chrX	Cufflinks	exon	147778655	147779463	0.043602	-	.	gene_id "LID20732-LID20733_CUFF.38433.1,LID20819-LID20820_CUFF.46496.1,LID21042-LID21043_CUFF.35946.1"; transcript_id "LID20732-LID20733_CUFF.38433.1,LID20819-LID20820_CUFF.46496.1,LID21042-LID21043_CUFF.35946.1"; new_id "cuff.tx_re11";
chr7	Cufflinks	exon	86643764	86644827	0.014676	-	.	gene_id "LID47032-LID47033_CUFF.77817.1"; transcript_id "LID47032-LID47033_CUFF.77817.1"; new_id "cuff.tx_re108";
chr6	Cufflinks	exon	140372519	140373697	0.007418	-	.	gene_id "LID20920-LID20921_CUFF.21734.1,LID20732-LID20733_CUFF.14448.1"; transcript_id "LID20920-LID20921_CUFF.21734.1,LID20732-LID20733_CUFF.14448.1"; new_id "cuff.tx_re148";
chr5	Cufflinks	exon	3343531	3343758	0.011894	-	.	gene_id "LID47032-LID47033_CUFF.50110.1"; transcript_id "LID47032-LID47033_CUFF.50110.1"; new_id "cuff.tx_re151";
chr2	Cufflinks	exon	29701079	29701205	0.011761	-	.	gene_id "LID47030-LID47031_CUFF.7860.1"; transcript_id "LID47030-LID47031_CUFF.7860.1"; new_id "cuff.tx_re253";
chr19	Cufflinks	exon	11986744	11987391	0.027042	-	.	gene_id "LID20821-LID20822_CUFF.60845.1"; transcript_id "LID20821-LID20822_CUFF.60845.1"; new_id "cuff.tx_re286";
chr18	Cufflinks	exon	11054180	11054878	0.094778	-	.	gene_id "LID20868-LID20869_CUFF.64996.1"; transcript_id "LID20868-LID20869_CUFF.64996.1"; new_id "cuff.tx_re310";
chr17	Cufflinks	exon	84105944	84106203	0.078886	-	.	gene_id "LID20821-LID20822_CUFF.58037.1"; transcript_id "LID20821-LID20822_CUFF.58037.1"; new_id "cuff.tx_re338";
chr15	Cufflinks	exon	59478620	59479754	0.014940	-	.	gene_id "LID20870-LID20871_CUFF.30431.1,LID20920-LID20921_CUFF.47035.2,LID20730-LID20731_CUFF.33300.1,LID21183-LID21184_CUFF.33634.1,LID47148-LID47149_CUFF.63951.3"; transcript_id "LID20870-LID20871_CUFF.30431.1,LID20920-LID20921_CUFF.47035.2,LID20730-LID20731_CUFF.33300.1,LID21183-LID21184_CUFF.33634.1,LID47148-LID47149_CUFF.63951.3"; new_id "cuff.tx_re362";
chr4	Cufflinks	exon	106512874	106513999	0.009128	+	.	gene_id "LID46950-LID46951_CUFF.34270.1,LID46985-LID46986_CUFF.38986.1"; transcript_id "LID46950-LID46951_CUFF.34270.1,LID46985-LID46986_CUFF.38986.1"; new_id "cuff.tx_re699";
chr3	Cufflinks	exon	89084193	89084581	0.008550	+	.	gene_id "LID47148-LID47149_CUFF.13373.1"; transcript_id "LID47148-LID47149_CUFF.13373.1"; new_id "cuff.tx_re728";
chr2	Cufflinks	exon	160934995	160936032	0.052807	+	.	gene_id "LID47036-LID47037_CUFF.25040.2,LID47030-LID47031_CUFF.12856.2,LID20920-LID20921_CUFF.7701.2,LID20872-LID20873_CUFF.6660.2,LID21040-LID21041_CUFF.5814.1,LID20924-LID20925_CUFF.8020.2,LID21179-LID21180_CUFF.6728.2,LID20922-LID20923_CUFF.10489.1,LID46950-LID46951_CUFF.19757.3,LID47144-LID47145_CUFF.9979.1"; transcript_id "LID47036-LID47037_CUFF.25040.2,LID47030-LID47031_CUFF.12856.2,LID20920-LID20921_CUFF.7701.2,LID20872-LID20873_CUFF.6660.2,LID21040-LID21041_CUFF.5814.1,LID20924-LID20925_CUFF.8020.2,LID21179-LID21180_CUFF.6728.2,LID20922-LID20923_CUFF.10489.1,LID46950-LID46951_CUFF.19757.3,LID47144-LID47145_CUFF.9979.1"; new_id "cuff.tx_re739";
chr11	Cufflinks	exon	118914912	118915483	0.003107	+	.	gene_id "LID46983-LID46984_CUFF.88987.1"; transcript_id "LID46983-LID46984_CUFF.88987.1"; new_id "cuff.tx_re958";
chr10	Cufflinks	exon	120787894	120788627	0.046830	+	.	gene_id "LID20819-LID20820_CUFF.27760.1,LID20732-LID20733_CUFF.23070.1,LID20821-LID20822_CUFF.37965.1"; transcript_id "LID20819-LID20820_CUFF.27760.1,LID20732-LID20733_CUFF.23070.1,LID20821-LID20822_CUFF.37965.1"; new_id "cuff.tx_re996";
chr10	Cufflinks	exon	108448214	108449783	0.013124	+	.	gene_id "LID46948-LID46949_CUFF.102315.1"; transcript_id "LID46948-LID46949_CUFF.102315.1"; new_id "cuff.tx_re999";
chr10	Cufflinks	exon	61245719	61247230	0.173644	+	.	gene_id "LID20732-LID20733_CUFF.22102.1,LID20924-LID20925_CUFF.34224.1,LID21040-LID21041_CUFF.25469.1,LID20730-LID20731_CUFF.23526.1,LID21038-LID21039_CUFF.37610.1,LID20821-LID20822_CUFF.36428.1"; transcript_id "LID20732-LID20733_CUFF.22102.1,LID20924-LID20925_CUFF.34224.1,LID21040-LID21041_CUFF.25469.1,LID20730-LID20731_CUFF.23526.1,LID21038-LID21039_CUFF.37610.1,LID20821-LID20822_CUFF.36428.1"; new_id "cuff.tx_re1020";
chr1	Cufflinks	exon	180206264	180206908	0.011200	+	.	gene_id "LID47036-LID47037_CUFF.10871.1,LID20821-LID20822_CUFF.3523.1,LID21040-LID21041_CUFF.2471.1,LID20730-LID20731_CUFF.2193.1"; transcript_id "LID47036-LID47037_CUFF.10871.1,LID20821-LID20822_CUFF.3523.1,LID21040-LID21041_CUFF.2471.1,LID20730-LID20731_CUFF.2193.1"; new_id "cuff.tx_re1033";
chr1	Cufflinks	exon	166388220	166389604	0.122850	+	.	gene_id "LID20728-LID20729_CUFF.2274.1"; transcript_id "LID20728-LID20729_CUFF.2274.1"; new_id "cuff.tx_re1038";
chrX	Cufflinks	exon	147778695	147779449	0.104255	-	.	gene_id "LID21040-LID21041_CUFF.44876.1"; transcript_id "LID21040-LID21041_CUFF.44876.1"; new_id "cuff.tx_re1086";
chrX	Cufflinks	exon	147768542	147768556	0.104255	-	.	gene_id "LID21040-LID21041_CUFF.44876.1"; transcript_id "LID21040-LID21041_CUFF.44876.1"; new_id "cuff.tx_re1086";
chrX	Cufflinks	exon	147779060	147779449	0.072195	-	.	gene_id "LID21038-LID21039_CUFF.67212.1"; transcript_id "LID21038-LID21039_CUFF.67212.1"; new_id "cuff.tx_re1087";
chrX	Cufflinks	exon	147775377	147775404	0.072195	-	.	gene_id "LID21038-LID21039_CUFF.67212.1"; transcript_id "LID21038-LID21039_CUFF.67212.1"; new_id "cuff.tx_re1087";
chr2	Cufflinks	exon	115901593	115901785	0.010903	-	.	gene_id "LID47036-LID47037_CUFF.20871.1"; transcript_id "LID47036-LID47037_CUFF.20871.1"; new_id "cuff.tx_re1678";
chr2	Cufflinks	exon	115900949	115901483	0.010903	-	.	gene_id "LID47036-LID47037_CUFF.20871.1"; transcript_id "LID47036-LID47037_CUFF.20871.1"; new_id "cuff.tx_re1678";
chr15	Cufflinks	exon	59479509	59479758	0.007261	-	.	gene_id "LID47030-LID47031_CUFF.78350.2"; transcript_id "LID47030-LID47031_CUFF.78350.2"; new_id "";
chr15	Cufflinks	exon	59479144	59479358	0.007261	-	.	gene_id "LID47030-LID47031_CUFF.78350.2"; transcript_id "LID47030-LID47031_CUFF.78350.2"; new_id "";
chr15	Cufflinks	exon	59478975	59479142	0.018813	-	.	gene_id "LID47030-LID47031_CUFF.78350.2"; transcript_id "LID47030-LID47031_CUFF.78350.2"; new_id "";
chr15	Cufflinks	exon	59478829	59478970	0.018813	-	.	gene_id "LID47030-LID47031_CUFF.78350.2"; transcript_id "LID47030-LID47031_CUFF.78350.2"; new_id "";
chr15	Cufflinks	exon	59479424	59479758	0.011552	-	.	gene_id "LID47030-LID47031_CUFF.78350.1"; transcript_id "LID47030-LID47031_CUFF.78350.1"; new_id "";
chr15	Cufflinks	exon	59479144	59479422	0.011552	-	.	gene_id "LID47030-LID47031_CUFF.78350.1"; transcript_id "LID47030-LID47031_CUFF.78350.1"; new_id "";
chr15	Cufflinks	exon	59478975	59479142	0.018813	-	.	gene_id "LID47030-LID47031_CUFF.78350.1"; transcript_id "LID47030-LID47031_CUFF.78350.1"; new_id "";
chr15	Cufflinks	exon	59478829	59478970	0.018813	-	.	gene_id "LID47030-LID47031_CUFF.78350.1"; transcript_id "LID47030-LID47031_CUFF.78350.1"; new_id "";
chr15	Cufflinks	exon	59479567	59479750	0.007681	-	.	gene_id "LID47148-LID47149_CUFF.63951.2"; transcript_id "LID47148-LID47149_CUFF.63951.2"; new_id "cuff.tx_re1954";
chr15	Cufflinks	exon	59478757	59479528	0.007681	-	.	gene_id "LID47148-LID47149_CUFF.63951.2"; transcript_id "LID47148-LID47149_CUFF.63951.2"; new_id "cuff.tx_re1954";
chr15	Cufflinks	exon	59479509	59479704	0.014630	-	.	gene_id "LID20920-LID20921_CUFF.47035.3,LID47144-LID47145_CUFF.61721.1"; transcript_id "LID20920-LID20921_CUFF.47035.3,LID47144-LID47145_CUFF.61721.1"; new_id "cuff.tx_re1955";
chr15	Cufflinks	exon	59478727	59479358	0.014630	-	.	gene_id "LID20920-LID20921_CUFF.47035.3,LID47144-LID47145_CUFF.61721.1"; transcript_id "LID20920-LID20921_CUFF.47035.3,LID47144-LID47145_CUFF.61721.1"; new_id "cuff.tx_re1955";
chr15	Cufflinks	exon	59479614	59479700	0.001357	-	.	gene_id "LID47148-LID47149_CUFF.63951.1"; transcript_id "LID47148-LID47149_CUFF.63951.1"; new_id "cuff.tx_re1956";
chr15	Cufflinks	exon	59479509	59479610	0.001357	-	.	gene_id "LID47148-LID47149_CUFF.63951.1"; transcript_id "LID47148-LID47149_CUFF.63951.1"; new_id "cuff.tx_re1956";
chr15	Cufflinks	exon	59478757	59479358	0.001357	-	.	gene_id "LID47148-LID47149_CUFF.63951.1"; transcript_id "LID47148-LID47149_CUFF.63951.1"; new_id "cuff.tx_re1956";
chr15	Cufflinks	exon	59479511	59479679	0.015269	-	.	gene_id "LID20920-LID20921_CUFF.47035.1"; transcript_id "LID20920-LID20921_CUFF.47035.1"; new_id "cuff.tx_re1957";
chr15	Cufflinks	exon	59478823	59479360	0.015269	-	.	gene_id "LID20920-LID20921_CUFF.47035.1"; transcript_id "LID20920-LID20921_CUFF.47035.1"; new_id "cuff.tx_re1957";
chr13	Cufflinks	exon	91600115	91600318	0.014987	-	.	gene_id "LID46985-LID46986_CUFF.120709.1"; transcript_id "LID46985-LID46986_CUFF.120709.1"; new_id "cuff.tx_re2133";
chr13	Cufflinks	exon	91599435	91600113	0.014987	-	.	gene_id "LID46985-LID46986_CUFF.120709.1"; transcript_id "LID46985-LID46986_CUFF.120709.1"; new_id "cuff.tx_re2133";
chr11	Cufflinks	exon	66340086	66340447	0.014996	-	.	gene_id "LID46985-LID46986_CUFF.102962.1"; transcript_id "LID46985-LID46986_CUFF.102962.1"; new_id "cuff.tx_re2233";
chr11	Cufflinks	exon	66340060	66340082	0.014996	-	.	gene_id "LID46985-LID46986_CUFF.102962.1"; transcript_id "LID46985-LID46986_CUFF.102962.1"; new_id "cuff.tx_re2233";
chr11	Cufflinks	exon	66339732	66340058	0.014996	-	.	gene_id "LID46985-LID46986_CUFF.102962.1"; transcript_id "LID46985-LID46986_CUFF.102962.1"; new_id "cuff.tx_re2233";
chr4	Cufflinks	exon	106512832	106513335	0.013034	+	.	gene_id "LID46948-LID46949_CUFF.40942.1"; transcript_id "LID46948-LID46949_CUFF.40942.1"; new_id "cuff.tx_re3003";
chr4	Cufflinks	exon	106513337	106513738	0.013034	+	.	gene_id "LID46948-LID46949_CUFF.40942.1"; transcript_id "LID46948-LID46949_CUFF.40942.1"; new_id "cuff.tx_re3003";
chr3	Cufflinks	exon	79090734	79091247	0.011126	+	.	gene_id "LID20732-LID20733_CUFF.6207.1"; transcript_id "LID20732-LID20733_CUFF.6207.1"; new_id "cuff.tx_re3094";
chr3	Cufflinks	exon	79091652	79091694	0.011126	+	.	gene_id "LID20732-LID20733_CUFF.6207.1"; transcript_id "LID20732-LID20733_CUFF.6207.1"; new_id "cuff.tx_re3094";
chr2	Cufflinks	exon	160935013	160935057	0.121720	+	.	gene_id "LID46987-LID46988_CUFF.26125.2"; transcript_id "LID46987-LID46988_CUFF.26125.2"; new_id "cuff.tx_re3145";
chr2	Cufflinks	exon	160935060	160935087	0.121720	+	.	gene_id "LID46987-LID46988_CUFF.26125.2"; transcript_id "LID46987-LID46988_CUFF.26125.2"; new_id "cuff.tx_re3145";
chr2	Cufflinks	exon	160935090	160935878	0.097650	+	.	gene_id "LID46987-LID46988_CUFF.26125.2"; transcript_id "LID46987-LID46988_CUFF.26125.2"; new_id "cuff.tx_re3145";
chr2	Cufflinks	exon	160935051	160935348	0.048615	+	.	gene_id "LID46946-LID46947_CUFF.25899.1"; transcript_id "LID46946-LID46947_CUFF.25899.1"; new_id "cuff.tx_re3148";
chr2	Cufflinks	exon	160935350	160936167	0.024670	+	.	gene_id "LID46946-LID46947_CUFF.25899.1"; transcript_id "LID46946-LID46947_CUFF.25899.1"; new_id "cuff.tx_re3148";
chr18	Cufflinks	exon	23197841	23198060	0.016193	+	.	gene_id "LID20922-LID20923_CUFF.70910.1"; transcript_id "LID20922-LID20923_CUFF.70910.1"; new_id "cuff.tx_re3290";
chr18	Cufflinks	exon	23198252	23198975	0.016193	+	.	gene_id "LID20922-LID20923_CUFF.70910.1"; transcript_id "LID20922-LID20923_CUFF.70910.1"; new_id "cuff.tx_re3290";
chr16	Cufflinks	exon	5007391	5007418	0.270512	+	.	gene_id "LID47144-LID47145_CUFF.63611.1"; transcript_id "LID47144-LID47145_CUFF.63611.1"; new_id "cuff.tx_re3463";
chr16	Cufflinks	exon	5007837	5007981	0.603416	+	.	gene_id "LID47144-LID47145_CUFF.63611.1"; transcript_id "LID47144-LID47145_CUFF.63611.1"; new_id "cuff.tx_re3463";
chr16	Cufflinks	exon	5008065	5008162	0.270512	+	.	gene_id "LID47144-LID47145_CUFF.63611.1"; transcript_id "LID47144-LID47145_CUFF.63611.1"; new_id "cuff.tx_re3463";
chr16	Cufflinks	exon	5008299	5008334	1.074069	+	.	gene_id "LID47144-LID47145_CUFF.63611.1"; transcript_id "LID47144-LID47145_CUFF.63611.1"; new_id "cuff.tx_re3463";
chr12	Cufflinks	exon	88640779	88641198	0.006950	+	.	gene_id "LID21042-LID21043_CUFF.25167.1"; transcript_id "LID21042-LID21043_CUFF.25167.1"; new_id "cuff.tx_re3733";
chr12	Cufflinks	exon	88641293	88641626	0.006950	+	.	gene_id "LID21042-LID21043_CUFF.25167.1"; transcript_id "LID21042-LID21043_CUFF.25167.1"; new_id "cuff.tx_re3733";
chr11	Cufflinks	exon	118914850	118915168	0.008768	+	.	gene_id "LID46946-LID46947_CUFF.127741.1"; transcript_id "LID46946-LID46947_CUFF.127741.1"; new_id "cuff.tx_re3826";
chr11	Cufflinks	exon	118915171	118915512	0.008768	+	.	gene_id "LID46946-LID46947_CUFF.127741.1"; transcript_id "LID46946-LID46947_CUFF.127741.1"; new_id "cuff.tx_re3826";
chr10	Cufflinks	exon	61245719	61247023	0.341191	+	.	gene_id "LID47032-LID47033_CUFF.106641.1"; transcript_id "LID47032-LID47033_CUFF.106641.1"; new_id "cuff.tx_re3959";
chr10	Cufflinks	exon	61247025	61247025	0.341191	+	.	gene_id "LID47032-LID47033_CUFF.106641.1"; transcript_id "LID47032-LID47033_CUFF.106641.1"; new_id "cuff.tx_re3959";
chr10	Cufflinks	exon	61247027	61247027	0.341191	+	.	gene_id "LID47032-LID47033_CUFF.106641.1"; transcript_id "LID47032-LID47033_CUFF.106641.1"; new_id "cuff.tx_re3959";
chr10	Cufflinks	exon	61247030	61247036	0.341191	+	.	gene_id "LID47032-LID47033_CUFF.106641.1"; transcript_id "LID47032-LID47033_CUFF.106641.1"; new_id "cuff.tx_re3959";
chr10	Cufflinks	exon	61247038	61247088	0.341191	+	.	gene_id "LID47032-LID47033_CUFF.106641.1"; transcript_id "LID47032-LID47033_CUFF.106641.1"; new_id "cuff.tx_re3959";
chr10	Cufflinks	exon	61247090	61247139	0.341191	+	.	gene_id "LID47032-LID47033_CUFF.106641.1"; transcript_id "LID47032-LID47033_CUFF.106641.1"; new_id "cuff.tx_re3959";
chr10	Cufflinks	exon	61247142	61247216	0.341191	+	.	gene_id "LID47032-LID47033_CUFF.106641.1"; transcript_id "LID47032-LID47033_CUFF.106641.1"; new_id "cuff.tx_re3959";
chr10	Cufflinks	exon	61247218	61247236	0.341191	+	.	gene_id "LID47032-LID47033_CUFF.106641.1"; transcript_id "LID47032-LID47033_CUFF.106641.1"; new_id "cuff.tx_re3959";
chr10	Cufflinks	exon	61247240	61247241	0.341191	+	.	gene_id "LID47032-LID47033_CUFF.106641.1"; transcript_id "LID47032-LID47033_CUFF.106641.1"; new_id "cuff.tx_re3959";
chr10	Cufflinks	exon	61247243	61247266	0.341191	+	.	gene_id "LID47032-LID47033_CUFF.106641.1"; transcript_id "LID47032-LID47033_CUFF.106641.1"; new_id "cuff.tx_re3959";
chr10	Cufflinks	exon	61247268	61247319	0.341191	+	.	gene_id "LID47032-LID47033_CUFF.106641.1"; transcript_id "LID47032-LID47033_CUFF.106641.1"; new_id "cuff.tx_re3959";
chr10	Cufflinks	exon	61247324	61247342	0.341191	+	.	gene_id "LID47032-LID47033_CUFF.106641.1"; transcript_id "LID47032-LID47033_CUFF.106641.1"; new_id "cuff.tx_re3959";
chr10	Cufflinks	exon	61247344	61247429	0.341191	+	.	gene_id "LID47032-LID47033_CUFF.106641.1"; transcript_id "LID47032-LID47033_CUFF.106641.1"; new_id "cuff.tx_re3959";