGGGAT--------------------------------AAAT-------ATGAGGTACTA-------CA------CGGAT-AATTGCCAGC s droPse3.chr3 1367627 48 - 19787792 TGA-TACAAACTACTGATT--------------------------------TATG---------AGATCGTTG-------GG------TGGGT-TTATTGATTC s droPer1.super_34 556468 48 - 916997 TGA-TACAAACTACTGATT--------------------------------TATG---------AGATCGTTG-------GG------TGGGT-TTATTGGTTC s droMir2.chr3 1410393 48 - 20862834 TGA-TATAAACTACTGATT--------------------------------TATG---------AGATCGTTG-------GG------TGGGT-TTATTGATTC a score=-57037.000000 s dm6.chr2R 24374400 23 + 25286936 --CTTATATG----TACGTGTGTGCTGCA-- s droSim1.chr2R 18713189 23 + 19596830 --CTTATACG----TACGTGTGTGCTGTG-- s droSec1.super_23 132486 23 + 989336 --CTTATACG----TACGTGTGTGCTGTG-- s droYak3.chr2R 20222616 19 + 21139217 --CTTA--------TACGTGTGTGCTTCA-- s droEre2.scaffold_4845 21620166 19 + 22589142 --CTTA--------TACGTGTGTGCTTCA-- s droBia2.KB462602 815250 19 + 3129309 --TCTA--------TAAGTGAGTGCTTAA-- s droSuz1.KI419649 12064598 19 - 14502029 --CTTA--------TAAGTGTGCGCTTAA-- s droAna3.scaffold_13266 5724875 7 - 19884421 --CATA--------------------TTA-- s droBip2.KB464407 1974692 7 + 2915140 --CATA--------------------TTT-- s droEug2.KB465067 617678 18 + 1515531 --CTTT--------TACGCGTG-GCTCAA-- s droEle2.KB458573 541696 7 - 5320397 --CCTA--------------------TAA-- s droKik2.KB459527 295175 19 - 1234237 --CACA--------GTGATTAGCTCACTA-- s droTak2.KB461535 160798 19 - 669855 --CTTA--------TATGTGTGCTTTTAA-- s droRho2.KB449310 56277 17 - 65043 --CTTA----------TATGTGTGTTTAA-- s droFic2.KB457177 97872 17 + 995874 --CTTA----------TACGTTCGCCTTA-- s droPse3.chr3 1367675 27 - 19787792 --CTTCCGTTTGACTTTGATTGTTGCCAA-- s droPer1.super_34 556516 27 - 916997 --CTTCCGTTTGACTTTGATTGTTGCCAA-- s droMir2.chr3 1410441 27 - 20862834 --CTTCCGTTTGACTTTGATTGTTACCAA-- s droMoj3.scaffold_6496 26169192 23 + 26866924 CTCATA--------TCTAATTACAATCTATT a score=28709.000000 s dm6.chr2R 24374423 5 + 25286936 GATGC s droSim1.chr2R 18713212 5 + 19596830 GATGC s droSec1.super_23 132509 5 + 989336 GATGC s droYak3.chr2R 20222635 5 + 21139217 GCCGC s droEre2.scaffold_4845 21620185 5 + 22589142 GACGC s droBia2.KB462602 815269 5 + 3129309 AATGC s droSuz1.KI419649 12064617 5 - 14502029 AATGC s droAna3.scaffold_13266 5724882 5 - 19884421 AATGC s droBip2.KB464407 1974699 5 + 2915140 AATGC s droEug2.KB465067 617696 5 + 1515531 ACTGC s droEle2.KB458573 541703 5 - 5320397 AATGC s droKik2.KB459527 295194 5 - 1234237 TATAG s droTak2.KB461535 160817 5 - 669855 AATGC s droRho2.KB449310 56294 5 - 65043 AATGC s droFic2.KB457177 97889 5 + 995874 AATAC s droPse3.chr3 1367702 5 - 19787792 GCGGC s droPer1.super_34 556543 5 - 916997 GCGGC s droMir2.chr3 1410468 5 - 20862834 GCGGC s droMoj3.scaffold_6496 26169215 3 + 26866924 --CAC s droGri2.scaffold_15245 925388 5 + 18325388 GTTGC a score=34454.000000 s dm6.chr2R 24374428 5 + 25286936 AAGCC s droSim1.chr2R 18713217 5 + 19596830 AAGCC s droSec1.super_23 132514 5 + 989336 AAGCC s droYak3.chr2R 20222640 5 + 21139217 AAGCC s droEre2.scaffold_4845 21620190 5 + 22589142 AAGCC s droBia2.KB462602 815274 5 + 3129309 AAGCT s droSuz1.KI419649 12064622 5 - 14502029 AAGCT s droAna3.scaffold_13266 5724887 5 - 19884421 AAACT s droBip2.KB464407 1974704 5 + 2915140 TAACT s droEug2.KB465067 617701 5 + 1515531 AAGCT s droEle2.KB458573 541708 5 - 5320397 AAGCT s droKik2.KB459527 295199 5 - 1234237 GGGCT s droTak2.KB461535 160822 5 - 669855 AAGCT s droRho2.KB449310 56299 5 - 65043 AAGCC s droFic2.KB457177 97894 5 + 995874 AAGCC s droPse3.chr3 1367707 5 - 19787792 CTGGC s droPer1.super_34 556548 5 - 916997 CTGGC s droMir2.chr3 1410473 5 - 20862834 CTGGC s droVir3.scaffold_12875 7374646 5 + 20611582 AAGCT s droMoj3.scaffold_6496 26169221 5 + 26866924 AAGCT s droGri2.scaffold_15245 925393 5 + 18325388 GAGCG a score=415150.000000 s dm6.chr2R 24374433 51 + 25286936 TGGGCACA---ATGTAACCTTT--ACATGAG-CAGCTCCACTTTCAGCCGCCTTCTG s droSim1.chr2R 18713222 51 + 19596830 TGGGCACA---ATGTAACCTTT--ACATGAG-CAGCTCCACTTTCAGCCGCCTTCTG s droSec1.super_23 132519 51 + 989336 TGGGCACA---ATGTAACCTTT--ACATGAG-CAGCTCCACTTTCAGCCGCCTTCTG s droYak3.chr2R 20222645 51 + 21139217 TGGGCACA---ATGTAACCTTT--ACATGAG-CAGCTCCACTTTCAGCCGCCTTCTG s droEre2.scaffold_4845 21620195 50 + 22589142 TGGGCACA---ATGTAACCTTT--ACATGAG-CAGCTCCACTTTCAGCCGCCTTCT- s droBia2.KB462602 815279 51 + 3129309 TGGGCAAA---AGGTAACCTTT--ACATGAG-CAGCTCCACTTTCAGCTGCCTTGCA s droSuz1.KI419649 12064627 51 - 14502029 TGGGCATA---ATGTAACCTTT--ACATGAG-CAGCTCCACTTTCCGCTGCCTTGCA s droAna3.scaffold_13266 5724892 52 - 19884421 TGGTCTTATAGCAGTAACCTTT--ACATGAG-CAGCTCCACTTTCAGCCAG--TCTA s droBip2.KB464407 1974709 48 + 2915140 TGGTCGTATAGTAGTAACCTTT--ACATGAG-CAGCTCCACTTTCAGCCAG------ s droEug2.KB465067 617706 51 + 1515531 TGGGCACA---ATGTAATCTTT--ACATGAG-CAGCTCCCCTTTCAGCTGCCTTCTA s droEle2.KB458573 541713 51 - 5320397 TGAGCACA---ATTTAACCTTT--ACACGAG-CAGCTCCACTTTCAGCTGCCTTCTA s droKik2.KB459527 295204 46 - 1234237 TGG--------CTGTAACCTTT--ACATGAG-CAGCTCCACTTTCAGCCGGCTTCGG s droTak2.KB461535 160827 51 - 669855 TGGGCACA---ATGTAACCTTT--ACATGAG-CAGCTCCACTTTCAGCTGCCTGCGG s droRho2.KB449310 56304 51 - 65043 TGGGCACA---ATGTAACCTTT--ACATGAG-CAGCTCCACTTTCAGCTgcctttta s droFic2.KB457177 97899 51 + 995874 TGGGCACA---ATGTAACCTTT--ACATGAA-CAGCTCCGCTTTCAGCTGCCTTCta s droPse3.chr3 1367712 42 - 19787792 CTGTCACT---CTGTAACCTCC--GCACGAG-CAGCTCCACTTTCAGC--------- s droPer1.super_34 556553 51 - 916997 CTGTCACT---CTGTAACCTCC--GCACGAG-CAGCTCCACTTTCAGCCCTCTCTCT s droMir2.chr3 1410478 42 - 20862834 CTGTCACT---CTGTAACCTCC--GCACGAG-CAGCTCCACTTTCAGC--------- s droWil2.CH963894 1338247 42 + 2843958 TGGTGACT---GTGTAACCTTT--GCATGAG-CAGCTCATCTTTCAAC--------- s droVir3.scaffold_12875 7374651 51 + 20611582 CATTCGCT---TTTTAACTCTTA-AGACGAT-CAGCAATGCATGCAG-AGGTCTTCG s droMoj3.scaffold_6496 26169226 49 + 26866924 CATACGCT---TTTTAACTCTTA-ACACGAT-CAGCAATGCGTGC---AGGTCTTTG s droGri2.scaffold_15245 925398 49 + 18325388 TAACAAC-----AGTAACAGTTGCAGGCGTTGCAGCAGT---TGCAATAGTTACTTA a score=1593645.000000 s dm6.chr2R 24374484 206 + 25286936 -------------------GTGTTGTCACCGG-------------TTTTTTCGCATCTGCT-------TGCTGC--AAC----TG---AAAA--C-CACGAGCGTAACAACA--GTTGCA-------CATGCA------------C--ATGTTGGT--GTCGCCAGCA---------------------------ACGTG-----GCCAAGTGTATCATGGC-------AACTTGGAGACAGTT---------------------TGTCGTC-GCT---GGT------------------------TTTGCTAATTAAAATGTCTTGGTGCTGTCACTCAAAAGG----CGGTCGC--------CTGATCCACTGGCCAagt--- s droSim1.chr2R 18713273 203 + 19596830 -------------------GTGTTGTCACCGG-------------TTTTTTCGCATCTGCT-------TGCTGC--AAC----TG---AAAA--C-CACGAGCGTAACAACA--GTTGCA-------CATGCA------------C--ATGCTGGT--GTCGCCAGCA---------------------------ACGTG-----GCCAAGTGTATCATGGC-------AACTTGGAGACAGTT---------------------TGTCGTC-GCT---GGT------------------------TTTGCTAATTAAAATGTCTTGGTGCTGTCACTCAAAAGG----CGGTCGC--------CTGATCCACTGGCCA------ s droSec1.super_23 132570 203 + 989336 -------------------GTGTTGTCACCGG-------------TTTTTTCGCATCTGCT-------TGCTGC--AAC----TG---AAAA--C-CACGAGCGTAACAACA--GTTGCA-------CATGCA------------C--ATGCTGGT--GTCGCCAGCA---------------------------ACGTG-----GCCAAGTGTATCATGGC-------AACTTGGAGACAGTT---------------------TGTCGTC-GCT---GGT------------------------TTTGCTAATTAAAATGTCTTGGTGCTGTCACTCAAAAGG----CGGTCGC--------CTGATCCACTGGCCA------ s droYak3.chr2R 20222696 223 + 21139217 -------------------GTTTGCTCaccgg---------ttttttttttcgcctctGCT-------TGCTGC--AACTGGATG---AAAA--C-CACGAGCGTAACAACA--GTTGCA-------CATGCAACATGCACATGGT--GTGTTGGT--GTCGCCAGCA---------------------------ACGTG-----GCCAAGTGTATCATGGC-------AACTTGGAGACAGTT---------------------TGTCGTC-GCT---GGT------------------------TTTGCTAATTAAAATGTCTTGGTGCTGTCACTCAAAAGG----CGGTCGC--------CTGATCCACTGGCca------ s droEre2.scaffold_4845 21620245 201 + 22589142 -------------------GTTGGCCCACCGG-------------TTTTTTCGCATCTCC---------GCTGC--AAC----TT---AAAA--C-CACGAGCGTAACAACA--GTTGCA-------CATGCA------------C--ATGTTGGT--GTCGCCAGCA---------------------------ACGTG-----GCCAAGTGTATCATGGC-------AACTTGGAGACAGTT---------------------TGTCGTC-GCT---GGC------------------------TCTGCTAATTAAAATGTCTTGGTGCTGTCACTCAAAAGG----CGGTCGC--------CTGATCCACTGGCCA------ s droBia2.KB462602 815330 185 + 3129309 -------------------GTTTTTCCCCCAG-----------CCTTTTTACGCATCTGC----------------AAC----TG---AAAA--C-CGCGAGCGTAACAACA--GTTGCA-------CATGCA------------C--ATGC----------------------------------------------TG-----GCCAAGTGTATCATGGC-------AACTTGGAGACAGTT---------------------TGTCGTC-GTT---GGT------------------------tttgctaattaaaatgtcttGGTGCTGTCACTCAAAAGGCGGTCGGTCGC--------CTGATCCACTGGCCA------ s droSuz1.KI419649 12064678 182 - 14502029 -------------------ATTTTTCCACTAG----------TCtttttttCGCATCTGC----------------AAC----AG---AAAA--C-CGCGAGCGTAACAACA--GTTGCA-------CATGCA------------C--ATGC----------------------------------------------TG-----GCCAAGTATATCATGGC-------AACTTGGAGACAGTT---------------------TGTCGTC-GTT---GGT------------------------TTTGCTAATTAAAATGTCTTGGTGCTGTCACTCAAAAGG----CGGTCGC--------CTGATCCACTGGCCA------ s droAna3.scaffold_13266 5724944 207 - 19884421 -------------------GTGCCTCCTCCTC-----CTCCTTGTTTTTTTTGCAGCTTTT------GTGGTGC--AAC----TG---AAAA--C-CGCGAGCGTAACAACA--GTTGCC-------GCTGCT------------G--CTGCTG----GTAGTTGGTA---------------------------GTGCG-----G-CAAGTGTATCATGGC-------AACTTGGAGACAGTT---------------------TGTCGTC-GCT---GGT------------------------CTTGCTAATTAAAATGTCTTGGTGCTGTCACTCAAAAGG----CGGTCGT--------CCGG-CCGCT-GCCA------ s droBip2.KB464407 1974757 198 + 2915140 -------------------ATGcctcctcct----------ttttttttgtggcagcttTT------GTGGTGC--AAC----TG---AAAA--C-CGCGAGCGTAACAACA--GTTGCA-------CATGTT------------G--CAGC--------GGCCGGTA---------------------------GTGCG-----G-CAAGTGTATCATGGC-------AACTTGGAGACAGTT---------------------TGTCGTC-GCT---GGT------------------------CTTGCTAATTAAAATGTCTTGGTGCTGTCACTCAAAAGG----CGGTCGT--------CCGG-ACGCT-GCCA------ s droEug2.KB465067 617757 187 + 1515531 -------------------GTTTTTT-------------------CCTTCTTGCAACTGCT-----------GC--AAC----TG---AAAA--C-CGCGAGCGTAACAACA--GTTGCA-------CATGCA------------C--ATGTTGGT--GTTGCCG---------------------------------TG-----GCCAAGTATATCATGGC-------AACTTGGAGACAGTT---------------------TGTCGTC-GTT---GGt------------------------tttgctaattaaaatatCTTGGTGCTGTCACTCAAAAGG----CGGTCGC--------CTGATCCACTGGCCA------ s droEle2.KB458573 541764 199 - 5320397 -------------------GTTGTTTTGCCCC----------TCtttttttCgcatctgc--------tgctgc--aac----tg---aaAA--C-CGCGAGCGTAACAACA--GTTGCA-------CATGCA------------C--ATGTTGGT--GTTGCCG---------------------------------TG-----GCCAAGTATATCATGGC-------AACTTGGAGACAGTT---------------------TGTCGTC-GTT---GGt------------------------tttgctaattaaaatgtCTTGGTGCTGTCACTCAAAAGG----CGGTCGC--------CTGATCCACTGGCCA------ s droKik2.KB459527 295250 173 - 1234237 -------------------CTTCAGCTACAGC---------TTCTGTTTTTTA------------------------------TG---AAGC--CTCGAGAGCGTAACAACA--GTTGCA-------CATGCT------------G--GTG-----------------------------------------------TT-----GCCAAGTATATCATGGC-------TACTTGGAGACAGTT---------------------TGTCGTC-GCT---GGC------------------------tttgctaattaaaatgtCTTGGTGCTGTCACTCAAAAGG----CAGTTGA--------CTGGCCAGTGGATCa------ s droTak2.KB461535 160878 198 - 669855 -------------------GTTTT-TCAccagtttttttcttttttttgttcgcaTCTGCT-------GGCTGC--TAC----AG---AAAA--C-CGCGAGCGTAACAACA--GTTGCA-------CATGCA------------C--ATGC----------------------------------------------TG-----GCCAAGTATATCATGGC-------AACTTGGAGACAGTT---------------------TGTCGTC-GTT---GGC------------------------TTTGCTAATTAAAATGTCTTGGTGCTGTCACTCAAAAGG----CGGTCGC--------CTGATCCACTGGCCA------ s droRho2.KB449310 56355 180 - 65043 -------------------gtttt---------------------ttttcccccat----------------GC--AAC----TG---AAAA--C-CGCGAGCGTAACAACA--GTTGCA-------CATGCA------------C--ATGTTGGT--GTTGCCG---------------------------------TG-----GCCAAGTATATCATGGC-------AACTTGGAGACAGTT---------------------TGTCGTC-GTT---GGC------------------------TTTGCTAATTAAAATGTCTTGGTGCTGTCACTCAAAAGG----CGGTCGC--------CTGATCCACTGGCCA------ s droFic2.KB457177 97950 197 + 995874 -------------------gtttttccccttt-------------tccactcGCATCTGCT-----------GC--AAC----TG---AAAA--C-CGCGAGCGTAACAACG--GTTGCA-------CATGCA------------C--ATGTTGGT--GTTGCCGCGG------------------------------TT-----GCCAAGTATATCATGGC-------AACTTGGAGACAGTT---------------------TGTCGTCGGTT---Ggt------------------------tttgctaattaaaatgtcTTGGTGCTGTCACTCAAAAGG----CGGTCGC--------CTGATCCACTGGCCA------ s droPse3.chr3 1367754 224 - 19787792 ----------------------------CCTC-------------TTTGTGCACCTCTGTCTGCCACTTGATGC--CAC----TG---AAAAGCC-CGCAAGCGTAACCACA--GTTGCA-------ACTGCCACAAGTGCaactt--ctgctgcc--gctgctgcta------------------ctgctgctgctgtt-----gccaagTATATCATGGC-------AACTTGGAGACAGTT---------------------TGTCGTC-GTT---GCT------------------------TTTGCTAATTAAAATGTCTTGGTGCTGTCACTCAAAAGG----CGGTCGT--------CTGATCCACTGGCCA------ s droPer1.super_34 556604 247 - 916997 -------------------GCCTT----CCTC-------------TTTGTGCACCTCTGTCTGCCACTTGATGC--CAC----TG---AAAAGCC-CGCAAGCGTAACAACA--GTTGCA-------ACTGCCACAAGTGCAACTT--ctgctgcc--gctgctgctactgctactgcttctgctgctgctgctgctgtt-----gcCAAGTATATCATGGC-------AACTTGGAGACAGTT---------------------TGTCGTC-GTT---GCT------------------------TTTGCTAATTAAAATGTCTTGGTGCTGTCACTCAAAAGG----CGGTCGT--------CTGATCCACTGGCCA------ s droMir2.chr3 1410520 242 - 20862834 ----------------------------CCCC-------------TTTGTGCACCTCTGTCTGCCACTTGATGC--CAC----TG---AAAAGCC-CGCAAGCGTAACAACA--GTTGCA-------ACTGCCACAAGTGCaactt--ctgctgcc--gctgctgctgctgctgctgctgctgctgctgctgctgctgtt-----gccaagTATATCATGGC-------AACTTGGAGACAGTT---------------------TGTCGTC-GTT---GCt------------------------tttgctaattaaaatgtcttGGTGCTGTCACTCAAAAGG----CGGTCGT--------CTGATCCACTGGCCA------ s droWil2.CH963894 1338289 127 + 2843958 -------------------------------------------------------------------------C--AAC---------------C-AGCGAGCGTAACAACA--GTTGCA-------CTTGTT-----------------GCTCGT--GTTGCTCAAG------------------------------TT-----GC--------------------------TGGAGACAGTT---------------------TGTCTTG-GCTTGGGGT------------------------TTTGCTAATTAAAATGTCTTGTGGCTGTCACTCAAAAGg----cggtcgt--------c-------------------- s droVir3.scaffold_12875 7374714 229 + 20611582 ---CTGCAACGCGTCAAGTGCGAATCTTCCTT-------------TGTTTTTG----------------GTTGC--AAC----TG---AAAA--C-CGCGAGCGTGACAACA--GTTGCA-------ACAGTT------------GCACAGTTGCTCAGTTGCTG---------------------------------CT-----GCCAAAAGTCGAGTTGC-----ACGACTTAGAGACACTTTGTCAG---------------CGCTGTT-GTT---GTT------------GCC--TGTGCTGCTTGCTAATTAAAATGTCTCGATGCTGTCACTCAAAAGG----CAGTCGC--------TCAAACCACTGGCCG---GCc s droMoj3.scaffold_6496 26169292 260 + 26866924 CAACTGCAACTCGTTGAGTGTGAATCTGCCTT-------------TGTTGTCG----------------ACTGCTGAGC----TGGCTGAAG--C-CGTGAACGCAACGACA--GCTGCA-------ACAGCT------------G--CAgttgtt--gctgcaa---------------------------------gt-----gccaaaagtcgagttgc-----gcgacttagatgcactttgtcaatgttgcagctgttgttgctgtt-gtt---gctgttgctgctgtagcc--agtgctgtttgctAATTAAAATGTCTTGATGCTGTCGCTCAAAAGG----CACTCGC--------TCGAACCACAGGCCG---GCT s droAlb1.JH854640 331978 253 + 406291 ---------------gtatctgtatctgcttT-------------TGTGGTTGTATTTGGT---CGCAAGTTGC--AAC----TG---AAAA--C-CGCGAGCGTAACAaca--gttgcagagttgcacagtt------------gcacagttggg-agttgcaa---------------------------------gttgcaagttgagagttgTGCTGCCAAAAGTGACTTAGAGACAGTTTGTCAA---------------CGGTGTT-GCT---GCT------------CGC--GTTGTTGTTC-CTAATTAAAATGTCTTGGCGCTGTCACTCAAAAGG----CAGTCGAGCGGTCGGTTGAGCCACTCAGCG---ATT s droGri2.scaffold_15245 925447 169 + 18325388 CTGCTGCCAAAAGTCAA----------------------------------------------------GTTGCACGAC----TT---AAAA-----GACAATttgtcaacgttgttgtt-------gttgtt------------g--ttgttgct--gttgctg---------------------------------ct-----gtt---------gttgc-----agtagt--------------------------------tgttgta-gtt---gtt------------gcCTGTGTGCTGTTTGCTAATTAAAATGTCTTGATGCTGTCACTCAAAAGG----CAGTCGC--------TCGA----------------- a score=-256109.000000 s dm6.chr2R 24374690 41 + 25286936 cgagtcgagt-cga-gtc-------gacga-gtc-TCTCGGT------TG---GCAGCGGA------ s droSim1.chr2R 18713476 34 + 19596830 -------AGT-CGA-GTC-------GACGA-GTC-GCTCGGT------TG---GCAGCGGA------ s droSec1.super_23 132773 34 + 989336 -------AGT-CGA-GCC-------GACGA-GTC-GCTCGGT------TG---GCAGCGGA------ s droYak3.chr2R 20222919 46 + 21139217 --agtcgagt-cga-gtcgagtaGAGTCGA-GTC-TCTTGGT------TG---CCAGCGga------ s droEre2.scaffold_4845 21620446 41 + 22589142 --AGTCGAGT-CGA-GTC-----GAGACGG-GTC-TCTCGGT------TG---CCAGCGGA------ s droBia2.KB462602 815515 31 + 3129309 -------AGT-CGA-GCC----------AA-GTC-GCTTGGT------TG---GCGGCaga------ s droSuz1.KI419649 12064860 31 - 14502029 -------AGT-CGA-GTC----------AA-CTC-GCTTGGT------TG---GCGGCGGA------ s droAna3.scaffold_13266 5725151 41 - 19884421 -------GATCCAC-TGC----ACTGGCGA-GGC-GACTGGT------TAGCGGCGGCAGA------ s droBip2.KB464407 1974955 37 + 2915140 -------GGT-CGG-TCC----ACTGGCGA-GGC-GACTGGT------TA---GAGGCAGA------ s droEug2.KB465067 617944 21 + 1515531 -------AGT-CG----C-------------------TTGGC------TG---GCAGCAGA------ s droEle2.KB458573 541963 21 - 5320397 -------AGT-CG----C-------------------TTGGC------TG---GCAGCAGA------ s droKik2.KB459527 295423 35 - 1234237 -------ggc-agacgac-------gacgacgga-ggacgga------cg---gcggc-ga------ s droTak2.KB461535 161076 32 - 669855 -------AGT-CGA-GTT----------GA-GTTGGCTTGGT------TG---CCGGCAGA------ s droRho2.KB449310 56535 21 - 65043 -------AGT-------C-----------------GCTTGGT------TG---GCAGCAGA------ s droFic2.KB457177 98147 21 + 995874 -------ACT-------C-----------------GCTCGGT------TG---GCAGCAGC------ s droPse3.chr3 1367978 20 - 19787792 -------AGC-----GAC--------------------TGGC------TG---GCAGCAga------ s droPer1.super_34 556851 20 - 916997 -------AGC-----GAC--------------------TGGC------TG---GCAGCAGA------ s droMir2.chr3 1410762 20 - 20862834 -------AGC-----GAC--------------------TGGC------TG---GCAGCAga------ s droWil2.CH963894 1338416 17 + 2843958 -------gtc-----gtc-------------gtc-------------------gtggtctt------ s droVir3.scaffold_12875 7374943 25 + 20611582 ---------------------------------------ggcagacgtca---gcaataacaacagc s droAlb1.JH854640 332231 14 + 406291 ------------------------------------------------CA---CCACTGGC--CGGC s droGri2.scaffold_15245 925616 28 + 18325388 -----------------------------------AGCCGGCAGACGTCC---acagcgacaacaa- a score=5393157.000000 s dm6.chr2R 24374731 557 + 25286936 CAACGAT-GAT----------GACGACGCCCATTTTAGTCAGC--AGT-----------CGGCGGCAACAAT---GCGATTTTGCCTTTCGCGAAAt-------------------gctgccgctgcctctgct----gc---------ctgtgctgctgctgctA----CAATTTCATTGGAAGTCCG------------------C-----------TG---ATGA----------------TGTGG----------CAGGGGCACGCGGCGTATGCGCAA---------------TGCCA-CTGCGATCTCCCTCGC-------------------------------------------------ACAAAATGGCGATCGCATTGTTACAGTTTGCAATTATTTTGATTTATTTTTTGT-------T------CG-------TCCCAGAGGTTGA--------------------------------------------------------------GCACTAATCAAAATTAAAATGACGCAT---TCGCTGCC--------------ATCCCATC-------------------------CAAGGCGATG-------------------CGAC----------------------GGCAACGA-----------------TGATGA------------------TGG-CCCCGC-----TCCGATCACCCT--GC------------------------------TCGCC------G----------------TAGAGCCAGAAATCAATATTCTAAATTCTTTAACGCGTGTGCACATTTAAGGCAAC--------GC------------CAGCTCATTGAGATGCGTGCCGGCAAACAGCCTGGCCAGCACTTATACGCAATTTCGCGCCATATTTGGTTCAAACATATTGG-A---------------TTTTTT---------------TGTCATC----TCGAC--G-------------------TC---------------TCCTTGCTCCCT----------------------------------------GCACT---TGGCTGGCATATAGAACAG------------------------------------CGGAC s droSim1.chr2R 18713510 558 + 19596830 CGACGAT-GAT----------GACGACGCCCATTTTAGTCAGC--AGT-----------CGGCGGCAACAAT---GCGATTTTGCCTTTCGCGAAAT-------------------GCTGCCGCTGCCTCTGCT----GC---------CTGTGCTGCGGCTGCTA----CAATTTCATTGGAAGTCCG------------------C-----------TG---GTGA----------------TGTGG----------CAGGGGCACGCGGCGTATGCGCAA---------------TGCCA-CTGCGATCTCCCTCGC-------------------------------------------------ACAAAATGGCGATCGCATTGTTACAGTTTGCAATTATTTTGATTTATTTTTTGT-------T------CG-------TCCCAGAGGTTGA--------------------------------------------------------------GCACTAATCAAAATTAAAATGACGCGT---TCGCTGCC--------------ATCCCATC-------------------------CAAGGCGATG-------------------CGAC----------------------GACGACGA-----------------TGATGA------------------CGG-CCCCGC-----GCCGATCACCCC--GC------------------------------TCGCC------G----------------GAGAGCCAGAAATCAATATTCTAAATTCTTTAACGCGTGTGCACATTTAAGGCAAC--------GC------------CAGCTCATTGAGATGCGTGCCGGCAAACAGCCTGGCCAGCACTTATACGCAATTTCGCGCCATATTTGGTTCAAACATATTGG-A--------------TTTTTTT---------------TGTCATC----TCGAC--G-------------------TC---------------TCCTTGCTCCCT----------------------------------------GCACT---TGGCTGGCATATAGAACAG------------------------------------CGCAC s droSec1.super_23 132807 551 + 989336 CGACGAT-GAT----------GACGACGCCCATTTTAGTAGGC--AGT-----------CGGCAGCAACAAT---GCGATTTTGCCTTTCGCGAAAT-------------------GCTACCGCTGCCTCTGCT----GC---------CTGT------GCTGCTA----CAATTTCATTGGAAGTCCG------------------C-----------TG---GTGA----------------TGTGG----------CACGGGCACGCGGCGTATGCGCAA---------------TGCCA-CTGCGATCTCCCTCGC-------------------------------------------------ACAAAATGGCGATCGCATTGTTACAGTTTGCAATTATTTTGATTTATTTTTTGT-------T------CG-------TCTCAGAGGTTGA--------------------------------------------------------------GCACTAATCAAAATTAAAATGACGCGT---TCGCTGCC--------------ATCCCATC-------------------------CAAGGCGATG-------------------CGAC----------------------GACGACGA-----------------TGATGA------------------TGG-CCCCGC-----GCCGATCACCCC--GC------------------------------TCGCC------G----------------GAGAGCCAGAAATCAATATTCTAAATTCTTTAACGCGTGTGCACATTTAAGGCAAC--------GC------------CAGCTCATTGAGATGCGTGCCGGCAAACAGCCTGGCCAGCACTTATACGCAATTTCGCGCCATATTTGGTTCAAACATATTGG-A---------------TTTTTT---------------TGTCATC----TCGAC--G-------------------TC---------------TCCTTGCTCCCT----------------------------------------GCACT---TGGCTGGCATATAGAACAG------------------------------------CGCAC s droYak3.chr2R 20222977 577 + 21139217 cgacgac-gat----------gacgacgcCCATTTTAGTCGGC--AGT-----------CAGCGGCAACAAT---GCGATTTTGCCTTTCGCGAAAt-------------------gctgcctctgctgctgct----a-------------------------------caATTTCATTGGAAGTCCG--------CTG---ATGTC-----------TG---ATGA----------------TGTGG----------CAGGggcacgcggcgtatgcgcaatgcg---------actgcga-ctgcgatcTCCCTCGC-------------------------------------------------ACAAAATGGCGATCGCATTGTTACAgtttgcaattattttgatttattttttgt-------t------cg-------tcCCCGCGCTTGA--------------------------------------------------------------GCactaatcaaaattaaaatgacGCGT---TCGCtgcc--------------atcccatcccatcccatcccatccaaGGCGATACGATGCGATG-------------------CGAC----------------------GACAACGA-----------------CGATGA------------------TGG-CCCCGC-----ACCGATCGCTCC--GC------------------------------TGGCC------G----------------GAGAGCCAGAAATCAATATTCTAAATTCTTTAACGCGTGTGCACATTTAAGGCAAC--------GC------------CAGCTCATTGAGATGCGTGCCGGCGAACAGCCCGGCCAGCACTTATACGCAATTTCGCGCCATATTTGGGCCAAACATATTGG-A---------------tttttt---------------tGTCATC----TCGAC--G-------------------TC---------------TCCTTGCTCCCT----------------------------------------GCACT---TGGCCGGCATATAGAACAG------------------------------------CGCAC s droEre2.scaffold_4845 21620487 562 + 22589142 CGGCGAT-GAT----------GACGACGCCCATTTTAGTCGGC--AGT-----------CAGCGGCAACAAT---GCGATTTTGCCTTTCGCGAAAC-------------------gctgccgctgctgctgct----gc---------tgctgctgctgttgctgcAGCCAATTTCATTGGAAGTCCG------------------C-----------TG---ATGA----------------TGTGG----------CAGGGGCACGCGGCGTATGCGCAA---------------TGCAA-CTGCGATCTCCCTCGC-------------------------------------------------ACAAAATGGCGATCGCATTGTTACAGTTTGCAATTATTTTGATTTATTTTTTGT-------T------CG-------TCCCAGAGGTTGA--------------------------------------------------------------GCACTAATCAAAATTAAAATGACGCGT---TCGCTGCC--------------ATCCCATC-------------------------CAAGGCGATG-------------------CGAC----------------------GACAACGA-----------------TGATGA------------------TAG-CCCCGC-----ACCGATCTCCCC--GC------------------------------TCGCC------G----------------GAGAGCCAGAAATCAATATTCTAAATTCTTTAACGCGTGTGCACATTTAAGGCAAC--------GC------------CAGCTCATTGAGATGCGTGCCGGCAAACAGCCTGGCCAGCACTTATACGCAATTTCGCGCCATATTTGGGCCAAACATATTGGTT---------------TTTTTT---------------TGTCATC----TCGAC--G-------------------TC---------------TCCTTGCTCCCT----------------------------------------GCACT---TGGCTGGCATATAGAACAG------------------------------------CGCAC s droBia2.KB462602 815567 566 + 3129309 cgtcgac-gat----------gacgacgCCCATTTT---------AGT-----------CAGCGGCAACAAT---GCGATTTTGCCTTTCGCGAaatgctgcc-------------gctgccgctgctgctgct----gc---------tgctgatgtggctgctA----CAATTTCATTGGAAGTCCG------------------C-----------TG---ATGA----------------TGTGG----------CAGGggcacgcggcgtatgcgcaa---------------tgcaATTTGCGATCTCCCTCGC-------------------------------------------------ACAAAATGGCGATCGCATTGTTACAGtttgcaattattttgatttattttttgt-------t------cg-------tcCCAGCGGTTCAG--------------------CCTGTG-----------------------------C---TGGCactaatcaaaattaaaatgacgCGT---TCGCTGCC--------------ATCCCATC-------------------------CAAGGC-ATG-------------------CGGT-------------------------------------------------------------------------G-CCCCGC-----GCCGATCGGCCC--GC------------------------------TCGCC-----AG----------------GAGAGCCAGAAATCAATATTCTAAATTCTTTAACGCGTGTGCACATTTAAGGCAAC--------GC------------CAGCTCATTGAGATGCGTGCCGGCAAACAGCCTGGCCAGCACTTATACGCAATTTCGCGCCATATTTGGTCCAAACatattgg-a---------------tttttt---------------tgtCATC----TCCTC--G-------------------TCGCCGTCGTAGTCGCCTCTTTGCTCCCT----------------------------------------GCACT---TGGCTGGCATATAGAACAG------------------------------------CAGAC s droSuz1.KI419649 12064900 563 - 14502029 CGTCGAC-GAT----------GACGACGCCCATTTT---------AGT-----------CAGCGGCAACAAT---GCGATTTTGCCTTTCGCgaaat-------------------gctgctgctgctgctgct----gc---------tgctgatgtggCTGCTA----CAATTTCATTGGAAGTCCG------------------C-----------TG---ATGA----------------TGTGG----------CAGGggcacgcggcgtatgcgcaa---------------tgcaATTTGCGATCTCCCTCGC-------------------------------------------------ACAAAATGGCGATCGCATTGTTACAGtttgcaattattttgatttattttttgt-------t------cg-------tCCCAGCGGTTCAG--------------------CCTGTG-----------------------------C---TGGCactaatcaaaattaaaatgacgCGT---TCGCTGCC--------------ATCCCATC-------------------------CAAGGC-ATT-------------------CGAT-------------------------------------------------------------------------G-GCCCGC-----ACCGATCGCCCC--GC------------------------------TCGCC-----AG----------------GAGAGCCAGAAATCAATATTCTAAATTCTTTAACGCGTGTGCACATTTAAGGCAAC--------GC------------CAGCTCATTGAGATGCGTGCCGGCAAACAGCCTGGCCAGCACTTATACGCAATTTCGCGCCATATTTGGTTCAAACatattgg-a------------ttttttttt---------------tgtcatc----tcgtc--g-------------------tcgtcgtcgtcgtcgcgtcTTTGCTCCCT----------------------------------------GCACT---TGGCTGGCATATAGAACAG------------------------------------CAGAC s droAna3.scaffold_13266 5725192 532 - 19884421 CGATGGC-GAT----------GACGACGCCCATTTTGGTCGAC--AGT--------------CGGCAACAAT---GCGATTTTACCTTTTCTGAATT-------------------GCTAGTGGTGCTGTTGCA----GC---------------AGTTGCTGCTA----CAATTTCATTGGAAGTCTG---------------------------------------------------------TGG----------CAGGGGCACGCGGCGTATGCGCAA---------------TGCAATTTGCGATCTCCCTCGC-------------------------------------------------ACAAAATGGCGATCGCATTGTTACAGTTTGCAATTATTTTGATTTATTTTTTT------------------------TGCCAGCGACTGTG--------------------CCTGTGCTCG---------TCGTCCCTG------CC---TGACACTAATCAAAATTAAAATGACGCGA---ACG-------------------ATACCAGA-------------------------CATGGCGATG-------------------TG----------------------------------------------------------------------------------------------CACGTC--GC------------------------------TCGCC------C----------------GAGAGTCAGAAATCAATATTCTAAATTCTTTAACGCGTGTGCACATTTAAGGCAAC--------GC------------CATCTCATTGAGATGCGTGCCGGCAAACAGCCTGGCCAGCACTTATACGCAATTTCGCGCCATATTTGGTTCAAACATATTGG-C---------------TTTTTT---------TTCGTACTTAATT----CTGCCTTG-------------------TC---------------TTTTTGCACCCA----------------------------------------GCACT---TGGCTGGCATATAGAACAG------------------------------------CAGTC s droBip2.KB464407 1974992 544 + 2915140 CGACGGC-GAT----------GACGACGCCCATTTTGGTCGAC--AGT--------------CGGCAACAAT---GCGATTTTGCCTTTTGTGAATT-------------------GCTagtggtgc-------------------------------tgctgcta----cAATTTCATTGGAAGTCTG---------------------------------------------------------TGG----------CAGGggcacgcggcgtatgcgcaa---------------tgcaATTTGCGATCTCCCTCGC-------------------------------------------------ACAAAATGGCGATCGCATTGTTacagtttgcaattattttgatttatttttttg-------t------cagagcctgtgcctgtgcctgtg--------------------tcTGTGCTCG---------TCGTCCCTG------CC---TGGCactaatcaaaattaaaatgacgCGA---ACG-------------------ATACCAGA-------------------------CATGGCGATG-------------------TG----------------------------------------------------------------------------------------------CACGTC--GC------------------------------TCGCC------C----------------GAGAGCCAGAAATCAATATTCTAAATTCTTTAACGCGTGTGCACATTTAAGGCAAC--------GC------------CATCTCATTGAGATGCGTGCCGGCAAACAGCCTGGCCAGCACTTATACGCAATTTCGCGCCATATTTGGTTCAAACatattgg-c---------------tttttttttgttttgtttgtattttatt----ctaccttg-------------------tc---------------tttttgCACCCA----------------------------------------GCACT---TGGCTGGCATATAGAACAGCCC------C--------------------------CAGTC s droEug2.KB465067 617968 562 + 1515531 CGTCGAC-GAT----------GACGACGCCCATTTTAGTCAGC--AGT-----------CAGCGGCAACAAT---GCGATTTTGCCTTTCGCGAACT-------------------GCCGctgcggttgctgtt----gc------------------tgctgcta----caaTTTCATTGGAAGTCCG------------------C-----------TG---ATGA----------------TGTGG----------CAGGggcacgcggcgtatgcgcaa---------------tgcaATTTGCGATCTCCCTCGC-------------------------------------------------ACAAAATGGCGATCGCATTGTTACAGTTTgcaattattttgatttattttttgt-------t------cg-------tCCCAGAGGTTCA--------------------------GTTCAG-----AGCTCAGCCCCT------GC---TGGCactaatcaaaattaaaatgacgCGT---CCG-------------------ATGCCATC-------------------------CAAGGCGATg-------------------cgac-------------------------gatga-----------------tgacga------------------tgg-cCCCGC-----ACCGATCACTTC--GC------------------------------TCGCC------G----------------GAGAGTCAGAAATCAATATTCTAAATTCTTTAACGCGTGTGCACATTTAAGGCAAC--------GC------------CAGCTCATTGAGATGCGTGCCGGCGAACAGCCTGGCCAGCACTTATACGCAATTTCGCGCCATATTTGGTCCAAGCATATTGG-A---------------tttttt---------------tGTCATC----TCGAC--G-------------------TC---------------TCTTTGCTCCCT----------------------------------------GCACT---TGGCTGGCATATAGAACAG-------------------------------------GCCC s droEle2.KB458573 542011 594 - 5320397 CGACAAC-GAT----------GACGACGCCCATTTTAGTCAGC----T-----------CAGCGGCAACAAT---GCGATTTTGCCTTTCGCGAAAt-------------------gctgccgctgctactgct----gc---------tactgttgctgctgcta----caaTTTCATTGGAAGTCCG------------------C-----------TG---ATG-------------------TGG----------CAGGggcacgcggcgtatgcgcaa---------------tgcaATTTGCGATCTCCCTCGC-------------------------------------------------ACAAAATGGCGATCGCATTGTTACAgtttgcaattattttgatttatttttttg-------tatgc--cg-------TCTCCGAGGGACA--------------------------------------------------------------GCactaatcaaaattaaaatgacgCTT---GCG-------------------ATACCATC-------------------------CAAGGCGATG-------------------CGATGCCAGGCGATGCGATGCGGTGCGACGACGA-----------------CAATGA------------------TGG-CCCCGC-----ACCGATCACGTC--GC--------------------TCCCC---GATCGCC------G----------------GAGAGTCAGAAATCAATATTCTAAATTCTTTAACGCGTGTGCACATTTAAGGCAAC--------GC------------CAGCTCATTGAGATGCGTGCCGGCGAACAGCCTGGCCAGCACTTATACGCAATTTCGCGCCATATTTGGTTCAAACATattgg-a---------------tttttt----tgtttttcttatctcGTC----TCGTCTTG-------------------TC---------------TCTTTGCTCCCT----------------------------------------GCACT---TGGCTGGCATATAGAACAG------------------------------------GCCAC s droKik2.KB459527 295458 539 - 1234237 cggcgac-gat----------gacgacgccCATTTT---------GGT-----------CACCGGCAACAAT---GCGATTTTGCCTTTcgc------------------------gttgctgctgc-------------------------------ggctgcta----cAATTTCATTGGAAGtctg------------------c-----------ag---ctgcagttgcagttgctgtttGCAG----------CGGGggcacgcggcgtatgcgcaa---------------tgcaATTTGCGATCTCCCTCGC-------------------------------------------------ACAAAATGGCGATCGCATTGTTAcagtttgcaattattttgatttacttTTTGT-------GCTGTCGCG-------TCTGCCCGGCTCC--------------------------------------------------------C---TGGCactaatcaaaattaaaatgacgCGA---TCGAT-----------------ACACCAGA-------------------------CATGGCAATG-------------------CGAT--------------------------TCGA-----------------GGATGA------------------TG----------------GGTCCCCCT--TC------------------------------TCGCC------G----------------GAGAGCCAGAAATCAATATTCTAAATTCTTTAACGCGTGTGCACATTTAAGGCAAC--------GC------------CAGCTCATTGAGATGCGTGCCGGCGAACAGCCTGGCCAGCACTTATACGCAATTTCGCGCCATATTTGGTCCAAACAtattgg-t---------------tgtttt---------------ttttttc----g------t-------------------tc---------------tcGCTGC---------------------------------------------ACACT---TGGCTAGCATATAGAACAGGCC------TG-----------AGAGCAG-------CAGGC s droTak2.KB461535 161114 555 - 669855 CGTCGAC-GAT----------GACGACGCCCATTTT---------AGT-----------CAGCGGCAACAAT---GCGATTTTGCCTTTCGCGaaat-------------------tctgctgctgctgctgct----gctgcggttgctgctgatgtggctgctA----CAATTTCATTGGAAGTCCG------------------C-----------TG---ATGA----------------TGTGG----------CAGGggcacgcggcgtatgcgcaa---------------tgcaATTTGCGATCTCCCTCGC-------------------------------------------------ACAAAATGGCGATCGCATTGTTACAGTTtgcaattattttgatttattttttgt-------t------cg-------tCGCA----------------------------------------------------------------------GCactaatcaaaattaaaatgacgCGT---TCGCTGCC--------------ATCCCATC-------------------------CAAGGC-ATT-------------------CGAT------------------------------------------------GCGAA------------------GGC-CCCCGA-----ACCGATCGCCTC--GC------------------------------TGGCC------G----------------GCGAGTCAGAAATCAATATTCTAAATTCTTTAACGCGTGTGCACATTTAAGGCAAC--------GC------------CAGCTCATTGAGATGCGTGCCGGCAAACAGCCTGGCCAGCACTTATACGCAATTTCGCGCCATATTTGGTTCAAAcatattgg-a--------------ttttttt---------------tgtcatc----TCGTC--G-------------------TCGACGTCGTTGTC---TCTTTGCTCCCT----------------------------------------GCACT---TGGCTGGCATATAGAACAG------------------------------------CAGAC s droRho2.KB449310 56568 575 - 65043 cgacgac-gat----------gacgacgcCCATTTTAGTCAGC----T-----------CGGCGGCAACAAT---GCGATTTTGCCTTTCGCGAAAT-------------------GCtgctattgctgctgct----gc------------------------ta----caaTTTCATTGGAAGTCCG------------------C-----------TG---A-------------------TGTGG----------CAGGggcacgcggcgtatgcgcaa---------------tgcaATTTGCGATCTCCCTCGC-------------------------------------------------ACAAAATGGCGATCGCATTGTTACAGtttgcaattattttgatttattttttttattcgtgt------CG-------TCTCTGAGGGACA-------------------------------------GTGGCAGCCTCT------GC---TGGCactaatcaaaattaaaatgacgCTG---GCG-------------------ATACCATC-------------------------CAAGGCGatg-------------------cgac----------------------gacgacga-----------------cgatga------------------tgg-CCCCGC-----ACCGATCACGTC--GC------------------------------TCGCC------G----------------GAGAGTCAGAAATCAATATTCTAAATTCTTTAACGCGTGTGCACATTTAAGGCAAC--------GC------------CAGCTCATTGAGATGCGTGCCGGCGAACAGCCTGGCCAGCACTTATACGCAATTTCGCGCCATATTTGGTTCAAACatattgg-tatttttttttttttttttttt---------------tgttattctcGTTGTC--G-------------------TC---------------TCTTTGCTCCCT----------------------------------------GCACT---TGGCTGGCATATAGAACAG------------------------------------GCCAC s droFic2.KB457177 98177 563 + 995874 CGGCGACGGAT----------GACGACGCCCATTTT---------AGT-----------CAGCGGCAACAAT---GCGATTTTGCCTTTCGCGAATTGTGGCTGAGGCAGCttacagctgctgctgctgctgct----gt---ttatgctgctgctgcggctggta----CAATTTCATTGGAAGTCCG------------------C-----------TG---A-------------------TGTGG----------CAGGggcacgcggcgtatgcgcaatgta---------tGTGCAATTTGCGATCTCCCTCGC-------------------------------------------------ACAAAATGGCGATCGCATTGTTACagtttgcaattattttgatttattttttgt------gc------cg-------TCCCAGAGGCTCA-------------------------------------------GCCTCT------GC---TGGCactaatcaaaattaaaatgacgCTC---GCG-------------------ATGCCATC-------------------------CAAGGCGATG-------------------CGAC-----------------------------------------------------------------------------------------------GAC--GT------------------------------TCGCT------G----------------GAGAGTCAGAAATCAATATTCTAAATTCTTTAACGCGTGTGCACATTTAAGGCAAC--------GC------------CAGCTCATTGAGATGCGTGCCGGCGAACAGCCTGGCCAGCACTTATACGCAATTTCGCGCCATATTTGGTCCAAACATAttgg-a-----tttttttctttttttt---------------tgttatc----tcGTC--G-------------------TC---------------TTTTTGCTCCCT----------------------------------------GCACT---TGGCTGGCATATAGAACAG-------------------------------------GCCC s droPse3.chr3 1368020 613 - 19787792 cgatgac-gac----------gacgacgcccaTTTT---------AGT-----------CAGCGGCAACAAT---GCgattttgccttt-------t-------------------gctgctgctgcctgtgct---------------tgtggctgtggctgcta----cAATTTCATTGGAAGTCTG---------------------------------------------------------TGG----------ACGGggcacgcggcgtatgcgcaa---------------tgcca-TTGCGATCTCCCTCGC-------------------------------------------------ACAAAATGGCGATCGCATTGTTACAGtttgcaattattttgatttattttttgt-------t------cg-------ctCCGTCGCTGCAGTGCCTCCAGTACTGTCTGCCCCTAcaccctgcctctgcctgtgcctct------acCTGTGGCactaatcaaaattaaaatgacgCGA---ACG-------------------ATACCAGA-------------------------CAAGGCGATG-------------------CCAC-----------------------------------------------GGATGA------------------TGT-CCCCGC-----ACTGTGcacgtc--gccgttgccgtcaccgtcaccgtcccCGTTGCCGGCC------A----------------GAGAGTCAGAAATCAATATTCTAAATTCTTTAACGCGTGTGCACATTTAAGGCAAC--------GC------------CAGCTCATTGAGATGCGTGCCGGCGAACAGCCTGGCCAGCACTTATACGCAATTTCGCGCCATATTTGGTCCAAACATATTGG-A---------------TTTTTT---------------------------------G-------------------TC-------------------------AG----------------------------------------GCACT---GGGCTGGCATATAGAACAGgct------cagacccagacccagaccaggccagaacgaac s droPer1.super_34 556893 625 - 916997 cgatgac-gac----------gacgacgCCCATTTT---------AGT-----------CAGCGGCAACAAT---GCGATTTTGCCTTT-------T-------------------GCTGCTGCTGCCTGTGCTTGTGGC---------TGTGGCTGTGGCTGCTA----CAATTTCATTGGAAGTCTG---------------------------------------------------------TGG----------ACGGGGCACGCGGCGTATGCGCAA---------------TGCCA-TTGCGATCTCCCTCGC-------------------------------------------------ACAAAATGGCGATCGCATTGTTACAGTTTGCAATTATTTTGATTTATTTTTTGT-------T------CG-------CTCCGTCGCTGCAGTGCCTCCAGTACTGTCTGCCCCTACACCCTGCCTCTGCCTGTGCCTCT------ACCTGTGGCACTAATCAAAATTAAAATGACGCGA---ACG-------------------ATACCAGA-------------------------CAAGGCGATG-------------------CCAC-----------------------------------------------GGATGA------------------TGT-CCCCGC-----ACTGTGCACGTC--GCCGTTGCCGTCACCGTCACCGTCCCCGTTGCCGGCC------A----------------GAGAGTCAGAAATCAATATTCTAAATTCTTTAACGCGTGTGCACATTTAAGGCAAC--------GC------------CAGCTCATTGAGATGCGTGCCGGCGAACAGCCTGGCCAGCACTTATACGCAATTTCGCGCCATATTTGGTCCAAACATATTGG-A---------------TTTTTT---------------------------------G-------------------TC-------------------------AG----------------------------------------GCACT---GGGCTGGCATATAGAACAGGCTCAGACccagacccagacccagaccaggccagaacgaac s droMir2.chr3 1410798 619 - 20862834 cgatgac-gac----------gacgacgcccaTTTT---------AGT-----------CAGCGGCAACAAT---GCgattttgccttt-------t-------------------gctgctgctgcctgtgct---------------tgtggctgtggctgcta----cAATTTCATTGGAAGTCTG---------------------------------------------------------TGG----------ACGGggcacgcggcgtatgcgcaa---------------tgcca-TTGCGATCTCCCTCGC-------------------------------------------------ACAAAATGGCGATCGCATTGTTACAgtttgcaattattttgatttattttttgt-------t------cg-------ctcCGTCGCTGCAGTGCCTCCAGTACTGTCTGCCCCTAcaccctgcctctgcctgtgcctctgcctcagcctgtGGCactaatcaaaattaaaatgacgCGA---ACG-------------------ATACCAGA-------------------------CAAGGCGATG-------------------CCAC-----------------------------------------------GGATGA------------------TGT-CCCCGC-----ACTGTGCACGTC--GCCGCtgccgtcaccgtcaccgtcccCGTTGCCGGCC------A----------------GAGAATCAGAAATCAATATTCTAAATTCTTTAACGCGTGTGCACATTTAAGGCAAC--------GC------------CAGCTCATTGAGATGCGTGCCGGCGAACAGCCTGGCCAGCACTTATACGCAATTTCGCGCCATATTTGGTCCAAACATATTGG-A---------------TTTTTT---------------------------------G-------------------TC-------------------------AG----------------------------------------GCACT---GGGCTGGCATATAGAACAggct------cagacccagacccagaccaggccagaacgaac s droWil2.CH963894 1338433 622 + 2843958 cgtcgac-gac----------gacgacgcccATTTT---------AGT-----------C-----CAACAATGCAGCAATTTTACCTTACGTG-----------------------TTTAAcgcagcgacaaca----ac------------------aactgcta----CAATTTCATTGGAAGTCTG------------------C--------GTGTG---ACGA----------------AGACT----------TTGGGAGACGtggcgtatgcgcaatatatacacacactctcccactctctctctctctctctgtctacgcctgtctgtctgtctgtctctgtttttttgtttttacactGGCAAAATGGCGATCGCATTGTTACagtttgcaattatttt---------------------t------cg-------CCTGA----------------------------------------------------------------------CCactaatcaaaattaaaatgatgCGA---TTG-AGCCACTTACAACAACAGACAGCAGA-------------------------GAAGGAGATAATGATTATGATGACGaagccgac----------------------gacgacga-----------------cgacga------------------cga-cgacgatgttGACGAATGTCATT--GT------------------------------TGGAC------GTAGGATCGCGACATTCGAGGCTCAGAAATCAATATTCTAAATTCTTTAACGCGTGTGCACATTTAAGGCAAA--------A--------------AGCTCATTGAGATGCGTGGCGGCTAACAGCCTGGCCAGCACTTATACGCAATTTCGCGCCATATTTGGAGCAAAcatattgg-t---------------tttttt---------------tttcgtt-----------t-------------------tt---------------tttttttttatc----------------------------------------ttacT---TGCCTGGCATATAGAACAG----------------------------------------- s droVir3.scaffold_12875 7375001 501 + 20611582 GGCAGAC-GAC----------GACGACGCCCATTTTGGTCAGT---GT-------GGTGCAGTGGCAACAAT---GCAATTTAACCATACGCG---T-------------------------------------------------------------CGCTGCTA----CAATTTCATTGGAAGTTGA--------------TGGCA-----------TG---ACGC-------AGTCGCAGTTGCAG----------GCGGCGCACGCTGCGTATGCGCAA---------------TGCC-------------------------------------------------------------------ACAAAATGGCGAACGCATTGTTACAGTTCACAATTATTTTTACCT----------------G------AG----------------------------------------------------------------------------------ACACTAATCAAAATTAAAATGATGCGA-TACTGCAACG--------------ATGTCG---------------------------------AACG-------------------TGGA------------------------TGA--------------------TGATGAGT----------------TGTCCCCTGC---------------AC--GT------------------------------TCGGT-----TA----------------CAGAGCCAGAAATCAATATTCTAAATTCTTTAACGCGTGTGCACATTTAAGGCAAC--------GAGTTGCG--CTCTTGGCTCATTGAAATGCGTGCCGGCGTGCAACGCGGCCAGCACTTATACGCAATTTCGCGCCATATTTGGTGCAAGCATATTG-----------------------------------------------------------------------------CT---------------TTTTTGTGCCAGACACACACACACAC-----CACACACAGTCTC--------TTACT---TGGCTGGCATATAGAACAG------------------------------------TCCCg s droMoj3.scaffold_6496 26169610 527 + 26866924 CAGAGAC-AAC----------GACAACGCCCATTTTGGTCAGC---GT-------GGTGCAGTGGCAGCAAT---GCAATTTAGCCATACGCG---T-------------------------------------------------------------CGCTGCTA----CAATTTCATTGGAagttga---------------ggcagttgaggcagttg---aggc-------agttgTAGTTGCAGT----TGC--GCAGCGCACGCTGCGTATGCGCAA---------------TGCC-------------------------------------------------------------------ACAAAATGGCGAACGCATTGTTACAGTTCGCAATTATTTTTGCC-----------------G------AG----------------------------------------------------------------------------------ACACTAATCAAAATTAAAATGATGCGA-GGCAGCTGCG--------------CTGTCGCG----------------------------GCCGCCG-------------------CGGC------------------------TGGC-------------------TGATGAGT----------------TGT-CCCTGC---------------AC--GT------------------------------TCGAT-----TA----------------CAGAGCCAGAAATCAATATTCTAAATTCTTTAACGCGTGTGCACATTTAAGGCAAC--------GAGCGCTG--CTCATGGCTCATTGAAATGCGTGCCGGCGAGCAACGCGGCCAGCACTTATACGCAATTTCGCGCCATATTTGGTCCAAGCATATTGT-T---------------TTTCCC--------------------------TCTTT--ATATTTTGTTTTTTCGTTTTCT---------------TTTCTGTGCCAG----------------------ACACAATCGC--------TGGCT---TGGCCGGCATATAGAA-------------------------------------------- s droAlb1.JH854640 332258 641 + 406291 CAACAAT-AAG----------AGCAACACCAA-------CAGA---GTTGCAACAGTCGCAGAGTCGTCAGT---CCAAGACGCCCATTTTGG---T-------------------CTCAATTGCGCTGtggca----gccagcaacaacaacaaccacgttGCTA----CAATTTCAttggaagctgctgctgctgctg--ttggca-----------tgcgaatgcgaatacgaattgtgattgcga----------attgcgaa---tgcgtatgcgcaa---------------tgcc-------------------------------------------------------------------aCAAAATGGCGATCGCATTGTTACAgttggcaattaattttacCT--------G-------G------GG----------------------------------------------------------------------------------GCactaatcaaaattaaaatgatgtgA-TACAGCGACT--------------ATGATGAGCGAGTTT------------------AATGTCACTG-------------------TCGA------------------------CAGTCGACACAGTCTTGTatctgtgctgtgt---------gttgaa-TGT-CCCTGC---------------TC--GA------------------------------TCCGTACATATA----------------CAGAGCCAGAAATCAATATTCTAAATTCTTTAACGCGTGTGCACATTTAAGGCAacgttcagttgagttgagctctCTTGACTCATTGAAATGCGTACCGGCGTGCAACGCGGCCAGCACTTATACGCAATTTCGCGCCATATTTGGTGCAGGCacattgc-t---------------tttttt--------------------------tctgc--g-------------------gC---------------TTTTTGgcccaagcacacacacacacgcacacactcacacttgcacGTACATTTACT---TGGCTGGCATATAGAACAG------------------------------------TCTGG s droGri2.scaffold_15245 925644 561 + 18325388 caacaac-aacagcagcagcaGACGACGCCCATTTTGGTCAGCTGTGT-------GTTGCAGTGGCAACAAT---GCAATTTAACCATACGCG---T-------------------------------------------------------------CACTGCTA----CAATTTCATTGGAAGTTGATGGCACAGTTGCACTGGCA----------------GTGCCAGTGCCAGTGGTAGTGGCAGTTTGCTGCCAACAGCGCACGAGACGTATGCGCAA---------------TGGA---------------CGG-------------------------------------------------ACAAAATGGCGAACGCATTGTTACAGTTCGCAATTATTTTTTTTT----TGCCA-------G------AG----------------------------------------------------------------------------------ACACTAATCAAAATTAAAATGATGCGACGACTGTTGC----------------TGTTGTG-------------------------GATGTCAATG-------------------TTGA------------------------TGATGA-----------------TGATGAGCTGGAGAGCTGTAGAGCTGT-CCCTGC---------------ACAGGT------------------------------TCGCT-----TA----------------CCGAGCCAGAAATCAATATTCTAAATTCTTTAACGCGTGTGCACATTTAAGGCAAC--------AAGC----------TGGCTCATTGAAATGCGCGCCGGCGTGCAACGCGGCCAGCACTTATACGCAATTTCGCGCCATATTTGGTGCAAGCATATTGC-T---------------TTTTTC--------------------------TTATT--TTTCTTCTT-----------CT---------------TTTTT-----------------------------------------------TTACTGTGTGGCACACACACACAAAAA------------------------------------CACAC a score=-301493.000000 s dm6.chr2R 24375288 37 + 25286936 -----------------CGG---------GTAGACAG----------AAGATCCCAGC----------------CGATCCCCAC--------TCC---CA s droSim1.chr2R 18714068 36 + 19596830 -----------------C-G---------GCCTACCG----------AAGATCCCAGC----------------CGATCCCCAC--------TCC---CA s droSec1.super_23 133358 37 + 989336 -----------------CGG---------GCAGACCG----------AAGATCCCAGC----------------CGATCTCCAC--------TCC---CA s droYak3.chr2R 20223554 23 + 21139217 -----------------CGG---------G----CCA----------CAGACCACAGA----------------------------------TCC---CA s droEre2.scaffold_4845 21621049 50 + 22589142 -----------------CGG---------GCGGACCA----------CAGACCACAGA---CCGCAGATCCCAGCCAAACCCAC--------TCC---CA s droBia2.KB462602 816133 38 + 3129309 -----------------CGG--------AGCAGTCCA----------GAGATCTCCCT----------------CCCGGTCCAA--------TCC---CA s droSuz1.KI419649 12065463 38 - 14502029 -----------------CGG--------AGCAGTCCA----------GAGATCTCCCT----------------CCCGATCCAA--------TCC---CA s droAna3.scaffold_13266 5725724 41 - 19884421 -----------------CCG-------GAGC----------------CAGATCTGGCT----------------ACGGCTCGGGAGGAGATCTCT---TA s droBip2.KB464407 1975536 32 + 2915140 -----------------CCG---------GC----------------CAGATCTGGCT---------------------CCGGGAGGAGA--TCT---TA s droEug2.KB465067 618530 36 + 1515531 -----------------CGG--------AGCAGACCG----------GAGATCTC--C----------------CGATCCCCAT--------TCC---CA s droEle2.KB458573 542605 33 - 5320397 -----------------AGA---------GCAAAGCG----------AAGATCTTCCA--------------------ATCCAT--------TCC---CA s droKik2.KB459527 295997 62 - 1234237 -----------------CAGGGTCTTGGAGCAGGATT----------GAGATCCCTCAAACTCGCATTCTACCTCCCCATCCAG--------GCG---CA s droTak2.KB461535 161669 39 - 669855 -----------------CGG--------CGCAATCCA----------GAGATCCCCGA---------------TCCCAATCCAA--------TCC---CA s droRho2.KB449310 57143 53 - 65043 -----------------GGA---------GCAAACCG----------CAGATCTCCCGATTCCAATTCCGATTCCTATTCCTAT--------TCC---CA s droFic2.KB457177 98740 45 + 995874 -----------------CGG--------AGCAGACCA----------GAGATCCCCGA---------TCCCAATCGCGACTCAC--------TCG---CA s droPse3.chr3 1368633 38 - 19787792 -----------------cag--------accagaccaagc-------cagatcaggca---------------------gccaT--------CCC-GGCA s droPer1.super_34 557518 38 - 916997 -----------------cag--------accagaccaagc-------cagatcagGCA---------------------GCCAT--------CCC-GGCA s droMir2.chr3 1411417 38 - 20862834 -----------------cag--------accagaccaagc-------cagatcaggca---------------------gccat--------cca-gGCA s droWil2.CH963894 1339055 23 + 2843958 -------------------G--------------CCA----------AAGAAAAACGA----------------------------------TCGAGGCA s droVir3.scaffold_12875 7375502 43 + 20611582 gcaagaccaggccgggccag--------accaggccagccagccaggcAGC------------------------------------------------- s droMoj3.scaffold_6496 26170137 31 + 26866924 ------------CGAGCCCG--------ACGGGGCCAGCCTGGCATGCAGC------------------------------------------------- s droAlb1.JH854640 332899 27 + 406291 CAG---------AAAGCCAG--------AACTGAACAGAT-------CAGC------------------------------------------------- a score=-10967.000000 s dm6.chr2R 24375325 7 + 25286936 GCCATCG s droSim1.chr2R 18714104 7 + 19596830 GCCATCC s droSec1.super_23 133395 7 + 989336 GCCATGC s droYak3.chr2R 20223577 7 + 21139217 GGCATCC s droEre2.scaffold_4845 21621099 7 + 22589142 GCCATCC s droBia2.KB462602 816171 1 + 3129309 A------ s droSuz1.KI419649 12065501 1 - 14502029 A------ s droAna3.scaffold_13266 5725765 5 - 19884421 GAACT-- s droBip2.KB464407 1975568 5 + 2915140 GAACT-- s droEug2.KB465067 618566 7 + 1515531 ATCATCC s droEle2.KB458573 542638 7 - 5320397 ATCATCT s droKik2.KB459527 296059 7 - 1234237 ATCATCT s droTak2.KB461535 161708 1 - 669855 A------ s droRho2.KB449310 57196 7 - 65043 ATCATCT s droFic2.KB457177 98785 7 + 995874 ATCACCC s droPse3.chr3 1368671 7 - 19787792 ATCATCC s droPer1.super_34 557556 7 - 916997 ATCATCC s droMir2.chr3 1411455 7 - 20862834 ATCATCC s droWil2.CH963894 1339078 7 + 2843958 ATCTTCT s anoGam1.chr3L 4072502 7 + 41284009 GCCATCG a score=2907298.000000 s dm6.chr2R 24375332 362 + 25286936 TGAGCTGCGCTTAGCC-TA--------AGATCAGCCT-------------------------GCC-------AGACTGTTTGTCTA------------CTCCA------CTAATCGG------------------------GT------------------------------------------GTCT-------TTG------CTT--GTTTCCTTCCAGGATGACCGATCGCCTACCTCGTCGGGCAACGAGTCGGATGATTCGTCGGACGTGGAGATGCCG---GCGGAGGCTG---CTGA---GGTG---GCAA---CCA-------------AGTTGC---CG-G------------CCAGCAA-A---------ACAGAGGTA---TCAGCGCCT------------C------------------CAGCAGCCTCAT---G------------CTCGGCGGCCACCGCTTCC---------------------TCTGGCCACAAAACCA---TGC---CAGCATTGAACTATCAGACTGAC-ACCAACAGCGGACCCTCAACGTCCA------CCGCC------GCCGG----------------------------------AGGA---GGAGG----CTCGGCGG------------------------------A---CAGCAAGTACGTCTACTCCGCTGCCTCGA s droSim1.chr2R 18714111 362 + 19596830 TGAGCTGCGCTTAGCC-CA--------AGATCAGCCT-------------------------GCC-------AGACTGTTTGTCTA------------CTCCA------CTAATCGG------------------------GT------------------------------------------GTCT-------TTG------CTT--GTTTCCTTCCAGGATGACCGATCGCCTACCTCGTCGGGCAACGAGTCGGATGATTCGTCGGACGTGGAGATGCCG---GTGGAGGCTG---CTGA---GGTG---GCAA---CCA-------------AGTTGC---CG-G------------CCAGCAA-A---------ACAGAGGTA---TCAGCGCCT------------C------------------CAGCAGCCTCTT---G------------CTCGGCGGCCACCGCGTCC---------------------TCTGGCCCCAAAACCA---TGC---CAGCATTGAACTATCAGACTGAC-ACCAACAGCGGACCCTCGACGTCCA------CGGCC------GCCGG----------------------------------AGGA---GGAGG----CTCGGCGG------------------------------A---CAGCAAGTACGTCTACTCAGCTGCCTCGA s droSec1.super_23 133402 362 + 989336 TGATCTGCGCTTAGCC-TA--------AGATCAGCCT-------------------------GCC-------AGACTGTTTGTCTA------------CTCCA------CTAATCGG------------------------GT------------------------------------------GTCT-------TTG------CTT--GTTTCCTTCCAGGATGACCGATCGCCTACCTCGTCGGGCAACGAGTCGGATGATTCGTCGGACGTTGAGATGCCG---GTGGAGGCTG---CTGA---GGTG---GCAA---CCA-------------AGTTGC---CG-G------------CCAGCAA-A---------ACAGAGGTA---TCAGCGCCT------------C------------------CAGCAGCCTCAT---G------------CTCGGCGGCCACCGCGTCC---------------------TCTGGCCCCAAAACCA---TGC---CAGCATTGAACTATCAGACTGAC-ACCAACAGCGGACCCTCGACGTCCA------CGGCC------GCCGG----------------------------------AGGA---GGAGG----CTCGGCGG------------------------------A---CAGCAAGTACGTCTACTCAGCTGCCTCGA s droYak3.chr2R 20223584 370 + 21139217 TAAGCTATGCTTAGCT-TAACTGCTTGAGATCAGCCT-------------------------GCC-------AGACTGTTTGTCTA------------CTCCG------CTAATCGG------------------------GT------------------------------------------GTCT-------TGG------CTT--CTTTCTTTCCAGGATGACCGATCGCCTACCTCGTCGGGCAACGAGTCGGATGATTCGTCGGACGTGGAGATGCCG---TTGGAGGCGG---CTGA---GGTG---GCAA---CCA-------------AGTTGC---CG-G------------CCAGCAA-A---------ACAGAGGTA---TCAGCGCCT------------C------------------CAGCTGCGTCTT---G------------CTCGGCGGCCACCGCGTCC---------------------TCTGGCCCCAAAACCA---TGC---CAGCATTGAACTACCAGACTGAG-ACCAACAGCGGACCCTCGACGTCCA------CGGCC------GCCGG----------------------------------AGGA---GCAGC----CTCGGCGG------------------------------A---CAGCAAGTACGTCTACTCAGCTGCCTCGA s droEre2.scaffold_4845 21621106 362 + 22589142 TAAGCTACGCTTAGCC-TA--------AGATCAGCCT-------------------------GCC-------AGACTGTTTGTCTA------------CTCCA------CTAATCGG------------------------GT------------------------------------------GTCT-------CTG------CTT--GTTTCTTTCCAGGATGACCGATCGCCTACCTCGTCGGGCAACGAGTCGGATGATTCGTCGGACGTGGAGATGCCG---GTGGAGGCTG---CTGA---GGTG---GCAA---CCA-------------AGTTGC---CG-G------------CCAGCAA-A---------ACAGAGGTA---ACAGCGCCT------------C------------------CAGCCGCCTCCT---G------------CTCGGCGTCTGCCGCGTCC---------------------TCTGGCCCCAAAACCA---TGC---CAGCATTGAACTATCAGACTGAG-ACCAACAGCGGACCCTCGACGTCCA------CGGCC------GCCGG----------------------------------AGGA---GGAGC----CTCGGCGG------------------------------A---CAGCAAGTACGTCTACTCAGCTGCCTCGA s droBia2.KB462602 816172 385 + 3129309 ----CTAAGCTTAGCCTTA--------AGATCAGCCC-----------------------AGACC-------AGACTGTTTGTCTA------------CATCG------CTAATCGG------------------------GT------------------------------------------GTCT-------TGGCTTCTTCTT--GTTTCTTTCCAGGATGACCGATCGCCTACCTCGTCGGGCAACGAGTCGGATGACTCGTCGGACGTGGAGATGCCG---GTGGAGGCAG---CCGA---GGTG---GCAG---CCA-------------GATCACAATCC-G------------CCAGCAA-A---------ACAGAGCTA---TCAGCGCCT------------C------------------CCGCTGCCGCAC---C------------ATCATCATCTGCCTCATCT---------------------TCTGGCCCCAAAACCA---TGC---CAGCATTGAACTATCAGACTGAG-ACCAACAACGGACCCTCGACGTCCA------CAGCC------GCTGGAGCAGca----------ggtggt---------ggagga---ggagc----cccGGCGG------------------------------A---CAGCAAGTACGTCTACTCGGCTGCCTCGA s droSuz1.KI419649 12065502 379 - 14502029 ----CTAAGCTTAGCCTTA--------AGATCAGCCC-----------------------AGACC-------AGACTGTTTGTCTA------------CATCG------CTAATCGG------------------------GT------------------------------------------GTCT-------TGG------CTT--GTTTCTTTCCAGGATGACCGATCGCCTACCTCGTCGGGCAACGAGTCGGATGACTCGTCGGATGTGGAGATGCCG---GCGGAGGCTG---CCGA---GGTG---GCAG---CCA-------------AGTCACAATCA-G------------CCAGCAA-A---------ACAGAGCTA---TCAGCGCCT------------C------------------CCGTTGCcgcaccatc------------atcatcatctgccTCATCT---------------------TCTGGCCCCAAAACCA---TGC---CAGCATTGACCTATCAGACTGAG-ACTAACAACGGACCCTCGACGTCCA------CAGcc------gctgg---agga----------ggaggt---------gcagGA---GGAGC----CCCAGCGG------------------------------A---CAGCAAGTACGTCTACTCGGCTGCCTCGA s droAna3.scaffold_13266 5725770 408 - 19884421 ----CGAGGCTAAGCCTCG--------AGATCATCGG------------------------TACC-------AGACTGTTTGGCTG------------CACCA------CTAATCGA------------------------CT------------------------------------------GTCT----GTCTAA------CTT--GATTTGTTCTAGGATGAGCGATCGCCGACATCGTCGGGCAACGAATCGGATGACTCCTCCGACGTGGAGATGCCGGGTGCCGAGGTAA---TCGA---GGTG---GCCA---GCAGCAAGGCGG---TGGCCACGG-TG-G------------CCAGCAA-A---------ACAGAGGTTGCTCCTGCCCCG------------C------------------CAGCCGCAGCGG---GAAGTTCCGGGGCAACGGCAACCACCTCAGCC------------ACGGGA---GCGGGCTCCAAGCCCA---TGC---CAGCGTTGAACTATCAGACTGAG-------AACGGACCTTCGACGTCCA------CAGGA------GCGGCAGCGGGA----------GCATCA---------GGAGGA---GGTGC----CTCGGCGG------------------------------A---CAGCAAGTATGTCTATCCAGCCGCCTCGT s droBip2.KB464407 1975573 405 + 2915140 ----CGAGGCTAAGCCTCG--------AGATCATCGG------------------------GACC-------AGACTGTTTGGCTG------------CACCA------CTAATCGA------------------------CT------------------------------------------GTCT----GTCTAA------CTT--GATTTGTTCTAGGATGAGCGATCACCGACATCGTCGGGCAACGAATCGGATGACTCCTCCGATGTGGAGATGCCGGGTGGCGAGGTAA---TCGA---GGTG---GCTA---CCAGCAAGGC------GGCCACGG-TG-G------------CCAGCAA-A---------ACAGAGGTAGCTCCTGCCCCA------------C------------------CAACCGCAGCGG---GAACGTCCGGGGCAACGGCAGTCACCACAGCC------------ACGGGA---GCGGGCACCAAGCCCA---TGC---CAGCATTGAACTATCAGACTGAG-------AACGGACCATCGACGTCCA------CAgga------gccggagcagca----------gcagcg---------ggagcg---ggagc----CCCAGCGG------------------------------A---CAGCAAGTATGTCTACTCAGCTGCCTCGT s droEug2.KB465067 618573 374 + 1515531 TAAACTAAGCTTAGCC-TA--------AGATCAGCAG-------------------------GCC-------AGACTGTTTGTCTA------------CAGCA------CTAATCGT------------------------GT------------------------------------------GTCT-------TTG------CTC--TTCTCTTTCCAGGATGACCGATCGCCTACTTCGTCCGGCAACGAGTCGGATGATTCGTCGGATGTGGAGATGCCG---GCGGAGGCTG---CCGA---TGTG---GCAA---CCA-------------AGCCAC---CA-G------------CCAGCAA-A---------ACAGAGCTA---TCAGCGCCGTCTTCTGCACCAT------------------CAGCAGCCACAT---C------------GTCGGCGGCTGCCTCATCT---------------------TCTGGATCCAAAACCA---TGC---CACCATTGAACTATCAGACTGAG-ACTAACAACGGACCCTCGACGTCCA------CAGCA------GCTGG----------------------------------AGGA---GGAGC----CCCGGCGG------------------------------A---CAGCAAGTATGTCTACTCAGCCGCTTCGA s droEle2.KB458573 542645 394 - 5320397 GAAACCAAGCTTAGCCTTA--------AGATCAACAA-------------------------ACC-------AGACGGTTTGTCTAC-----------CACCA------CTAATCGA------------------------GT------------------------------------------GTCT----CTGTGG------CTT--CTTTCCTTGCAGGATGACCGATCGCCCACTTCGTCGGGCAACGAATCGGATGATTCGTCGGATGTGGAGATGCCC---GTGGAGGCAG---CCGAGGTGGTG---GCCG---CCA-------------AGTTAA---CG-G------------CCAGCAA-A---------ACAGAGGCA---TCAGCTCCT------------C------------------CA---GTCACAT---C------------TTCAGCGGCTGCCTCATCT------------TCGTCAACTTCTGGCAGCAAGGCCA---TGC---CAGCATTGAACTATCAGACTGAG----AACACCGGACCCTCGACCTCCa------cagca------gctggaggagga----------ggagga---gggggcggagga---gCGGC----CCCGGCGG------------------------------A---CAGCAAGTATGTCTACCCAGCTGCCTCGT s droKik2.KB459527 296066 388 - 1234237 TAAACCTGGCTTAGCCATA--------AGATC----C-------------------------GCC-------AGACTGTTTGGCTGC---------AGCACCA------CTAATCGA------------------------AT------------------------------------------GTGT-------TT-------CTT--GGTTACTTGCAGGATGAACGATCGCCGACCTCGTCGGGCAACGAGTCGGATGATTCCTCGGATGTGGAGATGCCG---GGAGAGGTCT---CGGA---GGTGTCTGCCT---CCA-------------AGCTGC---CA-G------------CTAGCAA-AGCCGAGGCTACAGCGGTC---TCAGCGCCAGCCACCACAGCCA------------------CGGCAGCCACAT---C------------TGCGACGGGAGCCTCAACT---------------------TCGGGCTCCAAGCCGA---TGC---CAGCATTGAACTATCAGACTGAG-------AACGGACCCTCGACGTCCA------CAGCG------GCTGCGACAGC----------------------------GGGT---GGATC----AGCGGCGG------------------------------ACAGCAGCAAGTACGTCTACCCGGCCGCCTCCT s droTak2.KB461535 161709 365 - 669855 ----CTAGGCTTAGTCTTA--------AGATCAGCCC-------------------------ACC-------AGACTGTTTGTCTG------------CAGCA------CTAATCGG------------------------GT------------------------------------------GTCG-------TGG------CTT--TTTTCTTTCCAGGATGACCGATCGCCTACCTCGTCGGGCAACGAGTCGGATGATTCGTCGGATGTGGAGATGCCA---GCGGAGGCTG---CCGA---GGTG---GCGG---CCA-------------AGTCACAACCA-G------------CCAGCAA-A---------ACAGAGCTA---TCAGCGCCT------------C------------------CTGCGGCCGCAC---C---------------GTCTTCTGCCTCATCT---------------------GCTGGCCCCAAAACCA---TGC---CAGCATTGAACTATCAGACTGAG-ACTAACAACGGACCCTCGACGTCCA------CAggc------gctgg---agga----------ggagga---ggagggggagga---ggagc----CCCAGCGG------------------------------T---------------TTACTCGGCTGCCTCGA s droRho2.KB449310 57203 395 - 65043 CAAACTAAGCTTAGCCTTA--------AGATCAGCAG-------------------------ACC-------AGACTGTTTGTCTAC-----------CACCA------CTAATCGA------------------------GT------------------------------------------gtctttggctttgg------ctt--ctTTCTTTCCAGGATGACCGATCGCCTACTTCGTCGGGCAACGAGTCGGATGATTCGTCGGATGTGGAGATGCCA---GTCGAGGCAG---CCGA---GGTG---GCAT---CCA-------------AGTTAA---CG-G------------CCAGCAA-A---------ACAGAGGTA---TCACCGCCT------------CCT---------------GCAGCGGCCTCAT---C------------TTCGGCGGCGGCCTCATCT---------------------TCTGGCTCCAAAACCA---TGC---CAGCATTGAACTATCAGACTGAG----AACACCGGACCCTCGACCTCCA------CAGCA------gctgctggagga----------ggaggaggaggagggggagga---ggagc----CTCGGCGG------------------------------A---CAGCAAGTATGTTTACCCAGCTGCCTCAT s droFic2.KB457177 98792 370 + 995874 AAGactaagctaggct-ta--------agatCAGCAC-------------------------AGC-------AGACTGTTTGTCTAC-----------CATTA------TTAATCGT------------------------GT------------------------------------------GTCT------CTGG------CTT--GACTCTTTGCAGGATGACCGATCGCCTACCTCGTCCGGCAACGAGTCGGATGACTCGTCGGATGTGGAGATGCCG---GTGGAGGCTG---CCGA---GGCG---GCAG---CCA-------------AGCTCC---CG-G------------CCAGCAA-A---------ACAGAggct---cctccgcct------------cctgccgcctcagcggcagcagctgccacgT---C------------CTCGGCGGCAGCCTCATCT---------------------TCTGGCTCCAAGGCGA---TGC---CAGCTTTGAACTATCAGACTGAG----AACAACGGACCCTCGACGTCCG------C-------------------------------------------------AGGC---GGAGC----CCCGGCGG------------------------------A---CAGCAAGTACGTTTACCCAGCTGCCTCGA s droPse3.chr3 1368678 418 - 19787792 TCAACTTAGCTCTGGCTta--------agatcagcagcagcagctgcaacagtagcagcagcacc-------agactGTTTGGCTGCACAGCGAAGAACCCCA------CTAATCGA------------------------GT------------------------------------------Gtct----------------atc--ttttttttgcaggATGATCGATCGCCAACATCGTCGGGCAATGAGTCGGACGACTCTTCGGACGTGGAAATGCCC---GCTGAAGTGGTGTCCGA---GGTG---GTGG---CCA-CAA---------AAGTGC---CA-GCCAGTCAGGATCCCAGCAA-A---------Acagaggcaacggcagcggcg------------a------------------cTGCAACGACAT---C------------TGCAACGGCAACTGCAGTA---------------------GCGGCATCCAAGCCGA---TGC---CAGCACTGAGCTATCAGACTGAG-------AAAGGACCCTCAACGTCCA------CGGTAGCAACTGCCGG----------------------------------AGGC---GGATC----GTCGGGGG------------------------------A---TGGCAAATATGTCTATCCGGGAGCCTCCT s droPer1.super_34 557563 418 - 916997 TCAACTTAGCTCTGGCTTA--------AGATcagcatcagcagcagcaacagtagcagcagcacc-------agACTGTTTGGCTGCACAGCGAAGAACCCCA------CTAATCGA------------------------GT------------------------------------------GTCT----------------ATC--TTTTTTTTGCAGGATGATCGATCGCCAACATCGTCGGGCAATGAGTCGGACGACTCTTCGGACGTGGAAATGCCC---GCTGAAGTGGTGTCCGA---GGTG---GTGG---CCA-CAA---------AAGTGC---CA-GCCAGTCAGGATCCCAGCAA-A---------ACAGAGGCAACGGCAGCGGCG------------A------------------CTGCAACGACAT---C------------TGCAACGGCAACTGCAGTA---------------------GCGGCATCCAAGCCGA---TGC---CAGCACTGAGCTATCAGACTGAG-------AAAGGACCCTCAACGTCCA------CGGCAACAACTGCCGG----------------------------------AGGA---GGATC----GTCGGGGG------------------------------A---TGGCAAATATGTCTATCCGGGAGCCTCCT s droMir2.chr3 1411462 420 - 20862834 TCAACTTAGCTCTGGCTta--------agatcagcagcagcagtagcaacagtagcagcagcacc-------agactGTTTGGCTGCACAGCGAAGAACCCCA------CTAATCGA------------------------GT------------------------------------------gtct----------------atcttttttttttgcaggatGATCGATCGCCAACATCGTCGGGCAATGAGTCGGACGACTCTTCGGACGTGGAAATGCCC---GCTGAAGTGGTGTCCGA---GGTG---GTGG---CCA-CAA---------AAGTGC---CA-GCCAGTCAGGATCCCAGCAA-A---------Acagaggcaacggcagcggcg------------a------------------cTGCAACGACAT---c------------tgcaacggcaactgcagca---------------------gcggcatccaAGCCGA---TGC---CAGCACTGAGCTATCAGACTGAG-------AAAGGACCCTCAACGTCCA------CGGCAGCAACTGCCGG----------------------------------AGGA---GGATC----GTCGGGGG------------------------------A---TGGCAAATATGTCTATCCGGGAGCCTCCT s droWil2.CH963894 1339085 438 + 2843958 AACTACAGACTTAAGCTTA--------AGATCA---T-------------------------AGC-------AGACTGTTTGGCTA------------CAACAGCAAGTCTaatccatctctctctctctctctcttttctct------------------------------------------gttt----------------ctc--tttttcttttaggaTGAACGTTCACCTACTTCATCTGGCAATGAATCGGATGATTCTTCGGATGTGGAAATGCCA---AGTGAAGTCA---CAGA---GCTG---Gaca---gcagcaaggcagaattaaatac---tgtg------------tcagcagca---------acagcaaca---acagcagcg------------g------------------cagcagcagcca---g------------cacATCGACTATAGTGACTGGAGGGGGAGGAGTGGGAGCAGGGGGATCTAAGGCAA---TGC---CAGCATTAAACCACCAGACTGAT-------CAAGGACCCTCATCGTCAA------AAG--------GCTGCAGTGGGGCTGCAGCAGTGCAGCC-----------AACT---GCCGC----ATCATCGG------------------------------A---TAGCAAGTATGTCTATCCGGCTGCCTCGT s droVir3.scaffold_12875 7375545 363 + 20611582 -----TCATCTTTGGCTTA--------AGATCAG----------------------------ACC-------AGACTGTTTGGCTG------------CATCT----CTCTAATCTC------------------------TT------------------------------------------GCCT----------------CTT--CTTGTCTTGCAGGATGAGCGTTCGCCAACATCGTCGGGCAACGAATCGGATGATTCTTCGGATGTGGAAATGCCA---ATGCCGATGG---ATGC---CGAC---GCAG---CCA-------------AGTCAG---CG-C------------CTCAGGA-G---------CTCAAG------GCAGAGACA------------G------------------CAGCAGCAGCAG---G------------------------GTCGGCC---------------------GCTTGCAGCAAACCAA---TGCCAGCAGCTTTGAGCTATCAGACTGAG-------ACTGGACCCTCGACGTCCA------CGgca------gcaacaacagca----------gcagc------------agca---gcagc----atcggcag------------caacagcagcaCCTG---A---TAGCAAATATGTTTATCCGGCCACTTCAT s droMoj3.scaffold_6496 26170168 428 + 26866924 -----TCATCTTTGGCTTAAGATC---AGATCAG----------------------------ACC-------AGACTGTTTGGCTGCAA---------CAACT----ATCTAATCTC------------------------ctcactctctccctctctctctctctctctctctgtctctctTGGTCT----------------ATT--CTGGTCTGGCAGGATGATCGCTCGCCAACATCGTCGGGCAACGAATCGGATGACTCTTCGGATGTGGAAATGCCG---TTGCCAGCCG---ACGC---CGAC---CCTGTTTCCA-------------AGGCAG---CA-G------------CACATGA-G---------CTTAAG------CCAGAGACT------------G------------------CAGCGTCCGTAG---G------------------------------------------------------TGGCCCAAAATCAA---TGCCGGCCTCATTAATCTATCAGACTGAG-------ACGGGTgcatcgacgtccacagcggcggca------gcagcagcagca----------gcagc------------agcatcggcagc----atcaacagcgtcgccagcgacagcagcagcaccag---a---taacaaATACGTTTATCCGGCCACCTCGT s droAlb1.JH854640 332926 410 + 406291 -----TAAGCATTGGCTTA--------AGATCAA----------------------------ACC-------AGACTGTTTGGCTGCAG---------CATGT--GAAACTGAtttt------------------------ctttctctcct---------------------------------cttt----------------ttt--ctttatttgcagGATGATCGATCGCCAACATCTTCGGGAAATGAGTCCGATGATTCGTCGGATGTGGAGATGCCGAGCACGGCGGCAG---ATGC---GGAG---GCTG---TTA-------------AATCTG---GG-C------------CTCTTGA-A---------CTTAAG------TGTGAGCCA------------ACAGCGAGCTGCTCTT---CAGCGACAGTCG---C------------------------GACGACT---------------------GTTGGCCCCAAGCCAA---TGCCAATAGCATTGAATTATCAGACTGAG-------ACTGGAccatccacatcca------cagcA------GCACTGACAGCA----------GCATC------------AGTG---GCAGCGGGAAGCAGCGG----ACTAACTGCAGCCACGTCGtctgataa---taataaatacgttTATCCAGCGACATCGT s droGri2.scaffold_15245 926250 385 + 18325388 -----TCATCTTTGGCTTA--------AGATCAG----------------------------GCC-------AGACTGTTTGGCTGCAA---------CAGTT-----TCTAATCTG------------------------CCCC----------------------------------------TTCT----------------CTC--TCTTTGTTGCAGGATGAACGTTCACCAACATCGTCTGGCAATGAATCGGATGATTCGTCCGATGTTGAAATGCCA---ATGCCAACGG---ATGC---CGTC---GATGATGCCA-------------AGCCAA---CG-C------------CTCAGGA-T---------CTGAAA------GCTGAGgca------------gctgcag------------cagcagcagcag---c---agtaacagcTACTACTTCAGTATCTGCC---------------------ACTTGCCCCAAGGCAA---------CAGCATTGAGTTATCAGACTGAA-------TCGGGACCCTCGACATCCA------TGgca------tcatccgcagtg----------gcagc------------aaca---gcagt----------gg------------cagcaacagcaCCGG---A---TAGCAAATATGTTTATCCGGCTACCTCGT s anoGam1.chr3L 4072509 378 + 41284009 CAAGCCGTGTTCAAACAAATTGCCAATAAGTCAACTT-------------------------GTCGTTACTGACACTGTTTTCTTT------------TTCCC------CTACC---------------------------GC------------------------------------------TTCT----------------CTT--TTTCTTCCGCAGGATGATCGGTCGCCGATGTCGTCCGGCAGTGAATCGGACGATTATTCGCCCCCGGAATCGCCC---CCTCCAGGAC---CTAG---CGTT---AATA---CTAGCAG---------TAATAC---CA-A------------CGTCAAC-A---------GTAGTAATAA--TCATCATTT------------G------------------CAGCCGCAGCAA---C------------CGCAGCAA-------GGCA---------------------GCTCGAACGAAAGGCACACTAC---CAGAAGTG--CTGGTACACAGAGTGCAGGAAGTGGTGCAGCATCAAGCA------CTGCT------GCCGGCACAGCA----------ACAACA-----------AGCG---TGATG----ACC-----------------------------------G---CTTCAAGTGCTGCTGCT--GCTGCTACCA a score=641988.000000 s dm6.chr2R 24375694 33 + 25286936 TTGCCAACATACCGCAGAAGATGCTGAGGCAGC s droSim1.chr2R 18714473 33 + 19596830 TCGCTAACATACCGCAGAAGATGCTGAGGCAGC s droSec1.super_23 133764 33 + 989336 TTGCTAACATACCGCAGAAGATGCTGAGGCAGC s droYak3.chr2R 20223954 33 + 21139217 TTGCCAACATACCGCAGAAGATGCTGAGGCAGC s droEre2.scaffold_4845 21621468 33 + 22589142 TTGCCAACATACCGCAGAAGATGCTGAGGCAGC s droBia2.KB462602 816557 33 + 3129309 TTGCCAACATACCGCAGAAAATGCTGAGGCAAC s droSuz1.KI419649 12065881 33 - 14502029 TTGCCAACATACCGCAGAAAATGCTGAGGCAAC s droAna3.scaffold_13266 5726178 33 - 19884421 TTGCCAACATACCGCCCAAAATGTTGAGGCAAC s droBip2.KB464407 1975978 33 + 2915140 TTGCCAATATACCGCCCAAAATGTTGAGGCAAC s droEug2.KB465067 618947 33 + 1515531 TTGCCAACATACCGCAGAAAATGTTGAGGCAGC s droEle2.KB458573 543039 33 - 5320397 TTGCCAACATACCGCAGAAAATGCTGAGGCAAC s droKik2.KB459527 296454 33 - 1234237 TTGCCAATATACCGCAGAAGATGCTGAGGCAAC s droTak2.KB461535 162074 33 - 669855 TTGCCAACATACCGCAGAAAATGCTTAGGCAAC s droRho2.KB449310 57598 33 - 65043 TTGCCAACATACCGCAGAAAATGCTGAGGCAAC s droFic2.KB457177 99162 33 + 995874 TCGCCAACATACCGCAGAAGATGCTGCGGCAGC s droPse3.chr3 1369096 33 - 19787792 TTGCCAACATACCGCCGAAAATGTTGAGGCAAC s droPer1.super_34 557981 33 - 916997 TTGCCAACATACCGCCGAAAATGTTGAGGCAAC s droMir2.chr3 1411882 33 - 20862834 TTGCCAACATACCGCCGAAAATGTTGAGGCAAC s droWil2.CH963894 1339523 33 + 2843958 TTGCCAATATACCGCCGGATATGCTAAGACAAC s droVir3.scaffold_12875 7375908 33 + 20611582 TTGCCAATATACCGCCGGACATGTTGCGCCAGC s droMoj3.scaffold_6496 26170596 33 + 26866924 TCGCCAATATACCGCCGGACATGCTGCGCCATC s droAlb1.JH854640 333336 33 + 406291 TTGCCAACATACCTCCCGATATGCTGCGTCAGC s droGri2.scaffold_15245 926635 33 + 18325388 TCGCCAATATACCGCCGGATATGCTGCGTCAGC s musDom2.KB857237 78576 33 - 101287 TTAACAATGTAACGCAGGATGTGCTGTTACAAT s anoGam1.chr3L 4072887 33 + 41284009 TTAACGCCATCcagcagcaaattcagcaacagc a score=764491.000000 s dm6.chr2R 24375727 47 + 25286936 TCATCCAGTCAGGCCACTTGCAGGTGCACGCCGAAGAGGGTAAGTA-------G s droSim1.chr2R 18714506 47 + 19596830 TCATCCAGTCGGGCCACTTGCAGGTGCACGCCGAAGAGGGTGAGTA-------G s droSec1.super_23 133797 47 + 989336 TCATCCAGTCGGGCCACTTGCAGGTGCACGCCGAAGAGGGTGAGTA-------G s droYak3.chr2R 20223987 47 + 21139217 TCATCCAGTCGGGCCACTTGCAGGTGCACGCCGAAGAGGGTGAGTA-------G s droEre2.scaffold_4845 21621501 47 + 22589142 TCATCCAGTCGGGCCACTTGCAGGTGCACGCCGAAGAGGGTGAGTA-------G s droBia2.KB462602 816590 47 + 3129309 TCATACAGTCGGGACACTTGCAGCTGCACGCCGAAGAGGGTGGGTA-------C s droSuz1.KI419649 12065914 47 - 14502029 TCATACAGTCGGGACACTTGCAGCTGCACGCTGAAGAGGGTGGGTA-------C s droAna3.scaffold_13266 5726211 47 - 19884421 TGATACGGACCGGACACTTGCAACTGCACGCTGAGGAAGGTGAGTA-------A s droBip2.KB464407 1976011 47 + 2915140 TGATACGGACGGGACACTTGCAACTGCACGCCGAGGAAGGTGAGTA-------A s droEug2.KB465067 618980 47 + 1515531 TCATACAGTCGGGACACTTGCAGCTGCACGCTGAAGAAGGTGGGTA-------A s droEle2.KB458573 543072 47 - 5320397 TTATACAAACAGGACACTTGCAGCTCCACGCTGAAGAGGGTAAGAA-------A s droKik2.KB459527 296487 51 - 1234237 TGATACAGACAGGACACTTGCAGCTGCACGCCGAGGAGGGTGAGTGT---ACCA s droTak2.KB461535 162107 47 - 669855 TCATACAGTCGGGACACTTGCAGCTGCACGCCGAAGAGGGTGAGTA-------C s droRho2.KB449310 57631 47 - 65043 TCATACAGACAGGACACTTGCAGCTTCACGCTGAAGAGGGTGAGTA-------A s droFic2.KB457177 99195 47 + 995874 TCATACAGTCGGGTCACTTGCAGCTCCACGCTGAAGAGGGTGTGTG-------C s droPse3.chr3 1369129 47 - 19787792 TGATACAAACGGGACACTTGCAGCTGCACGCTGAAGAGGGTGAGTG-------T s droPer1.super_34 558014 47 - 916997 TGATACAAACGGGACACTTGCAGCTGCACGCTGAAGAGGGTGAGTG-------T s droMir2.chr3 1411915 47 - 20862834 TGATACAAACGGGACACTTGCAGCTGCACGCTGAAGAGGGTGAGTG-------T s droWil2.CH963894 1339556 54 + 2843958 TGATACAAACCGGACACTTGCAAGTCCATGCTGAAGAGGGTGAGTAGTAAACAA s droVir3.scaffold_12875 7375941 47 + 20611582 TAATACAATCGGGTCAATTGCAGGTGCATGCCGAAGAAGGTGGGTA-------G s droMoj3.scaffold_6496 26170629 40 + 26866924 TAATACAGTCGGGCCAATTACAGATTCATGCCGAAGAAGG-------------- s droAlb1.JH854640 333369 47 + 406291 TGATCCAAGCGGGCCAGTTGCAAGTCCATGCCGAAGAGGGTGAGTA-------T s droGri2.scaffold_15245 926668 47 + 18325388 TTATACAATCAGGACAGTTGCAGCTCCATGCCGAGGAAGGTGAGTA-------A s musDom2.KB857237 78609 47 - 101287 TAATAGAATCAGGCCATCTACAAGTACATACCGAAGAAGGTAAGTG-------A a score=-417959.000000 s dm6.chr2R 24375774 44 + 25286936 CTCTG-AAGTCC-CCAAGC-------A-----AAGT-----------------------------CCCA-------------------------ATATCTAA--CAGTTGCTTA----- s droSim1.chr2R 18714553 44 + 19596830 CTCTG-AAGTCC-CCAAGC-------A-----AAGT-----------------------------CCCA-------------------------ATACTTAA--TAGTTACTTA----- s droSec1.super_23 133844 44 + 989336 CTCTA-AAGTCC-CCAAGC-------A-----AAGT-----------------------------CCCA-------------------------ATACTTAA--TAATTACTTA----- s droYak3.chr2R 20224034 44 + 21139217 CACTG-AAATCT-CTCAGT-------A-----AAGC-----------------------------GCCA-------------------------GTTCTAAA--CAGATATCCA----- s droEre2.scaffold_4845 21621548 44 + 22589142 CACTG-AAATCC-CCAACT-------A-----AAAT-----------------------------CCCA-------------------------GTACTAAG--CCGACACCCA----- s droBia2.KB462602 816637 45 + 3129309 TGCGA-AAATCC-TTCCCC-------A-----GAAt-----------------------------ctga-------------------------aaactaaaaccaTTTACCC------ s droSuz1.KI419649 12065961 46 - 14502029 TACGG-AAATCC-CTCCTT-------A-----TGat-----------------------------ctaa-------------------------aaactaaataaacttTCCCA----- s droAna3.scaffold_13266 5726258 38 - 19884421 TCCGG--------CCCAAA-------A-----TCAG-----------------------------GCTA-------------------------GAACTTGA--CTAACTTCTG----- s droBip2.KB464407 1976058 43 + 2915140 TCAGA--------CCAACA-------ACATGGCTAG-----------------------------ACTA-------------------------AAGCTAAA--CTAACTCCTA----- s droEug2.KB465067 619027 40 + 1515531 CTTGC-TAACCC-CC-----------A-----AAAT-----------------------------CTGA-------------------------AATCCTAA--TACCTTCTGT----- s droEle2.KB458573 543119 44 - 5320397 CTTAA-AGAgct-ttttaa-------c-----aaaa-----------------------------tcaa-------------------------taaattaa--taaacctTTA----- s droKik2.KB459527 296538 38 - 1234237 CATAG-ATATCT-ATAGCT-------A-----TGatta---------------------------ctat-------------------------atactata--ta------------- s droTak2.KB461535 162154 47 - 669855 TATGGGAAATCC-CTTACT-----TAA-----AAAC-----------------------------CCTG-------------------------AAACTAAT--TACATTTTCC----- s droRho2.KB449310 57678 45 - 65043 CTTCA-AGATTTAATACCT-------A-----AAAT-----------------------------Ctct-------------------------aaattaaa--tactattaTC----- s droFic2.KB457177 99242 45 + 995874 CTCAC-AGATCT-CACCTT-------G-----AAGT-A---------------------------TTCA-------------------------GCTGTTAA--TCATATCCCG----- s droPse3.chr3 1369176 45 - 19787792 TGCAA-AGAGTA-CCG----------A-----AGGT-----------------------------TTCACCAT---------------------AGATTTCA--CGACTGTCTC----- s droPer1.super_34 558061 45 - 916997 TGCAA-AGACTA-CCG----------A-----AGGT-----------------------------TTCACCAT---------------------AGATTTCA--CGACTGTCTC----- s droMir2.chr3 1411962 45 - 20862834 TGCAA-AGATTA-CCG----------A-----AGAT-----------------------------TTCACCAT---------------------AGATTTCA--CGACTGTCTC----- s droWil2.CH963894 1339610 51 + 2843958 TGTGG-AAAATT-CTAAATGAGAACAA-----GAGA-----------------------------TAGA-------------------------AAACTtga--caaacatttt----- s droMoj3.scaffold_6496 26170673 15 + 26866924 -----------------------------------------------------------------AATT-------------------------ATATATTC--TAA------------ s droAlb1.JH854640 333419 15 + 406291 -----------------------------------------------------------------CCTT-------------------------AAAATTGA--TCA------------ s droGri2.scaffold_15245 926715 68 + 18325388 -------------------------------------TCTCCAATCTCAATTGACAAGAAATATTCCTTTGAATATACCCGCATATGATTGGCAATAGttaa--taa------------ s musDom2.KB857237 78656 39 - 101287 ----------------------AATAA-----AAGT-----------------------------TAGA-AAG---------------------AAATATTG--TCATTATTTATCTTA a score=135681.000000 s dm6.chr2R 24375818 15 + 25286936 A--C-CT-----ACAGATGGCAA s droSim1.chr2R 18714597 15 + 19596830 A--C-CT-----GCAGATGGCAA s droSec1.super_23 133888 15 + 989336 A--C-CT-----GCAGATGGCAA s droYak3.chr2R 20224078 15 + 21139217 A--C-TT-----ACAGATGGCAA s droEre2.scaffold_4845 21621592 15 + 22589142 A--C-TT-----ACAGATGGCAA s droBia2.KB462602 816682 13 + 3129309 -----TT-----ACAGATGGCAA s droSuz1.KI419649 12066007 14 - 14502029 A----TT-----ACAGATGGCAA s droAna3.scaffold_13266 5726296 17 - 19884421 TCTC-CC-----ACAGATGGCAA s droBip2.KB464407 1976101 17 + 2915140 TCTC-CC-----ACAGATGGCAA s droEug2.KB465067 619067 15 + 1515531 C--C-TT-----ACAGATGGCAA s droEle2.KB458573 543163 20 - 5320397 T--C-TCCCCAAACAGATGGCAA s droKik2.KB459527 296576 14 - 1234237 ---t-tc-----aCAGATGGCAA s droTak2.KB461535 162201 15 - 669855 C--C-CT-----ACAGATGGCAA s droRho2.KB449310 57723 15 - 65043 T--T-TA-----ACAGATGGCAA s droFic2.KB457177 99287 15 + 995874 C--T-TT-----GCAGATGGAAA s droPse3.chr3 1369221 17 - 19787792 TATC-CG-----CCAGATGGCAA s droPer1.super_34 558106 17 - 916997 TATC-CG-----CCAGATGGCAA s droMir2.chr3 1412007 17 - 20862834 TATC-CG-----CCAGATGGCAA s droWil2.CH963894 1339661 16 + 2843958 t--c-tt----ggcaGATGGCAA s droVir3.scaffold_12875 7376350 15 + 20611582 --AT-TT-----CCAGATGGCAA s droMoj3.scaffold_6496 26170735 16 + 26866924 --ATATT-----CCAGATGGCAA s droAlb1.JH854640 333457 15 + 406291 --ac-tC-----TTAGATGGCAA s droGri2.scaffold_15245 926834 15 + 18325388 --GT-TT-----TTAGATGGCAA s musDom2.KB857237 78695 15 - 101287 --Tc-tt-----aaatattacaa a score=1985628.000000 s dm6.chr2R 24375833 345 + 25286936 CCAGTATGTGACCATACCGCTCAGCTCCACAGCAGCCAATCTGATAAAGAGCAATAAGCTAACAGC---------------------CTC------------TGGATCAGG---AGCC---------------TCAGGATCGGGA---ACGCC------CGTC---AAGAACGA------TGCCAGTG---CCGATAA---GCCCTTGACCATCAAACAGGAGTTCGATTAG----CCCCC------AGCT--------------ACG---CCTACTGCTTATCATGA---GATAACTGAGA---ACT--------------GCGTTT---------ATCCACA--CTTGCC-CACA--------CCA-----TCTGGA---AA-AAT------CATCAGCAGGAGATTACCA-------------------TTACT----C----------------ACCCACT--ACTCTC-------TT----AAAGT------------CTATCCA----AAG-----------T---TTTCACGTCATCA-CCG----------GGG-ATGA---CGATCGCCTGC------------------------TA-----AGTCTAAGTCATA---------C-----T---------A s droSim1.chr2R 18714612 344 + 19596830 CCAGTATGTGACCATACCACTCAGCTCCACGGCAGCCAATCTGATAAAGAGCAATAAGCTAACAGC---------------------CTC------------TGGATCAGG---AGCC---------------TCAGGATCGGGA---ACGCC------CGCC---AAGAACGA------TGCCAGTG---CCGACAA---GCCCTTGACCATCAAACAGGAGTTCGATTAG----CCCCC------AGCT--------------ACG---CCCACTGCTTATCCTGA---GATAACTGATA---ACT--------------GCGTTT---------ATCCACA--CTTGCC-CACA--------CCA-----TCTGGA---AA-AAT------CATCAGCAGGAGATTACCA-------------------TTACT----C----------------ACCCACT--ACTCTC-------TT----AAAGT------------CTATCCA----AAG---------------TTTCGCGTCATCAGCCA----------GGG-ATGA---CGATCGCCTGC------------------------TA-----AGTCTAAGTCATA---------C-----T---------- s droSec1.super_23 133903 344 + 989336 CCAGTATGTGACCATACCACTCAGCTCCACGGCAGCCAATCTGATAAAGAGCAATAAGCTAACAGC---------------------CTC------------TGGATCAGG---AGCC---------------TCAGGATCGGGA---ACGCC------CGTC---AAGAACGA------TGCCAGTG---CCGATAA---GCCCTTCACCATCAAACAGGAGTTCGATTAG----CCCCC------AGCT--------------ACG---CCCAGTGCTTATCCTGA---GATAACTGATA---ACT--------------GCGTTT---------ATCCACA--CTTGCC-CACA--------CCA-----TCTGGA---AA-AAT------CATCAGCAGGAGATTACCA-------------------TTACT----C----------------ACCCACT--ACTCTC-------TT----AAAGT------------CTATCCA----AAG---------------TTTCGCGTCATCAGCCA----------GGG-ATGA---CGATCGCCTGC------------------------TA-----AGTCTAAGTCATA---------C-----T---------- s droYak3.chr2R 20224093 364 + 21139217 CCAGTATGTGACCATACCACTGAGCTCCACGGCAGCGAACCTGATAAAGAGCAACAAGCTAACAGC---------------------CTC------------CGGATCGGT---AGCC---------------CCAGGATCAGGA---ACGCC------CGTC---AAGAACGATGCGAGTGCCAGTT---CCGACAA---GCCGTTGACCATCAAACAGGAGTTCGATTAG----ccccc------agcc--------------acg---cccactgcttGTCC-------ACCACTGAGT---ACT--------------GCGTTT---------ATCCACA--CTTGCCACACA--------CCA-----TCTGG----GA-AAT------CATCAGCAGGAGATTACCA-------------------TTACT----CCATACCATTACTCCATACCCACT--ACTCTC-------TT----AAAGT------------CTATCCA----AAG-----------T---TTTCGCGTCATCAGCCG----------GGG-ATGA---CGATCGCCTGC------------------------TA-----CATCTAAGTCata---------c-----t---------a s droEre2.scaffold_4845 21621607 334 + 22589142 CCAGTATGTGACCATACCACTCAGCTCCACGGCAGCCAACCTGATAAAGAGCAATAAGCTAACAGC---------------------CTC------------TGGGTCG---------------------------------GGA---GCGCC------CGTC---AAGAACGA------TGCCAGTG---CCGACAA---GCCCTTGACCATCAAACAGGAGTTCGATTAG----CCCCC------AGCT--------------ACG---CCCACTGCTTATCC-------ACCACTGAGA---ACT--------------GCGTTT---------ATCCACA--CTTGCC-CGCA--------TCA-----TCTGGA---GA-AAT------CATCAGCAGGAGATTACCA-------------------TTACT----C----------------ACCCACT--ACTCCCCTAAAGTCT----AAAGT------------CTATCCA----AAG-----------T---TTTCGCGTCATCAGCCG----------GGG-ATGA---CGATCGCCTGC------------------------TA-----CGTCTAAGTCATA---------C-----T---------A s droBia2.KB462602 816695 357 + 3129309 TCAGTATGTCACCATACCACTCAGCTCCACGGCGGCCAATCTGATCAAGAGCAACAAGCTAAGCGC---------------------CTC------------TGGATCAGG---AGCC------CCGGGTGGATCGGTAACGGGA---GCTGC------AGTC---AAGAGCGA------TCCCAGCG---CCGAGAA---ACCCTTGACCATCAAACAGGAATACGATTAG----CCCCC------AGCC--------------ACGCTACCCACTGCTTATCC-------AATACTGAGA---ACT--------------GCGTTT---------AACCACA--CTTGCC-CAAA--------TCA-----TCTGAG---AA-AAGAAA---CATCAGCAGGAGATTACCA-------------------TTACA----C----------------ACCCACT--ACTCTC-------TT----AAAGT------------CTATCCA----AAG-----------T---TTTCGCGTCGTCTCTAA----------GGG-ATGA---CGATCGCCTGC------------------------TA-----AGTCTAAGTCata---------c-----t---------a s droSuz1.KI419649 12066021 355 - 14502029 TCAATATGTTACCATACCACTCAGCTCCACGGCGGCCAATCTGATCAAGAGCAACAAGCTAACAGC---------------------CTC------------TGGATCAGG---AACC------TCGGTT---TCGGTGCCGGGA---ACTCC------AGTC---AAGAGCGA------TCCCAGTG---CCGAAAA---ACCCTTGACCATCAAACAGGAATACGATTAG----CCCCC------AGCT--------------ACGCTACCCACTGCTTATCC-------AATACTGAGA---ACT--------------GCGTTT---------AACCACA--CTTGCC-CACa--------tca-----tcttaa---aa-aaaaaa--gcatcAGCAGGAGATTCCCA-------------------TTACA----C----------------ACCCACT--ACTCTC-------TT----AAAGT------------CTATCCA----AAG-----------T---TTTCGCGTCGTCTGTAA----------CGG-ATGA---CGATCGCCTGC------------------------TA-----AGTCTAAGTCata---------c-----t---------a s droAna3.scaffold_13266 5726313 361 - 19884421 CCAATATGTGACCATACCCCTCAGCTCCACAGCTGCCAACCTAATCAAAAGTAATAAGCTAACAAC---------------------CTC---------CAGCGGAACAGC---AACA------------------GGATCAGGG---ACATCGACTGCCAGC---AAAACGGA------TCCAAGTG---CCGAACA---ACCTTTGACCATTAAACAGGAATATGATTAG----CAACC----GAAGCT--------------A-----CACACTGCTTATCCCGAACCGGAAACTGAAA---ACT--------------GCGTTT---------ATCCACA----GGCC-CAAG--------CTTACAATCCTCAT---GG-AAC------CTTCAGCAGGAGATGCCCA-------------------TCAC----------------------ACACACT---CTCTA-------TT----AAAGT------------CTATCCA----AAG-----------TCTATTTCATGTCATCATCCA----------ATG-GTGACCTCGATCGCCTGC------------------------TA-----AGTCTAAGTCATA---------C-----T---------A s droBip2.KB464407 1976118 370 + 2915140 CCAATATGTGACCATACCCCTCAGCTCCACAGCGGCCAACCTAATCAAAAGTAACAAGCTAATAAC---------------------CTC---------CAGCGGAACAGC---AACA------------GGAACGGGATCAGGG---ACCTCGACTGGCACC---AAAACGGA------TCAAAGTG---CCGAACA---ACCCTTGACCATCAAACAGGAATATGATTAG----CAACC----GAAGCC--------------A-----CCCACTGCTTATCCAGAATCGGAAACTGAGA---ACT--------------GCGTTT---------ATCCACA----GGCC-CAAG--------CCC-CCATCCTCAT---GG-AACCAA--TCCTCAGCAGGAGATGCCCA-------------------TCAC----------------------ACACACT---CTCTA-------TT----AAAGT------------CTATCCA----AAG-----------TTTATTTCATGTCATCATCCA----------ATG-GTGACCTCGATCGCCTGC------------------------TA-----AGTCTAAGTCATA---------C-----T---------A s droEug2.KB465067 619082 346 + 1515531 TCAGTATGTGACCATACCACTCAGCTCCACGGCGGCAAATCTGATCAAGAGCAACAAGCTAACAGC---------------------CTC------------TGCATCAGG---AGCC---------------TCAGGAACAGGA---ACTCC------GGCC---AAGAGCGA------TACCAGTG---CCGAGAA---ACCCTTGACTATCAAACAGGAATACGATTAG----CCCCC------AGCT--------------ACG---CCCACTGCTTATCC-------AATACTGAGA---ACT--------------GCGTTT---------ATCCACA--CTTGCC-CAAA--------CCA-----TTTGAA---AA-AAG------CATCAGCAGGAGATTACCA-------------------TTACCATTAC----------------ACCCACA--ACTCTC-------TT----AAAGT------------CTATCCA----AAG-----------T---TTTTACGTCATCAGTCA----------GGG-ATGA---CGGTCGCCTGC------------------------TA-----AGTCTAAGTCata---------c-----t---------a s droEle2.KB458573 543183 330 - 5320397 TCAGTATGTAACCATACCACTCAGTTCCACGGCGGCCAACCTGATCAAAAGCAATAAGTTACAGGC---------------------TTC------------AGGAGGATC---GGCT---------------TCAGGAGGAGGC---ACCGC------ATCG---AAAAGCGA------TCCCAGTG---CCGAGAA---ACCCTTGAGCATCAAACAGGAATACGATTAg----ccccc------tgcc--------------acg---cccactgcctATCC-------CATACCGAGA---ACT--------------GCGTTT---------ATCCACA--CTTGCC-CACA--------ACA-----TCTGAAAAGAA-AAT------CATCAGCAGGAGATTACCA-------------------TCACA----C----------------AACCACT--ATTCTC-------TT----AAAGT------------CTATCCA----AAG-----------T---TTTCGTA--------------------------GA---CGATCGCCGGC------------------------TA-----AGTCTAAGTCata---------c-----t---------a s droKik2.KB459527 296590 366 - 1234237 TCAGTATGTGACCATACCCCTAAGCTCCACTGCAGCCAACCTGATCAAGAGCAATAAGCTATCGGTGGCCAATAGTGGACCCTCGGGCTC------------TGGATCAGC---AACA------------------GCTACAGGG---ACCGC------TGCC---AAGTCAGA------ACCAAGTG---CCGAAAA---ACCTCTGACCATTAAACAGGAATACGATTAGCATCCCACC------AGCC--------------ACG---TCCACTGCTTATCC-------AATACTGAGA---ACT--------------GCGTTT---------ATCcacacacttgcc-cacacacacactcaa-----tcTGAA---A-----------GATCAGCAGG--------A-------------------TCATA----C----------------AC-------ACTCTC-------TA----AAAGT------------CTATCCA----AAG---------------TTTTGTATCATCATCCATCTAaagatgatg-ctga---tgatCGCCTGC------------------------TA-----AGTCTAAGTCata---------c-----t---------a s droTak2.KB461535 162216 355 - 669855 TCAGTATGTTACCATACCACTCAGCTCCACGGCGGCCAATCTGATTAAGAGCAACAAGCTAACAGC---------------------CTC------------CGGATCAGG---AACT------TCGGCT---TCGGTTTCGGGA---ACTCC------AGCCTCTAAGAGCGA------TCCCAGTGCTCCCGAGAA---ACCCTTGACCATCAAACAGGAATACGATTAG----CCCCC-----------------------------------TGATTATCCAAG----ATTACTGAGA---ACT--------------GCGTTT---------AACCACA--CTTGCC-CACA--------CCA-----TCTTAG---AA-AGAAAACAGCATCAGCAGGAGATTACCA-------------------TTACA----CCATT------------ACCAATT--ACTCTC-------TT----AAAGT------------CTATCCA----AAG-----------T---TTTCGCGTCATCTGTGA----------GGG-ATGA---CGATCGCCTGC------------------------TA-----AGTCTAAGTCata---------c-----t---------a s droRho2.KB449310 57738 354 - 65043 TCAGTATGTGACCATACCACTCAGCTCCACGACGGCCAACCTAATCAAGAGCAATAAGTTAACAGC---------------------CTC---------AGCAGGATCAGG---AGCT---------------TCAGGATCAGGA---AATGC------ATCG---AAAAGCGA------TCCCAGTG---CCGAGAA---ACCCTTGACTATCAAACAGGAATATGATTAG----CCCCC------AGCT--------------ACG---CCCACTGCTTATCC-------AATACTGAGA---ACT--------------GCGTTT---------ATCCACA--CTTGCC-CACAAAAACA--CCA-----TCTGAA---AACAAA------CACCAGCAGGAGATTACCA-------------------TTACA----C----------------ACCCACTATACCCAC-------TT----AAAGT------------CTATCCA----AAG-----------T---TTTCGCGTCATCATCCA----------AGG-ATGA---CGATCGCCTGC------------------------TA-----AGTCTAAGTCata---------c-----t---------a s droFic2.KB457177 99302 345 + 995874 CCAGTACGTGACCATACCGCTCAGCTCCACGGCGGCCAACCTGATCAAGAGCAACAAGCTGAGCGC---------------------CTC------------TGGATCGGG---AGCT---------------TCGGGGTCAGGA---ACTGC------CACT---AAAAGCGA------TCCCCAAG---CCGAGAA---ACCCCTGACCATCAAGCAGGAGTACGATTAG----ccccc------agcc--------------acg---cccactgcttACCC-------AATACCGAGA---ACT--------------GCGTTT---------AACCACA--CTTGCC-CAGAA-------CCA-----TCTGAA---GG-AGAAA----CACCAGCAGGAGACCACCA-------------------TTACT----C----------------ACCCACA--GCTCTC-------TT----GAAGT------------CTATCCA----AAG-----------T---TTTCGCGTCACCTTCCA----------CGG-ATGA---CGATCCCCTGC------------------------TA-----AGTCTAAGTCATA---------C-----T---------G s droPse3.chr3 1369238 357 - 19787792 TCAATATGTGACTATCCCGCTCAGCTCCACGGCAGCCAGTCTGATCAAGGGAAACAAATTGGCGGC---------------------CTCATCGTCCAGCGGTGgtcctgg---aggaggaggcggaggcggaggaggagtgggatCCACGGC------TATC---AAGTCAGA------GCAAACAC---CCGAGAAAACATCGTTGGTTATCAAACAGGAGTATGATTAG----CACCC------CGCT--------------ACG---ACCACTGCTTGTCC-------AACACTGAGA---ACG--------------GCGTTT---------ATCAGCA--CTGGCC-CGca--------aca-----aaagaa---ga-ag-------cagcagcaagggaTCCCCA-------------------GTACC----C-------------------------GTCTTC-------GC----AAAGT------------CTATTTA----AAG-----------T---TTTC------------------------------A---CGATCGCCTGC------------------------TA-----ACTCTAAGTCAta---------c-----tactacgagta s droPer1.super_34 558123 357 - 916997 TCAATATGTGACTATCCCGCTCAGCTCCACGGCAGCCAGTCTGATCAAGGGCAACAAATTGGCGGC---------------------CTCATCGTCCAGCGGTGGTCCTgg---aggaggaggcggaggcggaggaggagTGGGTTCCACGGC------TATC---AAGTCAGA------GCAAACAC---CCGAGAAAGCATCGTTGGTTATCAAACAGGAGTATGATTAG----CACCC------CGCT--------------ACG---ACCACTGCTTGTCC-------AACACTGAGA---ACG--------------GCGTTT---------ATCAGCA--CTGGCC-CGCA--------ACA-----AAAGAA---GA-AG-------CAGCAGCAAGGGATCCCCA-------------------GTACC----C-------------------------GTCTTC-------GC----AAAGT------------CTATATA----AAG-----------T---TTTC------------------------------A---CGATCGCCTGC------------------------TA-----ACTCTAAGTCATA---------C-----TACTACGAGTA s droMir2.chr3 1412024 351 - 20862834 TCAATATGTGACTATCCCGCTCAGCTCCACGGCAGCCAGTCTGATCAAGGGCAACAAATTGGCGGC---------------------CTCATCGGCCAGCGGTGgtcctgg---agga------ggaggcggaggaggagtaggatcCACGGC------TATC---AAGTCAGA------GCAAACAC---CCGAGAAAGCATCGTTGATTATCAAACAGGAGTATGATTAG----CACCC------CGCT--------------ACG---ACCACTGCTTGTCC-------AACACTGAGA---ACG--------------GCGTTT---------ATCAGCA--CTGGCC-CGCA--------ACA-----aaacaa---ga-ag-------cagcagcaagggaTCCCCA-------------------GTACC----C-------------------------GTCTTC-------GC----AAAGT------------CTATTTA----AAG-----------T---TTTC------------------------------A---CGATCGCCTGC------------------------TA-----ACTCTAAGTCAta---------c-----tactacgagta s droWil2.CH963894 1339677 374 + 2843958 TCAATATGTGACTATACCACTGAGTTCTTCGGCAGCCAGTCTCATCAAGGGCAATAAGATGGCAGC---------------------CTC---------AAGTAGTACACA---GTCT---------------TCTAATCCT------GCTCA------AGTG---AAGTCTGA------GCAGGTGG---CAGAGAA---ACCCCTATCTATCAAACAGGAATACGATTAA----CCCTA------GCCT--------------TCT---AGCACcaaataacaaacaacaaaaactggaA---AAT--------------GCTTTTATACAGAAAATCTATA--CTTGCC-------------CCA-----TTTGCA---GA-ACC------CCGAAGCAGGCTACAATCA-------------TAATTTTCACG----C----------------ACACATT--AATCAA-------CC----AAAACCAGAAATAAATACTATCCA----AAG-----------T---TTTC-----ATCTTTCA----------TTGCATAA---CCG--GCCTGC------------------------TC--TCTCATCTAAgtcata---------catacgt---------a s droVir3.scaffold_12875 7376365 390 + 20611582 CCAGTATGTTACCATACCGCTGAGCTCTACAGTGGCCAGCTACATTAAAGGCAAGTCCACGCCAGC---------------------GGC------------TGCAACTGT---CACC--------------------------A---GCGCC------AATC-CGAAGTCTGA------GAAAAGTG---CCGAGAA---AACTTTATCCATCAAACAGGAATATGATTAA----CCGTTCTTCAATGCGCTGAAGCGGCATAAATG---GAGATTGCTTTTATGAC----AACAAATTGA-AAATA--------------TTATAA---------ATCCATA--TCTAAT-CATG--------CAA-----TCCAAG---AC-AAA------ATacacacacatctacacaagcccaaacacacgcacactcact----c----------------acacactc-acatat-------gc-acacaAGT------------CTAACCA----TAGTATACACGCGTC---TCTTATAATAATGTTGG----------TCAAAAGC---TGATCA-----------------------------TACATATACACCCAGTC--A---------------T---------A s droMoj3.scaffold_6496 26170751 337 + 26866924 TCAGTATGTTACCATACCGCTGAGCTCCACCGTGGCCAGTTACATCAAAGGCAAGTCCACGACAGG---------------------GGC------------------------CACG--------------------------A---GCTCC------CATC-CGAAGTCTGA------GAAAAGTA---CCGAGAA---GGCCTTATCCATAAAGCAGGAATATGACTAG------------CATAGCG----ATTGGCCTAAACG---GAGACTGGTTTTACGGG----CATATTTGGATACATG--------------CTGTAA---------ATCCATA--TCTAAT-------------CGA-----TCCAAG---AC-AAA------acacttacccatatacata----------------------------c----------------acacactc-acatac-------ac--------------------------------------acaTGCGTC---TTTGATGATAATGTGGA----------TCAGACGC---TGATCACCCACACA---------------TACACGCACACACACACCAAGTCata---------------t---------a s droAlb1.JH854640 333472 319 + 406291 CCAATATGTGACTATACCGCTGAGCTCCACAGCCGCCAGCTACATCAAGGGCAAGTCCGCAACGGC---------------------TGC------------GAACACAGTGAACACC--------------------------A---ATCCC------AACC-CGAAGTCTGA------GAAGAGTG---CCGATAA---AACTCTGTCCATCAAACAGGAGTACGATTAG----CCTcc---caaaatt---------------ta---caaattgcttttatgac----aacattttga-ataca---------------tGTAA---------ATCC----------T-------------CAA-----GCATAA---AT-CAT------AAACATAACAATAGCGATA------------------------------------------------------ACAGGA-------ACGATCCAAGT------------CTATCCATTGTTAGATCGCACTTGCT---TCTTGTGGCGGCATAG-------------------------TCA-----------------------------TA-----AGACCGATTCATA---------------C---------A s droGri2.scaffold_15245 926849 400 + 18325388 TCAGTATGTGACCATACCACTGAGCTCCACTGTAGCCAGCTACATTAAGGGCAAATCAACGGCTGC---------------------TGC---------------AACTGT---CACC--------------------------A---GCTCC------AACC-AGAAGTCTGA------GAAGAGTG---CCGAGAA---AATCTTATCAATTAAACAGGAATACGATTAA----CCGTTCTTCAATGCATTGCAGTGGCATAAATG---GAGATTGCTTTTATGAC----AACATTTGAATAAATACTGTATACTGTATTCTGTAA---------ATCCATA--TCCAAT-CATG--------CAA-----CTCAAG---AC-ACA------AT-CACAACCAGATACACA----------------------------C----------------A--------ACATAT-------AC-ACACAAGT------------CTATCCA----TAG-----------T---TTTTATCATAATATTGA----------TGCATTGC---TGTTCACCCACACACATCTACGCCCAAGTCACACatatatatatatatatctatatttatatatc-----t---------a a score=525039.000000 s dm6.chr2R 24376178 43 + 25286936 TATC---TAC-------T------------------ATACCGTAT----ATATACTATTTTTTATACCTATA-CAA s droSim1.chr2R 18714956 43 + 19596830 TATC---TAC-------T------------------ATACCGTAT----ATATACTATTTTTTATACCTATA-CAA s droSec1.super_23 134247 43 + 989336 TATC---TAC-------T------------------ATACCGTAT----ATATACTATTTTTTATACCTATA-CAA s droYak3.chr2R 20224457 61 + 21139217 tatc---tac-------tataccgataccgataccgataccgtat----atatactattttttatacctata-cAA s droEre2.scaffold_4845 21621941 43 + 22589142 TATC---TAC-------T------------------ATACCGTAT----ATATACTATTTTTTATACCTATA-CAA s droBia2.KB462602 817052 42 + 3129309 tatc---tac-------t------------------atatcgtat----atatacta-tttttatacctata-cAA s droSuz1.KI419649 12066376 42 - 14502029 tatc---tac-------t------------------atatcgtat----atatacta-tttttatacctata-cAA s droAna3.scaffold_13266 5726674 45 - 19884421 TATC---TAC-------T------------------ATATCGTAT--ACATATACTA-TTTTTATACCTAAAGTGA s droBip2.KB464407 1976488 45 + 2915140 TATC---TAT-------T------------------ATATCGTAT--ACatatacta-tttttatacctaaagtga s droEug2.KB465067 619428 43 + 1515531 tatc---tac-------t------------------atatcgtat----atatactattttttatacctata-caa s droEle2.KB458573 543513 42 - 5320397 tatc---tac-------t------------------atatcgcat----atatacta-tttttatacctata-caa s droKik2.KB459527 296956 45 - 1234237 tatc---tac-------tat----------------atatcgtat----acatactattttttatacctata-caa s droTak2.KB461535 162571 43 - 669855 tatc---tac-------t------------------ataccgtat----atatactattttttatacctata-cAA s droRho2.KB449310 58092 43 - 65043 tatc---tac-------t------------------atatcgtat----atatactattttttatacctata-cAA s droFic2.KB457177 99647 42 + 995874 TATC---TAC-------C------------------ATATCGTAT----ATATacta-tttttatacctata-CAT s droPse3.chr3 1369595 45 - 19787792 tatccatTAT-------T------------------ATGTCGTAc----ataaacta-tttttatacctata-taa s droPer1.super_34 558480 45 - 916997 TATCCATTAT-------T------------------ATGTCGTAC----ATAAACTA-TTTTTATACCTATA-TAA s droMir2.chr3 1412375 45 - 20862834 tatccatTAT-------T------------------ATGTCGTac----ataaacta-tttttatacctata-taa s droWil2.CH963894 1340051 26 + 2843958 tatc---tac-------t-----------------------ttat----atctatta-----------tata--ga s droVir3.scaffold_12875 7376755 53 + 20611582 TAAC---TATATACGTAT------------------ATATCAAATTTATATAGACTA-TTTTTATACCTATA-TAA s droMoj3.scaffold_6496 26171088 53 + 26866924 tatc---tatacacgtat------------------atatcatatttatatagatta-tttttatacctata-taA s droAlb1.JH854640 333791 53 + 406291 GTAC---AGTTTATAcgt------------------atatcatatttatatagaata-tttttctaCCTTTA-TAA s droGri2.scaffold_15245 927249 53 + 18325388 tatc---tatataCGCAT------------------AAAACATATTTATATAGACTA-TTTTTATACCTATA-TAA s anoGam1.chr3L 4083955 43 + 41284009 TATT---TAC-------T------------------TTGTATTAA----ATATACTTTTTGGCATACCCGTA-TAA a score=-13059.000000 s dm6.chr2R 24376221 2 + 25286936 -GG s droSim1.chr2R 18714999 2 + 19596830 -GG s droSec1.super_23 134290 2 + 989336 -GG s droYak3.chr2R 20224518 2 + 21139217 -GA s droEre2.scaffold_4845 21621984 2 + 22589142 -GG s droBia2.KB462602 817094 2 + 3129309 -GG s droSuz1.KI419649 12066418 2 - 14502029 -GA s droAna3.scaffold_13266 5726719 2 - 19884421 -AT s droBip2.KB464407 1976533 2 + 2915140 -ag s droEug2.KB465067 619471 2 + 1515531 -gg s droEle2.KB458573 543555 2 - 5320397 -ga s droKik2.KB459527 297001 2 - 1234237 -ca s droTak2.KB461535 162614 2 - 669855 -GG s droRho2.KB449310 58135 2 - 65043 -GG s droFic2.KB457177 99689 2 + 995874 -GG s droPse3.chr3 1369640 2 - 19787792 -aa s droPer1.super_34 558525 2 - 916997 -AA s droMir2.chr3 1412420 2 - 20862834 -aa s droWil2.CH963894 1340077 2 + 2843958 -gc s droVir3.scaffold_12875 7376808 2 + 20611582 -AA s droGri2.scaffold_15245 927305 1 + 18325388 --G s anoGam1.chr3L 4083998 2 + 41284009 TA- a score=-67658.000000 s dm6.chr2R 24376223 18 + 25286936 -----AGAAGTGAA--AAAA-A------------------------------ACA-C s droSim1.chr2R 18715001 19 + 19596830 -----AGAAGTGAA--AGGATA------------------------------ACA-C s droSec1.super_23 134292 19 + 989336 -----AGAAGTGAA--AGGATA------------------------------ACA-C s droYak3.chr2R 20224520 17 + 21139217 -----AGAAGTG----AAGTGA------------------------------ACA-C s droEre2.scaffold_4845 21621986 19 + 22589142 -----AGAAGTGAA--AAGAGA------------------------------ACT-C s droBia2.KB462602 817096 21 + 3129309 -----AGGAGTGAG--AAGAGATG----------------------------AAA-C s droSuz1.KI419649 12066420 22 - 14502029 -----AAAAGTGAG--AAGAGATG---------------------------AAAA-C s droAna3.scaffold_13266 5726721 22 - 19884421 -----GAAAATGAAAGAAAAAA------------------------------AGCGC s droBip2.KB464407 1976535 19 + 2915140 -----gaaaatgaa--aaaaaa------------------------------cgc-C s droEug2.KB465067 619473 49 + 1515531 -----agaagtgaa--aagaaaagtgaaaaagaaaaggaaaaggaaaaggaaaaa-c s droEle2.KB458573 543557 20 - 5320397 -----aaaaaggag--aagaaa------------------------------agAAC s droKik2.KB459527 297003 31 - 1234237 -----agaagaaaa--aagtgaagaaatgaaatg------------------aaa-c s droTak2.KB461535 162616 33 - 669855 -----AGAAGTGAG--AAGAgatgagaaaaaaaaga----------------aaa-c s droRho2.KB449310 58137 19 - 65043 -----AGATGTGAG--AGAAGA------------------------------AAA-C s droFic2.KB457177 99691 17 + 995874 -----CGAAGTGAA--AAGG--------------------------------AAA-C s droPse3.chr3 1369642 17 - 19787792 -----agaagagaa--ggag--------------------------------aaa-c s droPer1.super_34 558527 17 - 916997 -----AGAAGAGAA--GGAG--------------------------------AAA-C s droMir2.chr3 1412422 17 - 20862834 -----agaagagaa--ggag--------------------------------aaa-c s droWil2.CH963894 1340079 22 + 2843958 -----atatataaa--actattttt---------------------------ata-c s droGri2.scaffold_15245 927319 6 + 18325388 -----AGACAC---------------------------------------------- s anoGam1.chr3L 4084000 18 + 41284009 CTTTTATAAAATAA--ACAC------------------------------------- a score=60163.000000 s dm6.chr2R 24376241 4 + 25286936 CCTG s droSim1.chr2R 18715020 4 + 19596830 CCTG s droSec1.super_23 134311 4 + 989336 CCTG s droYak3.chr2R 20224537 4 + 21139217 CCTG s droEre2.scaffold_4845 21622005 4 + 22589142 CCTG s droBia2.KB462602 817117 4 + 3129309 CCTG s droSuz1.KI419649 12066442 4 - 14502029 CCTG s droAna3.scaffold_13266 5726743 4 - 19884421 CCTA s droBip2.KB464407 1976554 4 + 2915140 CCTA s droEug2.KB465067 619522 4 + 1515531 cctG s droEle2.KB458573 543577 4 - 5320397 CCTG s droKik2.KB459527 297034 4 - 1234237 ccTG s droTak2.KB461535 162649 4 - 669855 cctg s droRho2.KB449310 58156 4 - 65043 CCTG s droFic2.KB457177 99708 4 + 995874 CCTG s droPse3.chr3 1369659 4 - 19787792 cCAA s droPer1.super_34 558544 4 - 916997 CCAA s droMir2.chr3 1412439 4 - 20862834 cCAA s droWil2.CH963894 1340101 4 + 2843958 ccta s droMoj3.scaffold_6496 26171174 4 + 26866924 CCTG s droGri2.scaffold_15245 927331 4 + 18325388 CTTG s anoGam1.chr3L 4084018 4 + 41284009 CTTG a score=-57477.000000 s dm6.chr2R 24376245 8 + 25286936 AG------CTGGTA s droSim1.chr2R 18715024 8 + 19596830 AG------CTGGTA s droSec1.super_23 134315 8 + 989336 AG------CTGGTA s droYak3.chr2R 20224541 8 + 21139217 AG------CTGGTA s droEre2.scaffold_4845 21622009 8 + 22589142 AG------CTGGTA s droBia2.KB462602 817121 8 + 3129309 AT------CTGGTA s droSuz1.KI419649 12066446 8 - 14502029 AT------CTGGTA s droAna3.scaffold_13266 5726747 8 - 19884421 GT------TGGGTT s droBip2.KB464407 1976558 8 + 2915140 GT------TGGGTC s droEug2.KB465067 619526 8 + 1515531 AT------CTGGTA s droEle2.KB458573 543581 1 - 5320397 A------------- s droKik2.KB459527 297038 1 - 1234237 A------------- s droTak2.KB461535 162653 8 - 669855 AT------CTGGTA s droRho2.KB449310 58160 8 - 65043 AT------CTGGTA s droFic2.KB457177 99712 8 + 995874 AC------CTGGTA s droPse3.chr3 1369663 3 - 19787792 CC------C----- s droPer1.super_34 558548 3 - 916997 CC------C----- s droMir2.chr3 1412443 3 - 20862834 CC------C----- s droWil2.CH963894 1340105 8 + 2843958 aa------CTGCCT s droMoj3.scaffold_6496 26171178 8 + 26866924 GGAACTGC------ s droGri2.scaffold_15245 927335 2 + 18325388 GC------------ a score=7480.000000 s dm6.chr2R 24376253 3 + 25286936 CCC s droSim1.chr2R 18715032 3 + 19596830 CCC s droSec1.super_23 134323 3 + 989336 CCC s droYak3.chr2R 20224549 3 + 21139217 GCC s droEre2.scaffold_4845 21622017 3 + 22589142 CCC s droBia2.KB462602 817129 3 + 3129309 CCC s droSuz1.KI419649 12066454 3 - 14502029 CCC s droAna3.scaffold_13266 5726755 1 - 19884421 C-- s droBip2.KB464407 1976566 3 + 2915140 CCC s droEug2.KB465067 619534 3 + 1515531 CCC s droKik2.KB459527 297039 2 - 1234237 -TC s droTak2.KB461535 162661 3 - 669855 CCC s droRho2.KB449310 58168 3 - 65043 CCC s droFic2.KB457177 99720 3 + 995874 CCC s droWil2.CH963894 1340113 1 + 2843958 T-- s droVir3.scaffold_12875 7376846 3 + 20611582 CTC s droMoj3.scaffold_6496 26171186 3 + 26866924 CTC s droGri2.scaffold_15245 927337 3 + 18325388 ATC a score=497551.000000 s dm6.chr2R 24376256 52 + 25286936 AAGATGCCAGCG---------GCAT---ATCTAC------------AT--ACGTAAG-TTTTA---------AAA-GT-TTTGCAAGT------TA s droSim1.chr2R 18715035 52 + 19596830 AAGATGCCAGCG---------GCAT---ATCTAC------------AT--ACGTAAG-TTTTA---------AAA-GT-TTTGCAAGT------TA s droSec1.super_23 134326 51 + 989336 AAGATGCCAGCG---------GCA----ATCTAC------------AT--ACGTAAG-TTTTA---------AAA-GT-TTTGCAAGT------TA s droYak3.chr2R 20224552 52 + 21139217 AAGATGCCAGCG---------GCAT---ATCTAC------------AT--ACGtaag-tttta---------aaa-gt-tttgcaaGT------TA s droEre2.scaffold_4845 21622020 52 + 22589142 AAGATGCCAGCG---------GCAT---ATCTAC------------AT--ACGTAAG-TTTTA---------AAA-GT-TTTGCAAGT------TA s droBia2.KB462602 817132 52 + 3129309 AAGTGGCCAGCG---------GCAT---ATCTAC------------AT--ACgtaag-tttta---------aaa-gt-tttgcaaGT------TA s droSuz1.KI419649 12066457 52 - 14502029 AAGATGCCAGCG---------GCAT---AGCTAC------------AT--ACgtaag-tttta---------aaa-gt-tttgcaaGT------TA s droAna3.scaffold_13266 5726756 41 - 19884421 ---------------------ATAT---ATCTAC------------GT--ACGTAAG-TTTTA---------AAG-AGTTTTGCAGGT------TA s droBip2.KB464407 1976569 61 + 2915140 AAGATGCCCAGCggcatatatacat---atatat------------ct--acGTAAG-TTTTA---------AAG-AG-TTTGCAGGT------TA s droEug2.KB465067 619537 43 + 1515531 AAG------------------ATAT---ATCTAC------------AT--ACGTAAG-TTTTA---------AAC-GT-TTTGCAAGT------TA s droEle2.KB458573 543582 48 - 5320397 ----TGCCAGCG---------GCAT---ATCTAC------------AT--ACgtaag-tttta---------aaa-gt-tttgcaagT------TA s droKik2.KB459527 297041 52 - 1234237 GCGATGCCAGCG---------TCAT---ATCTAC------------GT--ACGtaag-tttta---------aaa-gt-tttgcaagt------ta s droTak2.KB461535 162664 52 - 669855 AAGATGCCAGCG---------GCAT---ATCTAC------------AT--ACGtaag-tttta---------aaa-gt-tttgcaaGT------TA s droRho2.KB449310 58171 52 - 65043 AAGATGCCAGCG---------GCAT---ATCTAC------------AT--ACGTAAG-tttga---------aaa-gt-tttgcaaGT------TA s droFic2.KB457177 99723 52 + 995874 AAGTTGCCAGCG---------GCAT---ATCCAC------------GT--ACGtaag-tttta---------aaa-gt-tttgcaagA------TA s droPse3.chr3 1369666 69 - 19787792 ----TGCCAACg---------gcat---atctacatatatgaaaCTAT--ACGTaag-tttacaaaaaaaaaaat-gt-tctgcAAGC------TA s droPer1.super_34 558551 68 - 916997 ----TGCCAACG---------GCAT---ATCTACATATATGAAACTAT--ACGTAAG-TTTAC-AAAAAAAAAAT-GT-TCTGCAAGC------TA s droMir2.chr3 1412446 67 - 20862834 ----TGCCAACg---------gcat---atctacatatatgaaaCTAT--ACGtaag-tttac--aaaaaaaaat-gt-tctgcaAGC------TA s droWil2.CH963894 1340114 49 + 2843958 ----TGGcagat---------aaat---atttac------------ataaatgtaaG-TTTTA----------AA-GT-TTCACAAGg------at s droVir3.scaffold_12875 7376849 48 + 20611582 AAGCTGTCGGAG---------GCAG---A--TAA------------TT--GCATAAG-TTATA---------AAA----TTTACAAGT------TC s droMoj3.scaffold_6496 26171189 49 + 26866924 AAGCTGTCAGAG---------GCAG---A--TGC------------TT--GCGTAAGTTTATA---------AAG----TTTACAAGT------TA s droAlb1.JH854640 333891 60 + 406291 GAGCTGTCAAAG---------GCAGATTA--TAC------------TT--ACATAAG-TTACA---------TAAAGT-TTTGAAAGTTTTGCATC s droGri2.scaffold_15245 927342 48 + 18325388 TCTCAGTCAGAG---------GCAG---A--TAA------------TC--AAATAAG-TTATA---------AAG----TTTACAAGT------TC a score=-45910.000000 s dm6.chr2R 24376308 22 + 25286936 TACA-------ACGTACAGG--CATC---------TGCTG--- s droSim1.chr2R 18715087 22 + 19596830 TACA-------ACGTACAGG--CATC---------TGCTG--- s droSec1.super_23 134377 22 + 989336 TACA-------ACGTACAGG--CATC---------TGCTG--- s droYak3.chr2R 20224604 29 + 21139217 TACAACAACATACGTGCAGG--CATC---------TGCTG--- s droEre2.scaffold_4845 21622072 22 + 22589142 TACA-------ACGTACAGG--CATC---------TGCTG--- s droBia2.KB462602 817184 23 + 3129309 TACA-------ACCTAAAGG--CATT--------AAACTG--- s droSuz1.KI419649 12066509 23 - 14502029 TACA-------ACCTAAAGG--CATT--------AAACTG--- s droBip2.KB464407 1976630 22 + 2915140 ----------------AAGG--CATTAAACTTGTATGATG--- s droEug2.KB465067 619580 23 + 1515531 TACA-------ACGTAAAGG--CATT--------AAACCG--- s droEle2.KB458573 543630 23 - 5320397 TGCA-------TCGTAAAGG--CATT--------ACACTG--- s droKik2.KB459527 297093 24 - 1234237 taaa-------tcataaaaaaccata---------aactG--- s droTak2.KB461535 162716 23 - 669855 TACA-------ACGTAAAGG--CATT--------AAACTG--- s droRho2.KB449310 58223 23 - 65043 TACA-------TCGTAATGG--CATT--------AAACTG--- s droFic2.KB457177 99775 23 + 995874 TACA-------ACGGAAAAG--CATT--------ACACTG--- s droPse3.chr3 1369735 16 - 19787792 --------------TGAAAG--CATC--------ATATTG--- s droPer1.super_34 558619 16 - 916997 --------------TGAAAG--CATC--------ATATTG--- s droMir2.chr3 1412513 16 - 20862834 --------------TGAAAA--CATC--------ATATTG--- s droWil2.CH963894 1340163 21 + 2843958 --ta-------agatgaatt--cata--------ataaag--- s droVir3.scaffold_12875 7376897 18 + 20611582 ---------------TATGA--GATT--------GAATCGCTG s droMoj3.scaffold_6496 26171238 18 + 26866924 ---------------ATTGA--GATT--------AAATACCGG s droAlb1.JH854640 333951 18 + 406291 ---------------GATGA--GATT--------GAATAAcag s droGri2.scaffold_15245 927390 18 + 18325388 ---------------TATGA--GATT--------GAATAACAG a score=1358118.000000 s dm6.chr2R 24376330 143 + 25286936 ATATCGA---------------------GAT-TGTATGA-GAAATG---GAA--------AA----------------------------------------TG--------------AGG---ATGATATGGATGTTCCTA--AATCGCAGAGATCAT-----------------------------------GTTGCTTTGTTACTAGTTTATATTG---TTTTATTAT-------ACAATAC-ATAAATAC--ATATAAACC-AC-TTTTTTTGCAT----AAAACC s droSim1.chr2R 18715109 142 + 19596830 ATATCGA---------------------GAT-TGTATGA-GAAATG---G-A--------AA----------------------------------------TG--------------AGG---ATGATATGGATGTTCCTA--AATCGCAGAGATCAT-----------------------------------GTTGCTTTGTTACTAGTTTATATTG---TTTTATTAT-------ACAATAC-ATAAATAC--ATATAAACC-AC-TTTTTTTGCAT----AAAACC s droSec1.super_23 134399 141 + 989336 ATATCGA---------------------GAT-TGTATGA-GAAATG---G-A--------AA----------------------------------------TG--------------AGG---ATGATGTGGATGTTCCTA--AATCGCAGAGATCAT-----------------------------------GTTGCTTTGTTACTAGTTTATATTG---TTTTATTAT-------ACAATAC-ATAAATAC--ATATAAACC-AC--TTTTTTGCAT----AAAACC s droYak3.chr2R 20224633 161 + 21139217 AAATCGAGATGAATTAT----GATCGATGAT-TGTATGA-GAAATG---GAA--------AA----------------------------------------CG--------------GGG---ATGATATGGATGTTCCTA--AATCGCAGAGATCAT-----------------------------------GTTGCTTTGTTACTAgtttatattg---ttttattat-------acaatac-ataaatac--atataaaccaac-tttttttgcat----aaaacc s droEre2.scaffold_4845 21622094 160 + 22589142 ATATCGAGATGAATTAT----GATCGGTGAT-TGTATGA-GAAATG---GAA--------AA----------------------------------------TG--------------AGG---ATGATATGGATGTTCCTA--AATCGCAGAGATCAT-----------------------------------GTTGCTTTGTTACTAGTTTATATTG---TTTTATTAT-------ACAATAC-ATAAATAC--ATATAAACC-AC-TTTTTTTGCAT----AAAACC s droBia2.KB462602 817207 163 + 3129309 ATATCGAGATGAACTAT----GATCGATGAT-TGTatga-gaaatg---gaa--------aa----------------------------------------cg-------gaATGTAAGG---ATGATATGGATGTTCCTA--AATCGCAGAGATCAT-----------------------------------GTTGCTTTGTTACTagtttatattg---ttttattat-------acagtac-ataaatac--at----aat-ac-tttttttgcat----aaaacc s droSuz1.KI419649 12066532 163 - 14502029 ATATCGAGATGAACTAT----GATCGATGAT-TGTATGA-GAAATG---GAT--------AA----------------------------------------TG-------GAAAGTAAGG---ATGATATGGATGTTCCTA--AACCGCAGAGATCAT-----------------------------------GTTGCTTTGTTACTagtttatattg---ttttattat-------acaatac-ataaatac--at----aat-ac-tttttttgcat----aaaacc s droAna3.scaffold_13266 5726815 145 - 19884421 ATGATGA---------------------AAC-TGAATTA-TGATCG---GAA--------AG----------------------------------------TG--------------AGG---ATGATATGGATGTTCCTA--AACCGCAGAGATCAT-----------------------------------GTTGCTTTGTTACTAGTTTATATTG---TTTTATTAT-------ACAATACAATGGATACATATATAAACC-AC-TTTTTTTGCAT----AAAAA- s droBip2.KB464407 1976652 143 + 2915140 -AAatga---------------------attatgaatta-tgaTCG---GAA--------AG----------------------------------------TG--------------AGG---ATGATATGGATGTTCCTA--AACCGCAGAGATCAT-----------------------------------GTTGCTTTGTTACTAgtttatattg---ttttattat-------acaaTACAACGGATAC--Atataaacc-ac-tttttttgcat----aaaaa- s droEug2.KB465067 619603 160 + 1515531 ATATCGAGATGAATTAG----GATCGATGAT-TGAATGA-TAAATG---GAG--------AA----------------------------------------CA--------------AGG---ATGATATGGATGTTCCTA--AACCGCAGAGATCAT-----------------------------------GTTGCTTTGTTACTagtttatattg---ttttattat-------acaacac-ataaatac--atataaacC-AC-tttttttGCAT----AAAACC s droEle2.KB458573 543653 159 - 5320397 ATATCGAGATGATTAAT----GATCGATGA--TAAATga-gaaatg---gaa--------aa----------------------------------------ca--------------agG---ATGATATGGATGTTCCTA--AATCGCAGAGATCAT-----------------------------------GTTGCTTTGTTACtagtttatattg---ttttattat-------acaatac-ataaatac--atataaacc-ac-tttttttgcat----aaaatc s droKik2.KB459527 297119 173 - 1234237 GTATCGAGATGAATTATGATCGATCGATGAT-TGAATGA-GAAATG---G-A--------AA----------------------------------------CA--------------AGGATAATGATATGGATGTTCCTA--AACCGCAGAGATCAT-----------------------------------GTTGCTTTGTTACTAGTTTATAtcg---ttttattata-aaaaaaaaatactgaaaatac--atataaatc-ac-tttttttgcat----aaaaag s droTak2.KB461535 162739 157 - 669855 --------------------ATATCGATGAT-TGAATGA-Gaaacg---gaa--------aa----------------------------------------tggaaaacggaaAGTAAGG---ATGATATGGATGTTCCTA--AATCACAGAGATCAT-----------------------------------GTTGCTTTGTTACTagtttatattg---ttttattat-------acaatac-ataaatac--atataaacc-AC--TTTTTTGCAT----AAAACC s droRho2.KB449310 58246 160 - 65043 ATATCGAGATGAATTAT----GATCGATGAT-TAAAtga-gaaatg---gaa--------aa----------------------------------------ca--------------agG---ATGATATGGATGTTCCTA--AATCGCAGAGATCAT-----------------------------------GTTGCTTTGTTACTagtttatattg---ttttattat-------acaatac-ataaatac--atataaacc-ac-tttttttgcat----aaaacc s droFic2.KB457177 99798 172 + 995874 ATATCGGGATGAATAC-----GATCGATGGT-TGAAtga-gaaatg---gaa--------aa----------------------------------------gggaaaatggaaaacaagg---ATGATATGGATGTTCCTA--AACCGCAGAGATCAT-----------------------------------GTTGCTTTGTTACTagtttatattg---ttttattat-------acaatac-atgaatat--atataaacc-aC--TTTTTTGCAT----AAAACC s droPse3.chr3 1369751 170 - 19787792 AGTTCGGGATCAA--------GATCGATAAA-GAGGGAA-GAAAGA---GAAGGATAATTGA----------------------------------------ta--------------atg---aggatgaggatgttCCTA--AACCGCAGAGGTCAA-----------------------------------GTTGCTTTGttaatagtttatattg---ttttattatattatatacaatac-ataaatat--atatgaaac-ac--ttttttgcat----ataaaa s droPer1.super_34 558635 163 - 916997 AGTTCGGGATCAA--------GATCGATAAG-GAGGGAA-GAAAGA---GAAG-------GA----------------------------------------TA--------------ATG---AGGATGAGGATGTTCCTA--AACCGCAGAGGTCAA-----------------------------------GTTGCTTTGTTAATAGtttatattg---ttttattatattatatacaatac-ataaatat--atatGAAAC-AC--TTTTTTGCAT----ATAAAA s droMir2.chr3 1412529 162 - 20862834 AGTTCGGGATCAA--------GATCGATAAA-G-gggaa-gaaaga---gaag-------ga----------------------------------------ta--------------atg---aggatgaggatgttcCTA--AACCGCAGAGGTCAA-----------------------------------GTTGCTTTGttaatagtttatattg---ttttattatattatatacaatac-ataaatat--atatgaaac-ac--ttttttgcat----ataaaa s droWil2.CH963894 1340187 173 + 2843958 -----------------------ataatgct-tatgcta-atgctaat-gat--------ga----------------------------------------tg--------------atg---atgatgatgatgttccTAACAGCTGCAGAGTTaatgaacaaacaaacaaaatattaaaagaaaaagatacGTTGCTTTGTTAATAgtttatattg---ttttattat-------actatat-atatatac--acatgaaat-at--------gaaa----aaaaac s droVir3.scaffold_12875 7376915 142 + 20611582 ---------------------------AGAT-GAAGTTA-ATGAGAT--GAG--------GA-----------------------------AATGATTATGCCG--------------ATG---ATGATGATAATGTTCCTA--AGCCGCAGATGAAAA-----------------------------------GTTGCTTTGTTAATAGTTTATATTGT--TTTTATTAT-------ATTATAC-----------ACATAAACC-AC-TTTTTTTGCAA----AACAAC s droMoj3.scaffold_6496 26171256 132 + 26866924 ---------------------------AGAT-GGAGTTA-ATGAGA------------------------------------------------------------------------ACG---ATGATGATCATGTTCCTA--GGCTGCAGATGAAAA-----------------------------------GTTGCTTTGTTAATAGTTTATTTGATTGTTCTATTATATG----ATGATAC-----------ACATGGACC-GT-TTTTGCCACAACAACAACAAC s droAlb1.JH854640 333969 138 + 406291 ---------------------------agat-cagatcagatcagatcagaa--------ga-----------------------------gatcagaAGTTTG--------------GC-------AGAATGATGTTCCTA--AGCTGCAGATATAAA-----------------------------------GTTGCTTTGTTAATagtttatattg---ttttattat-------att-tac-----------agataaacc-at-tttt-ttgcaa----aacaat s droGri2.scaffold_15245 927408 172 + 18325388 ---------------------------AGAT-GAAGTTA-AGGAGG---AAG--------GAGTCAACatgatgatgatgatgatgatgatgatgatgatgctg--------------atg---aagctgatgatgTTCCTA--AGCTGCCGATATAAA-----------------------------------GTTGCTTTGTTAATAGTTTATATTG---TTTTATTAT-------ATTATAC-----------ATATAAACC-ACATTTTTTTGCCA--ACAACACC #eof