# HG changeset patch
# User iuc
# Date 1589389049 14400
# Node ID 2dfbcb88d16a30253659e93dcbbb69388b62f927

"planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"

diff -r 000000000000 -r 2dfbcb88d16a test-data/control1.bam
Binary file test-data/control1.bam has changed
diff -r 000000000000 -r 2dfbcb88d16a test-data/control2.bam
Binary file test-data/control2.bam has changed
diff -r 000000000000 -r 2dfbcb88d16a test-data/gtf.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gtf.gtf	Wed May 13 12:57:29 2020 -0400
@@ -0,0 +1,779 @@
+chrX	refGene	exon	14118058	14118761	.	+	.	gene_id "l(1)G0007"; transcript_id "NM_167396"; exon_number "3"; exon_id "NM_167396.3"; gene_name "l(1)G0007";
+chrX	refGene	3UTR	14118656	14118761	.	+	.	gene_id "l(1)G0007"; transcript_id "NM_167396"; exon_number "3"; exon_id "NM_167396.3"; gene_name "l(1)G0007";
+chr2L	refGene	exon	18711071	18711733	.	-	.	gene_id "Irk3"; transcript_id "NM_136059"; exon_number "1"; exon_id "NM_136059.1"; gene_name "Irk3";
+chr2L	refGene	3UTR	18711071	18711336	.	-	.	gene_id "Irk3"; transcript_id "NM_136059"; exon_number "1"; exon_id "NM_136059.1"; gene_name "Irk3";
+chr2L	refGene	exon	11128807	11129335	.	+	.	gene_id "Nup160"; transcript_id "NM_135649"; exon_number "14"; exon_id "NM_135649.14"; gene_name "Nup160";
+chr2L	refGene	3UTR	11128927	11129335	.	+	.	gene_id "Nup160"; transcript_id "NM_135649"; exon_number "14"; exon_id "NM_135649.14"; gene_name "Nup160";
+chr2L	refGene	exon	10324379	10324990	.	+	.	gene_id "CG4995"; transcript_id "NM_135536"; exon_number "5"; exon_id "NM_135536.5"; gene_name "CG4995";
+chr2L	refGene	CDS	10324379	10324962	.	+	2	gene_id "CG4995"; transcript_id "NM_135536"; exon_number "5"; exon_id "NM_135536.5"; gene_name "CG4995";
+chr2L	refGene	3UTR	10324966	10324990	.	+	.	gene_id "CG4995"; transcript_id "NM_135536"; exon_number "5"; exon_id "NM_135536.5"; gene_name "CG4995";
+chr2L	refGene	stop_codon	10324963	10324965	.	+	0	gene_id "CG4995"; transcript_id "NM_135536"; exon_number "1"; exon_id "NM_135536.1"; gene_name "CG4995";
+chr2L	refGene	exon	6487562	6488372	.	-	.	gene_id "KFase"; transcript_id "NM_135192"; exon_number "1"; exon_id "NM_135192.1"; gene_name "KFase";
+chr2L	refGene	3UTR	6487562	6487596	.	-	.	gene_id "KFase"; transcript_id "NM_135192"; exon_number "1"; exon_id "NM_135192.1"; gene_name "KFase";
+chr2L	refGene	exon	6063562	6063771	.	-	.	gene_id "Fbw5"; transcript_id "NM_135145"; exon_number "1"; exon_id "NM_135145.1"; gene_name "Fbw5";
+chr2L	refGene	3UTR	6063562	6063687	.	-	.	gene_id "Fbw5"; transcript_id "NM_135145"; exon_number "1"; exon_id "NM_135145.1"; gene_name "Fbw5";
+chr2L	refGene	exon	4461657	4462563	.	-	.	gene_id "CG15443"; transcript_id "NM_134995"; exon_number "1"; exon_id "NM_134995.1"; gene_name "CG15443";
+chr2L	refGene	3UTR	4461657	4461823	.	-	.	gene_id "CG15443"; transcript_id "NM_134995"; exon_number "1"; exon_id "NM_134995.1"; gene_name "CG15443";
+chr2L	refGene	exon	5521281	5522007	.	-	.	gene_id "CG7371"; transcript_id "NM_135087"; exon_number "1"; exon_id "NM_135087.1"; gene_name "CG7371";
+chr2L	refGene	3UTR	5521281	5521377	.	-	.	gene_id "CG7371"; transcript_id "NM_135087"; exon_number "1"; exon_id "NM_135087.1"; gene_name "CG7371";
+chr2L	refGene	stop_codon	5521378	5521380	.	-	0	gene_id "CG7371"; transcript_id "NM_135087"; exon_number "1"; exon_id "NM_135087.1"; gene_name "CG7371";
+chr2L	refGene	exon	4969285	4970216	.	+	.	gene_id "CG3756"; transcript_id "NM_135041"; exon_number "2"; exon_id "NM_135041.2"; gene_name "CG3756";
+chr2L	refGene	3UTR	4970147	4970216	.	+	.	gene_id "CG3756"; transcript_id "NM_135041"; exon_number "2"; exon_id "NM_135041.2"; gene_name "CG3756";
+chr2L	refGene	exon	4815680	4815891	.	+	.	gene_id "CG15629"; transcript_id "NM_135015"; exon_number "4"; exon_id "NM_135015.4"; gene_name "CG15629";
+chr2L	refGene	CDS	4815680	4815779	.	+	1	gene_id "CG15629"; transcript_id "NM_135015"; exon_number "4"; exon_id "NM_135015.4"; gene_name "CG15629";
+chr2R	refGene	exon	3709615	3709990	.	-	.	gene_id "cathD"; transcript_id "NM_143756"; exon_number "1"; exon_id "NM_143756.1"; gene_name "cathD";
+chr2R	refGene	3UTR	3709615	3709729	.	-	.	gene_id "cathD"; transcript_id "NM_143756"; exon_number "1"; exon_id "NM_143756.1"; gene_name "cathD";
+chr2R	refGene	exon	11428922	11430003	.	+	.	gene_id "Vha36-1"; transcript_id "NM_143730"; exon_number "1"; exon_id "NM_143730.1"; gene_name "Vha36-1";
+chr2R	refGene	CDS	11429042	11429779	.	+	0	gene_id "Vha36-1"; transcript_id "NM_143730"; exon_number "1"; exon_id "NM_143730.1"; gene_name "Vha36-1";
+chr3R	refGene	exon	27625356	27626336	.	-	.	gene_id "CG42233"; transcript_id "NM_143642"; exon_number "1"; exon_id "NM_143642.1"; gene_name "CG42233";
+chr3R	refGene	3UTR	27625356	27625893	.	-	.	gene_id "CG42233"; transcript_id "NM_143642"; exon_number "1"; exon_id "NM_143642.1"; gene_name "CG42233";
+chr3R	refGene	exon	25629467	25630105	.	+	.	gene_id "CG7789"; transcript_id "NM_143471"; exon_number "2"; exon_id "NM_143471.2"; gene_name "CG7789";
+chr3R	refGene	3UTR	25630009	25630105	.	+	.	gene_id "CG7789"; transcript_id "NM_143471"; exon_number "2"; exon_id "NM_143471.2"; gene_name "CG7789";
+chr3R	refGene	exon	25499702	25499945	.	+	.	gene_id "ppk19"; transcript_id "NM_143451"; exon_number "5"; exon_id "NM_143451.5"; gene_name "ppk19";
+chr3R	refGene	CDS	25499702	25499942	.	+	1	gene_id "ppk19"; transcript_id "NM_143451"; exon_number "5"; exon_id "NM_143451.5"; gene_name "ppk19";
+chr2R	refGene	exon	16152361	16152650	.	-	.	gene_id "CR43812"; transcript_id "NR_073891"; exon_number "1"; exon_id "NR_073891.1"; gene_name "CR43812";
+chr3L	refGene	exon	22726252	22726688	.	-	.	gene_id "CG11241"; transcript_id "NM_168960"; exon_number "1"; exon_id "NM_168960.1"; gene_name "CG11241";
+chr3L	refGene	3UTR	22726252	22726553	.	-	.	gene_id "CG11241"; transcript_id "NM_168960"; exon_number "1"; exon_id "NM_168960.1"; gene_name "CG11241";
+chr3L	refGene	exon	19538783	19539064	.	+	.	gene_id "Rcd7"; transcript_id "NM_168803"; exon_number "2"; exon_id "NM_168803.2"; gene_name "Rcd7";
+chr3L	refGene	CDS	19538784	19539064	.	+	0	gene_id "Rcd7"; transcript_id "NM_168803"; exon_number "2"; exon_id "NM_168803.2"; gene_name "Rcd7";
+chr2R	refGene	exon	12953476	12954959	.	-	.	gene_id "CG30460"; transcript_id "NM_001169701"; exon_number "1"; exon_id "NM_001169701.1"; gene_name "CG30460";
+chr2R	refGene	3UTR	12953476	12954286	.	-	.	gene_id "CG30460"; transcript_id "NM_001169701"; exon_number "1"; exon_id "NM_001169701.1"; gene_name "CG30460";
+chr2R	refGene	exon	10755738	10756067	.	-	.	gene_id "Inr-a"; transcript_id "NM_001169682"; exon_number "2"; exon_id "NM_001169682.2"; gene_name "Inr-a";
+chr2R	refGene	CDS	10755738	10756067	.	-	0	gene_id "Inr-a"; transcript_id "NM_001169682"; exon_number "2"; exon_id "NM_001169682.2"; gene_name "Inr-a";
+chr2L	refGene	exon	21157444	21157647	.	-	.	gene_id "CG9249"; transcript_id "NM_001169558"; exon_number "1"; exon_id "NM_001169558.1"; gene_name "CG9249";
+chr2L	refGene	CDS	21157520	21157647	.	-	2	gene_id "CG9249"; transcript_id "NM_001169558"; exon_number "1"; exon_id "NM_001169558.1"; gene_name "CG9249";
+chr3R	refGene	exon	11102162	11103277	.	-	.	gene_id "MRG15"; transcript_id "NM_142185"; exon_number "1"; exon_id "NM_142185.1"; gene_name "MRG15";
+chr3R	refGene	3UTR	11102162	11102306	.	-	.	gene_id "MRG15"; transcript_id "NM_142185"; exon_number "1"; exon_id "NM_142185.1"; gene_name "MRG15";
+chr2L	refGene	exon	115365	116488	.	-	.	gene_id "CG13694"; transcript_id "NM_134648"; exon_number "1"; exon_id "NM_134648.1"; gene_name "CG13694";
+chr2L	refGene	3UTR	115365	115712	.	-	.	gene_id "CG13694"; transcript_id "NM_134648"; exon_number "1"; exon_id "NM_134648.1"; gene_name "CG13694";
+chr2LHet	refGene	exon	20723	21383	.	-	.	gene_id "CG12567"; transcript_id "NM_001170362"; exon_number "2"; exon_id "NM_001170362.2"; gene_name "CG12567";
+chr2LHet	refGene	CDS	20723	21383	.	-	0	gene_id "CG12567"; transcript_id "NM_001170362"; exon_number "2"; exon_id "NM_001170362.2"; gene_name "CG12567";
+chr2L	refGene	exon	12035194	12036137	.	+	.	gene_id "CG18788"; transcript_id "NM_144408"; exon_number "3"; exon_id "NM_144408.3"; gene_name "CG18788";
+chr2L	refGene	3UTR	12035986	12036137	.	+	.	gene_id "CG18788"; transcript_id "NM_144408"; exon_number "3"; exon_id "NM_144408.3"; gene_name "CG18788";
+chr3L	refGene	exon	357981	358486	.	+	.	gene_id "Roc1b"; transcript_id "NM_144356"; exon_number "1"; exon_id "NM_144356.1"; gene_name "Roc1b";
+chr3L	refGene	CDS	358031	358396	.	+	0	gene_id "Roc1b"; transcript_id "NM_144356"; exon_number "1"; exon_id "NM_144356.1"; gene_name "Roc1b";
+chr2R	refGene	exon	10044555	10044651	.	-	.	gene_id "CG13018"; transcript_id "NM_144123"; exon_number "1"; exon_id "NM_144123.1"; gene_name "CG13018";
+chr2R	refGene	3UTR	10044555	10044609	.	-	.	gene_id "CG13018"; transcript_id "NM_144123"; exon_number "1"; exon_id "NM_144123.1"; gene_name "CG13018";
+chr2R	refGene	CDS	10044613	10044651	.	-	0	gene_id "CG13018"; transcript_id "NM_144123"; exon_number "1"; exon_id "NM_144123.1"; gene_name "CG13018";
+chr2R	refGene	stop_codon	10044610	10044612	.	-	0	gene_id "CG13018"; transcript_id "NM_144123"; exon_number "1"; exon_id "NM_144123.1"; gene_name "CG13018";
+chrX	refGene	exon	8486279	8486423	.	-	.	gene_id "CG12659"; transcript_id "NM_167163"; exon_number "3"; exon_id "NM_167163.3"; gene_name "CG12659";
+chrX	refGene	5UTR	8486279	8486423	.	-	.	gene_id "CG12659"; transcript_id "NM_167163"; exon_number "3"; exon_id "NM_167163.3"; gene_name "CG12659";
+chr2L	refGene	exon	5055982	5058248	.	-	.	gene_id "CG31918"; transcript_id "NM_135060"; exon_number "1"; exon_id "NM_135060.1"; gene_name "CG31918";
+chr2L	refGene	3UTR	5055982	5056246	.	-	.	gene_id "CG31918"; transcript_id "NM_135060"; exon_number "1"; exon_id "NM_135060.1"; gene_name "CG31918";
+chr2L	refGene	exon	5062636	5063442	.	-	.	gene_id "CR43820"; transcript_id "NR_073722"; exon_number "1"; exon_id "NR_073722.1"; gene_name "CR43820";
+chr3R	refGene	exon	4830231	4831053	.	+	.	gene_id "CG11980"; transcript_id "NM_169251"; exon_number "2"; exon_id "NM_169251.2"; gene_name "CG11980";
+chr3R	refGene	3UTR	4830973	4831053	.	+	.	gene_id "CG11980"; transcript_id "NM_169251"; exon_number "2"; exon_id "NM_169251.2"; gene_name "CG11980";
+chr2R	refGene	exon	17573705	17574110	.	-	.	gene_id "Tbp"; transcript_id "NM_079081"; exon_number "1"; exon_id "NM_079081.1"; gene_name "Tbp";
+chr2R	refGene	3UTR	17573705	17573831	.	-	.	gene_id "Tbp"; transcript_id "NM_079081"; exon_number "1"; exon_id "NM_079081.1"; gene_name "Tbp";
+chr3L	refGene	exon	15965259	15968196	.	-	.	gene_id "brm"; transcript_id "NM_168641"; exon_number "3"; exon_id "NM_168641.3"; gene_name "brm";
+chr3L	refGene	CDS	15965259	15968196	.	-	0	gene_id "brm"; transcript_id "NM_168641"; exon_number "3"; exon_id "NM_168641.3"; gene_name "brm";
+chr3L	refGene	exon	9069958	9070556	.	+	.	gene_id "Tequila"; transcript_id "NM_168315"; exon_number "6"; exon_id "NM_168315.6"; gene_name "Tequila";
+chr3L	refGene	3UTR	9070122	9070556	.	+	.	gene_id "Tequila"; transcript_id "NM_168315"; exon_number "6"; exon_id "NM_168315.6"; gene_name "Tequila";
+chr3L	refGene	exon	2267870	2268530	.	+	.	gene_id "obst-I"; transcript_id "NM_167943"; exon_number "1"; exon_id "NM_167943.1"; gene_name "obst-I";
+chr3L	refGene	CDS	2267870	2268526	.	+	0	gene_id "obst-I"; transcript_id "NM_167943"; exon_number "1"; exon_id "NM_167943.1"; gene_name "obst-I";
+chr2L	refGene	exon	115365	116182	.	-	.	gene_id "CG13694"; transcript_id "NM_001272868"; exon_number "1"; exon_id "NM_001272868.1"; gene_name "CG13694";
+chr2L	refGene	3UTR	115365	115712	.	-	.	gene_id "CG13694"; transcript_id "NM_001272868"; exon_number "1"; exon_id "NM_001272868.1"; gene_name "CG13694";
+chr3L	refGene	exon	9420487	9421771	.	+	.	gene_id "Shc"; transcript_id "NM_079944"; exon_number "2"; exon_id "NM_079944.2"; gene_name "Shc";
+chr3L	refGene	CDS	9420487	9421531	.	+	1	gene_id "Shc"; transcript_id "NM_079944"; exon_number "2"; exon_id "NM_079944.2"; gene_name "Shc";
+chr3L	refGene	exon	9479548	9480455	.	-	.	gene_id "pall"; transcript_id "NM_140068"; exon_number "1"; exon_id "NM_140068.1"; gene_name "pall";
+chr3L	refGene	3UTR	9479548	9479722	.	-	.	gene_id "pall"; transcript_id "NM_140068"; exon_number "1"; exon_id "NM_140068.1"; gene_name "pall";
+chr2R	refGene	exon	12115905	12117379	.	+	.	gene_id "Tsf3"; transcript_id "NM_079035"; exon_number "4"; exon_id "NM_079035.4"; gene_name "Tsf3";
+chr2R	refGene	CDS	12115905	12117281	.	+	0	gene_id "Tsf3"; transcript_id "NM_079035"; exon_number "4"; exon_id "NM_079035.4"; gene_name "Tsf3";
+chr2R	refGene	exon	10766861	10767682	.	-	.	gene_id "Cyp6a9"; transcript_id "NM_079024"; exon_number "1"; exon_id "NM_079024.1"; gene_name "Cyp6a9";
+chr2R	refGene	3UTR	10766861	10767263	.	-	.	gene_id "Cyp6a9"; transcript_id "NM_079024"; exon_number "1"; exon_id "NM_079024.1"; gene_name "Cyp6a9";
+chr3L	refGene	exon	6952240	6952686	.	+	.	gene_id "Surf1"; transcript_id "NM_080019"; exon_number "4"; exon_id "NM_080019.4"; gene_name "Surf1";
+chr3L	refGene	3UTR	6952622	6952686	.	+	.	gene_id "Surf1"; transcript_id "NM_080019"; exon_number "4"; exon_id "NM_080019.4"; gene_name "Surf1";
+chr3L	refGene	exon	9363295	9363802	.	-	.	gene_id "Fdxh"; transcript_id "NM_079269"; exon_number "1"; exon_id "NM_079269.1"; gene_name "Fdxh";
+chr3L	refGene	3UTR	9363295	9363450	.	-	.	gene_id "Fdxh"; transcript_id "NM_079269"; exon_number "1"; exon_id "NM_079269.1"; gene_name "Fdxh";
+chr2R	refGene	exon	20916469	20917609	.	+	.	gene_id "uzip"; transcript_id "NM_079137"; exon_number "5"; exon_id "NM_079137.5"; gene_name "uzip";
+chr2R	refGene	CDS	20916469	20916873	.	+	0	gene_id "uzip"; transcript_id "NM_079137"; exon_number "5"; exon_id "NM_079137.5"; gene_name "uzip";
+chr2R	refGene	exon	19415328	19415963	.	-	.	gene_id "bw"; transcript_id "NM_079100"; exon_number "1"; exon_id "NM_079100.1"; gene_name "bw";
+chr2R	refGene	3UTR	19415328	19415775	.	-	.	gene_id "bw"; transcript_id "NM_079100"; exon_number "1"; exon_id "NM_079100.1"; gene_name "bw";
+chrX	refGene	exon	12989478	12989770	.	+	.	gene_id "CG2200"; transcript_id "NM_132624"; exon_number "3"; exon_id "NM_132624.3"; gene_name "CG2200";
+chrX	refGene	3UTR	12989539	12989770	.	+	.	gene_id "CG2200"; transcript_id "NM_132624"; exon_number "3"; exon_id "NM_132624.3"; gene_name "CG2200";
+chrX	refGene	exon	9977415	9978875	.	+	.	gene_id "CG2972"; transcript_id "NM_132375"; exon_number "2"; exon_id "NM_132375.2"; gene_name "CG2972";
+chrX	refGene	CDS	9977415	9978755	.	+	0	gene_id "CG2972"; transcript_id "NM_132375"; exon_number "2"; exon_id "NM_132375.2"; gene_name "CG2972";
+chrX	refGene	exon	8329051	8330244	.	-	.	gene_id "CG12125"; transcript_id "NM_132248"; exon_number "2"; exon_id "NM_132248.2"; gene_name "CG12125";
+chrX	refGene	CDS	8329051	8330244	.	-	0	gene_id "CG12125"; transcript_id "NM_132248"; exon_number "2"; exon_id "NM_132248.2"; gene_name "CG12125";
+chrX	refGene	exon	8292973	8294036	.	+	.	gene_id "CG10555"; transcript_id "NM_132246"; exon_number "1"; exon_id "NM_132246.1"; gene_name "CG10555";
+chrX	refGene	5UTR	8292973	8293427	.	+	.	gene_id "CG10555"; transcript_id "NM_132246"; exon_number "1"; exon_id "NM_132246.1"; gene_name "CG10555";
+chrX	refGene	exon	7810988	7811478	.	+	.	gene_id "snz"; transcript_id "NM_132193"; exon_number "11"; exon_id "NM_132193.11"; gene_name "snz";
+chrX	refGene	CDS	7810988	7811353	.	+	0	gene_id "snz"; transcript_id "NM_132193"; exon_number "11"; exon_id "NM_132193.11"; gene_name "snz";
+chrX	refGene	exon	5211462	5213104	.	+	.	gene_id "Sas10"; transcript_id "NM_131987"; exon_number "1"; exon_id "NM_131987.1"; gene_name "Sas10";
+chrX	refGene	3UTR	5212824	5213104	.	+	.	gene_id "Sas10"; transcript_id "NM_131987"; exon_number "1"; exon_id "NM_131987.1"; gene_name "Sas10";
+chrX	refGene	exon	4891572	4892219	.	+	.	gene_id "CG12680"; transcript_id "NM_131973"; exon_number "1"; exon_id "NM_131973.1"; gene_name "CG12680";
+chrX	refGene	CDS	4891572	4892216	.	+	0	gene_id "CG12680"; transcript_id "NM_131973"; exon_number "1"; exon_id "NM_131973.1"; gene_name "CG12680";
+chrX	refGene	exon	822831	824131	.	-	.	gene_id "CG3708"; transcript_id "NM_130515"; exon_number "1"; exon_id "NM_130515.1"; gene_name "CG3708";
+chrX	refGene	3UTR	822831	822928	.	-	.	gene_id "CG3708"; transcript_id "NM_130515"; exon_number "1"; exon_id "NM_130515.1"; gene_name "CG3708";
+chr2L	refGene	exon	10324379	10324990	.	+	.	gene_id "CG4995"; transcript_id "NM_001273396"; exon_number "4"; exon_id "NM_001273396.4"; gene_name "CG4995";
+chr2L	refGene	CDS	10324379	10324962	.	+	2	gene_id "CG4995"; transcript_id "NM_001273396"; exon_number "4"; exon_id "NM_001273396.4"; gene_name "CG4995";
+chr2L	refGene	3UTR	10324966	10324990	.	+	.	gene_id "CG4995"; transcript_id "NM_001273396"; exon_number "4"; exon_id "NM_001273396.4"; gene_name "CG4995";
+chr2L	refGene	stop_codon	10324963	10324965	.	+	0	gene_id "CG4995"; transcript_id "NM_001273396"; exon_number "1"; exon_id "NM_001273396.1"; gene_name "CG4995";
+chr2R	refGene	exon	12953476	12954959	.	-	.	gene_id "CG30460"; transcript_id "NM_001144214"; exon_number "1"; exon_id "NM_001144214.1"; gene_name "CG30460";
+chr2R	refGene	3UTR	12953476	12954286	.	-	.	gene_id "CG30460"; transcript_id "NM_001144214"; exon_number "1"; exon_id "NM_001144214.1"; gene_name "CG30460";
+chr2R	refGene	exon	12953476	12954959	.	-	.	gene_id "CG30460"; transcript_id "NM_001144213"; exon_number "1"; exon_id "NM_001144213.1"; gene_name "CG30460";
+chr2R	refGene	3UTR	12953476	12954286	.	-	.	gene_id "CG30460"; transcript_id "NM_001144213"; exon_number "1"; exon_id "NM_001144213.1"; gene_name "CG30460";
+chr3R	refGene	exon	7790396	7791208	.	-	.	gene_id "CG12213"; transcript_id "NM_001104284"; exon_number "1"; exon_id "NM_001104284.1"; gene_name "CG12213";
+chr3R	refGene	3UTR	7790396	7791146	.	-	.	gene_id "CG12213"; transcript_id "NM_001104284"; exon_number "1"; exon_id "NM_001104284.1"; gene_name "CG12213";
+chr3R	refGene	exon	7790396	7791208	.	-	.	gene_id "CG12213"; transcript_id "NM_169442"; exon_number "1"; exon_id "NM_169442.1"; gene_name "CG12213";
+chr3R	refGene	3UTR	7790396	7791146	.	-	.	gene_id "CG12213"; transcript_id "NM_169442"; exon_number "1"; exon_id "NM_169442.1"; gene_name "CG12213";
+chr3R	refGene	exon	7790396	7791208	.	-	.	gene_id "CG12213"; transcript_id "NM_001275560"; exon_number "1"; exon_id "NM_001275560.1"; gene_name "CG12213";
+chr3R	refGene	3UTR	7790396	7791146	.	-	.	gene_id "CG12213"; transcript_id "NM_001275560"; exon_number "1"; exon_id "NM_001275560.1"; gene_name "CG12213";
+chr2L	refGene	exon	6674682	6675062	.	-	.	gene_id "cort"; transcript_id "NM_001273215"; exon_number "1"; exon_id "NM_001273215.1"; gene_name "cort";
+chr2L	refGene	3UTR	6674682	6674799	.	-	.	gene_id "cort"; transcript_id "NM_001273215"; exon_number "1"; exon_id "NM_001273215.1"; gene_name "cort";
+chr2L	refGene	exon	6674682	6675062	.	-	.	gene_id "cort"; transcript_id "NM_078770"; exon_number "1"; exon_id "NM_078770.1"; gene_name "cort";
+chr2L	refGene	3UTR	6674682	6674799	.	-	.	gene_id "cort"; transcript_id "NM_078770"; exon_number "1"; exon_id "NM_078770.1"; gene_name "cort";
+chr3R	refGene	exon	9860740	9861000	.	-	.	gene_id "CG9922"; transcript_id "NM_001275627"; exon_number "1"; exon_id "NM_001275627.1"; gene_name "CG9922";
+chr3R	refGene	3UTR	9860740	9860901	.	-	.	gene_id "CG9922"; transcript_id "NM_001275627"; exon_number "1"; exon_id "NM_001275627.1"; gene_name "CG9922";
+chr3L	refGene	exon	18605667	18605863	.	+	.	gene_id "CG32199"; transcript_id "NM_168770"; exon_number "3"; exon_id "NM_168770.3"; gene_name "CG32199";
+chr3L	refGene	CDS	18605667	18605863	.	+	1	gene_id "CG32199"; transcript_id "NM_168770"; exon_number "3"; exon_id "NM_168770.3"; gene_name "CG32199";
+chr3R	refGene	exon	9860740	9861000	.	-	.	gene_id "CG9922"; transcript_id "NM_142072"; exon_number "1"; exon_id "NM_142072.1"; gene_name "CG9922";
+chr3R	refGene	3UTR	9860740	9860901	.	-	.	gene_id "CG9922"; transcript_id "NM_142072"; exon_number "1"; exon_id "NM_142072.1"; gene_name "CG9922";
+chr3R	refGene	exon	1295185	1296181	.	-	.	gene_id "mRpL44"; transcript_id "NM_141284"; exon_number "1"; exon_id "NM_141284.1"; gene_name "mRpL44";
+chr3R	refGene	3UTR	1295185	1295282	.	-	.	gene_id "mRpL44"; transcript_id "NM_141284"; exon_number "1"; exon_id "NM_141284.1"; gene_name "mRpL44";
+chr3L	refGene	exon	8233400	8233701	.	-	.	gene_id "CG7213"; transcript_id "NM_139938"; exon_number "4"; exon_id "NM_139938.4"; gene_name "CG7213";
+chr3L	refGene	CDS	8233400	8233577	.	-	0	gene_id "CG7213"; transcript_id "NM_139938"; exon_number "4"; exon_id "NM_139938.4"; gene_name "CG7213";
+chr3L	refGene	exon	19538704	19539064	.	+	.	gene_id "Rcd7"; transcript_id "NM_140868"; exon_number "1"; exon_id "NM_140868.1"; gene_name "Rcd7";
+chr3L	refGene	CDS	19538784	19539064	.	+	0	gene_id "Rcd7"; transcript_id "NM_140868"; exon_number "1"; exon_id "NM_140868.1"; gene_name "Rcd7";
+chr3L	refGene	exon	6964679	6965329	.	-	.	gene_id "CG10063"; transcript_id "NM_139811"; exon_number "1"; exon_id "NM_139811.1"; gene_name "CG10063";
+chr3L	refGene	3UTR	6964679	6964757	.	-	.	gene_id "CG10063"; transcript_id "NM_139811"; exon_number "1"; exon_id "NM_139811.1"; gene_name "CG10063";
+chr3L	refGene	exon	17901685	17902783	.	+	.	gene_id "CG14353"; transcript_id "NM_140768"; exon_number "2"; exon_id "NM_140768.2"; gene_name "CG14353";
+chr3L	refGene	3UTR	17902538	17902783	.	+	.	gene_id "CG14353"; transcript_id "NM_140768"; exon_number "2"; exon_id "NM_140768.2"; gene_name "CG14353";
+chr3L	refGene	exon	5805165	5805328	.	+	.	gene_id "CG5537"; transcript_id "NM_139733"; exon_number "3"; exon_id "NM_139733.3"; gene_name "CG5537";
+chr3L	refGene	3UTR	5805165	5805328	.	+	.	gene_id "CG5537"; transcript_id "NM_139733"; exon_number "3"; exon_id "NM_139733.3"; gene_name "CG5537";
+chr3L	refGene	exon	5760117	5761233	.	-	.	gene_id "Ppat-Dpck"; transcript_id "NM_139728"; exon_number "1"; exon_id "NM_139728.1"; gene_name "Ppat-Dpck";
+chr3L	refGene	3UTR	5760117	5760235	.	-	.	gene_id "Ppat-Dpck"; transcript_id "NM_139728"; exon_number "1"; exon_id "NM_139728.1"; gene_name "Ppat-Dpck";
+chr3R	refGene	exon	1418969	1420421	.	+	.	gene_id "Vha26"; transcript_id "NM_079513"; exon_number "5"; exon_id "NM_079513.5"; gene_name "Vha26";
+chr3R	refGene	3UTR	1419077	1420421	.	+	.	gene_id "Vha26"; transcript_id "NM_079513"; exon_number "5"; exon_id "NM_079513.5"; gene_name "Vha26";
+chr3R	refGene	exon	1418969	1420421	.	+	.	gene_id "Vha26"; transcript_id "NM_169073"; exon_number "4"; exon_id "NM_169073.4"; gene_name "Vha26";
+chr3R	refGene	3UTR	1419077	1420421	.	+	.	gene_id "Vha26"; transcript_id "NM_169073"; exon_number "4"; exon_id "NM_169073.4"; gene_name "Vha26";
+chr2R	refGene	exon	11427059	11427908	.	-	.	gene_id "CG8187"; transcript_id "NM_137201"; exon_number "1"; exon_id "NM_137201.1"; gene_name "CG8187";
+chr2R	refGene	3UTR	11427059	11427534	.	-	.	gene_id "CG8187"; transcript_id "NM_137201"; exon_number "1"; exon_id "NM_137201.1"; gene_name "CG8187";
+chr2L	refGene	exon	8305586	8306741	.	+	.	gene_id "CG7840"; transcript_id "NM_135359"; exon_number "1"; exon_id "NM_135359.1"; gene_name "CG7840";
+chr2L	refGene	3UTR	8306666	8306741	.	+	.	gene_id "CG7840"; transcript_id "NM_135359"; exon_number "1"; exon_id "NM_135359.1"; gene_name "CG7840";
+chr2L	refGene	exon	9787352	9788499	.	+	.	gene_id "IP3K1"; transcript_id "NM_135469"; exon_number "4"; exon_id "NM_135469.4"; gene_name "IP3K1";
+chr2L	refGene	CDS	9787352	9788168	.	+	1	gene_id "IP3K1"; transcript_id "NM_135469"; exon_number "4"; exon_id "NM_135469.4"; gene_name "IP3K1";
+chr2L	refGene	exon	9961018	9962104	.	+	.	gene_id "CR43683"; transcript_id "NR_073752"; exon_number "1"; exon_id "NR_073752.1"; gene_name "CR43683";
+chr2L	refGene	exon	4446670	4447851	.	-	.	gene_id "MFS18"; transcript_id "NM_134991"; exon_number "1"; exon_id "NM_134991.1"; gene_name "MFS18";
+chr2L	refGene	3UTR	4446670	4446987	.	-	.	gene_id "MFS18"; transcript_id "NM_134991"; exon_number "1"; exon_id "NM_134991.1"; gene_name "MFS18";
+chr2L	refGene	exon	4461657	4462563	.	-	.	gene_id "CG15443"; transcript_id "NM_001273100"; exon_number "1"; exon_id "NM_001273100.1"; gene_name "CG15443";
+chr2L	refGene	3UTR	4461657	4461823	.	-	.	gene_id "CG15443"; transcript_id "NM_001273100"; exon_number "1"; exon_id "NM_001273100.1"; gene_name "CG15443";
+chr2L	refGene	exon	21159272	21160783	.	+	.	gene_id "CG9248"; transcript_id "NM_165356"; exon_number "2"; exon_id "NM_165356.2"; gene_name "CG9248";
+chr2L	refGene	3UTR	21160568	21160783	.	+	.	gene_id "CG9248"; transcript_id "NM_165356"; exon_number "2"; exon_id "NM_165356.2"; gene_name "CG9248";
+chr2L	refGene	exon	20829608	20830073	.	+	.	gene_id "CG31673"; transcript_id "NM_165346"; exon_number "1"; exon_id "NM_165346.1"; gene_name "CG31673";
+chr2L	refGene	CDS	20829670	20830073	.	+	0	gene_id "CG31673"; transcript_id "NM_165346"; exon_number "1"; exon_id "NM_165346.1"; gene_name "CG31673";
+chr2L	refGene	exon	18133588	18134826	.	-	.	gene_id "kel"; transcript_id "NM_165242"; exon_number "4"; exon_id "NM_165242.4"; gene_name "kel";
+chr2L	refGene	CDS	18133617	18134826	.	-	1	gene_id "kel"; transcript_id "NM_165242"; exon_number "4"; exon_id "NM_165242.4"; gene_name "kel";
+chr2R	refGene	exon	19918493	19918725	.	-	.	gene_id "CG30172"; transcript_id "NM_166649"; exon_number "2"; exon_id "NM_166649.2"; gene_name "CG30172";
+chr2R	refGene	CDS	19918493	19918688	.	-	0	gene_id "CG30172"; transcript_id "NM_166649"; exon_number "2"; exon_id "NM_166649.2"; gene_name "CG30172";
+chrX	refGene	exon	8916051	8916272	.	+	.	gene_id "rdgA"; transcript_id "NM_001201636"; exon_number "12"; exon_id "NM_001201636.12"; gene_name "rdgA";
+chrX	refGene	CDS	8916051	8916272	.	+	2	gene_id "rdgA"; transcript_id "NM_001201636"; exon_number "12"; exon_id "NM_001201636.12"; gene_name "rdgA";
+chrX	refGene	exon	8916051	8916272	.	+	.	gene_id "rdgA"; transcript_id "NM_001201635"; exon_number "12"; exon_id "NM_001201635.12"; gene_name "rdgA";
+chrX	refGene	CDS	8916051	8916272	.	+	2	gene_id "rdgA"; transcript_id "NM_001201635"; exon_number "12"; exon_id "NM_001201635.12"; gene_name "rdgA";
+chr3L	refGene	exon	11683326	11683412	.	-	.	gene_id "pallidin"; transcript_id "NM_001169948"; exon_number "2"; exon_id "NM_001169948.2"; gene_name "pallidin";
+chr3L	refGene	3UTR	11683326	11683412	.	-	.	gene_id "pallidin"; transcript_id "NM_001169948"; exon_number "2"; exon_id "NM_001169948.2"; gene_name "pallidin";
+chr3R	refGene	exon	9950148	9950584	.	-	.	gene_id "140up"; transcript_id "NM_057603"; exon_number "1"; exon_id "NM_057603.1"; gene_name "140up";
+chr3R	refGene	3UTR	9950148	9950226	.	-	.	gene_id "140up"; transcript_id "NM_057603"; exon_number "1"; exon_id "NM_057603.1"; gene_name "140up";
+chr3L	refGene	exon	7233144	7233345	.	+	.	gene_id "BHD"; transcript_id "NM_139833"; exon_number "3"; exon_id "NM_139833.3"; gene_name "BHD";
+chr3L	refGene	3UTR	7233265	7233345	.	+	.	gene_id "BHD"; transcript_id "NM_139833"; exon_number "3"; exon_id "NM_139833.3"; gene_name "BHD";
+chr3R	refGene	exon	18217911	18219247	.	-	.	gene_id "CG13857"; transcript_id "NM_142778"; exon_number "1"; exon_id "NM_142778.1"; gene_name "CG13857";
+chr3R	refGene	3UTR	18217911	18218211	.	-	.	gene_id "CG13857"; transcript_id "NM_142778"; exon_number "1"; exon_id "NM_142778.1"; gene_name "CG13857";
+chr3R	refGene	exon	16416746	16417333	.	-	.	gene_id "CG4159"; transcript_id "NM_142642"; exon_number "1"; exon_id "NM_142642.1"; gene_name "CG4159";
+chr3R	refGene	3UTR	16416746	16416807	.	-	.	gene_id "CG4159"; transcript_id "NM_142642"; exon_number "1"; exon_id "NM_142642.1"; gene_name "CG4159";
+chr3R	refGene	exon	14985332	14985600	.	-	.	gene_id "CG11779"; transcript_id "NM_142529"; exon_number "4"; exon_id "NM_142529.4"; gene_name "CG11779";
+chr3R	refGene	5UTR	14985428	14985600	.	-	.	gene_id "CG11779"; transcript_id "NM_142529"; exon_number "4"; exon_id "NM_142529.4"; gene_name "CG11779";
+chr3R	refGene	exon	13621717	13622039	.	+	.	gene_id "CG7713"; transcript_id "NM_142398"; exon_number "5"; exon_id "NM_142398.5"; gene_name "CG7713";
+chr3R	refGene	3UTR	13621801	13622039	.	+	.	gene_id "CG7713"; transcript_id "NM_142398"; exon_number "5"; exon_id "NM_142398.5"; gene_name "CG7713";
+chr3R	refGene	exon	12149648	12150850	.	+	.	gene_id "CG6901"; transcript_id "NM_142274"; exon_number "3"; exon_id "NM_142274.3"; gene_name "CG6901";
+chr3R	refGene	CDS	12149648	12150772	.	+	0	gene_id "CG6901"; transcript_id "NM_142274"; exon_number "3"; exon_id "NM_142274.3"; gene_name "CG6901";
+chr3L	refGene	exon	259043	259913	.	-	.	gene_id "Tudor-SN"; transcript_id "NM_001274266"; exon_number "1"; exon_id "NM_001274266.1"; gene_name "Tudor-SN";
+chr3L	refGene	3UTR	259043	259502	.	-	.	gene_id "Tudor-SN"; transcript_id "NM_001274266"; exon_number "1"; exon_id "NM_001274266.1"; gene_name "Tudor-SN";
+chr3L	refGene	exon	260311	261746	.	-	.	gene_id "Tudor-SN"; transcript_id "NM_001274266"; exon_number "2"; exon_id "NM_001274266.2"; gene_name "Tudor-SN";
+chr3L	refGene	CDS	260311	261746	.	-	2	gene_id "Tudor-SN"; transcript_id "NM_001274266"; exon_number "2"; exon_id "NM_001274266.2"; gene_name "Tudor-SN";
+chr3L	refGene	exon	260311	261746	.	-	.	gene_id "Tudor-SN"; transcript_id "NM_138177"; exon_number "2"; exon_id "NM_138177.2"; gene_name "Tudor-SN";
+chr3L	refGene	CDS	260311	261746	.	-	2	gene_id "Tudor-SN"; transcript_id "NM_138177"; exon_number "2"; exon_id "NM_138177.2"; gene_name "Tudor-SN";
+chr3L	refGene	exon	16837307	16837685	.	+	.	gene_id "TSG101"; transcript_id "NM_079396"; exon_number "7"; exon_id "NM_079396.7"; gene_name "TSG101";
+chr3L	refGene	3UTR	16837494	16837685	.	+	.	gene_id "TSG101"; transcript_id "NM_079396"; exon_number "7"; exon_id "NM_079396.7"; gene_name "TSG101";
+chr3L	refGene	exon	21722775	21723554	.	-	.	gene_id "CG14570"; transcript_id "NM_141096"; exon_number "1"; exon_id "NM_141096.1"; gene_name "CG14570";
+chr3L	refGene	3UTR	21722775	21722841	.	-	.	gene_id "CG14570"; transcript_id "NM_141096"; exon_number "1"; exon_id "NM_141096.1"; gene_name "CG14570";
+chr3L	refGene	exon	8124529	8125034	.	-	.	gene_id "CG7504"; transcript_id "NM_001144435"; exon_number "1"; exon_id "NM_001144435.1"; gene_name "CG7504";
+chr3L	refGene	3UTR	8124529	8124896	.	-	.	gene_id "CG7504"; transcript_id "NM_001144435"; exon_number "1"; exon_id "NM_001144435.1"; gene_name "CG7504";
+chr3L	refGene	exon	8124529	8125034	.	-	.	gene_id "CG7504"; transcript_id "NM_139920"; exon_number "1"; exon_id "NM_139920.1"; gene_name "CG7504";
+chr3L	refGene	3UTR	8124529	8124896	.	-	.	gene_id "CG7504"; transcript_id "NM_139920"; exon_number "1"; exon_id "NM_139920.1"; gene_name "CG7504";
+chr3L	refGene	exon	8188951	8189673	.	+	.	gene_id "MED24"; transcript_id "NM_139928"; exon_number "7"; exon_id "NM_139928.7"; gene_name "MED24";
+chr3L	refGene	3UTR	8189576	8189673	.	+	.	gene_id "MED24"; transcript_id "NM_139928"; exon_number "7"; exon_id "NM_139928.7"; gene_name "MED24";
+chr3L	refGene	exon	16837668	16837962	.	-	.	gene_id "CG9669"; transcript_id "NM_140668"; exon_number "1"; exon_id "NM_140668.1"; gene_name "CG9669";
+chr3L	refGene	3UTR	16837668	16837724	.	-	.	gene_id "CG9669"; transcript_id "NM_140668"; exon_number "1"; exon_id "NM_140668.1"; gene_name "CG9669";
+chr3L	refGene	exon	3897444	3897940	.	-	.	gene_id "CG14980"; transcript_id "NM_139578"; exon_number "1"; exon_id "NM_139578.1"; gene_name "CG14980";
+chr3L	refGene	3UTR	3897444	3897458	.	-	.	gene_id "CG14980"; transcript_id "NM_139578"; exon_number "1"; exon_id "NM_139578.1"; gene_name "CG14980";
+chr3L	refGene	exon	2642184	2642887	.	-	.	gene_id "CG14949"; transcript_id "NM_139477"; exon_number "1"; exon_id "NM_139477.1"; gene_name "CG14949";
+chr3L	refGene	CDS	2642416	2642887	.	-	1	gene_id "CG14949"; transcript_id "NM_139477"; exon_number "1"; exon_id "NM_139477.1"; gene_name "CG14949";
+chr3L	refGene	exon	11683326	11683412	.	-	.	gene_id "pallidin"; transcript_id "NM_140237"; exon_number "2"; exon_id "NM_140237.2"; gene_name "pallidin";
+chr3L	refGene	CDS	11683326	11683412	.	-	0	gene_id "pallidin"; transcript_id "NM_140237"; exon_number "2"; exon_id "NM_140237.2"; gene_name "pallidin";
+chr2L	refGene	exon	10485538	10485790	.	-	.	gene_id "CG7456"; transcript_id "NM_135569"; exon_number "1"; exon_id "NM_135569.1"; gene_name "CG7456";
+chr2L	refGene	CDS	10485751	10485790	.	-	1	gene_id "CG7456"; transcript_id "NM_135569"; exon_number "1"; exon_id "NM_135569.1"; gene_name "CG7456";
+chr2L	refGene	exon	10981487	10982395	.	+	.	gene_id "SCAR"; transcript_id "NM_001259037"; exon_number "6"; exon_id "NM_001259037.6"; gene_name "SCAR";
+chr2L	refGene	3UTR	10981666	10982395	.	+	.	gene_id "SCAR"; transcript_id "NM_001259037"; exon_number "6"; exon_id "NM_001259037.6"; gene_name "SCAR";
+chr2L	refGene	exon	10981487	10982395	.	+	.	gene_id "SCAR"; transcript_id "NM_001259038"; exon_number "6"; exon_id "NM_001259038.6"; gene_name "SCAR";
+chr2L	refGene	3UTR	10981666	10982395	.	+	.	gene_id "SCAR"; transcript_id "NM_001259038"; exon_number "6"; exon_id "NM_001259038.6"; gene_name "SCAR";
+chr2L	refGene	exon	10981487	10982395	.	+	.	gene_id "SCAR"; transcript_id "NM_001273439"; exon_number "7"; exon_id "NM_001273439.7"; gene_name "SCAR";
+chr2L	refGene	3UTR	10981666	10982395	.	+	.	gene_id "SCAR"; transcript_id "NM_001273439"; exon_number "7"; exon_id "NM_001273439.7"; gene_name "SCAR";
+chr2L	refGene	exon	10981487	10982395	.	+	.	gene_id "SCAR"; transcript_id "NM_001273440"; exon_number "5"; exon_id "NM_001273440.5"; gene_name "SCAR";
+chr2L	refGene	3UTR	10981723	10982395	.	+	.	gene_id "SCAR"; transcript_id "NM_001273440"; exon_number "5"; exon_id "NM_001273440.5"; gene_name "SCAR";
+chr2L	refGene	exon	10981487	10982395	.	+	.	gene_id "SCAR"; transcript_id "NM_135633"; exon_number "5"; exon_id "NM_135633.5"; gene_name "SCAR";
+chr2L	refGene	3UTR	10981666	10982395	.	+	.	gene_id "SCAR"; transcript_id "NM_135633"; exon_number "5"; exon_id "NM_135633.5"; gene_name "SCAR";
+chr2L	refGene	exon	1132332	1134098	.	-	.	gene_id "Iris"; transcript_id "NM_134726"; exon_number "1"; exon_id "NM_134726.1"; gene_name "Iris";
+chr2L	refGene	3UTR	1132332	1132477	.	-	.	gene_id "Iris"; transcript_id "NM_134726"; exon_number "1"; exon_id "NM_134726.1"; gene_name "Iris";
+chr2L	refGene	exon	10324379	10324990	.	+	.	gene_id "CG4995"; transcript_id "NM_164915"; exon_number "4"; exon_id "NM_164915.4"; gene_name "CG4995";
+chr2L	refGene	CDS	10324379	10324962	.	+	2	gene_id "CG4995"; transcript_id "NM_164915"; exon_number "4"; exon_id "NM_164915.4"; gene_name "CG4995";
+chr2L	refGene	3UTR	10324966	10324990	.	+	.	gene_id "CG4995"; transcript_id "NM_164915"; exon_number "4"; exon_id "NM_164915.4"; gene_name "CG4995";
+chr2L	refGene	stop_codon	10324963	10324965	.	+	0	gene_id "CG4995"; transcript_id "NM_164915"; exon_number "1"; exon_id "NM_164915.1"; gene_name "CG4995";
+chr2L	refGene	exon	10324379	10324990	.	+	.	gene_id "CG4995"; transcript_id "NM_164914"; exon_number "5"; exon_id "NM_164914.5"; gene_name "CG4995";
+chr2L	refGene	CDS	10324379	10324962	.	+	2	gene_id "CG4995"; transcript_id "NM_164914"; exon_number "5"; exon_id "NM_164914.5"; gene_name "CG4995";
+chr2L	refGene	3UTR	10324966	10324990	.	+	.	gene_id "CG4995"; transcript_id "NM_164914"; exon_number "5"; exon_id "NM_164914.5"; gene_name "CG4995";
+chr2L	refGene	stop_codon	10324963	10324965	.	+	0	gene_id "CG4995"; transcript_id "NM_164914"; exon_number "1"; exon_id "NM_164914.1"; gene_name "CG4995";
+chr3R	refGene	exon	4576502	4578463	.	-	.	gene_id "CG34135"; transcript_id "NM_001275456"; exon_number "2"; exon_id "NM_001275456.2"; gene_name "CG34135";
+chr3R	refGene	5UTR	4576638	4578463	.	-	.	gene_id "CG34135"; transcript_id "NM_001275456"; exon_number "2"; exon_id "NM_001275456.2"; gene_name "CG34135";
+chr3R	refGene	exon	4576502	4580132	.	-	.	gene_id "CG11768"; transcript_id "NM_001260065"; exon_number "2"; exon_id "NM_001260065.2"; gene_name "CG11768";
+chr3R	refGene	3UTR	4576502	4579830	.	-	.	gene_id "CG11768"; transcript_id "NM_001260065"; exon_number "2"; exon_id "NM_001260065.2"; gene_name "CG11768";
+chr3R	refGene	exon	4538628	4541390	.	-	.	gene_id "Cks85A"; transcript_id "NM_001275454"; exon_number "1"; exon_id "NM_001275454.1"; gene_name "Cks85A";
+chr3R	refGene	3UTR	4538628	4541158	.	-	.	gene_id "Cks85A"; transcript_id "NM_001275454"; exon_number "1"; exon_id "NM_001275454.1"; gene_name "Cks85A";
+chr3R	refGene	exon	603219	604061	.	-	.	gene_id "CG14655"; transcript_id "NM_141237"; exon_number "1"; exon_id "NM_141237.1"; gene_name "CG14655";
+chr3R	refGene	3UTR	603219	603549	.	-	.	gene_id "CG14655"; transcript_id "NM_141237"; exon_number "1"; exon_id "NM_141237.1"; gene_name "CG14655";
+chr3L	refGene	exon	16404102	16404939	.	-	.	gene_id "fax"; transcript_id "NM_079382"; exon_number "5"; exon_id "NM_079382.5"; gene_name "fax";
+chr3L	refGene	CDS	16404102	16404518	.	-	0	gene_id "fax"; transcript_id "NM_079382"; exon_number "5"; exon_id "NM_079382.5"; gene_name "fax";
+chr3L	refGene	exon	16404102	16404939	.	-	.	gene_id "fax"; transcript_id "NM_001014587"; exon_number "5"; exon_id "NM_001014587.5"; gene_name "fax";
+chr3L	refGene	CDS	16404102	16404518	.	-	0	gene_id "fax"; transcript_id "NM_001014587"; exon_number "5"; exon_id "NM_001014587.5"; gene_name "fax";
+chrX	refGene	exon	8916051	8916272	.	+	.	gene_id "rdgA"; transcript_id "NM_001103446"; exon_number "11"; exon_id "NM_001103446.11"; gene_name "rdgA";
+chrX	refGene	CDS	8916051	8916272	.	+	2	gene_id "rdgA"; transcript_id "NM_001103446"; exon_number "11"; exon_id "NM_001103446.11"; gene_name "rdgA";
+chr2L	refGene	exon	16305355	16305940	.	+	.	gene_id "c(2)M"; transcript_id "NM_135944"; exon_number "8"; exon_id "NM_135944.8"; gene_name "c(2)M";
+chr2L	refGene	3UTR	16305480	16305940	.	+	.	gene_id "c(2)M"; transcript_id "NM_135944"; exon_number "8"; exon_id "NM_135944.8"; gene_name "c(2)M";
+chr3L	refGene	exon	16106985	16107241	.	+	.	gene_id "Taf4"; transcript_id "NM_001144486"; exon_number "2"; exon_id "NM_001144486.2"; gene_name "Taf4";
+chr3L	refGene	5UTR	16106985	16107241	.	+	.	gene_id "Taf4"; transcript_id "NM_001144486"; exon_number "2"; exon_id "NM_001144486.2"; gene_name "Taf4";
+chr3L	refGene	exon	16106996	16107241	.	+	.	gene_id "Taf4"; transcript_id "NM_001169982"; exon_number "2"; exon_id "NM_001169982.2"; gene_name "Taf4";
+chr3L	refGene	5UTR	16106996	16107241	.	+	.	gene_id "Taf4"; transcript_id "NM_001169982"; exon_number "2"; exon_id "NM_001169982.2"; gene_name "Taf4";
+chr3L	refGene	exon	16106985	16107241	.	+	.	gene_id "Taf4"; transcript_id "NM_001274998"; exon_number "2"; exon_id "NM_001274998.2"; gene_name "Taf4";
+chr3L	refGene	5UTR	16106985	16107241	.	+	.	gene_id "Taf4"; transcript_id "NM_001274998"; exon_number "2"; exon_id "NM_001274998.2"; gene_name "Taf4";
+chr3L	refGene	exon	16106985	16107241	.	+	.	gene_id "Taf4"; transcript_id "NM_001274999"; exon_number "2"; exon_id "NM_001274999.2"; gene_name "Taf4";
+chr3L	refGene	5UTR	16106985	16107241	.	+	.	gene_id "Taf4"; transcript_id "NM_001274999"; exon_number "2"; exon_id "NM_001274999.2"; gene_name "Taf4";
+chr3L	refGene	exon	16106985	16107241	.	+	.	gene_id "Taf4"; transcript_id "NM_176333"; exon_number "2"; exon_id "NM_176333.2"; gene_name "Taf4";
+chr3L	refGene	5UTR	16106985	16107241	.	+	.	gene_id "Taf4"; transcript_id "NM_176333"; exon_number "2"; exon_id "NM_176333.2"; gene_name "Taf4";
+chr3L	refGene	exon	16106985	16107241	.	+	.	gene_id "Taf4"; transcript_id "NM_079378"; exon_number "2"; exon_id "NM_079378.2"; gene_name "Taf4";
+chr3L	refGene	5UTR	16106985	16107241	.	+	.	gene_id "Taf4"; transcript_id "NM_079378"; exon_number "2"; exon_id "NM_079378.2"; gene_name "Taf4";
+chr3L	refGene	exon	16106890	16107241	.	+	.	gene_id "Taf4"; transcript_id "NM_168651"; exon_number "1"; exon_id "NM_168651.1"; gene_name "Taf4";
+chr3L	refGene	5UTR	16106890	16107241	.	+	.	gene_id "Taf4"; transcript_id "NM_168651"; exon_number "1"; exon_id "NM_168651.1"; gene_name "Taf4";
+chr3L	refGene	exon	19792378	19792432	.	+	.	gene_id "Ir76a"; transcript_id "NM_001104177"; exon_number "1"; exon_id "NM_001104177.1"; gene_name "Ir76a";
+chr3L	refGene	CDS	19792378	19792432	.	+	0	gene_id "Ir76a"; transcript_id "NM_001104177"; exon_number "1"; exon_id "NM_001104177.1"; gene_name "Ir76a";
+chr3R	refGene	exon	464266	464561	.	-	.	gene_id "CG9775"; transcript_id "NM_169012"; exon_number "2"; exon_id "NM_169012.2"; gene_name "CG9775";
+chr3R	refGene	CDS	464266	464561	.	-	1	gene_id "CG9775"; transcript_id "NM_169012"; exon_number "2"; exon_id "NM_169012.2"; gene_name "CG9775";
+chr3R	refGene	exon	463732	464561	.	-	.	gene_id "CG9775"; transcript_id "NM_001170036"; exon_number "1"; exon_id "NM_001170036.1"; gene_name "CG9775";
+chr3R	refGene	CDS	464156	464561	.	-	1	gene_id "CG9775"; transcript_id "NM_001170036"; exon_number "1"; exon_id "NM_001170036.1"; gene_name "CG9775";
+chr3R	refGene	exon	464266	464561	.	-	.	gene_id "CG9775"; transcript_id "NM_141225"; exon_number "2"; exon_id "NM_141225.2"; gene_name "CG9775";
+chr3R	refGene	CDS	464266	464561	.	-	1	gene_id "CG9775"; transcript_id "NM_141225"; exon_number "2"; exon_id "NM_141225.2"; gene_name "CG9775";
+chr3R	refGene	exon	464266	464561	.	-	.	gene_id "CG9775"; transcript_id "NM_001275328"; exon_number "2"; exon_id "NM_001275328.2"; gene_name "CG9775";
+chr3R	refGene	CDS	464266	464561	.	-	1	gene_id "CG9775"; transcript_id "NM_001275328"; exon_number "2"; exon_id "NM_001275328.2"; gene_name "CG9775";
+chr3L	refGene	exon	16096532	16097378	.	-	.	gene_id "IntS9"; transcript_id "NM_140581"; exon_number "1"; exon_id "NM_140581.1"; gene_name "IntS9";
+chr3L	refGene	3UTR	16096532	16096580	.	-	.	gene_id "IntS9"; transcript_id "NM_140581"; exon_number "1"; exon_id "NM_140581.1"; gene_name "IntS9";
+chr3L	refGene	exon	15965259	15968196	.	-	.	gene_id "brm"; transcript_id "NM_080498"; exon_number "3"; exon_id "NM_080498.3"; gene_name "brm";
+chr3L	refGene	CDS	15965259	15968196	.	-	0	gene_id "brm"; transcript_id "NM_080498"; exon_number "3"; exon_id "NM_080498.3"; gene_name "brm";
+chr3L	refGene	exon	15965259	15968196	.	-	.	gene_id "brm"; transcript_id "NM_168640"; exon_number "3"; exon_id "NM_168640.3"; gene_name "brm";
+chr3L	refGene	CDS	15965259	15968196	.	-	0	gene_id "brm"; transcript_id "NM_168640"; exon_number "3"; exon_id "NM_168640.3"; gene_name "brm";
+chr3L	refGene	exon	15965259	15968196	.	-	.	gene_id "brm"; transcript_id "NM_001274977"; exon_number "3"; exon_id "NM_001274977.3"; gene_name "brm";
+chr3L	refGene	CDS	15965259	15968196	.	-	0	gene_id "brm"; transcript_id "NM_001274977"; exon_number "3"; exon_id "NM_001274977.3"; gene_name "brm";
+chr3L	refGene	exon	15965259	15968196	.	-	.	gene_id "brm"; transcript_id "NM_001274978"; exon_number "3"; exon_id "NM_001274978.3"; gene_name "brm";
+chr3L	refGene	CDS	15965259	15968196	.	-	0	gene_id "brm"; transcript_id "NM_001274978"; exon_number "3"; exon_id "NM_001274978.3"; gene_name "brm";
+chr3L	refGene	exon	15965259	15968196	.	-	.	gene_id "brm"; transcript_id "NM_080497"; exon_number "3"; exon_id "NM_080497.3"; gene_name "brm";
+chr3L	refGene	CDS	15965259	15968196	.	-	0	gene_id "brm"; transcript_id "NM_080497"; exon_number "3"; exon_id "NM_080497.3"; gene_name "brm";
+chr3L	refGene	exon	21190649	21190737	.	-	.	gene_id "CG33054"; transcript_id "NM_176375"; exon_number "2"; exon_id "NM_176375.2"; gene_name "CG33054";
+chr3L	refGene	CDS	21190649	21190737	.	-	0	gene_id "CG33054"; transcript_id "NM_176375"; exon_number "2"; exon_id "NM_176375.2"; gene_name "CG33054";
+chr3L	refGene	exon	21190511	21190737	.	-	.	gene_id "CG33054"; transcript_id "NM_176376"; exon_number "1"; exon_id "NM_176376.1"; gene_name "CG33054";
+chr3L	refGene	CDS	21190585	21190737	.	-	0	gene_id "CG33054"; transcript_id "NM_176376"; exon_number "1"; exon_id "NM_176376.1"; gene_name "CG33054";
+chr2L	refGene	exon	4973719	4973852	.	-	.	gene_id "l(2)05714"; transcript_id "NM_001273133"; exon_number "3"; exon_id "NM_001273133.3"; gene_name "l(2)05714";
+chr2L	refGene	5UTR	4973719	4973852	.	-	.	gene_id "l(2)05714"; transcript_id "NM_001273133"; exon_number "3"; exon_id "NM_001273133.3"; gene_name "l(2)05714";
+chr2R	refGene	exon	10755738	10756067	.	-	.	gene_id "Inr-a"; transcript_id "NM_001202002"; exon_number "8"; exon_id "NM_001202002.8"; gene_name "Inr-a";
+chr2R	refGene	CDS	10755738	10756067	.	-	0	gene_id "Inr-a"; transcript_id "NM_001202002"; exon_number "8"; exon_id "NM_001202002.8"; gene_name "Inr-a";
+chr2L	refGene	exon	2155753	2156790	.	+	.	gene_id "CG15382"; transcript_id "NM_134806"; exon_number "1"; exon_id "NM_134806.1"; gene_name "CG15382";
+chr2L	refGene	3UTR	2156257	2156790	.	+	.	gene_id "CG15382"; transcript_id "NM_134806"; exon_number "1"; exon_id "NM_134806.1"; gene_name "CG15382";
+chr2L	refGene	exon	2226753	2227305	.	-	.	gene_id "CR44114"; transcript_id "NR_073695"; exon_number "1"; exon_id "NR_073695.1"; gene_name "CR44114";
+chr3L	refGene	exon	15553826	15555783	.	-	.	gene_id "CG7739"; transcript_id "NM_140519"; exon_number "1"; exon_id "NM_140519.1"; gene_name "CG7739";
+chr3L	refGene	3UTR	15553826	15554185	.	-	.	gene_id "CG7739"; transcript_id "NM_140519"; exon_number "1"; exon_id "NM_140519.1"; gene_name "CG7739";
+chr2L	refGene	exon	13177150	13178978	.	+	.	gene_id "CG5439"; transcript_id "NM_135763"; exon_number "1"; exon_id "NM_135763.1"; gene_name "CG5439";
+chr2L	refGene	5UTR	13177150	13177250	.	+	.	gene_id "CG5439"; transcript_id "NM_135763"; exon_number "1"; exon_id "NM_135763.1"; gene_name "CG5439";
+chr2L	refGene	CDS	13177251	13178810	.	+	0	gene_id "CG5439"; transcript_id "NM_135763"; exon_number "1"; exon_id "NM_135763.1"; gene_name "CG5439";
+chr2L	refGene	start_codon	13177251	13177253	.	+	0	gene_id "CG5439"; transcript_id "NM_135763"; exon_number "1"; exon_id "NM_135763.1"; gene_name "CG5439";
+chr3L	refGene	exon	8717967	8718160	.	+	.	gene_id "CG6511"; transcript_id "NM_001274668"; exon_number "5"; exon_id "NM_001274668.5"; gene_name "CG6511";
+chr3L	refGene	CDS	8717967	8718160	.	+	1	gene_id "CG6511"; transcript_id "NM_001274668"; exon_number "5"; exon_id "NM_001274668.5"; gene_name "CG6511";
+chr3L	refGene	exon	8718226	8719208	.	+	.	gene_id "CG6511"; transcript_id "NM_001274668"; exon_number "6"; exon_id "NM_001274668.6"; gene_name "CG6511";
+chr3L	refGene	3UTR	8718612	8719208	.	+	.	gene_id "CG6511"; transcript_id "NM_001274668"; exon_number "6"; exon_id "NM_001274668.6"; gene_name "CG6511";
+chr3L	refGene	exon	8717967	8718160	.	+	.	gene_id "CG6511"; transcript_id "NM_139995"; exon_number "5"; exon_id "NM_139995.5"; gene_name "CG6511";
+chr3L	refGene	CDS	8717967	8718160	.	+	1	gene_id "CG6511"; transcript_id "NM_139995"; exon_number "5"; exon_id "NM_139995.5"; gene_name "CG6511";
+chr3L	refGene	exon	8718226	8719208	.	+	.	gene_id "CG6511"; transcript_id "NM_139995"; exon_number "6"; exon_id "NM_139995.6"; gene_name "CG6511";
+chr3L	refGene	3UTR	8718612	8719208	.	+	.	gene_id "CG6511"; transcript_id "NM_139995"; exon_number "6"; exon_id "NM_139995.6"; gene_name "CG6511";
+chr3R	refGene	exon	8252776	8253599	.	+	.	gene_id "Sas"; transcript_id "NM_141938"; exon_number "2"; exon_id "NM_141938.2"; gene_name "Sas";
+chr3R	refGene	3UTR	8253559	8253599	.	+	.	gene_id "Sas"; transcript_id "NM_141938"; exon_number "2"; exon_id "NM_141938.2"; gene_name "Sas";
+chr2R	refGene	exon	12953476	12954959	.	-	.	gene_id "CG30460"; transcript_id "NM_001103885"; exon_number "1"; exon_id "NM_001103885.1"; gene_name "CG30460";
+chr2R	refGene	3UTR	12953476	12954286	.	-	.	gene_id "CG30460"; transcript_id "NM_001103885"; exon_number "1"; exon_id "NM_001103885.1"; gene_name "CG30460";
+chr3L	refGene	exon	14035548	14036786	.	+	.	gene_id "Hsc70Cb"; transcript_id "NM_001274893"; exon_number "6"; exon_id "NM_001274893.6"; gene_name "Hsc70Cb";
+chr3L	refGene	3UTR	14036172	14036786	.	+	.	gene_id "Hsc70Cb"; transcript_id "NM_001274893"; exon_number "6"; exon_id "NM_001274893.6"; gene_name "Hsc70Cb";
+chr2R	refGene	exon	13748834	13749096	.	+	.	gene_id "CG14490"; transcript_id "NM_137430"; exon_number "2"; exon_id "NM_137430.2"; gene_name "CG14490";
+chr2R	refGene	3UTR	13749019	13749096	.	+	.	gene_id "CG14490"; transcript_id "NM_137430"; exon_number "2"; exon_id "NM_137430.2"; gene_name "CG14490";
+chr3R	refGene	exon	8822404	8822647	.	+	.	gene_id "CG7488"; transcript_id "NM_141991"; exon_number "2"; exon_id "NM_141991.2"; gene_name "CG7488";
+chr3R	refGene	3UTR	8822592	8822647	.	+	.	gene_id "CG7488"; transcript_id "NM_141991"; exon_number "2"; exon_id "NM_141991.2"; gene_name "CG7488";
+chr3L	refGene	exon	22858978	22859060	.	+	.	gene_id "CG33170"; transcript_id "NM_001275295"; exon_number "3"; exon_id "NM_001275295.3"; gene_name "CG33170";
+chr3L	refGene	CDS	22858978	22859060	.	+	0	gene_id "CG33170"; transcript_id "NM_001275295"; exon_number "3"; exon_id "NM_001275295.3"; gene_name "CG33170";
+chr3L	refGene	exon	5132719	5133573	.	+	.	gene_id "CHMP2B"; transcript_id "NM_139690"; exon_number "1"; exon_id "NM_139690.1"; gene_name "CHMP2B";
+chr3L	refGene	3UTR	5133484	5133573	.	+	.	gene_id "CHMP2B"; transcript_id "NM_139690"; exon_number "1"; exon_id "NM_139690.1"; gene_name "CHMP2B";
+chr3L	refGene	exon	5359905	5360481	.	+	.	gene_id "membrin"; transcript_id "NM_139703"; exon_number "2"; exon_id "NM_139703.2"; gene_name "membrin";
+chr3L	refGene	3UTR	5360419	5360481	.	+	.	gene_id "membrin"; transcript_id "NM_139703"; exon_number "2"; exon_id "NM_139703.2"; gene_name "membrin";
+chr3L	refGene	exon	12498474	12499587	.	-	.	gene_id "CG10654"; transcript_id "NM_001274838"; exon_number "1"; exon_id "NM_001274838.1"; gene_name "CG10654";
+chr3L	refGene	3UTR	12498474	12498909	.	-	.	gene_id "CG10654"; transcript_id "NM_001274838"; exon_number "1"; exon_id "NM_001274838.1"; gene_name "CG10654";
+chr3L	refGene	CDS	12498913	12499587	.	-	0	gene_id "CG10654"; transcript_id "NM_001274838"; exon_number "1"; exon_id "NM_001274838.1"; gene_name "CG10654";
+chr3L	refGene	stop_codon	12498910	12498912	.	-	0	gene_id "CG10654"; transcript_id "NM_001274838"; exon_number "1"; exon_id "NM_001274838.1"; gene_name "CG10654";
+chr3L	refGene	exon	12498864	12499587	.	-	.	gene_id "CG10654"; transcript_id "NM_140326"; exon_number "1"; exon_id "NM_140326.1"; gene_name "CG10654";
+chr3L	refGene	3UTR	12498864	12498909	.	-	.	gene_id "CG10654"; transcript_id "NM_140326"; exon_number "1"; exon_id "NM_140326.1"; gene_name "CG10654";
+chr3L	refGene	CDS	12498913	12499587	.	-	0	gene_id "CG10654"; transcript_id "NM_140326"; exon_number "1"; exon_id "NM_140326.1"; gene_name "CG10654";
+chr3L	refGene	stop_codon	12498910	12498912	.	-	0	gene_id "CG10654"; transcript_id "NM_140326"; exon_number "1"; exon_id "NM_140326.1"; gene_name "CG10654";
+chr3L	refGene	exon	9363295	9363802	.	-	.	gene_id "Fdxh"; transcript_id "NM_001202146"; exon_number "1"; exon_id "NM_001202146.1"; gene_name "Fdxh";
+chr3L	refGene	3UTR	9363295	9363450	.	-	.	gene_id "Fdxh"; transcript_id "NM_001202146"; exon_number "1"; exon_id "NM_001202146.1"; gene_name "Fdxh";
+chr3L	refGene	exon	7659266	7686955	.	-	.	gene_id "Ank2"; transcript_id "NM_001202141"; exon_number "6"; exon_id "NM_001202141.6"; gene_name "Ank2";
+chr3L	refGene	CDS	7659266	7686955	.	-	2	gene_id "Ank2"; transcript_id "NM_001202141"; exon_number "6"; exon_id "NM_001202141.6"; gene_name "Ank2";
+chr3L	refGene	exon	12395395	12397390	.	-	.	gene_id "CG32103"; transcript_id "NM_206345"; exon_number "1"; exon_id "NM_206345.1"; gene_name "CG32103";
+chr3L	refGene	3UTR	12395395	12397154	.	-	.	gene_id "CG32103"; transcript_id "NM_206345"; exon_number "1"; exon_id "NM_206345.1"; gene_name "CG32103";
+chr3L	refGene	exon	19259573	19261560	.	-	.	gene_id "CG9629"; transcript_id "NM_140842"; exon_number "1"; exon_id "NM_140842.1"; gene_name "CG9629";
+chr3L	refGene	3UTR	19259573	19259936	.	-	.	gene_id "CG9629"; transcript_id "NM_140842"; exon_number "1"; exon_id "NM_140842.1"; gene_name "CG9629";
+chr3L	refGene	exon	5805165	5805328	.	+	.	gene_id "CG5537"; transcript_id "NM_001274522"; exon_number "3"; exon_id "NM_001274522.3"; gene_name "CG5537";
+chr3L	refGene	3UTR	5805176	5805328	.	+	.	gene_id "CG5537"; transcript_id "NM_001274522"; exon_number "3"; exon_id "NM_001274522.3"; gene_name "CG5537";
+chr3L	refGene	exon	5804486	5805328	.	+	.	gene_id "CG5537"; transcript_id "NM_001274523"; exon_number "2"; exon_id "NM_001274523.2"; gene_name "CG5537";
+chr3L	refGene	3UTR	5805030	5805328	.	+	.	gene_id "CG5537"; transcript_id "NM_001274523"; exon_number "2"; exon_id "NM_001274523.2"; gene_name "CG5537";
+chr3L	refGene	exon	6584579	6587040	.	+	.	gene_id "CG18769"; transcript_id "NM_144449"; exon_number "8"; exon_id "NM_144449.8"; gene_name "CG18769";
+chr3L	refGene	3UTR	6584822	6587040	.	+	.	gene_id "CG18769"; transcript_id "NM_144449"; exon_number "8"; exon_id "NM_144449.8"; gene_name "CG18769";
+chr3RHet	refGene	exon	1896444	1898929	.	-	.	gene_id "Alg-2"; transcript_id "NM_001015400"; exon_number "1"; exon_id "NM_001015400.1"; gene_name "Alg-2";
+chr3RHet	refGene	3UTR	1896444	1898328	.	-	.	gene_id "Alg-2"; transcript_id "NM_001015400"; exon_number "1"; exon_id "NM_001015400.1"; gene_name "Alg-2";
+chr2LHet	refGene	exon	20723	21383	.	-	.	gene_id "CG12567"; transcript_id "NM_001015383"; exon_number "2"; exon_id "NM_001015383.2"; gene_name "CG12567";
+chr2LHet	refGene	CDS	20723	21383	.	-	0	gene_id "CG12567"; transcript_id "NM_001015383"; exon_number "2"; exon_id "NM_001015383.2"; gene_name "CG12567";
+chr2L	refGene	exon	18133588	18134826	.	-	.	gene_id "kel"; transcript_id "NM_057241"; exon_number "4"; exon_id "NM_057241.4"; gene_name "kel";
+chr2L	refGene	CDS	18133588	18134826	.	-	1	gene_id "kel"; transcript_id "NM_057241"; exon_number "4"; exon_id "NM_057241.4"; gene_name "kel";
+chr2R	refGene	exon	5475458	5475835	.	-	.	gene_id "clos"; transcript_id "NM_001103776"; exon_number "1"; exon_id "NM_001103776.1"; gene_name "clos";
+chr2R	refGene	3UTR	5475458	5475510	.	-	.	gene_id "clos"; transcript_id "NM_001103776"; exon_number "1"; exon_id "NM_001103776.1"; gene_name "clos";
+chr3L	refGene	exon	9128809	9129001	.	-	.	gene_id "Use1"; transcript_id "NM_140032"; exon_number "1"; exon_id "NM_140032.1"; gene_name "Use1";
+chr3L	refGene	3UTR	9128809	9128957	.	-	.	gene_id "Use1"; transcript_id "NM_140032"; exon_number "1"; exon_id "NM_140032.1"; gene_name "Use1";
+chr2R	refGene	exon	19696768	19698907	.	+	.	gene_id "CG5543"; transcript_id "NM_137988"; exon_number "1"; exon_id "NM_137988.1"; gene_name "CG5543";
+chr2R	refGene	3UTR	19698850	19698907	.	+	.	gene_id "CG5543"; transcript_id "NM_137988"; exon_number "1"; exon_id "NM_137988.1"; gene_name "CG5543";
+chrX	refGene	exon	14476169	14476388	.	-	.	gene_id "mRpS25"; transcript_id "NM_078598"; exon_number "1"; exon_id "NM_078598.1"; gene_name "mRpS25";
+chrX	refGene	3UTR	14476169	14476216	.	-	.	gene_id "mRpS25"; transcript_id "NM_078598"; exon_number "1"; exon_id "NM_078598.1"; gene_name "mRpS25";
+chrX	refGene	exon	8916051	8916272	.	+	.	gene_id "rdgA"; transcript_id "NM_078537"; exon_number "12"; exon_id "NM_078537.12"; gene_name "rdgA";
+chrX	refGene	CDS	8916051	8916272	.	+	2	gene_id "rdgA"; transcript_id "NM_078537"; exon_number "12"; exon_id "NM_078537.12"; gene_name "rdgA";
+chrX	refGene	exon	15360217	15361300	.	-	.	gene_id "CG15642"; transcript_id "NM_132800"; exon_number "1"; exon_id "NM_132800.1"; gene_name "CG15642";
+chrX	refGene	3UTR	15360217	15360865	.	-	.	gene_id "CG15642"; transcript_id "NM_132800"; exon_number "1"; exon_id "NM_132800.1"; gene_name "CG15642";
+chrX	refGene	exon	14118058	14118761	.	+	.	gene_id "l(1)G0007"; transcript_id "NM_132719"; exon_number "4"; exon_id "NM_132719.4"; gene_name "l(1)G0007";
+chrX	refGene	3UTR	14118656	14118761	.	+	.	gene_id "l(1)G0007"; transcript_id "NM_132719"; exon_number "4"; exon_id "NM_132719.4"; gene_name "l(1)G0007";
+chrX	refGene	exon	21217349	21217885	.	+	.	gene_id "dod"; transcript_id "NM_078704"; exon_number "3"; exon_id "NM_078704.3"; gene_name "dod";
+chrX	refGene	3UTR	21217459	21217885	.	+	.	gene_id "dod"; transcript_id "NM_078704"; exon_number "3"; exon_id "NM_078704.3"; gene_name "dod";
+chr3LHet	refGene	exon	600380	601061	.	-	.	gene_id "MED21"; transcript_id "NM_001015223"; exon_number "1"; exon_id "NM_001015223.1"; gene_name "MED21";
+chr3LHet	refGene	3UTR	600380	600674	.	-	.	gene_id "MED21"; transcript_id "NM_001015223"; exon_number "1"; exon_id "NM_001015223.1"; gene_name "MED21";
+chr3LHet	refGene	exon	600380	601061	.	-	.	gene_id "MED21"; transcript_id "NM_001015224"; exon_number "1"; exon_id "NM_001015224.1"; gene_name "MED21";
+chr3LHet	refGene	3UTR	600380	600674	.	-	.	gene_id "MED21"; transcript_id "NM_001015224"; exon_number "1"; exon_id "NM_001015224.1"; gene_name "MED21";
+chr3L	refGene	exon	23777506	23780505	.	+	.	gene_id "CG43968"; transcript_id "NM_001275309"; exon_number "2"; exon_id "NM_001275309.2"; gene_name "CG43968";
+chr3L	refGene	CDS	23777506	23780502	.	+	0	gene_id "CG43968"; transcript_id "NM_001275309"; exon_number "2"; exon_id "NM_001275309.2"; gene_name "CG43968";
+chr3L	refGene	exon	10685630	10685908	.	-	.	gene_id "CG33493"; transcript_id "NM_001274757"; exon_number "1"; exon_id "NM_001274757.1"; gene_name "CG33493";
+chr3L	refGene	3UTR	10685630	10685858	.	-	.	gene_id "CG33493"; transcript_id "NM_001274757"; exon_number "1"; exon_id "NM_001274757.1"; gene_name "CG33493";
+chr3L	refGene	exon	10685676	10686267	.	-	.	gene_id "CG33493"; transcript_id "NM_206316"; exon_number "1"; exon_id "NM_206316.1"; gene_name "CG33493";
+chr3L	refGene	3UTR	10685676	10685914	.	-	.	gene_id "CG33493"; transcript_id "NM_206316"; exon_number "1"; exon_id "NM_206316.1"; gene_name "CG33493";
+chr3L	refGene	exon	20234367	20234640	.	+	.	gene_id "CG6951"; transcript_id "NM_168838"; exon_number "1"; exon_id "NM_168838.1"; gene_name "CG6951";
+chr3L	refGene	5UTR	20234367	20234640	.	+	.	gene_id "CG6951"; transcript_id "NM_168838"; exon_number "1"; exon_id "NM_168838.1"; gene_name "CG6951";
+chr3L	refGene	exon	20308234	20308638	.	-	.	gene_id "CR43875"; transcript_id "NR_073957"; exon_number "1"; exon_id "NR_073957.1"; gene_name "CR43875";
+chr2R	refGene	exon	18381802	18383903	.	-	.	gene_id "px"; transcript_id "NM_001274207"; exon_number "1"; exon_id "NM_001274207.1"; gene_name "px";
+chr2R	refGene	3UTR	18381802	18383835	.	-	.	gene_id "px"; transcript_id "NM_001274207"; exon_number "1"; exon_id "NM_001274207.1"; gene_name "px";
+chr2R	refGene	exon	18775097	18775316	.	-	.	gene_id "Gmer"; transcript_id "NM_137890"; exon_number "1"; exon_id "NM_137890.1"; gene_name "Gmer";
+chr2R	refGene	3UTR	18775097	18775148	.	-	.	gene_id "Gmer"; transcript_id "NM_137890"; exon_number "1"; exon_id "NM_137890.1"; gene_name "Gmer";
+chr2L	refGene	exon	6125879	6126595	.	-	.	gene_id "WDR79"; transcript_id "NM_135153"; exon_number "1"; exon_id "NM_135153.1"; gene_name "WDR79";
+chr2L	refGene	3UTR	6125879	6125931	.	-	.	gene_id "WDR79"; transcript_id "NM_135153"; exon_number "1"; exon_id "NM_135153.1"; gene_name "WDR79";
+chr3L	refGene	exon	4281116	4281585	.	+	.	gene_id "CG1311"; transcript_id "NM_001274482"; exon_number "9"; exon_id "NM_001274482.9"; gene_name "CG1311";
+chr3L	refGene	3UTR	4281347	4281585	.	+	.	gene_id "CG1311"; transcript_id "NM_001274482"; exon_number "9"; exon_id "NM_001274482.9"; gene_name "CG1311";
+chr3L	refGene	exon	4281116	4281585	.	+	.	gene_id "CG1311"; transcript_id "NM_139627"; exon_number "9"; exon_id "NM_139627.9"; gene_name "CG1311";
+chr3L	refGene	3UTR	4281347	4281585	.	+	.	gene_id "CG1311"; transcript_id "NM_139627"; exon_number "9"; exon_id "NM_139627.9"; gene_name "CG1311";
+chr3L	refGene	exon	4261038	4261305	.	+	.	gene_id "CG1309"; transcript_id "NM_139623"; exon_number "5"; exon_id "NM_139623.5"; gene_name "CG1309";
+chr3L	refGene	CDS	4261038	4261305	.	+	1	gene_id "CG1309"; transcript_id "NM_139623"; exon_number "5"; exon_id "NM_139623.5"; gene_name "CG1309";
+chr3R	refGene	exon	9094859	9095551	.	-	.	gene_id "CG8449"; transcript_id "NM_169499"; exon_number "1"; exon_id "NM_169499.1"; gene_name "CG8449";
+chr3R	refGene	3UTR	9094859	9095041	.	-	.	gene_id "CG8449"; transcript_id "NM_169499"; exon_number "1"; exon_id "NM_169499.1"; gene_name "CG8449";
+chr2R	refGene	exon	17205298	17207308	.	-	.	gene_id "CG33655"; transcript_id "NM_001169765"; exon_number "1"; exon_id "NM_001169765.1"; gene_name "CG33655";
+chr2R	refGene	3UTR	17205298	17207083	.	-	.	gene_id "CG33655"; transcript_id "NM_001169765"; exon_number "1"; exon_id "NM_001169765.1"; gene_name "CG33655";
+chr2R	refGene	exon	19792186	19792792	.	+	.	gene_id "CG13562"; transcript_id "NM_138005"; exon_number "4"; exon_id "NM_138005.4"; gene_name "CG13562";
+chr2R	refGene	3UTR	19792617	19792792	.	+	.	gene_id "CG13562"; transcript_id "NM_138005"; exon_number "4"; exon_id "NM_138005.4"; gene_name "CG13562";
+chr2R	refGene	exon	17546261	17546980	.	-	.	gene_id "Rae1"; transcript_id "NM_137753"; exon_number "1"; exon_id "NM_137753.1"; gene_name "Rae1";
+chr2R	refGene	3UTR	17546261	17546347	.	-	.	gene_id "Rae1"; transcript_id "NM_137753"; exon_number "1"; exon_id "NM_137753.1"; gene_name "Rae1";
+chr2R	refGene	exon	17181907	17182715	.	-	.	gene_id "CG9752"; transcript_id "NM_137729"; exon_number "1"; exon_id "NM_137729.1"; gene_name "CG9752";
+chr2R	refGene	3UTR	17181907	17181939	.	-	.	gene_id "CG9752"; transcript_id "NM_137729"; exon_number "1"; exon_id "NM_137729.1"; gene_name "CG9752";
+chr3R	refGene	exon	9949885	9950584	.	-	.	gene_id "140up"; transcript_id "NM_001275632"; exon_number "1"; exon_id "NM_001275632.1"; gene_name "140up";
+chr3R	refGene	3UTR	9949885	9950226	.	-	.	gene_id "140up"; transcript_id "NM_001275632"; exon_number "1"; exon_id "NM_001275632.1"; gene_name "140up";
+chr2L	refGene	exon	20064261	20064572	.	-	.	gene_id "vls"; transcript_id "NM_136175"; exon_number "1"; exon_id "NM_136175.1"; gene_name "vls";
+chr2L	refGene	3UTR	20064261	20064385	.	-	.	gene_id "vls"; transcript_id "NM_136175"; exon_number "1"; exon_id "NM_136175.1"; gene_name "vls";
+chr2L	refGene	exon	21102586	21103970	.	-	.	gene_id "CR43809"; transcript_id "NR_073816"; exon_number "1"; exon_id "NR_073816.1"; gene_name "CR43809";
+chr2LHet	refGene	exon	20723	21383	.	-	.	gene_id "CG12567"; transcript_id "NM_001015384"; exon_number "2"; exon_id "NM_001015384.2"; gene_name "CG12567";
+chr2LHet	refGene	CDS	20723	21383	.	-	0	gene_id "CG12567"; transcript_id "NM_001015384"; exon_number "2"; exon_id "NM_001015384.2"; gene_name "CG12567";
+chr2LHet	refGene	exon	20723	21373	.	-	.	gene_id "CG12567"; transcript_id "NM_001110861"; exon_number "2"; exon_id "NM_001110861.2"; gene_name "CG12567";
+chr2LHet	refGene	3UTR	20723	21367	.	-	.	gene_id "CG12567"; transcript_id "NM_001110861"; exon_number "2"; exon_id "NM_001110861.2"; gene_name "CG12567";
+chr2LHet	refGene	exon	20723	21569	.	-	.	gene_id "CG12567"; transcript_id "NM_001170363"; exon_number "2"; exon_id "NM_001170363.2"; gene_name "CG12567";
+chr2LHet	refGene	3UTR	20723	21414	.	-	.	gene_id "CG12567"; transcript_id "NM_001170363"; exon_number "2"; exon_id "NM_001170363.2"; gene_name "CG12567";
+chr2R	refGene	exon	402893	403824	.	-	.	gene_id "RpL38"; transcript_id "NM_001273771"; exon_number "1"; exon_id "NM_001273771.1"; gene_name "RpL38";
+chr2R	refGene	CDS	403615	403824	.	-	0	gene_id "RpL38"; transcript_id "NM_001273771"; exon_number "1"; exon_id "NM_001273771.1"; gene_name "RpL38";
+chr2R	refGene	exon	403505	403824	.	-	.	gene_id "RpL38"; transcript_id "NM_001042975"; exon_number "1"; exon_id "NM_001042975.1"; gene_name "RpL38";
+chr2R	refGene	CDS	403615	403824	.	-	0	gene_id "RpL38"; transcript_id "NM_001042975"; exon_number "1"; exon_id "NM_001042975.1"; gene_name "RpL38";
+chr3L	refGene	exon	20382951	20384487	.	-	.	gene_id "CR43944"; transcript_id "NR_073958"; exon_number "1"; exon_id "NR_073958.1"; gene_name "CR43944";
+chrX	refGene	exon	8916051	8916272	.	+	.	gene_id "rdgA"; transcript_id "NM_001042799"; exon_number "12"; exon_id "NM_001042799.12"; gene_name "rdgA";
+chrX	refGene	CDS	8916051	8916272	.	+	2	gene_id "rdgA"; transcript_id "NM_001042799"; exon_number "12"; exon_id "NM_001042799.12"; gene_name "rdgA";
+chrX	refGene	exon	3465577	3466033	.	+	.	gene_id "CG32792"; transcript_id "NM_001042795"; exon_number "5"; exon_id "NM_001042795.5"; gene_name "CG32792";
+chrX	refGene	CDS	3465577	3465830	.	+	2	gene_id "CG32792"; transcript_id "NM_001042795"; exon_number "5"; exon_id "NM_001042795.5"; gene_name "CG32792";
+chrX	refGene	exon	10031932	10032746	.	+	.	gene_id "CG34104"; transcript_id "NM_001042802"; exon_number "7"; exon_id "NM_001042802.7"; gene_name "CG34104";
+chrX	refGene	3UTR	10031937	10032746	.	+	.	gene_id "CG34104"; transcript_id "NM_001042802"; exon_number "7"; exon_id "NM_001042802.7"; gene_name "CG34104";
+chr2R	refGene	exon	20758822	20759032	.	+	.	gene_id "Atf-2"; transcript_id "NM_001038884"; exon_number "2"; exon_id "NM_001038884.2"; gene_name "Atf-2";
+chr2R	refGene	3UTR	20758932	20759032	.	+	.	gene_id "Atf-2"; transcript_id "NM_001038884"; exon_number "2"; exon_id "NM_001038884.2"; gene_name "Atf-2";
+chr3R	refGene	exon	4808454	4809273	.	-	.	gene_id "RagA"; transcript_id "NM_141593"; exon_number "1"; exon_id "NM_141593.1"; gene_name "RagA";
+chr3R	refGene	3UTR	4808454	4808834	.	-	.	gene_id "RagA"; transcript_id "NM_141593"; exon_number "1"; exon_id "NM_141593.1"; gene_name "RagA";
+chr3R	refGene	exon	4760735	4761009	.	-	.	gene_id "CR44020"; transcript_id "NR_073991"; exon_number "2"; exon_id "NR_073991.2"; gene_name "CR44020";
+chr3R	refGene	exon	4769187	4770620	.	-	.	gene_id "CG11964"; transcript_id "NM_141590"; exon_number "3"; exon_id "NM_141590.3"; gene_name "CG11964";
+chr3R	refGene	CDS	4769187	4770620	.	-	0	gene_id "CG11964"; transcript_id "NM_141590"; exon_number "3"; exon_id "NM_141590.3"; gene_name "CG11964";
+chr3R	refGene	exon	4830231	4831053	.	+	.	gene_id "CG11980"; transcript_id "NM_141600"; exon_number "3"; exon_id "NM_141600.3"; gene_name "CG11980";
+chr3R	refGene	3UTR	4830973	4831053	.	+	.	gene_id "CG11980"; transcript_id "NM_141600"; exon_number "3"; exon_id "NM_141600.3"; gene_name "CG11980";
+chr3R	refGene	exon	4830231	4831053	.	+	.	gene_id "CG11980"; transcript_id "NM_169250"; exon_number "3"; exon_id "NM_169250.3"; gene_name "CG11980";
+chr3R	refGene	3UTR	4830973	4831053	.	+	.	gene_id "CG11980"; transcript_id "NM_169250"; exon_number "3"; exon_id "NM_169250.3"; gene_name "CG11980";
+chr2R	refGene	exon	14296516	14297340	.	+	.	gene_id "GstE9"; transcript_id "NM_166279"; exon_number "1"; exon_id "NM_166279.1"; gene_name "GstE9";
+chr2R	refGene	3UTR	14297262	14297340	.	+	.	gene_id "GstE9"; transcript_id "NM_166279"; exon_number "1"; exon_id "NM_166279.1"; gene_name "GstE9";
+chr3L	refGene	exon	8975312	8976573	.	-	.	gene_id "Galk"; transcript_id "NM_168307"; exon_number "1"; exon_id "NM_168307.1"; gene_name "Galk";
+chr3L	refGene	3UTR	8975312	8976386	.	-	.	gene_id "Galk"; transcript_id "NM_168307"; exon_number "1"; exon_id "NM_168307.1"; gene_name "Galk";
+chr2R	refGene	exon	19780589	19780941	.	-	.	gene_id "Upf3"; transcript_id "NM_166629"; exon_number "1"; exon_id "NM_166629.1"; gene_name "Upf3";
+chr2R	refGene	3UTR	19780589	19780698	.	-	.	gene_id "Upf3"; transcript_id "NM_166629"; exon_number "1"; exon_id "NM_166629.1"; gene_name "Upf3";
+chr2R	refGene	stop_codon	19780699	19780701	.	-	0	gene_id "Upf3"; transcript_id "NM_166629"; exon_number "1"; exon_id "NM_166629.1"; gene_name "Upf3";
+chr2R	refGene	exon	17554252	17555099	.	+	.	gene_id "CG42365"; transcript_id "NM_166469"; exon_number "1"; exon_id "NM_166469.1"; gene_name "CG42365";
+chr2R	refGene	3UTR	17555004	17555099	.	+	.	gene_id "CG42365"; transcript_id "NM_166469"; exon_number "1"; exon_id "NM_166469.1"; gene_name "CG42365";
+chr2R	refGene	exon	3461391	3461663	.	+	.	gene_id "Vps13"; transcript_id "NM_001273852"; exon_number "15"; exon_id "NM_001273852.15"; gene_name "Vps13";
+chr2R	refGene	CDS	3461391	3461663	.	+	2	gene_id "Vps13"; transcript_id "NM_001273852"; exon_number "15"; exon_id "NM_001273852.15"; gene_name "Vps13";
+chr2R	refGene	exon	3461391	3461663	.	+	.	gene_id "Vps13"; transcript_id "NM_136455"; exon_number "15"; exon_id "NM_136455.15"; gene_name "Vps13";
+chr2R	refGene	CDS	3461391	3461663	.	+	2	gene_id "Vps13"; transcript_id "NM_136455"; exon_number "15"; exon_id "NM_136455.15"; gene_name "Vps13";
+chr2R	refGene	exon	16445897	16447458	.	+	.	gene_id "lms"; transcript_id "NM_137647"; exon_number "3"; exon_id "NM_137647.3"; gene_name "lms";
+chr2R	refGene	3UTR	16446647	16447458	.	+	.	gene_id "lms"; transcript_id "NM_137647"; exon_number "3"; exon_id "NM_137647.3"; gene_name "lms";
+chr2R	refGene	exon	13453284	13454499	.	-	.	gene_id "ns2"; transcript_id "NM_137388"; exon_number "1"; exon_id "NM_137388.1"; gene_name "ns2";
+chr2R	refGene	3UTR	13453284	13453363	.	-	.	gene_id "ns2"; transcript_id "NM_137388"; exon_number "1"; exon_id "NM_137388.1"; gene_name "ns2";
+chr2R	refGene	exon	12953476	12954959	.	-	.	gene_id "CG30460"; transcript_id "NM_137342"; exon_number "1"; exon_id "NM_137342.1"; gene_name "CG30460";
+chr2R	refGene	3UTR	12953476	12954286	.	-	.	gene_id "CG30460"; transcript_id "NM_137342"; exon_number "1"; exon_id "NM_137342.1"; gene_name "CG30460";
+chr2R	refGene	exon	11900178	11901329	.	+	.	gene_id "CG8389"; transcript_id "NM_137232"; exon_number "4"; exon_id "NM_137232.4"; gene_name "CG8389";
+chr2R	refGene	3UTR	11901042	11901329	.	+	.	gene_id "CG8389"; transcript_id "NM_137232"; exon_number "4"; exon_id "NM_137232.4"; gene_name "CG8389";
+chr2R	refGene	exon	8041411	8041768	.	+	.	gene_id "CG8407"; transcript_id "NM_001169653"; exon_number "4"; exon_id "NM_001169653.4"; gene_name "CG8407";
+chr2R	refGene	3UTR	8041576	8041768	.	+	.	gene_id "CG8407"; transcript_id "NM_001169653"; exon_number "4"; exon_id "NM_001169653.4"; gene_name "CG8407";
+chr2R	refGene	exon	8041411	8041768	.	+	.	gene_id "CG8407"; transcript_id "NM_136890"; exon_number "3"; exon_id "NM_136890.3"; gene_name "CG8407";
+chr2R	refGene	3UTR	8041576	8041768	.	+	.	gene_id "CG8407"; transcript_id "NM_136890"; exon_number "3"; exon_id "NM_136890.3"; gene_name "CG8407";
+chr2R	refGene	exon	8521671	8523187	.	-	.	gene_id "CG33671"; transcript_id "NM_001273993"; exon_number "1"; exon_id "NM_001273993.1"; gene_name "CG33671";
+chr2R	refGene	3UTR	8521671	8521758	.	-	.	gene_id "CG33671"; transcript_id "NM_001273993"; exon_number "1"; exon_id "NM_001273993.1"; gene_name "CG33671";
+chr2R	refGene	exon	8521671	8523646	.	-	.	gene_id "CG33671"; transcript_id "NM_001032241"; exon_number "1"; exon_id "NM_001032241.1"; gene_name "CG33671";
+chr2R	refGene	3UTR	8521671	8521758	.	-	.	gene_id "CG33671"; transcript_id "NM_001032241"; exon_number "1"; exon_id "NM_001032241.1"; gene_name "CG33671";
+chr2R	refGene	exon	8521671	8523646	.	-	.	gene_id "CG33672"; transcript_id "NM_001032242"; exon_number "1"; exon_id "NM_001032242.1"; gene_name "CG33672";
+chr2R	refGene	3UTR	8521671	8523328	.	-	.	gene_id "CG33672"; transcript_id "NM_001032242"; exon_number "1"; exon_id "NM_001032242.1"; gene_name "CG33672";
+chr2R	refGene	exon	9108444	9108881	.	-	.	gene_id "Fsn"; transcript_id "NM_165973"; exon_number "1"; exon_id "NM_165973.1"; gene_name "Fsn";
+chr2R	refGene	3UTR	9108444	9108786	.	-	.	gene_id "Fsn"; transcript_id "NM_165973"; exon_number "1"; exon_id "NM_165973.1"; gene_name "Fsn";
+chr2R	refGene	exon	9108444	9108881	.	-	.	gene_id "Fsn"; transcript_id "NM_137005"; exon_number "1"; exon_id "NM_137005.1"; gene_name "Fsn";
+chr2R	refGene	3UTR	9108444	9108786	.	-	.	gene_id "Fsn"; transcript_id "NM_137005"; exon_number "1"; exon_id "NM_137005.1"; gene_name "Fsn";
+chr2R	refGene	exon	4984436	4985641	.	-	.	gene_id "CG8078"; transcript_id "NM_136607"; exon_number "1"; exon_id "NM_136607.1"; gene_name "CG8078";
+chr2R	refGene	3UTR	4984436	4984815	.	-	.	gene_id "CG8078"; transcript_id "NM_136607"; exon_number "1"; exon_id "NM_136607.1"; gene_name "CG8078";
+chr2R	refGene	exon	4972167	4972827	.	+	.	gene_id "CNT1"; transcript_id "NM_136603"; exon_number "6"; exon_id "NM_136603.6"; gene_name "CNT1";
+chr2R	refGene	3UTR	4972205	4972827	.	+	.	gene_id "CNT1"; transcript_id "NM_136603"; exon_number "6"; exon_id "NM_136603.6"; gene_name "CNT1";
+chr2R	refGene	exon	11900178	11901329	.	+	.	gene_id "CG8389"; transcript_id "NM_166132"; exon_number "4"; exon_id "NM_166132.4"; gene_name "CG8389";
+chr2R	refGene	3UTR	11901042	11901329	.	+	.	gene_id "CG8389"; transcript_id "NM_166132"; exon_number "4"; exon_id "NM_166132.4"; gene_name "CG8389";
+chr2R	refGene	exon	10755738	10756067	.	-	.	gene_id "Inr-a"; transcript_id "NM_137155"; exon_number "8"; exon_id "NM_137155.8"; gene_name "Inr-a";
+chr2R	refGene	CDS	10755738	10756067	.	-	0	gene_id "Inr-a"; transcript_id "NM_137155"; exon_number "8"; exon_id "NM_137155.8"; gene_name "Inr-a";
+chr2R	refGene	exon	9747854	9748795	.	-	.	gene_id "CG16935"; transcript_id "NM_137070"; exon_number "1"; exon_id "NM_137070.1"; gene_name "CG16935";
+chr2R	refGene	3UTR	9747854	9747935	.	-	.	gene_id "CG16935"; transcript_id "NM_137070"; exon_number "1"; exon_id "NM_137070.1"; gene_name "CG16935";
+chr2R	refGene	exon	8374314	8375491	.	+	.	gene_id "Dh44-R2"; transcript_id "NM_136945"; exon_number "11"; exon_id "NM_136945.11"; gene_name "Dh44-R2";
+chr2R	refGene	3UTR	8374411	8375491	.	+	.	gene_id "Dh44-R2"; transcript_id "NM_136945"; exon_number "11"; exon_id "NM_136945.11"; gene_name "Dh44-R2";
+chr2R	refGene	exon	8064935	8066035	.	-	.	gene_id "EndoG"; transcript_id "NM_136893"; exon_number "1"; exon_id "NM_136893.1"; gene_name "EndoG";
+chr2R	refGene	3UTR	8064935	8065045	.	-	.	gene_id "EndoG"; transcript_id "NM_136893"; exon_number "1"; exon_id "NM_136893.1"; gene_name "EndoG";
+chr2R	refGene	exon	6714934	6716361	.	-	.	gene_id "CG12344"; transcript_id "NM_136775"; exon_number "1"; exon_id "NM_136775.1"; gene_name "CG12344";
+chr2R	refGene	3UTR	6714934	6716160	.	-	.	gene_id "CG12344"; transcript_id "NM_136775"; exon_number "1"; exon_id "NM_136775.1"; gene_name "CG12344";
+chr2R	refGene	exon	6709744	6710826	.	-	.	gene_id "CG12343"; transcript_id "NM_136773"; exon_number "1"; exon_id "NM_136773.1"; gene_name "CG12343";
+chr2R	refGene	3UTR	6709744	6710087	.	-	.	gene_id "CG12343"; transcript_id "NM_136773"; exon_number "1"; exon_id "NM_136773.1"; gene_name "CG12343";
+chr2R	refGene	exon	3856756	3857013	.	+	.	gene_id "nito"; transcript_id "NM_136495"; exon_number "4"; exon_id "NM_136495.4"; gene_name "nito";
+chr2R	refGene	3UTR	3856756	3857013	.	+	.	gene_id "nito"; transcript_id "NM_136495"; exon_number "4"; exon_id "NM_136495.4"; gene_name "nito";
+chr2L	refGene	exon	21159272	21160783	.	+	.	gene_id "CG9248"; transcript_id "NM_136249"; exon_number "3"; exon_id "NM_136249.3"; gene_name "CG9248";
+chr2L	refGene	3UTR	21160568	21160783	.	+	.	gene_id "CG9248"; transcript_id "NM_136249"; exon_number "3"; exon_id "NM_136249.3"; gene_name "CG9248";
+chr2L	refGene	exon	21157433	21158243	.	-	.	gene_id "CG9249"; transcript_id "NM_136248"; exon_number "1"; exon_id "NM_136248.1"; gene_name "CG9249";
+chr2L	refGene	CDS	21157520	21158243	.	-	1	gene_id "CG9249"; transcript_id "NM_136248"; exon_number "1"; exon_id "NM_136248.1"; gene_name "CG9249";
+chr3L	refGene	exon	19860588	19861745	.	-	.	gene_id "Rab8"; transcript_id "NM_079448"; exon_number "1"; exon_id "NM_079448.1"; gene_name "Rab8";
+chr3L	refGene	3UTR	19860588	19861652	.	-	.	gene_id "Rab8"; transcript_id "NM_079448"; exon_number "1"; exon_id "NM_079448.1"; gene_name "Rab8";
+chr3L	refGene	exon	19860808	19861745	.	-	.	gene_id "Rab8"; transcript_id "NM_001259908"; exon_number "1"; exon_id "NM_001259908.1"; gene_name "Rab8";
+chr3L	refGene	3UTR	19860808	19861652	.	-	.	gene_id "Rab8"; transcript_id "NM_001259908"; exon_number "1"; exon_id "NM_001259908.1"; gene_name "Rab8";
+chr2L	refGene	exon	18711071	18711733	.	-	.	gene_id "Irk3"; transcript_id "NM_001144363"; exon_number "1"; exon_id "NM_001144363.1"; gene_name "Irk3";
+chr2L	refGene	3UTR	18711071	18711336	.	-	.	gene_id "Irk3"; transcript_id "NM_001144363"; exon_number "1"; exon_id "NM_001144363.1"; gene_name "Irk3";
+chr3L	refGene	exon	8905410	8905771	.	-	.	gene_id "mfr"; transcript_id "NM_001144444"; exon_number "14"; exon_id "NM_001144444.14"; gene_name "mfr";
+chr3L	refGene	5UTR	8905410	8905771	.	-	.	gene_id "mfr"; transcript_id "NM_001144444"; exon_number "14"; exon_id "NM_001144444.14"; gene_name "mfr";
+chr3L	refGene	exon	22858978	22859060	.	+	.	gene_id "CG33170"; transcript_id "NM_001144528"; exon_number "3"; exon_id "NM_001144528.3"; gene_name "CG33170";
+chr3L	refGene	CDS	22858978	22859060	.	+	0	gene_id "CG33170"; transcript_id "NM_001144528"; exon_number "3"; exon_id "NM_001144528.3"; gene_name "CG33170";
+chr3R	refGene	exon	6234340	6234597	.	-	.	gene_id "Irp-1B"; transcript_id "NM_079579"; exon_number "1"; exon_id "NM_079579.1"; gene_name "Irp-1B";
+chr3R	refGene	3UTR	6234340	6234486	.	-	.	gene_id "Irp-1B"; transcript_id "NM_079579"; exon_number "1"; exon_id "NM_079579.1"; gene_name "Irp-1B";
+chr3R	refGene	exon	7447188	7447666	.	-	.	gene_id "CG6808"; transcript_id "NM_169411"; exon_number "1"; exon_id "NM_169411.1"; gene_name "CG6808";
+chr3R	refGene	3UTR	7447188	7447446	.	-	.	gene_id "CG6808"; transcript_id "NM_169411"; exon_number "1"; exon_id "NM_169411.1"; gene_name "CG6808";
+chr3R	refGene	exon	9502271	9502666	.	+	.	gene_id "lkb1"; transcript_id "NM_169544"; exon_number "1"; exon_id "NM_169544.1"; gene_name "lkb1";
+chr3R	refGene	5UTR	9502271	9502666	.	+	.	gene_id "lkb1"; transcript_id "NM_169544"; exon_number "1"; exon_id "NM_169544.1"; gene_name "lkb1";
+chr3R	refGene	exon	9223557	9224305	.	+	.	gene_id "CG14377"; transcript_id "NM_169524"; exon_number "1"; exon_id "NM_169524.1"; gene_name "CG14377";
+chr3R	refGene	3UTR	9223907	9224305	.	+	.	gene_id "CG14377"; transcript_id "NM_169524"; exon_number "1"; exon_id "NM_169524.1"; gene_name "CG14377";
+chrX	refGene	exon	19036145	19037801	.	-	.	gene_id "RhoGAP18B"; transcript_id "NM_001144748"; exon_number "1"; exon_id "NM_001144748.1"; gene_name "RhoGAP18B";
+chrX	refGene	3UTR	19036145	19037617	.	-	.	gene_id "RhoGAP18B"; transcript_id "NM_001144748"; exon_number "1"; exon_id "NM_001144748.1"; gene_name "RhoGAP18B";
+chr3L	refGene	exon	22858978	22859134	.	+	.	gene_id "CG33170"; transcript_id "NM_176391"; exon_number "3"; exon_id "NM_176391.3"; gene_name "CG33170";
+chr3L	refGene	CDS	22858978	22859061	.	+	0	gene_id "CG33170"; transcript_id "NM_176391"; exon_number "3"; exon_id "NM_176391.3"; gene_name "CG33170";
+chr3L	refGene	3UTR	22859065	22859134	.	+	.	gene_id "CG33170"; transcript_id "NM_176391"; exon_number "3"; exon_id "NM_176391.3"; gene_name "CG33170";
+chr3L	refGene	stop_codon	22859062	22859064	.	+	0	gene_id "CG33170"; transcript_id "NM_176391"; exon_number "1"; exon_id "NM_176391.1"; gene_name "CG33170";
+chrX	refGene	exon	6898793	6899011	.	-	.	gene_id "Inx7"; transcript_id "NM_176698"; exon_number "3"; exon_id "NM_176698.3"; gene_name "Inx7";
+chrX	refGene	5UTR	6898796	6899011	.	-	.	gene_id "Inx7"; transcript_id "NM_176698"; exon_number "3"; exon_id "NM_176698.3"; gene_name "Inx7";
+chr2R	refGene	exon	12953476	12954959	.	-	.	gene_id "CG30460"; transcript_id "NM_206149"; exon_number "1"; exon_id "NM_206149.1"; gene_name "CG30460";
+chr2R	refGene	3UTR	12953476	12954286	.	-	.	gene_id "CG30460"; transcript_id "NM_206149"; exon_number "1"; exon_id "NM_206149.1"; gene_name "CG30460";
+chr2R	refGene	exon	12953476	12954959	.	-	.	gene_id "CG30460"; transcript_id "NM_206150"; exon_number "1"; exon_id "NM_206150.1"; gene_name "CG30460";
+chr2R	refGene	3UTR	12953476	12954286	.	-	.	gene_id "CG30460"; transcript_id "NM_206150"; exon_number "1"; exon_id "NM_206150.1"; gene_name "CG30460";
+chr2R	refGene	exon	12953476	12954959	.	-	.	gene_id "CG30460"; transcript_id "NM_206148"; exon_number "1"; exon_id "NM_206148.1"; gene_name "CG30460";
+chr2R	refGene	3UTR	12953476	12954286	.	-	.	gene_id "CG30460"; transcript_id "NM_206148"; exon_number "1"; exon_id "NM_206148.1"; gene_name "CG30460";
+chr2L	refGene	exon	9959248	9961617	.	-	.	gene_id "CG5850"; transcript_id "NM_001259026"; exon_number "1"; exon_id "NM_001259026.1"; gene_name "CG5850";
+chr2L	refGene	3UTR	9959248	9961354	.	-	.	gene_id "CG5850"; transcript_id "NM_001259026"; exon_number "1"; exon_id "NM_001259026.1"; gene_name "CG5850";
+chr2L	refGene	exon	9787352	9788499	.	+	.	gene_id "IP3K1"; transcript_id "NM_001259025"; exon_number "4"; exon_id "NM_001259025.4"; gene_name "IP3K1";
+chr2L	refGene	CDS	9787352	9788168	.	+	1	gene_id "IP3K1"; transcript_id "NM_001259025"; exon_number "4"; exon_id "NM_001259025.4"; gene_name "IP3K1";
+chr3R	refGene	exon	7447188	7447666	.	-	.	gene_id "CG6808"; transcript_id "NM_001260126"; exon_number "1"; exon_id "NM_001260126.1"; gene_name "CG6808";
+chr3R	refGene	3UTR	7447188	7447446	.	-	.	gene_id "CG6808"; transcript_id "NM_001260126"; exon_number "1"; exon_id "NM_001260126.1"; gene_name "CG6808";
+chr3R	refGene	exon	3836629	3836956	.	-	.	gene_id "CG10435"; transcript_id "NM_141502"; exon_number "1"; exon_id "NM_141502.1"; gene_name "CG10435";
+chr3R	refGene	3UTR	3836629	3836830	.	-	.	gene_id "CG10435"; transcript_id "NM_141502"; exon_number "1"; exon_id "NM_141502.1"; gene_name "CG10435";
+chr3R	refGene	exon	13621717	13622039	.	+	.	gene_id "CG7713"; transcript_id "NM_001260230"; exon_number "4"; exon_id "NM_001260230.4"; gene_name "CG7713";
+chr3R	refGene	3UTR	13621801	13622039	.	+	.	gene_id "CG7713"; transcript_id "NM_001260230"; exon_number "4"; exon_id "NM_001260230.4"; gene_name "CG7713";
+chr3R	refGene	exon	13621717	13622039	.	+	.	gene_id "CG7713"; transcript_id "NM_001260229"; exon_number "5"; exon_id "NM_001260229.5"; gene_name "CG7713";
+chr3R	refGene	3UTR	13621801	13622039	.	+	.	gene_id "CG7713"; transcript_id "NM_001260229"; exon_number "5"; exon_id "NM_001260229.5"; gene_name "CG7713";
+chr3R	refGene	exon	7462899	7463460	.	+	.	gene_id "CR44137"; transcript_id "NR_073997"; exon_number "1"; exon_id "NR_073997.1"; gene_name "CR44137";
+chr3R	refGene	exon	20680218	20681667	.	-	.	gene_id "HdacX"; transcript_id "NM_001260367"; exon_number "1"; exon_id "NM_001260367.1"; gene_name "HdacX";
+chr3R	refGene	3UTR	20680218	20680824	.	-	.	gene_id "HdacX"; transcript_id "NM_001260367"; exon_number "1"; exon_id "NM_001260367.1"; gene_name "HdacX";
+chr3R	refGene	exon	4576502	4578463	.	-	.	gene_id "CG34135"; transcript_id "NM_001043224"; exon_number "2"; exon_id "NM_001043224.2"; gene_name "CG34135";
+chr3R	refGene	5UTR	4576638	4578463	.	-	.	gene_id "CG34135"; transcript_id "NM_001043224"; exon_number "2"; exon_id "NM_001043224.2"; gene_name "CG34135";
+chr3R	refGene	exon	4576502	4580132	.	-	.	gene_id "CG34135"; transcript_id "NM_001043223"; exon_number "2"; exon_id "NM_001043223.2"; gene_name "CG34135";
+chr3R	refGene	5UTR	4576638	4580132	.	-	.	gene_id "CG34135"; transcript_id "NM_001043223"; exon_number "2"; exon_id "NM_001043223.2"; gene_name "CG34135";
+chrX	refGene	exon	8329051	8330244	.	-	.	gene_id "CG12125"; transcript_id "NM_001169231"; exon_number "2"; exon_id "NM_001169231.2"; gene_name "CG12125";
+chrX	refGene	CDS	8329051	8330244	.	-	0	gene_id "CG12125"; transcript_id "NM_001169231"; exon_number "2"; exon_id "NM_001169231.2"; gene_name "CG12125";
+chr3R	refGene	exon	16416746	16417333	.	-	.	gene_id "CG4159"; transcript_id "NM_001170193"; exon_number "1"; exon_id "NM_001170193.1"; gene_name "CG4159";
+chr3R	refGene	3UTR	16416746	16416807	.	-	.	gene_id "CG4159"; transcript_id "NM_001170193"; exon_number "1"; exon_id "NM_001170193.1"; gene_name "CG4159";
+chrX	refGene	exon	3465577	3466033	.	+	.	gene_id "CG32792"; transcript_id "NM_001144679"; exon_number "6"; exon_id "NM_001144679.6"; gene_name "CG32792";
+chrX	refGene	CDS	3465577	3465830	.	+	2	gene_id "CG32792"; transcript_id "NM_001144679"; exon_number "6"; exon_id "NM_001144679.6"; gene_name "CG32792";
+chr2R	refGene	exon	19792186	19792792	.	+	.	gene_id "CG13562"; transcript_id "NM_001259555"; exon_number "5"; exon_id "NM_001259555.5"; gene_name "CG13562";
+chr2R	refGene	3UTR	19792617	19792792	.	+	.	gene_id "CG13562"; transcript_id "NM_001259555"; exon_number "5"; exon_id "NM_001259555.5"; gene_name "CG13562";
+chr3L	refGene	exon	19861136	19861745	.	-	.	gene_id "Rab8"; transcript_id "NM_001259907"; exon_number "1"; exon_id "NM_001259907.1"; gene_name "Rab8";
+chr3L	refGene	3UTR	19861136	19861652	.	-	.	gene_id "Rab8"; transcript_id "NM_001259907"; exon_number "1"; exon_id "NM_001259907.1"; gene_name "Rab8";
+chr3L	refGene	exon	16837668	16837962	.	-	.	gene_id "CG9669"; transcript_id "NM_001259878"; exon_number "1"; exon_id "NM_001259878.1"; gene_name "CG9669";
+chr3L	refGene	3UTR	16837668	16837724	.	-	.	gene_id "CG9669"; transcript_id "NM_001259878"; exon_number "1"; exon_id "NM_001259878.1"; gene_name "CG9669";
+chr3R	refGene	exon	3714818	3715872	.	+	.	gene_id "CG10092"; transcript_id "NM_001275422"; exon_number "5"; exon_id "NM_001275422.5"; gene_name "CG10092";
+chr3R	refGene	3UTR	3714972	3715872	.	+	.	gene_id "CG10092"; transcript_id "NM_001275422"; exon_number "5"; exon_id "NM_001275422.5"; gene_name "CG10092";
+chr3R	refGene	exon	8302987	8303989	.	-	.	gene_id "alphagamma-element:CR32865"; transcript_id "NR_002020"; exon_number "2"; exon_id "NR_002020.2"; gene_name "alphagamma-element:CR32865";
+chr3R	refGene	exon	1433980	1435042	.	+	.	gene_id "CR43628"; transcript_id "NR_048327"; exon_number "3"; exon_id "NR_048327.3"; gene_name "CR43628";
+chr2R	refGene	exon	15287274	15288840	.	+	.	gene_id "CR43430"; transcript_id "NR_048145"; exon_number "1"; exon_id "NR_048145.1"; gene_name "CR43430";
+chr2R	refGene	exon	8763587	8764785	.	+	.	gene_id "CR43468"; transcript_id "NR_048099"; exon_number "2"; exon_id "NR_048099.2"; gene_name "CR43468";
+chrX	refGene	exon	12864509	12865007	.	-	.	gene_id "CR43636"; transcript_id "NR_047800"; exon_number "1"; exon_id "NR_047800.1"; gene_name "CR43636";
+chrX	refGene	exon	7766860	7767673	.	+	.	gene_id "CR43615"; transcript_id "NR_047779"; exon_number "1"; exon_id "NR_047779.1"; gene_name "CR43615";
+chrUextra	refGene	exon	21314107	21314290	.	-	.	gene_id "Su(Ste):CR42422"; transcript_id "NR_026616"; exon_number "4"; exon_id "NR_026616.4"; gene_name "Su(Ste):CR42422";
+chrUextra	refGene	exon	14493536	14493887	.	-	.	gene_id "CR41583"; transcript_id "NR_003998"; exon_number "4"; exon_id "NR_003998.4"; gene_name "CR41583";
+chrUextra	refGene	exon	16450512	16450821	.	-	.	gene_id "CR41583"; transcript_id "NR_003998_2"; exon_number "5"; exon_id "NR_003998_2.5"; gene_name "CR41583";
+chrUextra	refGene	exon	21242017	21242310	.	+	.	gene_id "CR41583"; transcript_id "NR_003998_5"; exon_number "1"; exon_id "NR_003998_5.1"; gene_name "CR41583";
+chrUextra	refGene	exon	21598582	21599121	.	+	.	gene_id "CR41583"; transcript_id "NR_003998_5"; exon_number "2"; exon_id "NR_003998_5.2"; gene_name "CR41583";
+chrX	refGene	exon	18880	19093	.	+	.	gene_id "CR40469"; transcript_id "NR_003723"; exon_number "1"; exon_id "NR_003723.1"; gene_name "CR40469";
+chr3R	refGene	exon	7048136	7048564	.	-	.	gene_id "CR31144"; transcript_id "NR_037759"; exon_number "1"; exon_id "NR_037759.1"; gene_name "CR31144";
+chr3R	refGene	exon	5605241	5608415	.	-	.	gene_id "CR31514"; transcript_id "NR_037757"; exon_number "1"; exon_id "NR_037757.1"; gene_name "CR31514";
+chr3R	refGene	exon	27594101	27595145	.	+	.	gene_id "pncr017:3R"; transcript_id "NR_002507"; exon_number "2"; exon_id "NR_002507.2"; gene_name "pncr017:3R";
+chr3R	refGene	exon	27043086	27043384	.	-	.	gene_id "RNaseP:RNA"; transcript_id "NR_002092"; exon_number "1"; exon_id "NR_002092.1"; gene_name "RNaseP:RNA";
+chr3R	refGene	exon	2902612	2903703	.	+	.	gene_id "CG1943"; transcript_id "NM_001275397"; exon_number "2"; exon_id "NM_001275397.2"; gene_name "CG1943";
+chr3R	refGene	3UTR	2902998	2903703	.	+	.	gene_id "CG1943"; transcript_id "NM_001275397"; exon_number "2"; exon_id "NM_001275397.2"; gene_name "CG1943";
+chr3R	refGene	exon	2951993	2953194	.	-	.	gene_id "CG10068"; transcript_id "NM_141438"; exon_number "1"; exon_id "NM_141438.1"; gene_name "CG10068";
+chr3R	refGene	3UTR	2951993	2952493	.	-	.	gene_id "CG10068"; transcript_id "NM_141438"; exon_number "1"; exon_id "NM_141438.1"; gene_name "CG10068";
+chr3R	refGene	exon	11102162	11103292	.	-	.	gene_id "MRG15"; transcript_id "NM_001275659"; exon_number "1"; exon_id "NM_001275659.1"; gene_name "MRG15";
+chr3R	refGene	3UTR	11102162	11102306	.	-	.	gene_id "MRG15"; transcript_id "NM_001275659"; exon_number "1"; exon_id "NM_001275659.1"; gene_name "MRG15";
+chr3R	refGene	exon	11143217	11144007	.	+	.	gene_id "CG14866"; transcript_id "NM_001144585"; exon_number "3"; exon_id "NM_001144585.3"; gene_name "CG14866";
+chr3R	refGene	3UTR	11143861	11144007	.	+	.	gene_id "CG14866"; transcript_id "NM_001144585"; exon_number "3"; exon_id "NM_001144585.3"; gene_name "CG14866";
+chr3R	refGene	exon	11143217	11144007	.	+	.	gene_id "CG14866"; transcript_id "NM_142187"; exon_number "2"; exon_id "NM_142187.2"; gene_name "CG14866";
+chr3R	refGene	3UTR	11143861	11144007	.	+	.	gene_id "CG14866"; transcript_id "NM_142187"; exon_number "2"; exon_id "NM_142187.2"; gene_name "CG14866";
+chr3R	refGene	exon	11157306	11158270	.	-	.	gene_id "FK506-bp1"; transcript_id "NM_079640"; exon_number "1"; exon_id "NM_079640.1"; gene_name "FK506-bp1";
+chr3R	refGene	CDS	11157429	11158270	.	-	2	gene_id "FK506-bp1"; transcript_id "NM_079640"; exon_number "1"; exon_id "NM_079640.1"; gene_name "FK506-bp1";
+chr3R	refGene	exon	11196340	11197934	.	-	.	gene_id "CG6136"; transcript_id "NM_001275671"; exon_number "3"; exon_id "NM_001275671.3"; gene_name "CG6136";
+chr3R	refGene	5UTR	11197536	11197934	.	-	.	gene_id "CG6136"; transcript_id "NM_001275671"; exon_number "3"; exon_id "NM_001275671.3"; gene_name "CG6136";
+chr3R	refGene	exon	11195758	11197934	.	-	.	gene_id "CG6136"; transcript_id "NM_142203"; exon_number "1"; exon_id "NM_142203.1"; gene_name "CG6136";
+chr3R	refGene	5UTR	11197536	11197934	.	-	.	gene_id "CG6136"; transcript_id "NM_142203"; exon_number "1"; exon_id "NM_142203.1"; gene_name "CG6136";
+chr3R	refGene	exon	11196537	11197934	.	-	.	gene_id "CG6136"; transcript_id "NM_001202295"; exon_number "1"; exon_id "NM_001202295.1"; gene_name "CG6136";
+chr3R	refGene	5UTR	11197536	11197934	.	-	.	gene_id "CG6136"; transcript_id "NM_001202295"; exon_number "1"; exon_id "NM_001202295.1"; gene_name "CG6136";
+chr3R	refGene	exon	12470794	12471668	.	-	.	gene_id "CG10324"; transcript_id "NM_142314"; exon_number "1"; exon_id "NM_142314.1"; gene_name "CG10324";
+chr3R	refGene	3UTR	12470794	12470895	.	-	.	gene_id "CG10324"; transcript_id "NM_142314"; exon_number "1"; exon_id "NM_142314.1"; gene_name "CG10324";
+chr3R	refGene	exon	12825833	12827295	.	-	.	gene_id "CG16941"; transcript_id "NM_142326"; exon_number "4"; exon_id "NM_142326.4"; gene_name "CG16941";
+chr3R	refGene	CDS	12825833	12827295	.	-	1	gene_id "CG16941"; transcript_id "NM_142326"; exon_number "4"; exon_id "NM_142326.4"; gene_name "CG16941";
+chr3R	refGene	exon	13511411	13512083	.	-	.	gene_id "CG31249"; transcript_id "NM_169774"; exon_number "1"; exon_id "NM_169774.1"; gene_name "CG31249";
+chr3R	refGene	CDS	13511731	13512083	.	-	2	gene_id "CG31249"; transcript_id "NM_169774"; exon_number "1"; exon_id "NM_169774.1"; gene_name "CG31249";
+chr3R	refGene	exon	14012095	14013597	.	+	.	gene_id "Arp5"; transcript_id "NM_142427"; exon_number "2"; exon_id "NM_142427.2"; gene_name "Arp5";
+chr3R	refGene	3UTR	14013547	14013597	.	+	.	gene_id "Arp5"; transcript_id "NM_142427"; exon_number "2"; exon_id "NM_142427.2"; gene_name "Arp5";
+chr3R	refGene	exon	14012095	14013597	.	+	.	gene_id "Arp5"; transcript_id "NM_001275768"; exon_number "2"; exon_id "NM_001275768.2"; gene_name "Arp5";
+chr3R	refGene	3UTR	14013547	14013597	.	+	.	gene_id "Arp5"; transcript_id "NM_001275768"; exon_number "2"; exon_id "NM_001275768.2"; gene_name "Arp5";
+chr3R	refGene	exon	14985821	14986385	.	-	.	gene_id "CG42358"; transcript_id "NM_142530"; exon_number "1"; exon_id "NM_142530.1"; gene_name "CG42358";
+chr3R	refGene	3UTR	14985821	14985954	.	-	.	gene_id "CG42358"; transcript_id "NM_142530"; exon_number "1"; exon_id "NM_142530.1"; gene_name "CG42358";
+chr3R	refGene	exon	15691139	15694492	.	-	.	gene_id "CG4562"; transcript_id "NM_001275816"; exon_number "1"; exon_id "NM_001275816.1"; gene_name "CG4562";
+chr3R	refGene	3UTR	15691139	15693191	.	-	.	gene_id "CG4562"; transcript_id "NM_001275816"; exon_number "1"; exon_id "NM_001275816.1"; gene_name "CG4562";
+chr3R	refGene	exon	16436973	16438411	.	-	.	gene_id "CG15923"; transcript_id "NM_001104376"; exon_number "1"; exon_id "NM_001104376.1"; gene_name "CG15923";
+chr3R	refGene	3UTR	16436973	16438330	.	-	.	gene_id "CG15923"; transcript_id "NM_001104376"; exon_number "1"; exon_id "NM_001104376.1"; gene_name "CG15923";
+chr3R	refGene	exon	16436973	16438411	.	-	.	gene_id "CG15923"; transcript_id "NM_001275840"; exon_number "1"; exon_id "NM_001275840.1"; gene_name "CG15923";
+chr3R	refGene	3UTR	16436973	16438279	.	-	.	gene_id "CG15923"; transcript_id "NM_001275840"; exon_number "1"; exon_id "NM_001275840.1"; gene_name "CG15923";
+chr3R	refGene	exon	16648854	16649078	.	+	.	gene_id "RpS20"; transcript_id "NM_079697"; exon_number "4"; exon_id "NM_079697.4"; gene_name "RpS20";
+chr3R	refGene	3UTR	16648968	16649078	.	+	.	gene_id "RpS20"; transcript_id "NM_079697"; exon_number "4"; exon_id "NM_079697.4"; gene_name "RpS20";
+chr3R	refGene	exon	16649035	16649461	.	-	.	gene_id "CG17272"; transcript_id "NM_142660"; exon_number "1"; exon_id "NM_142660.1"; gene_name "CG17272";
+chr3R	refGene	3UTR	16649035	16649110	.	-	.	gene_id "CG17272"; transcript_id "NM_142660"; exon_number "1"; exon_id "NM_142660.1"; gene_name "CG17272";
+chr3R	refGene	exon	16738144	16738591	.	+	.	gene_id "CR44106"; transcript_id "NR_074034"; exon_number "2"; exon_id "NR_074034.2"; gene_name "CR44106";
+chr3R	refGene	exon	16930768	16932293	.	-	.	gene_id "sec15"; transcript_id "NM_142685"; exon_number "1"; exon_id "NM_142685.1"; gene_name "sec15";
+chr3R	refGene	3UTR	16930768	16931186	.	-	.	gene_id "sec15"; transcript_id "NM_142685"; exon_number "1"; exon_id "NM_142685.1"; gene_name "sec15";
+chr3R	refGene	exon	16942839	16943266	.	+	.	gene_id "ppan"; transcript_id "NM_057631"; exon_number "3"; exon_id "NM_057631.3"; gene_name "ppan";
+chr3R	refGene	CDS	16942839	16943266	.	+	1	gene_id "ppan"; transcript_id "NM_057631"; exon_number "3"; exon_id "NM_057631.3"; gene_name "ppan";
+chr3R	refGene	exon	17849419	17850063	.	+	.	gene_id "mRpL35"; transcript_id "NM_142744"; exon_number "2"; exon_id "NM_142744.2"; gene_name "mRpL35";
+chr3R	refGene	3UTR	17849931	17850063	.	+	.	gene_id "mRpL35"; transcript_id "NM_142744"; exon_number "2"; exon_id "NM_142744.2"; gene_name "mRpL35";
+chr3R	refGene	exon	17855162	17855801	.	-	.	gene_id "CG13409"; transcript_id "NM_142747"; exon_number "1"; exon_id "NM_142747.1"; gene_name "CG13409";
+chr3R	refGene	3UTR	17855162	17855427	.	-	.	gene_id "CG13409"; transcript_id "NM_142747"; exon_number "1"; exon_id "NM_142747.1"; gene_name "CG13409";
+chr3R	refGene	exon	19080792	19081345	.	-	.	gene_id "wda"; transcript_id "NM_142879"; exon_number "1"; exon_id "NM_142879.1"; gene_name "wda";
+chr3R	refGene	3UTR	19080792	19081215	.	-	.	gene_id "wda"; transcript_id "NM_142879"; exon_number "1"; exon_id "NM_142879.1"; gene_name "wda";
+chr3R	refGene	exon	19585205	19585645	.	-	.	gene_id "CG10219"; transcript_id "NM_142924"; exon_number "1"; exon_id "NM_142924.1"; gene_name "CG10219";
+chr3R	refGene	3UTR	19585205	19585443	.	-	.	gene_id "CG10219"; transcript_id "NM_142924"; exon_number "1"; exon_id "NM_142924.1"; gene_name "CG10219";
+chr3R	refGene	exon	19988551	19988882	.	-	.	gene_id "mRpS24"; transcript_id "NM_079752"; exon_number "1"; exon_id "NM_079752.1"; gene_name "mRpS24";
+chr3R	refGene	CDS	19988596	19988882	.	-	2	gene_id "mRpS24"; transcript_id "NM_079752"; exon_number "1"; exon_id "NM_079752.1"; gene_name "mRpS24";
+chr3R	refGene	exon	20046825	20047348	.	+	.	gene_id "cav"; transcript_id "NM_170134"; exon_number "1"; exon_id "NM_170134.1"; gene_name "cav";
+chr3R	refGene	5UTR	20046825	20047348	.	+	.	gene_id "cav"; transcript_id "NM_170134"; exon_number "1"; exon_id "NM_170134.1"; gene_name "cav";
+chr3R	refGene	exon	20046825	20047475	.	+	.	gene_id "cav"; transcript_id "NM_170135"; exon_number "1"; exon_id "NM_170135.1"; gene_name "cav";
+chr3R	refGene	5UTR	20046825	20047463	.	+	.	gene_id "cav"; transcript_id "NM_170135"; exon_number "1"; exon_id "NM_170135.1"; gene_name "cav";
+chr3R	refGene	exon	20047253	20047647	.	+	.	gene_id "cav"; transcript_id "NM_079753"; exon_number "1"; exon_id "NM_079753.1"; gene_name "cav";
+chr3R	refGene	5UTR	20047253	20047629	.	+	.	gene_id "cav"; transcript_id "NM_079753"; exon_number "1"; exon_id "NM_079753.1"; gene_name "cav";
+chr3R	refGene	exon	20345347	20345800	.	-	.	gene_id "CR44021"; transcript_id "NR_074058"; exon_number "1"; exon_id "NR_074058.1"; gene_name "CR44021";
+chr3R	refGene	exon	20707188	20707554	.	-	.	gene_id "CG31121"; transcript_id "NM_170180"; exon_number "1"; exon_id "NM_170180.1"; gene_name "CG31121";
+chr3R	refGene	3UTR	20707188	20707323	.	-	.	gene_id "CG31121"; transcript_id "NM_170180"; exon_number "1"; exon_id "NM_170180.1"; gene_name "CG31121";
+chr3R	refGene	exon	20707188	20707554	.	-	.	gene_id "CG31121"; transcript_id "NM_170179"; exon_number "1"; exon_id "NM_170179.1"; gene_name "CG31121";
+chr3R	refGene	3UTR	20707188	20707323	.	-	.	gene_id "CG31121"; transcript_id "NM_170179"; exon_number "1"; exon_id "NM_170179.1"; gene_name "CG31121";
+chr3R	refGene	exon	21317007	21318979	.	-	.	gene_id "CR44179"; transcript_id "NR_074059"; exon_number "1"; exon_id "NR_074059.1"; gene_name "CR44179";
+chr3R	refGene	exon	21509345	21510238	.	-	.	gene_id "RpL27"; transcript_id "NM_001276039"; exon_number "1"; exon_id "NM_001276039.1"; gene_name "RpL27";
+chr3R	refGene	3UTR	21509345	21509816	.	-	.	gene_id "RpL27"; transcript_id "NM_001276039"; exon_number "1"; exon_id "NM_001276039.1"; gene_name "RpL27";
+chr3R	refGene	exon	22810427	22811428	.	+	.	gene_id "CG14253"; transcript_id "NM_143260"; exon_number "5"; exon_id "NM_143260.5"; gene_name "CG14253";
+chr3R	refGene	3UTR	22810980	22811428	.	+	.	gene_id "CG14253"; transcript_id "NM_143260"; exon_number "5"; exon_id "NM_143260.5"; gene_name "CG14253";
+chr3R	refGene	exon	22810427	22811428	.	+	.	gene_id "CG14253"; transcript_id "NM_001276074"; exon_number "7"; exon_id "NM_001276074.7"; gene_name "CG14253";
+chr3R	refGene	3UTR	22810980	22811428	.	+	.	gene_id "CG14253"; transcript_id "NM_001276074"; exon_number "7"; exon_id "NM_001276074.7"; gene_name "CG14253";
+chr3R	refGene	exon	22810427	22811428	.	+	.	gene_id "CG14253"; transcript_id "NM_170300"; exon_number "6"; exon_id "NM_170300.6"; gene_name "CG14253";
+chr3R	refGene	3UTR	22810980	22811428	.	+	.	gene_id "CG14253"; transcript_id "NM_170300"; exon_number "6"; exon_id "NM_170300.6"; gene_name "CG14253";
+chr3R	refGene	exon	22810427	22811428	.	+	.	gene_id "CG14253"; transcript_id "NM_170301"; exon_number "6"; exon_id "NM_170301.6"; gene_name "CG14253";
+chr3R	refGene	3UTR	22810980	22811428	.	+	.	gene_id "CG14253"; transcript_id "NM_170301"; exon_number "6"; exon_id "NM_170301.6"; gene_name "CG14253";
+chr3R	refGene	exon	22810427	22811428	.	+	.	gene_id "CG14253"; transcript_id "NM_170302"; exon_number "6"; exon_id "NM_170302.6"; gene_name "CG14253";
+chr3R	refGene	3UTR	22810980	22811428	.	+	.	gene_id "CG14253"; transcript_id "NM_170302"; exon_number "6"; exon_id "NM_170302.6"; gene_name "CG14253";
+chr3R	refGene	exon	22810427	22811428	.	+	.	gene_id "CG14253"; transcript_id "NM_170303"; exon_number "6"; exon_id "NM_170303.6"; gene_name "CG14253";
+chr3R	refGene	3UTR	22810980	22811428	.	+	.	gene_id "CG14253"; transcript_id "NM_170303"; exon_number "6"; exon_id "NM_170303.6"; gene_name "CG14253";
+chr3R	refGene	exon	23085772	23086137	.	+	.	gene_id "CR44049"; transcript_id "NR_074063"; exon_number "1"; exon_id "NR_074063.1"; gene_name "CR44049";
+chr3R	refGene	exon	23086189	23087670	.	+	.	gene_id "CR44049"; transcript_id "NR_074063"; exon_number "2"; exon_id "NR_074063.2"; gene_name "CR44049";
+chr3R	refGene	exon	23111808	23113170	.	+	.	gene_id "CG3368"; transcript_id "NM_143298"; exon_number "3"; exon_id "NM_143298.3"; gene_name "CG3368";
+chr3R	refGene	3UTR	23113038	23113170	.	+	.	gene_id "CG3368"; transcript_id "NM_143298"; exon_number "3"; exon_id "NM_143298.3"; gene_name "CG3368";
+chr3R	refGene	exon	23117257	23117715	.	-	.	gene_id "CG3348"; transcript_id "NM_144004"; exon_number "1"; exon_id "NM_144004.1"; gene_name "CG3348";
+chr3R	refGene	3UTR	23117257	23117381	.	-	.	gene_id "CG3348"; transcript_id "NM_144004"; exon_number "1"; exon_id "NM_144004.1"; gene_name "CG3348";
+chr3R	refGene	exon	25698263	25698986	.	+	.	gene_id "CG34133"; transcript_id "NM_001043308"; exon_number "6"; exon_id "NM_001043308.6"; gene_name "CG34133";
+chr3R	refGene	CDS	25698263	25698986	.	+	1	gene_id "CG34133"; transcript_id "NM_001043308"; exon_number "6"; exon_id "NM_001043308.6"; gene_name "CG34133";
+chr3R	refGene	exon	25698263	25698986	.	+	.	gene_id "CG34133"; transcript_id "NM_001043307"; exon_number "7"; exon_id "NM_001043307.7"; gene_name "CG34133";
+chr3R	refGene	CDS	25698263	25698986	.	+	1	gene_id "CG34133"; transcript_id "NM_001043307"; exon_number "7"; exon_id "NM_001043307.7"; gene_name "CG34133";
+chr3R	refGene	exon	25698427	25698986	.	+	.	gene_id "CG34133"; transcript_id "NM_143485"; exon_number "8"; exon_id "NM_143485.8"; gene_name "CG34133";
+chr3R	refGene	CDS	25698427	25698986	.	+	2	gene_id "CG34133"; transcript_id "NM_143485"; exon_number "8"; exon_id "NM_143485.8"; gene_name "CG34133";
+chr3R	refGene	exon	25860262	25860461	.	-	.	gene_id "CR44045"; transcript_id "NR_074065"; exon_number "1"; exon_id "NR_074065.1"; gene_name "CR44045";
+chr3R	refGene	exon	27039536	27040506	.	+	.	gene_id "CG1542"; transcript_id "NM_143593"; exon_number "3"; exon_id "NM_143593.3"; gene_name "CG1542";
+chr3R	refGene	3UTR	27040310	27040506	.	+	.	gene_id "CG1542"; transcript_id "NM_143593"; exon_number "3"; exon_id "NM_143593.3"; gene_name "CG1542";
+chr3R	refGene	exon	27420514	27421323	.	-	.	gene_id "RpL6"; transcript_id "NM_143619"; exon_number "1"; exon_id "NM_143619.1"; gene_name "RpL6";
+chr3R	refGene	CDS	27420649	27421323	.	-	0	gene_id "RpL6"; transcript_id "NM_143619"; exon_number "1"; exon_id "NM_143619.1"; gene_name "RpL6";
+chr3R	refGene	exon	27420514	27421185	.	-	.	gene_id "RpL6"; transcript_id "NM_170554"; exon_number "1"; exon_id "NM_170554.1"; gene_name "RpL6";
+chr3R	refGene	CDS	27420649	27421185	.	-	0	gene_id "RpL6"; transcript_id "NM_170554"; exon_number "1"; exon_id "NM_170554.1"; gene_name "RpL6";
+chr4	refGene	exon	348791	352013	.	+	.	gene_id "CG32850"; transcript_id "NM_001272124"; exon_number "4"; exon_id "NM_001272124.4"; gene_name "CG32850";
+chr4	refGene	3UTR	348791	352013	.	+	.	gene_id "CG32850"; transcript_id "NM_001272124"; exon_number "4"; exon_id "NM_001272124.4"; gene_name "CG32850";
+chr4	refGene	exon	473598	474573	.	+	.	gene_id "CaMKI"; transcript_id "NM_079883"; exon_number "9"; exon_id "NM_079883.9"; gene_name "CaMKI";
+chr4	refGene	CDS	473598	473822	.	+	0	gene_id "CaMKI"; transcript_id "NM_079883"; exon_number "9"; exon_id "NM_079883.9"; gene_name "CaMKI";
+chr4	refGene	exon	473598	474573	.	+	.	gene_id "CaMKI"; transcript_id "NM_166764"; exon_number "8"; exon_id "NM_166764.8"; gene_name "CaMKI";
+chr4	refGene	CDS	473598	473822	.	+	0	gene_id "CaMKI"; transcript_id "NM_166764"; exon_number "8"; exon_id "NM_166764.8"; gene_name "CaMKI";
+chr4	refGene	exon	473598	474573	.	+	.	gene_id "CaMKI"; transcript_id "NM_166760"; exon_number "11"; exon_id "NM_166760.11"; gene_name "CaMKI";
+chr4	refGene	CDS	473598	473822	.	+	0	gene_id "CaMKI"; transcript_id "NM_166760"; exon_number "11"; exon_id "NM_166760.11"; gene_name "CaMKI";
+chr4	refGene	exon	473598	474573	.	+	.	gene_id "CaMKI"; transcript_id "NM_166761"; exon_number "9"; exon_id "NM_166761.9"; gene_name "CaMKI";
+chr4	refGene	CDS	473598	473822	.	+	0	gene_id "CaMKI"; transcript_id "NM_166761"; exon_number "9"; exon_id "NM_166761.9"; gene_name "CaMKI";
+chr4	refGene	exon	473598	474573	.	+	.	gene_id "CaMKI"; transcript_id "NM_166759"; exon_number "10"; exon_id "NM_166759.10"; gene_name "CaMKI";
+chr4	refGene	CDS	473598	473822	.	+	0	gene_id "CaMKI"; transcript_id "NM_166759"; exon_number "10"; exon_id "NM_166759.10"; gene_name "CaMKI";
+chr4	refGene	exon	1055914	1058048	.	-	.	gene_id "CaMKII"; transcript_id "NM_001169361"; exon_number "1"; exon_id "NM_001169361.1"; gene_name "CaMKII";
+chr4	refGene	3UTR	1055914	1057903	.	-	.	gene_id "CaMKII"; transcript_id "NM_001169361"; exon_number "1"; exon_id "NM_001169361.1"; gene_name "CaMKII";
+chr4	refGene	exon	1055914	1058048	.	-	.	gene_id "CaMKII"; transcript_id "NM_166810"; exon_number "1"; exon_id "NM_166810.1"; gene_name "CaMKII";
+chr4	refGene	3UTR	1055914	1057903	.	-	.	gene_id "CaMKII"; transcript_id "NM_166810"; exon_number "1"; exon_id "NM_166810.1"; gene_name "CaMKII";
+chr4	refGene	exon	1055914	1058048	.	-	.	gene_id "CaMKII"; transcript_id "NM_166811"; exon_number "1"; exon_id "NM_166811.1"; gene_name "CaMKII";
+chr4	refGene	3UTR	1055914	1057903	.	-	.	gene_id "CaMKII"; transcript_id "NM_166811"; exon_number "1"; exon_id "NM_166811.1"; gene_name "CaMKII";
+chr4	refGene	exon	1055914	1058048	.	-	.	gene_id "CaMKII"; transcript_id "NM_001014696"; exon_number "1"; exon_id "NM_001014696.1"; gene_name "CaMKII";
+chr4	refGene	3UTR	1055914	1057903	.	-	.	gene_id "CaMKII"; transcript_id "NM_001014696"; exon_number "1"; exon_id "NM_001014696.1"; gene_name "CaMKII";
+chr4	refGene	exon	1055914	1058048	.	-	.	gene_id "CaMKII"; transcript_id "NM_001272153"; exon_number "1"; exon_id "NM_001272153.1"; gene_name "CaMKII";
+chr4	refGene	3UTR	1055914	1057903	.	-	.	gene_id "CaMKII"; transcript_id "NM_001272153"; exon_number "1"; exon_id "NM_001272153.1"; gene_name "CaMKII";
+chr4	refGene	exon	1055914	1058048	.	-	.	gene_id "CaMKII"; transcript_id "NM_001272154"; exon_number "1"; exon_id "NM_001272154.1"; gene_name "CaMKII";
+chr4	refGene	3UTR	1055914	1057903	.	-	.	gene_id "CaMKII"; transcript_id "NM_001272154"; exon_number "1"; exon_id "NM_001272154.1"; gene_name "CaMKII";
+chr4	refGene	exon	1055914	1058048	.	-	.	gene_id "CaMKII"; transcript_id "NM_001272155"; exon_number "1"; exon_id "NM_001272155.1"; gene_name "CaMKII";
+chr4	refGene	3UTR	1055914	1057903	.	-	.	gene_id "CaMKII"; transcript_id "NM_001272155"; exon_number "1"; exon_id "NM_001272155.1"; gene_name "CaMKII";
+chr4	refGene	exon	1055914	1058048	.	-	.	gene_id "CaMKII"; transcript_id "NM_079896"; exon_number "1"; exon_id "NM_079896.1"; gene_name "CaMKII";
+chr4	refGene	3UTR	1055914	1057903	.	-	.	gene_id "CaMKII"; transcript_id "NM_079896"; exon_number "1"; exon_id "NM_079896.1"; gene_name "CaMKII";
+chr4	refGene	exon	1055914	1058048	.	-	.	gene_id "CaMKII"; transcript_id "NM_166812"; exon_number "1"; exon_id "NM_166812.1"; gene_name "CaMKII";
+chr4	refGene	3UTR	1055914	1057903	.	-	.	gene_id "CaMKII"; transcript_id "NM_166812"; exon_number "1"; exon_id "NM_166812.1"; gene_name "CaMKII";
+chr4	refGene	exon	1055914	1058048	.	-	.	gene_id "CaMKII"; transcript_id "NM_166813"; exon_number "1"; exon_id "NM_166813.1"; gene_name "CaMKII";
+chr4	refGene	3UTR	1055914	1057903	.	-	.	gene_id "CaMKII"; transcript_id "NM_166813"; exon_number "1"; exon_id "NM_166813.1"; gene_name "CaMKII";
+chr4	refGene	exon	1212983	1213163	.	+	.	gene_id "CG33521"; transcript_id "NM_001014703"; exon_number "11"; exon_id "NM_001014703.11"; gene_name "CG33521";
+chr4	refGene	3UTR	1212986	1213163	.	+	.	gene_id "CG33521"; transcript_id "NM_001014703"; exon_number "11"; exon_id "NM_001014703.11"; gene_name "CG33521";
+chr4	refGene	exon	1212983	1213163	.	+	.	gene_id "CG33521"; transcript_id "NM_001258506"; exon_number "11"; exon_id "NM_001258506.11"; gene_name "CG33521";
+chr4	refGene	3UTR	1212986	1213163	.	+	.	gene_id "CG33521"; transcript_id "NM_001258506"; exon_number "11"; exon_id "NM_001258506.11"; gene_name "CG33521";
+chr4	refGene	exon	1212983	1213320	.	+	.	gene_id "CG33521"; transcript_id "NM_001014705"; exon_number "11"; exon_id "NM_001014705.11"; gene_name "CG33521";
+chr4	refGene	3UTR	1212986	1213320	.	+	.	gene_id "CG33521"; transcript_id "NM_001014705"; exon_number "11"; exon_id "NM_001014705.11"; gene_name "CG33521";
+chr4	refGene	exon	1212983	1213482	.	+	.	gene_id "CG33521"; transcript_id "NM_001014702"; exon_number "11"; exon_id "NM_001014702.11"; gene_name "CG33521";
+chr4	refGene	3UTR	1212986	1213482	.	+	.	gene_id "CG33521"; transcript_id "NM_001014702"; exon_number "11"; exon_id "NM_001014702.11"; gene_name "CG33521";
+chrX	refGene	exon	518440	518798	.	+	.	gene_id "CG13369"; transcript_id "NM_130494"; exon_number "3"; exon_id "NM_130494.3"; gene_name "CG13369";
+chrX	refGene	3UTR	518753	518798	.	+	.	gene_id "CG13369"; transcript_id "NM_130494"; exon_number "3"; exon_id "NM_130494.3"; gene_name "CG13369";
+chrX	refGene	exon	1587418	1587876	.	+	.	gene_id "CG14798"; transcript_id "NM_130582"; exon_number "3"; exon_id "NM_130582.3"; gene_name "CG14798";
+chrX	refGene	CDS	1587418	1587727	.	+	1	gene_id "CG14798"; transcript_id "NM_130582"; exon_number "3"; exon_id "NM_130582.3"; gene_name "CG14798";
+chrX	refGene	exon	1784646	1785515	.	+	.	gene_id "mRpL16"; transcript_id "NM_001272219"; exon_number "3"; exon_id "NM_001272219.3"; gene_name "mRpL16";
+chrX	refGene	3UTR	1785263	1785515	.	+	.	gene_id "mRpL16"; transcript_id "NM_001272219"; exon_number "3"; exon_id "NM_001272219.3"; gene_name "mRpL16";
+chrX	refGene	exon	8303696	8305691	.	-	.	gene_id "lawc"; transcript_id "NM_001258650"; exon_number "4"; exon_id "NM_001258650.4"; gene_name "lawc";
+chrX	refGene	5UTR	8304008	8305691	.	-	.	gene_id "lawc"; transcript_id "NM_001258650"; exon_number "4"; exon_id "NM_001258650.4"; gene_name "lawc";
+chrX	refGene	exon	8582660	8582935	.	-	.	gene_id "Ppt1"; transcript_id "NM_167166"; exon_number "1"; exon_id "NM_167166.1"; gene_name "Ppt1";
+chrX	refGene	3UTR	8582660	8582812	.	-	.	gene_id "Ppt1"; transcript_id "NM_167166"; exon_number "1"; exon_id "NM_167166.1"; gene_name "Ppt1";
+chrX	refGene	exon	8916051	8916272	.	+	.	gene_id "rdgA"; transcript_id "NM_001272437"; exon_number "12"; exon_id "NM_001272437.12"; gene_name "rdgA";
+chrX	refGene	CDS	8916051	8916272	.	+	2	gene_id "rdgA"; transcript_id "NM_001272437"; exon_number "12"; exon_id "NM_001272437.12"; gene_name "rdgA";
+chrX	refGene	exon	8918657	8921648	.	+	.	gene_id "rdgA"; transcript_id "NM_001272437"; exon_number "16"; exon_id "NM_001272437.16"; gene_name "rdgA";
+chrX	refGene	3UTR	8918865	8921648	.	+	.	gene_id "rdgA"; transcript_id "NM_001272437"; exon_number "16"; exon_id "NM_001272437.16"; gene_name "rdgA";
+chrX	refGene	exon	8916051	8916272	.	+	.	gene_id "rdgA"; transcript_id "NM_001272438"; exon_number "12"; exon_id "NM_001272438.12"; gene_name "rdgA";
+chrX	refGene	CDS	8916051	8916272	.	+	2	gene_id "rdgA"; transcript_id "NM_001272438"; exon_number "12"; exon_id "NM_001272438.12"; gene_name "rdgA";
+chrX	refGene	exon	8918657	8923509	.	+	.	gene_id "rdgA"; transcript_id "NM_001272438"; exon_number "16"; exon_id "NM_001272438.16"; gene_name "rdgA";
+chrX	refGene	3UTR	8918865	8923509	.	+	.	gene_id "rdgA"; transcript_id "NM_001272438"; exon_number "16"; exon_id "NM_001272438.16"; gene_name "rdgA";
+chrX	refGene	exon	8916051	8916272	.	+	.	gene_id "rdgA"; transcript_id "NM_001103447"; exon_number "10"; exon_id "NM_001103447.10"; gene_name "rdgA";
+chrX	refGene	CDS	8916051	8916272	.	+	2	gene_id "rdgA"; transcript_id "NM_001103447"; exon_number "10"; exon_id "NM_001103447.10"; gene_name "rdgA";
+chrX	refGene	exon	9046556	9048273	.	-	.	gene_id "His3.3B"; transcript_id "NM_001272445"; exon_number "1"; exon_id "NM_001272445.1"; gene_name "His3.3B";
+chrX	refGene	3UTR	9046556	9048144	.	-	.	gene_id "His3.3B"; transcript_id "NM_001272445"; exon_number "1"; exon_id "NM_001272445.1"; gene_name "His3.3B";
+chrX	refGene	exon	9088305	9089366	.	+	.	gene_id "CG12106"; transcript_id "NM_132308"; exon_number "2"; exon_id "NM_132308.2"; gene_name "CG12106";
+chrX	refGene	3UTR	9088769	9089366	.	+	.	gene_id "CG12106"; transcript_id "NM_132308"; exon_number "2"; exon_id "NM_132308.2"; gene_name "CG12106";
+chrX	refGene	exon	9088783	9089254	.	-	.	gene_id "CG12118"; transcript_id "NM_001272451"; exon_number "1"; exon_id "NM_001272451.1"; gene_name "CG12118";
+chrX	refGene	CDS	9088955	9089254	.	-	0	gene_id "CG12118"; transcript_id "NM_001272451"; exon_number "1"; exon_id "NM_001272451.1"; gene_name "CG12118";
+chrX	refGene	exon	9088783	9089254	.	-	.	gene_id "CG12118"; transcript_id "NM_132309"; exon_number "1"; exon_id "NM_132309.1"; gene_name "CG12118";
+chrX	refGene	CDS	9088955	9089254	.	-	0	gene_id "CG12118"; transcript_id "NM_132309"; exon_number "1"; exon_id "NM_132309.1"; gene_name "CG12118";
+chrX	refGene	exon	9088783	9089254	.	-	.	gene_id "CG12118"; transcript_id "NM_176720"; exon_number "1"; exon_id "NM_176720.1"; gene_name "CG12118";
+chrX	refGene	CDS	9088955	9089254	.	-	0	gene_id "CG12118"; transcript_id "NM_176720"; exon_number "1"; exon_id "NM_176720.1"; gene_name "CG12118";
+chrX	refGene	exon	10674926	10676128	.	-	.	gene_id "sesB"; transcript_id "NM_167247"; exon_number "1"; exon_id "NM_167247.1"; gene_name "sesB";
+chrX	refGene	3UTR	10674926	10675653	.	-	.	gene_id "sesB"; transcript_id "NM_167247"; exon_number "1"; exon_id "NM_167247.1"; gene_name "sesB";
+chrX	refGene	exon	10675026	10676128	.	-	.	gene_id "sesB"; transcript_id "NM_167248"; exon_number "1"; exon_id "NM_167248.1"; gene_name "sesB";
+chrX	refGene	3UTR	10675026	10675653	.	-	.	gene_id "sesB"; transcript_id "NM_167248"; exon_number "1"; exon_id "NM_167248.1"; gene_name "sesB";
+chrX	refGene	exon	10675026	10676128	.	-	.	gene_id "sesB"; transcript_id "NM_078554"; exon_number "1"; exon_id "NM_078554.1"; gene_name "sesB";
+chrX	refGene	3UTR	10675026	10675653	.	-	.	gene_id "sesB"; transcript_id "NM_078554"; exon_number "1"; exon_id "NM_078554.1"; gene_name "sesB";
+chrX	refGene	exon	10675026	10676128	.	-	.	gene_id "sesB"; transcript_id "NM_167246"; exon_number "1"; exon_id "NM_167246.1"; gene_name "sesB";
+chrX	refGene	3UTR	10675026	10675653	.	-	.	gene_id "sesB"; transcript_id "NM_167246"; exon_number "1"; exon_id "NM_167246.1"; gene_name "sesB";
+chrX	refGene	exon	12607694	12609320	.	-	.	gene_id "Smr"; transcript_id "NM_001272562"; exon_number "8"; exon_id "NM_001272562.8"; gene_name "Smr";
+chrX	refGene	CDS	12607694	12609320	.	-	1	gene_id "Smr"; transcript_id "NM_001272562"; exon_number "8"; exon_id "NM_001272562.8"; gene_name "Smr";
+chrX	refGene	exon	12607694	12609302	.	-	.	gene_id "Smr"; transcript_id "NM_167334"; exon_number "8"; exon_id "NM_167334.8"; gene_name "Smr";
+chrX	refGene	CDS	12607694	12609302	.	-	1	gene_id "Smr"; transcript_id "NM_167334"; exon_number "8"; exon_id "NM_167334.8"; gene_name "Smr";
+chrX	refGene	exon	12607694	12609302	.	-	.	gene_id "Smr"; transcript_id "NM_167335"; exon_number "8"; exon_id "NM_167335.8"; gene_name "Smr";
+chrX	refGene	CDS	12607694	12609302	.	-	1	gene_id "Smr"; transcript_id "NM_167335"; exon_number "8"; exon_id "NM_167335.8"; gene_name "Smr";
+chrX	refGene	exon	12607694	12609302	.	-	.	gene_id "Smr"; transcript_id "NM_080536"; exon_number "8"; exon_id "NM_080536.8"; gene_name "Smr";
+chrX	refGene	CDS	12607694	12609302	.	-	1	gene_id "Smr"; transcript_id "NM_080536"; exon_number "8"; exon_id "NM_080536.8"; gene_name "Smr";
+chrX	refGene	exon	16199192	16201410	.	+	.	gene_id "CG3679"; transcript_id "NM_001272674"; exon_number "3"; exon_id "NM_001272674.3"; gene_name "CG3679";
+chrX	refGene	3UTR	16200248	16201410	.	+	.	gene_id "CG3679"; transcript_id "NM_001272674"; exon_number "3"; exon_id "NM_001272674.3"; gene_name "CG3679";
+chrX	refGene	exon	16779109	16779892	.	+	.	gene_id "Rcp"; transcript_id "NM_132947"; exon_number "3"; exon_id "NM_132947.3"; gene_name "Rcp";
+chrX	refGene	3UTR	16779550	16779892	.	+	.	gene_id "Rcp"; transcript_id "NM_132947"; exon_number "3"; exon_id "NM_132947.3"; gene_name "Rcp";
+chrX	refGene	exon	16779109	16779892	.	+	.	gene_id "Rcp"; transcript_id "NM_206770"; exon_number "4"; exon_id "NM_206770.4"; gene_name "Rcp";
+chrX	refGene	3UTR	16779550	16779892	.	+	.	gene_id "Rcp"; transcript_id "NM_206770"; exon_number "4"; exon_id "NM_206770.4"; gene_name "Rcp";
+chrX	refGene	exon	19510696	19511958	.	-	.	gene_id "CG12788"; transcript_id "NM_001272782"; exon_number "1"; exon_id "NM_001272782.1"; gene_name "CG12788";
+chrX	refGene	3UTR	19510696	19510942	.	-	.	gene_id "CG12788"; transcript_id "NM_001272782"; exon_number "1"; exon_id "NM_001272782.1"; gene_name "CG12788";
+chrX	refGene	exon	19510696	19512220	.	-	.	gene_id "Tim9b"; transcript_id "NM_001031903"; exon_number "1"; exon_id "NM_001031903.1"; gene_name "Tim9b";
+chrX	refGene	3UTR	19510696	19511983	.	-	.	gene_id "Tim9b"; transcript_id "NM_001031903"; exon_number "1"; exon_id "NM_001031903.1"; gene_name "Tim9b";
+chrX	refGene	exon	19510696	19512220	.	-	.	gene_id "CG12788"; transcript_id "NM_001272783"; exon_number "1"; exon_id "NM_001272783.1"; gene_name "CG12788";
+chrX	refGene	3UTR	19510696	19510942	.	-	.	gene_id "CG12788"; transcript_id "NM_001272783"; exon_number "1"; exon_id "NM_001272783.1"; gene_name "CG12788";
+chrX	refGene	exon	19510696	19512220	.	-	.	gene_id "CG12788"; transcript_id "NM_134485"; exon_number "1"; exon_id "NM_134485.1"; gene_name "CG12788";
+chrX	refGene	3UTR	19510696	19510942	.	-	.	gene_id "CG12788"; transcript_id "NM_134485"; exon_number "1"; exon_id "NM_134485.1"; gene_name "CG12788";
diff -r 000000000000 -r 2dfbcb88d16a test-data/te.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/te.gtf	Wed May 13 12:57:29 2020 -0400
@@ -0,0 +1,866 @@
+chr4	dm3_rmsk	exon	343119	348355	.	+	.	gene_id "Stalker2_I"; transcript_id "Stalker2_I_dup2"; family_id "Gypsy"; class_id "LTR";
+chr4	dm3_rmsk	exon	954243	955152	.	-	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup25"; family_id "CR1"; class_id "LINE";
+chr4	dm3_rmsk	exon	1281301	1285200	.	-	.	gene_id "TART"; transcript_id "TART_dup3"; family_id "telomeric"; class_id "LINE";
+chr4	dm3_rmsk	exon	1298748	1302519	.	-	.	gene_id "HETA"; transcript_id "HETA_dup2"; family_id "telomeric"; class_id "LINE";
+chr4	dm3_rmsk	exon	1325146	1336223	.	-	.	gene_id "TART"; transcript_id "TART_dup10"; family_id "telomeric"; class_id "LINE";
+chr4	dm3_rmsk	exon	1338128	1349150	.	-	.	gene_id "TART"; transcript_id "TART_dup15"; family_id "telomeric"; class_id "LINE";
+chrU	dm3_rmsk	exon	191398	191854	.	+	.	gene_id "BURDOCK_I"; transcript_id "BURDOCK_I_dup3"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	276311	276724	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup5"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	276725	281011	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup7"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	357869	358422	.	-	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup58"; family_id "CR1"; class_id "LINE";
+chrU	dm3_rmsk	exon	444361	445162	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup10"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	445163	445576	.	-	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup8"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	560147	564265	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup5"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	585727	586749	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup7"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	923349	923833	.	-	.	gene_id "T412LTR"; transcript_id "T412LTR"; family_id "LTR"; class_id "LTR";
+chrU	dm3_rmsk	exon	923724	930674	.	-	.	gene_id "DM412"; transcript_id "DM412_dup20"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	930358	930842	.	-	.	gene_id "T412LTR"; transcript_id "T412LTR_dup1"; family_id "LTR"; class_id "LTR";
+chrU	dm3_rmsk	exon	977434	977847	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup9"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	977848	984017	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup11"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	1068318	1074427	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup12"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	1145421	1151606	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup14"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	1183521	1184031	.	-	.	gene_id "DNAREP1_DM"; transcript_id "DNAREP1_DM_dup737"; family_id "Penelope"; class_id "LINE";
+chrU	dm3_rmsk	exon	1210262	1212598	.	-	.	gene_id "Gypsy12_LTR"; transcript_id "Gypsy12_LTR_dup7"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	1217990	1220370	.	-	.	gene_id "Gypsy12_LTR"; transcript_id "Gypsy12_LTR_dup8"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	1223765	1226146	.	-	.	gene_id "Gypsy12_LTR"; transcript_id "Gypsy12_LTR_dup9"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	1293346	1293758	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup12"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	1293759	1298196	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup15"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	1308708	1311586	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup17"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	1420117	1423754	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup22"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	1443400	1449972	.	-	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup15"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	1572762	1573180	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup24"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	1722014	1722692	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup27"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	1781498	1782154	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup10"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	1805831	1807913	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup29"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	1881961	1886692	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup29"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	1886693	1887052	.	-	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup16"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	1896226	1896818	.	+	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup28"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	1902819	1903411	.	+	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup29"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	2048219	2050481	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup35"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	2051056	2057160	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup36"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	2092493	2094999	.	+	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup152"; family_id "CR1"; class_id "LINE";
+chrU	dm3_rmsk	exon	2247039	2253619	.	+	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup25"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	2328705	2329297	.	+	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup30"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	2472019	2472186	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup48"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	2581052	2581507	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup31"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	2691771	2694411	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup51"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	3096181	3099337	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup53"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	3312718	3313508	.	+	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup27"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	3371327	3372261	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup61"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	3503665	3504199	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup69"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	3578157	3578336	.	+	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup4"; family_id "Copia"; class_id "LTR";
+chrU	dm3_rmsk	exon	3625425	3626082	.	+	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup20"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	3770053	3770709	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup22"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	3777432	3777737	.	+	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup40"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	3837334	3839552	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup76"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	4015850	4017758	.	+	.	gene_id "TART_B1"; transcript_id "TART_B1_dup3"; family_id "telomeric"; class_id "LINE";
+chrU	dm3_rmsk	exon	4116367	4117555	.	+	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup48"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	4126825	4127440	.	+	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup28"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	4236892	4237987	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup83"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	4345607	4346049	.	-	.	gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup83"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	4838081	4838523	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup59"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	5189745	5189910	.	-	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup237"; family_id "CR1"; class_id "LINE";
+chrU	dm3_rmsk	exon	5190657	5191171	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup93"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	5475097	5476840	.	-	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup62"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	5524199	5524856	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup36"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	5553424	5553622	.	+	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup8"; family_id "Copia"; class_id "LTR";
+chrU	dm3_rmsk	exon	5690556	5690753	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup9"; family_id "Copia"; class_id "LTR";
+chrU	dm3_rmsk	exon	5767489	5772171	.	+	.	gene_id "TART_B1"; transcript_id "TART_B1_dup7"; family_id "telomeric"; class_id "LINE";
+chrU	dm3_rmsk	exon	5951132	5951685	.	-	.	gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup99"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	5977542	5978155	.	-	.	gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup4"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	6001421	6002602	.	-	.	gene_id "DOC3_DM"; transcript_id "DOC3_DM_dup51"; family_id "Jockey"; class_id "LINE";
+chrU	dm3_rmsk	exon	6086408	6086991	.	-	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup45"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	6179002	6180525	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup103"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	6224902	6228880	.	+	.	gene_id "Gypsy6_I"; transcript_id "Gypsy6_I_dup42"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	6309683	6309880	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup12"; family_id "Copia"; class_id "LTR";
+chrU	dm3_rmsk	exon	6473514	6473693	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup13"; family_id "Copia"; class_id "LTR";
+chrU	dm3_rmsk	exon	6628271	6628930	.	+	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup41"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	6677331	6677601	.	+	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup70"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	6731465	6734022	.	+	.	gene_id "TART_B1"; transcript_id "TART_B1_dup11"; family_id "telomeric"; class_id "LINE";
+chrU	dm3_rmsk	exon	6945365	6947093	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup111"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	6987604	6988260	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup42"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	7126511	7127835	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup114"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	7264880	7267505	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup116"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	7308561	7309535	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup119"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	7329574	7329736	.	-	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup81"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	7332248	7332896	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup122"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	7332960	7334528	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup124"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	7487018	7487473	.	-	.	gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup111"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	7519432	7520276	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup127"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	7748631	7750155	.	+	.	gene_id "Gypsy12_LTR"; transcript_id "Gypsy12_LTR_dup78"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	7828761	7829083	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup132"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	7881322	7881911	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup48"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	7907279	7907794	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup135"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	8033433	8034022	.	+	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup51"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	8137658	8137976	.	+	.	gene_id "TIRANT_I"; transcript_id "TIRANT_I_dup20"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	8244488	8244933	.	-	.	gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup113"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	8371984	8372439	.	-	.	gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup115"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	8374715	8375214	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup144"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	8427074	8427271	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup15"; family_id "Copia"; class_id "LTR";
+chrU	dm3_rmsk	exon	8523917	8524479	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup55"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	8639171	8640550	.	+	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup91"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	8647157	8647861	.	+	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup306"; family_id "CR1"; class_id "LINE";
+chrU	dm3_rmsk	exon	8711610	8712130	.	+	.	gene_id "Gypsy_DS"; transcript_id "Gypsy_DS_dup11"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	8720854	8721046	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup107"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	8721047	8721460	.	-	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup29"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	8731513	8731702	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup17"; family_id "Copia"; class_id "LTR";
+chrU	dm3_rmsk	exon	8772055	8772757	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup157"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	8809472	8809792	.	-	.	gene_id "TIRANT_I"; transcript_id "TIRANT_I_dup23"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	8899308	8899741	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup62"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	9007353	9007909	.	-	.	gene_id "Stalker2_I"; transcript_id "Stalker2_I_dup42"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	9013996	9014409	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup30"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	9014410	9014542	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup110"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	9043750	9044112	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup31"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	9044113	9044332	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup111"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	9194346	9194700	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup63"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	9280618	9281548	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup176"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	9409569	9410084	.	+	.	gene_id "T412LTR"; transcript_id "T412LTR_dup4"; family_id "LTR"; class_id "LTR";
+chrU	dm3_rmsk	exon	9409769	9410183	.	+	.	gene_id "DM412"; transcript_id "DM412_dup60"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	9423981	9424974	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup181"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	9466785	9467907	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup183"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	9476659	9477397	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup68"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	9480221	9480307	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup69"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	9549357	9549872	.	+	.	gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup7"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	9693207	9693297	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup120"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	9693298	9693711	.	-	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup32"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	9841738	9842180	.	-	.	gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup125"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	9890510	9891080	.	-	.	gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup9"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	9917593	9917947	.	-	.	gene_id "DM412"; transcript_id "DM412_dup62"; family_id "Gypsy"; class_id "LTR";
+chrU	dm3_rmsk	exon	9917630	9918110	.	-	.	gene_id "T412LTR"; transcript_id "T412LTR_dup5"; family_id "LTR"; class_id "LTR";
+chrU	dm3_rmsk	exon	9931601	9932153	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup196"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	10820	12794	.	+	.	gene_id "TAHRE"; transcript_id "TAHRE_dup104"; family_id "telomeric"; class_id "LINE";
+chrX	dm3_rmsk	exon	19112	19196	.	+	.	gene_id "TAHRE"; transcript_id "TAHRE_dup105"; family_id "telomeric"; class_id "LINE";
+chrX	dm3_rmsk	exon	189895	197508	.	-	.	gene_id "DM412"; transcript_id "DM412_dup64"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	445510	453014	.	+	.	gene_id "DM412"; transcript_id "DM412_dup65"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	706355	706755	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup33"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	706756	710761	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup122"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	927440	935019	.	+	.	gene_id "DM412"; transcript_id "DM412_dup66"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	1251868	1253278	.	-	.	gene_id "IVK_DM"; transcript_id "IVK_DM_dup17"; family_id "I"; class_id "LINE";
+chrX	dm3_rmsk	exon	1825142	1831621	.	-	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup57"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	1849398	1854645	.	-	.	gene_id "Stalker2_I"; transcript_id "Stalker2_I_dup49"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	3073073	3079644	.	+	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup58"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	3387608	3395852	.	-	.	gene_id "ROO_I"; transcript_id "ROO_I_dup129"; family_id "Pao"; class_id "LTR";
+chrX	dm3_rmsk	exon	3395853	3396280	.	-	.	gene_id "ROO_LTR"; transcript_id "ROO_LTR_dup45"; family_id "Pao"; class_id "LTR";
+chrX	dm3_rmsk	exon	3495547	3495974	.	-	.	gene_id "ROO_LTR"; transcript_id "ROO_LTR_dup47"; family_id "Pao"; class_id "LTR";
+chrX	dm3_rmsk	exon	3508115	3508542	.	-	.	gene_id "ROO_LTR"; transcript_id "ROO_LTR_dup49"; family_id "Pao"; class_id "LTR";
+chrX	dm3_rmsk	exon	3880951	3881464	.	-	.	gene_id "T412LTR"; transcript_id "T412LTR_dup6"; family_id "LTR"; class_id "LTR";
+chrX	dm3_rmsk	exon	3881355	3888326	.	-	.	gene_id "DM412"; transcript_id "DM412_dup67"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	3888013	3888526	.	-	.	gene_id "T412LTR"; transcript_id "T412LTR_dup7"; family_id "LTR"; class_id "LTR";
+chrX	dm3_rmsk	exon	4051980	4052393	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup36"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	4052394	4058543	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup124"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	4722487	4728965	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup197"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	5285684	5286482	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup126"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	5286483	5286896	.	-	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup39"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	5418929	5420968	.	+	.	gene_id "DM412"; transcript_id "DM412_dup68"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	5420945	5422734	.	+	.	gene_id "DM412"; transcript_id "DM412_dup69"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	6065672	6066329	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup74"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	6066330	6072388	.	-	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup125"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	6072389	6073046	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup75"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	6340461	6344677	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup128"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	6344678	6345091	.	-	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup41"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	9693025	9699191	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup129"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	9699192	9699605	.	-	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup43"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	9989251	9989664	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup44"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	9989665	9994170	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup130"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	10032303	10032783	.	+	.	gene_id "T412LTR"; transcript_id "T412LTR_dup8"; family_id "LTR"; class_id "LTR";
+chrX	dm3_rmsk	exon	10032470	10039372	.	+	.	gene_id "DM412"; transcript_id "DM412_dup70"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	10039263	10039743	.	+	.	gene_id "T412LTR"; transcript_id "T412LTR_dup9"; family_id "LTR"; class_id "LTR";
+chrX	dm3_rmsk	exon	10419160	10419572	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup46"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	10419573	10425740	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup132"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	11206576	11213009	.	-	.	gene_id "Stalker2_I"; transcript_id "Stalker2_I_dup51"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	11527919	11534087	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup133"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	11534088	11534501	.	-	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup50"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	12608970	12609026	.	-	.	gene_id "ROO_I"; transcript_id "ROO_I_dup330"; family_id "Pao"; class_id "LTR";
+chrX	dm3_rmsk	exon	14052861	14056866	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup135"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	14056867	14057280	.	-	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup52"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	14446249	14452816	.	-	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup59"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	19030640	19031120	.	+	.	gene_id "T412LTR"; transcript_id "T412LTR_dup10"; family_id "LTR"; class_id "LTR";
+chrX	dm3_rmsk	exon	19030807	19035865	.	+	.	gene_id "DM412"; transcript_id "DM412_dup71"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	19037021	19037501	.	+	.	gene_id "T412LTR"; transcript_id "T412LTR_dup11"; family_id "LTR"; class_id "LTR";
+chrX	dm3_rmsk	exon	19691843	19698056	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup198"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	19927404	19927817	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup57"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	19927818	19929771	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup140"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	21329782	21335151	.	-	.	gene_id "IVK_DM"; transcript_id "IVK_DM_dup19"; family_id "I"; class_id "LINE";
+chrX	dm3_rmsk	exon	21395076	21395730	.	-	.	gene_id "ROO_I"; transcript_id "ROO_I_dup450"; family_id "Pao"; class_id "LTR";
+chrX	dm3_rmsk	exon	21421820	21423555	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup146"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	21423556	21423969	.	-	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup60"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	21512181	21519806	.	-	.	gene_id "DM412"; transcript_id "DM412_dup74"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	21519811	21524347	.	-	.	gene_id "Stalker2_I"; transcript_id "Stalker2_I_dup54"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	21547758	21549716	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup201"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	21549795	21551471	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup202"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	21552015	21558368	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup204"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	21580844	21582367	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup207"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	21586806	21587822	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup208"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	21604473	21610607	.	-	.	gene_id "Gypsy6_I"; transcript_id "Gypsy6_I_dup71"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	21615912	21617588	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup210"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	21642451	21643491	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup213"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	21644907	21645298	.	-	.	gene_id "Gypsy6_I"; transcript_id "Gypsy6_I_dup76"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	22022378	22022791	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup62"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	22022792	22027540	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup147"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	22175530	22176216	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup150"; family_id "Gypsy"; class_id "LTR";
+chrX	dm3_rmsk	exon	22176217	22176630	.	-	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup66"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	2112686	2119254	.	-	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup63"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	2565593	2566006	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup74"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	2566007	2569028	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup159"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	2772653	2773066	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup76"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	2773067	2776969	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup161"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	4662398	4668884	.	-	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup64"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	4973719	4973842	.	-	.	gene_id "S2_DM"; transcript_id "S2_DM_dup7"; family_id "Tc1"; class_id "DNA";
+chr2L	dm3_rmsk	exon	4973823	4973927	.	-	.	gene_id "S2_DM"; transcript_id "S2_DM_dup8"; family_id "Tc1"; class_id "DNA";
+chr2L	dm3_rmsk	exon	7977135	7977547	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup78"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	7977548	7983640	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup164"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	8594934	8601102	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup165"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	8601103	8601516	.	-	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup81"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	10593415	10599983	.	-	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup65"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	10876598	10877011	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup82"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	10877012	10883182	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup166"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	12067385	12067798	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup84"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	12067799	12073965	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup167"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	12781859	12782516	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup77"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	12782517	12788586	.	-	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup128"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	12788587	12789244	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup78"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	13449518	13450176	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup79"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	13450177	13456236	.	-	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup129"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	13456237	13456895	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup80"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	14984971	14991457	.	+	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup66"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	15586465	15586878	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup86"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	15586879	15593045	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup168"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	15683783	15684440	.	+	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup81"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	15684441	15686758	.	+	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup130"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	15718780	15719437	.	+	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup82"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	15719438	15721755	.	+	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup131"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	15726912	15727569	.	+	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup83"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	16154206	16160372	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup169"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	16160373	16160787	.	-	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup89"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	17144903	17151477	.	-	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup67"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	19147425	19147838	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup90"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	19147839	19153988	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup170"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	19658198	19664770	.	-	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup68"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	20156132	20156835	.	-	.	gene_id "POGO"; transcript_id "POGO_dup19"; family_id "Pogo"; class_id "DNA";
+chr2L	dm3_rmsk	exon	20157736	20158439	.	-	.	gene_id "POGO"; transcript_id "POGO_dup20"; family_id "Pogo"; class_id "DNA";
+chr2L	dm3_rmsk	exon	20835864	20836522	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup84"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	21406236	21406838	.	-	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup123"; family_id "Gypsy"; class_id "LTR";
+chr2L	dm3_rmsk	exon	22786818	22788162	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup218"; family_id "Gypsy"; class_id "LTR";
+chr2R	dm3_rmsk	exon	29494	29691	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup23"; family_id "Copia"; class_id "LTR";
+chr2R	dm3_rmsk	exon	33561	33757	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup24"; family_id "Copia"; class_id "LTR";
+chr2R	dm3_rmsk	exon	37627	37795	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup25"; family_id "Copia"; class_id "LTR";
+chr2R	dm3_rmsk	exon	62686	66864	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup221"; family_id "Gypsy"; class_id "LTR";
+chr2R	dm3_rmsk	exon	290249	291158	.	+	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup460"; family_id "CR1"; class_id "LINE";
+chr2R	dm3_rmsk	exon	320405	321649	.	+	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup138"; family_id "Gypsy"; class_id "LTR";
+chr2R	dm3_rmsk	exon	333623	334869	.	+	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup142"; family_id "Gypsy"; class_id "LTR";
+chr2R	dm3_rmsk	exon	352453	354318	.	-	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup144"; family_id "Gypsy"; class_id "LTR";
+chr2R	dm3_rmsk	exon	1208416	1208645	.	-	.	gene_id "DNAREP1_DM"; transcript_id "DNAREP1_DM_dup2748"; family_id "Penelope"; class_id "LINE";
+chr2R	dm3_rmsk	exon	1268080	1274651	.	+	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup84"; family_id "Gypsy"; class_id "LTR";
+chr2R	dm3_rmsk	exon	1275172	1281362	.	-	.	gene_id "Stalker2_I"; transcript_id "Stalker2_I_dup63"; family_id "Gypsy"; class_id "LTR";
+chr2R	dm3_rmsk	exon	1316559	1318957	.	-	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup536"; family_id "CR1"; class_id "LINE";
+chr2R	dm3_rmsk	exon	1469711	1470864	.	+	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup547"; family_id "CR1"; class_id "LINE";
+chr2R	dm3_rmsk	exon	2204690	2208130	.	-	.	gene_id "Copia2_I"; transcript_id "Copia2_I_dup101"; family_id "Copia"; class_id "LTR";
+chr2R	dm3_rmsk	exon	2218252	2224794	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup227"; family_id "Gypsy"; class_id "LTR";
+chr2R	dm3_rmsk	exon	2254749	2254934	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup27"; family_id "Copia"; class_id "LTR";
+chr2R	dm3_rmsk	exon	2261767	2261952	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup28"; family_id "Copia"; class_id "LTR";
+chr2R	dm3_rmsk	exon	2840244	2846730	.	+	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup86"; family_id "Gypsy"; class_id "LTR";
+chr2R	dm3_rmsk	exon	3150161	3156328	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup210"; family_id "Gypsy"; class_id "LTR";
+chr2R	dm3_rmsk	exon	3156329	3156741	.	-	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup106"; family_id "Gypsy"; class_id "LTR";
+chr2R	dm3_rmsk	exon	3994550	3994963	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup107"; family_id "Gypsy"; class_id "LTR";
+chr2R	dm3_rmsk	exon	3994964	3998866	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup211"; family_id "Gypsy"; class_id "LTR";
+chr2R	dm3_rmsk	exon	7304683	7305764	.	+	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup88"; family_id "Gypsy"; class_id "LTR";
+chr2R	dm3_rmsk	exon	9616211	9622776	.	+	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup89"; family_id "Gypsy"; class_id "LTR";
+chr2R	dm3_rmsk	exon	10972539	10972952	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup110"; family_id "Gypsy"; class_id "LTR";
+chr2R	dm3_rmsk	exon	10972953	10979116	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup215"; family_id "Gypsy"; class_id "LTR";
+chr2R	dm3_rmsk	exon	15957285	15958055	.	-	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup90"; family_id "Gypsy"; class_id "LTR";
+chr2R	dm3_rmsk	exon	17039987	17040847	.	+	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup94"; family_id "Gypsy"; class_id "LTR";
+chr2R	dm3_rmsk	exon	19417152	19424670	.	-	.	gene_id "DM412"; transcript_id "DM412_dup82"; family_id "Gypsy"; class_id "LTR";
+chr2R	dm3_rmsk	exon	19801877	19809443	.	-	.	gene_id "DM412"; transcript_id "DM412_dup83"; family_id "Gypsy"; class_id "LTR";
+chr2R	dm3_rmsk	exon	20034646	20035128	.	-	.	gene_id "T412LTR"; transcript_id "T412LTR_dup13"; family_id "LTR"; class_id "LTR";
+chr2R	dm3_rmsk	exon	20035019	20041999	.	-	.	gene_id "DM412"; transcript_id "DM412_dup84"; family_id "Gypsy"; class_id "LTR";
+chr2R	dm3_rmsk	exon	20041684	20042166	.	-	.	gene_id "T412LTR"; transcript_id "T412LTR_dup14"; family_id "LTR"; class_id "LTR";
+chr2R	dm3_rmsk	exon	20064814	20072241	.	-	.	gene_id "DM412"; transcript_id "DM412_dup85"; family_id "Gypsy"; class_id "LTR";
+chr2R	dm3_rmsk	exon	20535163	20542666	.	-	.	gene_id "DM412"; transcript_id "DM412_dup86"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	403154	409321	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup216"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	409322	409735	.	-	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup115"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	1047407	1054568	.	-	.	gene_id "DM412"; transcript_id "DM412_dup87"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	1054555	1055161	.	-	.	gene_id "DM412"; transcript_id "DM412_dup88"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	1219647	1220216	.	+	.	gene_id "DM412"; transcript_id "DM412_dup89"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	1220203	1227326	.	+	.	gene_id "DM412"; transcript_id "DM412_dup90"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	4328954	4335856	.	+	.	gene_id "DM412"; transcript_id "DM412_dup91"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	5292308	5292965	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup97"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	5292966	5299027	.	-	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup149"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	5299028	5299685	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup98"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	7370471	7370884	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup117"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	7370885	7371685	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup217"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	7787281	7793447	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup219"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	7793448	7793861	.	-	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup120"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	7880360	7881722	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup228"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	9070082	9070595	.	+	.	gene_id "T412LTR"; transcript_id "T412LTR_dup17"; family_id "LTR"; class_id "LTR";
+chr3L	dm3_rmsk	exon	9070282	9077180	.	+	.	gene_id "DM412"; transcript_id "DM412_dup92"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	9077071	9077584	.	+	.	gene_id "T412LTR"; transcript_id "T412LTR_dup18"; family_id "LTR"; class_id "LTR";
+chr3L	dm3_rmsk	exon	9123704	9127416	.	-	.	gene_id "DM412"; transcript_id "DM412_dup93"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	9526908	9534410	.	+	.	gene_id "DM412"; transcript_id "DM412_dup94"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	11557936	11565503	.	+	.	gene_id "DM412"; transcript_id "DM412_dup95"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	13260258	13260342	.	-	.	gene_id "ROO_I"; transcript_id "ROO_I_dup1029"; family_id "Pao"; class_id "LTR";
+chr3L	dm3_rmsk	exon	14818714	14825517	.	+	.	gene_id "Stalker2_I"; transcript_id "Stalker2_I_dup66"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	15418565	15419184	.	+	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup96"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	16609665	16610078	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup121"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	16610079	16614098	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup220"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	17510135	17517635	.	-	.	gene_id "DM412"; transcript_id "DM412_dup96"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	17912044	17912904	.	-	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup97"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	18704339	18709588	.	-	.	gene_id "Stalker2_I"; transcript_id "Stalker2_I_dup67"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	19813441	19813921	.	-	.	gene_id "T412LTR"; transcript_id "T412LTR_dup19"; family_id "LTR"; class_id "LTR";
+chr3L	dm3_rmsk	exon	19813812	19820779	.	-	.	gene_id "DM412"; transcript_id "DM412_dup97"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	19820466	19820946	.	-	.	gene_id "T412LTR"; transcript_id "T412LTR_dup20"; family_id "LTR"; class_id "LTR";
+chr3L	dm3_rmsk	exon	20327933	20328517	.	-	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup132"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	20334190	20334783	.	-	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup133"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	20583219	20583700	.	+	.	gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup12"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	21236884	21244408	.	+	.	gene_id "DM412"; transcript_id "DM412_dup98"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	22754546	22759914	.	+	.	gene_id "IVK_DM"; transcript_id "IVK_DM_dup40"; family_id "I"; class_id "LINE";
+chr3L	dm3_rmsk	exon	22797386	22803956	.	+	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup99"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	22806024	22812083	.	+	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup158"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	22983017	22983430	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup124"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	22983431	22989521	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup228"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	23150298	23150955	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup106"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	23150956	23157025	.	-	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup159"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	23157026	23157683	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup107"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	23159066	23159723	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup108"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	23159724	23165793	.	-	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup160"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	23165794	23166451	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup109"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	23296135	23297324	.	-	.	gene_id "DMRT1B"; transcript_id "DMRT1B_dup239"; family_id "R1"; class_id "LINE";
+chr3L	dm3_rmsk	exon	23309691	23310346	.	-	.	gene_id "PROTOP_B"; transcript_id "PROTOP_B_dup304"; family_id "P"; class_id "DNA";
+chr3L	dm3_rmsk	exon	23365825	23372408	.	+	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup100"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	23378792	23385373	.	-	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup101"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	23415043	23418949	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup230"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	23464990	23466103	.	+	.	gene_id "Gypsy3_I"; transcript_id "Gypsy3_I_dup62"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	23492288	23496191	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup235"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	23566127	23571153	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup236"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	23665822	23667053	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup239"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	23667051	23667540	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup240"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	23771950	23772323	.	+	.	gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup171"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	23800784	23802508	.	-	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup669"; family_id "CR1"; class_id "LINE";
+chr3L	dm3_rmsk	exon	23877394	23877591	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup29"; family_id "Copia"; class_id "LTR";
+chr3L	dm3_rmsk	exon	23881877	23882073	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup30"; family_id "Copia"; class_id "LTR";
+chr3L	dm3_rmsk	exon	23906997	23908404	.	+	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup691"; family_id "CR1"; class_id "LINE";
+chr3L	dm3_rmsk	exon	23968584	23969241	.	+	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup115"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	24131239	24137265	.	-	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup168"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	24190735	24191392	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup119"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	24195937	24196594	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup120"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	24265766	24272339	.	+	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup111"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	24402882	24408921	.	+	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup174"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	24467900	24472283	.	+	.	gene_id "Gypsy6_I"; transcript_id "Gypsy6_I_dup114"; family_id "Gypsy"; class_id "LTR";
+chr3L	dm3_rmsk	exon	24512256	24513726	.	+	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup746"; family_id "CR1"; class_id "LINE";
+chr3R	dm3_rmsk	exon	85005	91064	.	+	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup175"; family_id "Gypsy"; class_id "LTR";
+chr3R	dm3_rmsk	exon	3557455	3562699	.	+	.	gene_id "Stalker2_I"; transcript_id "Stalker2_I_dup82"; family_id "Gypsy"; class_id "LTR";
+chr3R	dm3_rmsk	exon	3917683	3919320	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup276"; family_id "Gypsy"; class_id "LTR";
+chr3R	dm3_rmsk	exon	3919321	3919734	.	-	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup135"; family_id "Gypsy"; class_id "LTR";
+chr3R	dm3_rmsk	exon	4694573	4694985	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup136"; family_id "Gypsy"; class_id "LTR";
+chr3R	dm3_rmsk	exon	4694986	4697176	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup277"; family_id "Gypsy"; class_id "LTR";
+chr3R	dm3_rmsk	exon	4723998	4724411	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup138"; family_id "Gypsy"; class_id "LTR";
+chr3R	dm3_rmsk	exon	4724412	4724498	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup279"; family_id "Gypsy"; class_id "LTR";
+chr3R	dm3_rmsk	exon	5130941	5137128	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup243"; family_id "Gypsy"; class_id "LTR";
+chr3R	dm3_rmsk	exon	6022729	6023142	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup140"; family_id "Gypsy"; class_id "LTR";
+chr3R	dm3_rmsk	exon	6023143	6027676	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup283"; family_id "Gypsy"; class_id "LTR";
+chr3R	dm3_rmsk	exon	6167799	6173891	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup285"; family_id "Gypsy"; class_id "LTR";
+chr3R	dm3_rmsk	exon	6173892	6174304	.	-	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup143"; family_id "Gypsy"; class_id "LTR";
+chr3R	dm3_rmsk	exon	6892543	6896548	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup287"; family_id "Gypsy"; class_id "LTR";
+chr3R	dm3_rmsk	exon	6896549	6896962	.	-	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup145"; family_id "Gypsy"; class_id "LTR";
+chr3R	dm3_rmsk	exon	8294200	8294397	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup31"; family_id "Copia"; class_id "LTR";
+chr3R	dm3_rmsk	exon	8295389	8295558	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup32"; family_id "Copia"; class_id "LTR";
+chr3R	dm3_rmsk	exon	8299366	8299535	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup35"; family_id "Copia"; class_id "LTR";
+chr3R	dm3_rmsk	exon	8300958	8301127	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup37"; family_id "Copia"; class_id "LTR";
+chr3R	dm3_rmsk	exon	8302550	8302719	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup39"; family_id "Copia"; class_id "LTR";
+chr3R	dm3_rmsk	exon	8303884	8304053	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup40"; family_id "Copia"; class_id "LTR";
+chr3R	dm3_rmsk	exon	8305497	8305666	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup42"; family_id "Copia"; class_id "LTR";
+chr3R	dm3_rmsk	exon	8308326	8308495	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup45"; family_id "Copia"; class_id "LTR";
+chr3R	dm3_rmsk	exon	8313462	8313631	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup48"; family_id "Copia"; class_id "LTR";
+chr3R	dm3_rmsk	exon	8316291	8316460	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup51"; family_id "Copia"; class_id "LTR";
+chr3R	dm3_rmsk	exon	8325323	8325492	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup53"; family_id "Copia"; class_id "LTR";
+chr3R	dm3_rmsk	exon	10928275	10928755	.	-	.	gene_id "T412LTR"; transcript_id "T412LTR_dup21"; family_id "LTR"; class_id "LTR";
+chr3R	dm3_rmsk	exon	10934859	10935305	.	-	.	gene_id "DM412"; transcript_id "DM412_dup107"; family_id "Gypsy"; class_id "LTR";
+chr3R	dm3_rmsk	exon	10934992	10935472	.	-	.	gene_id "T412LTR"; transcript_id "T412LTR_dup22"; family_id "LTR"; class_id "LTR";
+chr3R	dm3_rmsk	exon	11426941	11427422	.	-	.	gene_id "T412LTR"; transcript_id "T412LTR_dup23"; family_id "LTR"; class_id "LTR";
+chr3R	dm3_rmsk	exon	11427313	11434238	.	-	.	gene_id "DM412"; transcript_id "DM412_dup108"; family_id "Gypsy"; class_id "LTR";
+chr3R	dm3_rmsk	exon	11433924	11434405	.	-	.	gene_id "T412LTR"; transcript_id "T412LTR_dup24"; family_id "LTR"; class_id "LTR";
+chr3R	dm3_rmsk	exon	13334998	13342488	.	+	.	gene_id "DM412"; transcript_id "DM412_dup109"; family_id "Gypsy"; class_id "LTR";
+chr3R	dm3_rmsk	exon	13859073	13865652	.	+	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup114"; family_id "Gypsy"; class_id "LTR";
+chr3R	dm3_rmsk	exon	16340057	16340908	.	+	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup116"; family_id "Gypsy"; class_id "LTR";
+chr3R	dm3_rmsk	exon	19677352	19683927	.	-	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup117"; family_id "Gypsy"; class_id "LTR";
+chr3R	dm3_rmsk	exon	22043124	22047018	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup289"; family_id "Gypsy"; class_id "LTR";
+chr3R	dm3_rmsk	exon	22047019	22047431	.	-	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup147"; family_id "Gypsy"; class_id "LTR";
+chr3R	dm3_rmsk	exon	22384740	22390952	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup245"; family_id "Gypsy"; class_id "LTR";
+chr3R	dm3_rmsk	exon	22966292	22973844	.	+	.	gene_id "DM412"; transcript_id "DM412_dup110"; family_id "Gypsy"; class_id "LTR";
+chr3R	dm3_rmsk	exon	23701891	23708060	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup290"; family_id "Gypsy"; class_id "LTR";
+chr3R	dm3_rmsk	exon	24425799	24425915	.	-	.	gene_id "LINEJ1_DM"; transcript_id "LINEJ1_DM_dup144"; family_id "Jockey"; class_id "LINE";
+chr3R	dm3_rmsk	exon	24590095	24596647	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup246"; family_id "Gypsy"; class_id "LTR";
+chr3R	dm3_rmsk	exon	26201316	26208883	.	+	.	gene_id "DM412"; transcript_id "DM412_dup111"; family_id "Gypsy"; class_id "LTR";
+chr3R	dm3_rmsk	exon	27495986	27496134	.	-	.	gene_id "DNAREP1_DM"; transcript_id "DNAREP1_DM_dup4623"; family_id "Penelope"; class_id "LINE";
+chrXHet	dm3_rmsk	exon	92917	93113	.	+	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup55"; family_id "Copia"; class_id "LTR";
+chrXHet	dm3_rmsk	exon	98805	99001	.	+	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup56"; family_id "Copia"; class_id "LTR";
+chrXHet	dm3_rmsk	exon	104691	104887	.	+	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup57"; family_id "Copia"; class_id "LTR";
+chrXHet	dm3_rmsk	exon	110576	110772	.	+	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup58"; family_id "Copia"; class_id "LTR";
+chrXHet	dm3_rmsk	exon	116461	116657	.	+	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup59"; family_id "Copia"; class_id "LTR";
+chrXHet	dm3_rmsk	exon	122349	122545	.	+	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup60"; family_id "Copia"; class_id "LTR";
+chrXHet	dm3_rmsk	exon	128221	128417	.	+	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup61"; family_id "Copia"; class_id "LTR";
+chrXHet	dm3_rmsk	exon	132522	132719	.	+	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup62"; family_id "Copia"; class_id "LTR";
+chrYHet	dm3_rmsk	exon	79707	80691	.	-	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup771"; family_id "CR1"; class_id "LINE";
+chrYHet	dm3_rmsk	exon	181984	182181	.	+	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup64"; family_id "Copia"; class_id "LTR";
+chrYHet	dm3_rmsk	exon	314592	317225	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup252"; family_id "Gypsy"; class_id "LTR";
+chrYHet	dm3_rmsk	exon	321875	324507	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup254"; family_id "Gypsy"; class_id "LTR";
+chrYHet	dm3_rmsk	exon	338562	339218	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup134"; family_id "Gypsy"; class_id "LTR";
+chr2LHet	dm3_rmsk	exon	22078	22201	.	+	.	gene_id "DNAREP1_DM"; transcript_id "DNAREP1_DM_dup4748"; family_id "Penelope"; class_id "LINE";
+chr2LHet	dm3_rmsk	exon	237708	243077	.	+	.	gene_id "IVK_DM"; transcript_id "IVK_DM_dup49"; family_id "I"; class_id "LINE";
+chr2LHet	dm3_rmsk	exon	319022	322935	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup263"; family_id "Gypsy"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	321363	324230	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup266"; family_id "Gypsy"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	396896	397012	.	-	.	gene_id "HELENA"; transcript_id "HELENA_dup3"; family_id "Jockey"; class_id "LINE";
+chr2RHet	dm3_rmsk	exon	401410	401722	.	+	.	gene_id "Gypsy_I"; transcript_id "Gypsy_I_dup117"; family_id "Gypsy"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	412537	413738	.	+	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup825"; family_id "CR1"; class_id "LINE";
+chr2RHet	dm3_rmsk	exon	422796	423997	.	+	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup827"; family_id "CR1"; class_id "LINE";
+chr2RHet	dm3_rmsk	exon	579626	585667	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup272"; family_id "Gypsy"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	711188	717988	.	-	.	gene_id "Stalker2_I"; transcript_id "Stalker2_I_dup87"; family_id "Gypsy"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	845370	850300	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup278"; family_id "Gypsy"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	906168	912510	.	+	.	gene_id "TABOR_I"; transcript_id "TABOR_I_dup14"; family_id "Gypsy"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	1070316	1070759	.	+	.	gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup200"; family_id "Gypsy"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	1096471	1097123	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup138"; family_id "Gypsy"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	1097124	1102831	.	-	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup193"; family_id "Gypsy"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	1103201	1103853	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup139"; family_id "Gypsy"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	1103854	1109562	.	-	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup195"; family_id "Gypsy"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	1109932	1110584	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup140"; family_id "Gypsy"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	1430601	1435981	.	-	.	gene_id "IVK_DM"; transcript_id "IVK_DM_dup57"; family_id "I"; class_id "LINE";
+chr2RHet	dm3_rmsk	exon	1578556	1579063	.	+	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup142"; family_id "Gypsy"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	1595646	1595867	.	+	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup143"; family_id "Gypsy"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	1662407	1663532	.	-	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup925"; family_id "CR1"; class_id "LINE";
+chr2RHet	dm3_rmsk	exon	1671374	1671829	.	-	.	gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup207"; family_id "Gypsy"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	1732318	1732515	.	+	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup66"; family_id "Copia"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	1756050	1757426	.	+	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup931"; family_id "CR1"; class_id "LINE";
+chr2RHet	dm3_rmsk	exon	1759026	1763079	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup283"; family_id "Gypsy"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	1766744	1767869	.	+	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup934"; family_id "CR1"; class_id "LINE";
+chr2RHet	dm3_rmsk	exon	1829805	1830461	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup148"; family_id "Gypsy"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	1937252	1938427	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup287"; family_id "Gypsy"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	2126851	2127507	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup150"; family_id "Gypsy"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	2205238	2211812	.	+	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup155"; family_id "Gypsy"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	2266184	2266380	.	+	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup959"; family_id "CR1"; class_id "LINE";
+chr2RHet	dm3_rmsk	exon	2266388	2267371	.	-	.	gene_id "Gypsy12_LTR"; transcript_id "Gypsy12_LTR_dup172"; family_id "Gypsy"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	2271200	2271396	.	+	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup960"; family_id "CR1"; class_id "LINE";
+chr2RHet	dm3_rmsk	exon	2576017	2576497	.	-	.	gene_id "T412LTR"; transcript_id "T412LTR_dup29"; family_id "LTR"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	2576388	2583339	.	-	.	gene_id "DM412"; transcript_id "DM412_dup120"; family_id "Gypsy"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	2583026	2583506	.	-	.	gene_id "T412LTR"; transcript_id "T412LTR_dup30"; family_id "LTR"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	2620135	2626569	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup294"; family_id "Gypsy"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	2649149	2649806	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup151"; family_id "Gypsy"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	2876877	2877347	.	+	.	gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup214"; family_id "Gypsy"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	3240766	3242314	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup353"; family_id "Gypsy"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	3242315	3242729	.	-	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup169"; family_id "Gypsy"; class_id "LTR";
+chr2RHet	dm3_rmsk	exon	3277824	3279072	.	-	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup223"; family_id "Gypsy"; class_id "LTR";
+chr3LHet	dm3_rmsk	exon	354910	357822	.	+	.	gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup220"; family_id "Gypsy"; class_id "LTR";
+chr3LHet	dm3_rmsk	exon	483329	484050	.	-	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup1079"; family_id "CR1"; class_id "LINE";
+chr3LHet	dm3_rmsk	exon	509933	513445	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup302"; family_id "Gypsy"; class_id "LTR";
+chr3LHet	dm3_rmsk	exon	549647	552049	.	+	.	gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup223"; family_id "Gypsy"; class_id "LTR";
+chr3LHet	dm3_rmsk	exon	792236	794266	.	+	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup1098"; family_id "CR1"; class_id "LINE";
+chr3LHet	dm3_rmsk	exon	823538	825639	.	+	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup1102"; family_id "CR1"; class_id "LINE";
+chr3LHet	dm3_rmsk	exon	956253	956909	.	+	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup163"; family_id "Gypsy"; class_id "LTR";
+chr3LHet	dm3_rmsk	exon	957266	962595	.	+	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup240"; family_id "Gypsy"; class_id "LTR";
+chr3LHet	dm3_rmsk	exon	983668	986473	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup315"; family_id "Gypsy"; class_id "LTR";
+chr3LHet	dm3_rmsk	exon	1030809	1031465	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup167"; family_id "Gypsy"; class_id "LTR";
+chr3LHet	dm3_rmsk	exon	1151071	1155572	.	+	.	gene_id "Gypsy_I"; transcript_id "Gypsy_I_dup153"; family_id "Gypsy"; class_id "LTR";
+chr3LHet	dm3_rmsk	exon	1160221	1165073	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup319"; family_id "Gypsy"; class_id "LTR";
+chr3LHet	dm3_rmsk	exon	1373023	1377857	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup320"; family_id "Gypsy"; class_id "LTR";
+chr3LHet	dm3_rmsk	exon	1538514	1544203	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup323"; family_id "Gypsy"; class_id "LTR";
+chr3LHet	dm3_rmsk	exon	1683469	1684123	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup173"; family_id "Gypsy"; class_id "LTR";
+chr3LHet	dm3_rmsk	exon	1690175	1690811	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup174"; family_id "Gypsy"; class_id "LTR";
+chr3LHet	dm3_rmsk	exon	1737851	1738507	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup175"; family_id "Gypsy"; class_id "LTR";
+chr3LHet	dm3_rmsk	exon	1744573	1744770	.	+	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup67"; family_id "Copia"; class_id "LTR";
+chr3LHet	dm3_rmsk	exon	1774179	1777159	.	-	.	gene_id "Stalker2_I"; transcript_id "Stalker2_I_dup106"; family_id "Gypsy"; class_id "LTR";
+chr3LHet	dm3_rmsk	exon	1923212	1923837	.	+	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup177"; family_id "Gypsy"; class_id "LTR";
+chr3LHet	dm3_rmsk	exon	2034838	2037212	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup329"; family_id "Gypsy"; class_id "LTR";
+chr3LHet	dm3_rmsk	exon	2119474	2126010	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup330"; family_id "Gypsy"; class_id "LTR";
+chr3LHet	dm3_rmsk	exon	2197643	2198319	.	-	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup1188"; family_id "CR1"; class_id "LINE";
+chr3LHet	dm3_rmsk	exon	2228211	2230060	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup332"; family_id "Gypsy"; class_id "LTR";
+chr3LHet	dm3_rmsk	exon	2388150	2391546	.	-	.	gene_id "IVK_DM"; transcript_id "IVK_DM_dup87"; family_id "I"; class_id "LINE";
+chr3LHet	dm3_rmsk	exon	2493951	2500000	.	-	.	gene_id "Gypsy6_I"; transcript_id "Gypsy6_I_dup178"; family_id "Gypsy"; class_id "LTR";
+chr3LHet	dm3_rmsk	exon	2501208	2501456	.	-	.	gene_id "ACCORD2_I"; transcript_id "ACCORD2_I_dup230"; family_id "Gypsy"; class_id "LTR";
+chr3LHet	dm3_rmsk	exon	2523539	2528337	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup334"; family_id "Gypsy"; class_id "LTR";
+chr3LHet	dm3_rmsk	exon	2529719	2534595	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup336"; family_id "Gypsy"; class_id "LTR";
+chr3RHet	dm3_rmsk	exon	103505	104162	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup181"; family_id "Gypsy"; class_id "LTR";
+chr3RHet	dm3_rmsk	exon	115978	118430	.	+	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup1232"; family_id "CR1"; class_id "LINE";
+chr3RHet	dm3_rmsk	exon	168333	168746	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup185"; family_id "Gypsy"; class_id "LTR";
+chr3RHet	dm3_rmsk	exon	168747	173788	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup414"; family_id "Gypsy"; class_id "LTR";
+chr3RHet	dm3_rmsk	exon	174269	174682	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup186"; family_id "Gypsy"; class_id "LTR";
+chr3RHet	dm3_rmsk	exon	174683	177140	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup416"; family_id "Gypsy"; class_id "LTR";
+chr3RHet	dm3_rmsk	exon	235339	236750	.	+	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup1237"; family_id "CR1"; class_id "LINE";
+chr3RHet	dm3_rmsk	exon	391520	393355	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup345"; family_id "Gypsy"; class_id "LTR";
+chr3RHet	dm3_rmsk	exon	621179	625027	.	-	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup1258"; family_id "CR1"; class_id "LINE";
+chr3RHet	dm3_rmsk	exon	708787	710560	.	+	.	gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup266"; family_id "Gypsy"; class_id "LTR";
+chr3RHet	dm3_rmsk	exon	714932	715949	.	+	.	gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup269"; family_id "Gypsy"; class_id "LTR";
+chr3RHet	dm3_rmsk	exon	735903	736888	.	+	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup1270"; family_id "CR1"; class_id "LINE";
+chr3RHet	dm3_rmsk	exon	1048132	1048714	.	+	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup201"; family_id "Gypsy"; class_id "LTR";
+chr3RHet	dm3_rmsk	exon	1274333	1279708	.	+	.	gene_id "IVK_DM"; transcript_id "IVK_DM_dup92"; family_id "I"; class_id "LINE";
+chr3RHet	dm3_rmsk	exon	1391501	1397669	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup430"; family_id "Gypsy"; class_id "LTR";
+chr3RHet	dm3_rmsk	exon	1397670	1398083	.	-	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup194"; family_id "Gypsy"; class_id "LTR";
+chr3RHet	dm3_rmsk	exon	1725207	1725866	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup189"; family_id "Gypsy"; class_id "LTR";
+chr3RHet	dm3_rmsk	exon	1969336	1971537	.	-	.	gene_id "Gypsy_I"; transcript_id "Gypsy_I_dup201"; family_id "Gypsy"; class_id "LTR";
+chr3RHet	dm3_rmsk	exon	1976195	1976261	.	-	.	gene_id "DM176_I"; transcript_id "DM176_I_dup171"; family_id "Gypsy"; class_id "LTR";
+chr3RHet	dm3_rmsk	exon	1976257	1976371	.	-	.	gene_id "DM176_I"; transcript_id "DM176_I_dup172"; family_id "Gypsy"; class_id "LTR";
+chr3RHet	dm3_rmsk	exon	2012595	2015484	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup357"; family_id "Gypsy"; class_id "LTR";
+chr3RHet	dm3_rmsk	exon	2132247	2132697	.	-	.	gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup294"; family_id "Gypsy"; class_id "LTR";
+chr3RHet	dm3_rmsk	exon	2137589	2140535	.	+	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup1362"; family_id "CR1"; class_id "LINE";
+chr3RHet	dm3_rmsk	exon	2152093	2154363	.	+	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup1364"; family_id "CR1"; class_id "LINE";
+chr3RHet	dm3_rmsk	exon	2162807	2163464	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup191"; family_id "Gypsy"; class_id "LTR";
+chr3RHet	dm3_rmsk	exon	2166224	2169074	.	-	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup287"; family_id "Gypsy"; class_id "LTR";
+chr3RHet	dm3_rmsk	exon	2174172	2174747	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup193"; family_id "Gypsy"; class_id "LTR";
+chr3RHet	dm3_rmsk	exon	2502594	2502988	.	-	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup217"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	263872	264250	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup197"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	417914	418576	.	-	.	gene_id "Baggins1"; transcript_id "Baggins1_dup329"; family_id "LOA"; class_id "LINE";
+chrUextra	dm3_rmsk	exon	490459	490644	.	+	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup69"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	534429	535172	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup455"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	558971	559475	.	+	.	gene_id "Gypsy6_I"; transcript_id "Gypsy6_I_dup207"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	561513	561682	.	+	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup70"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	632088	632637	.	+	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup219"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	666562	666767	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup456"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	748847	750174	.	+	.	gene_id "Gypsy12_LTR"; transcript_id "Gypsy12_LTR_dup193"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	781576	782842	.	+	.	gene_id "TART"; transcript_id "TART_dup264"; family_id "telomeric"; class_id "LINE";
+chrUextra	dm3_rmsk	exon	1105430	1106023	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup207"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	1136603	1137798	.	-	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup295"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	1206989	1207411	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup382"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	1207512	1207872	.	-	.	gene_id "DM412"; transcript_id "DM412_dup150"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	1207558	1208072	.	-	.	gene_id "T412LTR"; transcript_id "T412LTR_dup34"; family_id "LTR"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	1214193	1214388	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup71"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	1263999	1264196	.	+	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup72"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	1283624	1283793	.	+	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup74"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	1337297	1338164	.	+	.	gene_id "Gypsy12_LTR"; transcript_id "Gypsy12_LTR_dup199"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	1479272	1479814	.	+	.	gene_id "IVK_DM"; transcript_id "IVK_DM_dup115"; family_id "I"; class_id "LINE";
+chrUextra	dm3_rmsk	exon	1491307	1491476	.	+	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup76"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	1553696	1553892	.	+	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup1507"; family_id "CR1"; class_id "LINE";
+chrUextra	dm3_rmsk	exon	1558560	1558972	.	+	.	gene_id "Baggins1"; transcript_id "Baggins1_dup350"; family_id "LOA"; class_id "LINE";
+chrUextra	dm3_rmsk	exon	1566550	1567649	.	-	.	gene_id "TART"; transcript_id "TART_dup297"; family_id "telomeric"; class_id "LINE";
+chrUextra	dm3_rmsk	exon	1634074	1634271	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup77"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	1674843	1675634	.	+	.	gene_id "Gypsy12_LTR"; transcript_id "Gypsy12_LTR_dup206"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	1682961	1683896	.	+	.	gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup339"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	1802357	1803441	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup392"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	1874696	1875287	.	-	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup224"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	1943630	1944699	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup398"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	2168853	2169605	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup404"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	2169603	2169894	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup405"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	2270032	2270229	.	+	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup80"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	2275702	2275899	.	+	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup81"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	2295331	2295528	.	+	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup82"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	2329835	2330219	.	-	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup227"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	2548657	2549227	.	+	.	gene_id "TART_B1"; transcript_id "TART_B1_dup92"; family_id "telomeric"; class_id "LINE";
+chrUextra	dm3_rmsk	exon	2553740	2553861	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup218"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	2559253	2560254	.	+	.	gene_id "Gypsy12_LTR"; transcript_id "Gypsy12_LTR_dup229"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	2623068	2624066	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup427"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	2821009	2821596	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup436"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	2822098	2822482	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup438"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	2826450	2827057	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup440"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	2892734	2893715	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup443"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	3035810	3036529	.	+	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup1570"; family_id "CR1"; class_id "LINE";
+chrUextra	dm3_rmsk	exon	3052810	3053324	.	+	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup237"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	3058643	3059056	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup209"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	3059057	3059176	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup495"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	3129560	3129757	.	+	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup84"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	3203233	3203707	.	+	.	gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup26"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	3343187	3343846	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup226"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	3457873	3458356	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup227"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	3535293	3536032	.	-	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup1586"; family_id "CR1"; class_id "LINE";
+chrUextra	dm3_rmsk	exon	3577563	3578217	.	+	.	gene_id "IVK_DM"; transcript_id "IVK_DM_dup124"; family_id "I"; class_id "LINE";
+chrUextra	dm3_rmsk	exon	3619388	3619704	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup228"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	3922644	3923216	.	+	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup350"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	4113357	4113963	.	-	.	gene_id "POGO"; transcript_id "POGO_dup58"; family_id "Pogo"; class_id "DNA";
+chrUextra	dm3_rmsk	exon	4221101	4221566	.	+	.	gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup379"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	4268697	4269186	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup497"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	4308781	4308977	.	+	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup1604"; family_id "CR1"; class_id "LINE";
+chrUextra	dm3_rmsk	exon	4331740	4332657	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup499"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	4344371	4344921	.	-	.	gene_id "Gypsy12_LTR"; transcript_id "Gypsy12_LTR_dup265"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	4362616	4363106	.	+	.	gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup380"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	4372298	4372494	.	+	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup1605"; family_id "CR1"; class_id "LINE";
+chrUextra	dm3_rmsk	exon	4506984	4507430	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup237"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	4534961	4535282	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup509"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	4643605	4644074	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup239"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	4649981	4650177	.	-	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup1615"; family_id "CR1"; class_id "LINE";
+chrUextra	dm3_rmsk	exon	4667366	4667714	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup513"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	4743405	4743601	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup86"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	4770443	4770927	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup240"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	4799955	4800151	.	+	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup1616"; family_id "CR1"; class_id "LINE";
+chrUextra	dm3_rmsk	exon	4806564	4807465	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup517"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	4834620	4835060	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup518"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	4903649	4904547	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup520"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	5002630	5003323	.	+	.	gene_id "DM412"; transcript_id "DM412_dup163"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	5199146	5199460	.	+	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup255"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	5410456	5410970	.	+	.	gene_id "T412LTR"; transcript_id "T412LTR_dup35"; family_id "LTR"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	5419739	5420020	.	-	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup258"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	5467623	5467819	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup87"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	5468267	5469145	.	+	.	gene_id "Stalker2_I"; transcript_id "Stalker2_I_dup157"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	5525509	5525875	.	+	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup249"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	5566323	5566520	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup88"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	5639085	5639356	.	+	.	gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup27"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	5645896	5646768	.	-	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup1631"; family_id "CR1"; class_id "LINE";
+chrUextra	dm3_rmsk	exon	5871695	5872156	.	-	.	gene_id "ROVER-I_DM"; transcript_id "ROVER-I_DM_dup287"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	5894742	5895604	.	-	.	gene_id "TART"; transcript_id "TART_dup471"; family_id "telomeric"; class_id "LINE";
+chrUextra	dm3_rmsk	exon	5939997	5940317	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup256"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	5968183	5968380	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup90"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	5973645	5974503	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup551"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	5989011	5989803	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup552"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	6006291	6007150	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup553"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	6057681	6057850	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup91"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	6214785	6215147	.	+	.	gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup28"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	6275627	6276474	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup556"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	6356315	6356488	.	+	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup92"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	6415169	6415678	.	+	.	gene_id "TIRANT_I"; transcript_id "TIRANT_I_dup109"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	6477616	6478058	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup259"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	6596063	6596902	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup566"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	6726414	6727249	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup574"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	6731093	6731592	.	-	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup1651"; family_id "CR1"; class_id "LINE";
+chrUextra	dm3_rmsk	exon	6777120	6777571	.	-	.	gene_id "Gypsy6_I"; transcript_id "Gypsy6_I_dup257"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	6817033	6817865	.	-	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup411"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	6841514	6842113	.	-	.	gene_id "Stalker2_I"; transcript_id "Stalker2_I_dup170"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	6903682	6904071	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup261"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	6907402	6907941	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup584"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	6920422	6921251	.	+	.	gene_id "DM412"; transcript_id "DM412_dup170"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	6992859	6993661	.	-	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup412"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	7102128	7102952	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup593"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	7150450	7150988	.	+	.	gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup30"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	7235015	7235497	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup263"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	7315986	7316645	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup600"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	7334043	7334240	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup95"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	7370695	7370891	.	+	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup1665"; family_id "CR1"; class_id "LINE";
+chrUextra	dm3_rmsk	exon	7446279	7446798	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup606"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	7507585	7508242	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup265"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	7588853	7588998	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup267"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	7616213	7617024	.	+	.	gene_id "Gypsy12_LTR"; transcript_id "Gypsy12_LTR_dup342"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	7702096	7702404	.	-	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup269"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	7734930	7735285	.	-	.	gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup31"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	7900550	7901354	.	-	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup428"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	7922267	7922830	.	-	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup272"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	8078372	8078451	.	+	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup1684"; family_id "CR1"; class_id "LINE";
+chrUextra	dm3_rmsk	exon	8250902	8251698	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup550"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	8271783	8272323	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup636"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	8290345	8291138	.	-	.	gene_id "TART_B1"; transcript_id "TART_B1_dup139"; family_id "telomeric"; class_id "LINE";
+chrUextra	dm3_rmsk	exon	8314031	8314435	.	-	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup260"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	8459459	8459943	.	+	.	gene_id "T412LTR"; transcript_id "T412LTR_dup39"; family_id "LTR"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	8459627	8460144	.	+	.	gene_id "DM412"; transcript_id "DM412_dup172"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	8478977	8479082	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup553"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	8479083	8479496	.	-	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup219"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	8532787	8533222	.	-	.	gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup435"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	8560978	8561767	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup645"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	8590054	8590223	.	+	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup100"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	8734305	8735091	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup557"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	8806116	8806901	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup654"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	8833870	8834362	.	+	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup276"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	8872012	8872417	.	+	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup277"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	8926762	8926958	.	-	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup1699"; family_id "CR1"; class_id "LINE";
+chrUextra	dm3_rmsk	exon	9061442	9062185	.	-	.	gene_id "Gypsy12_LTR"; transcript_id "Gypsy12_LTR_dup356"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	9101936	9102517	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup659"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	9118656	9118814	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup559"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	9118815	9119228	.	-	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup222"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	9136851	9137035	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup101"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	9250524	9251301	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup662"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	9351400	9351889	.	-	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup1706"; family_id "CR1"; class_id "LINE";
+chrUextra	dm3_rmsk	exon	9487421	9487729	.	+	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup282"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	9580526	9581298	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup669"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	9771332	9772101	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup672"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	9849567	9849768	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup281"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	9856519	9856717	.	-	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup286"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	9861728	9862489	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup673"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	9899335	9899815	.	-	.	gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup33"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	9935491	9935857	.	+	.	gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup34"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	9935858	9935990	.	+	.	gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup35"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	9994442	9995207	.	-	.	gene_id "Gypsy6_I"; transcript_id "Gypsy6_I_dup282"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	10381383	10382143	.	-	.	gene_id "Gypsy6_I"; transcript_id "Gypsy6_I_dup286"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	10486351	10487110	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup697"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	10539624	10540301	.	+	.	gene_id "DM412"; transcript_id "DM412_dup184"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	10543476	10543672	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup107"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	10619983	10620180	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup108"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	11073586	11074338	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup714"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	11164747	11165497	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup574"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	11167300	11168050	.	+	.	gene_id "IVK_DM"; transcript_id "IVK_DM_dup143"; family_id "I"; class_id "LINE";
+chrUextra	dm3_rmsk	exon	11320396	11321145	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup721"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	11379012	11379760	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup725"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	11560510	11560996	.	-	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup298"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	11582535	11583278	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup733"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	11648555	11649291	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup735"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	11729718	11730462	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup740"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	11747463	11748207	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup580"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	11766055	11766797	.	+	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup490"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	11916285	11917027	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup747"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	11919657	11920399	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup748"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	12017406	12018147	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup752"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	12023632	12023801	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup109"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	12084875	12085287	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup228"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	12085288	12085501	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup582"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	12111673	12112413	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup758"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	12170543	12170736	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup110"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	12210874	12211613	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup759"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	12320847	12321585	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup585"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	12392963	12393700	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup765"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	12445757	12446494	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup766"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	12468359	12469095	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup768"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	12502676	12503268	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup772"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	12574033	12574537	.	+	.	gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup494"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	12608080	12608347	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup229"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	12608348	12608815	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup586"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	12746217	12746386	.	+	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup111"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	12761216	12761385	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup112"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	12762629	12763363	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup781"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	12791845	12792001	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup588"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	12792002	12792415	.	-	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup230"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	12801853	12802586	.	-	.	gene_id "DM412"; transcript_id "DM412_dup191"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	13003552	13003917	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup231"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	13003918	13004284	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup590"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	13012838	13013035	.	+	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup113"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	13031417	13031757	.	+	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup301"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	13090101	13090449	.	-	.	gene_id "T412LTR"; transcript_id "T412LTR_dup41"; family_id "LTR"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	13095090	13095821	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup790"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	13145823	13146552	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup792"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	13195854	13196413	.	+	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup304"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	13203200	13203369	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup114"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	13359258	13359976	.	+	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup527"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	13368369	13369097	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup801"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	13513532	13514102	.	-	.	gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup38"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	13568026	13568291	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup232"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	13568292	13568753	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup593"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	13689617	13690340	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup811"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	13699538	13700264	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup596"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	13863890	13864605	.	+	.	gene_id "DM412"; transcript_id "DM412_dup198"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	13898531	13898702	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup309"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	13912672	13913280	.	+	.	gene_id "Gypsy6_I"; transcript_id "Gypsy6_I_dup312"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	14161352	14162074	.	+	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup545"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	14234569	14235290	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup835"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	14420512	14420954	.	-	.	gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup39"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	14429265	14429985	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup839"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	14480972	14481691	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup841"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	14585098	14585815	.	+	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup555"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	14641608	14642326	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup844"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	14643246	14643964	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup845"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	14801198	14801911	.	-	.	gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup40"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	14918063	14918779	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup853"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	15010326	15011041	.	+	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup564"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	15128635	15129292	.	+	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup317"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	15145715	15146429	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup860"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	15182390	15182946	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup319"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	15320001	15320714	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup867"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	15336281	15336994	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup869"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	15411173	15411820	.	+	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup322"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	15612583	15612802	.	+	.	gene_id "POGO"; transcript_id "POGO_dup66"; family_id "Pogo"; class_id "DNA";
+chrUextra	dm3_rmsk	exon	15640191	15640901	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup883"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	15724535	15725245	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup884"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	15812893	15813373	.	+	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup278"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	16121328	16121525	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup120"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	16144641	16144838	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup121"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	16219727	16220433	.	-	.	gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup280"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	16354882	16355051	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup122"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	16419763	16420468	.	+	.	gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup41"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	16443943	16444408	.	-	.	gene_id "T412LTR"; transcript_id "T412LTR_dup42"; family_id "LTR"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	16450018	16450214	.	-	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup1790"; family_id "CR1"; class_id "LINE";
+chrUextra	dm3_rmsk	exon	16453089	16453509	.	+	.	gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup544"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	16529332	16529408	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup237"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	16529409	16530033	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup622"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	16837298	16837913	.	-	.	gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup42"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	16862996	16863696	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup915"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	16992168	16992869	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup920"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	17001792	17002493	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup922"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	17027456	17028157	.	-	.	gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup43"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	17221404	17221817	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup238"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	17221818	17221904	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup626"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	17530604	17530896	.	+	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup316"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	17768434	17768846	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup240"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	17768847	17768942	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup630"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	17786236	17786432	.	+	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup1803"; family_id "CR1"; class_id "LINE";
+chrUextra	dm3_rmsk	exon	17913642	17913836	.	+	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup334"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	18148886	18149054	.	+	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup123"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	18492386	18493072	.	+	.	gene_id "Copia2_I"; transcript_id "Copia2_I_dup423"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	18536680	18537370	.	+	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup636"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	18578603	18579293	.	-	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup637"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	18870829	18871517	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup974"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	18899228	18899915	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup977"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	18907108	18907779	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup642"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	19142583	19143269	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup989"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	19144944	19145630	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup990"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	19208740	19209153	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup242"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	19209154	19209331	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup644"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	19226168	19226623	.	+	.	gene_id "T412LTR"; transcript_id "T412LTR_dup43"; family_id "LTR"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	19328097	19328776	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup997"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	19335638	19335834	.	+	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup1810"; family_id "CR1"; class_id "LINE";
+chrUextra	dm3_rmsk	exon	19460722	19460965	.	-	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup322"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	19573658	19574297	.	+	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup344"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	19604935	19605408	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup345"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	19610833	19611098	.	+	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup323"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	19663660	19664337	.	-	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup1813"; family_id "CR1"; class_id "LINE";
+chrUextra	dm3_rmsk	exon	19695763	19696445	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1009"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	19749726	19750030	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup347"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	19824016	19824697	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1015"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	19851352	19852032	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1017"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	19870877	19871557	.	+	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup656"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	20052745	20053274	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1021"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	20105098	20105612	.	-	.	gene_id "T412LTR"; transcript_id "T412LTR_dup44"; family_id "LTR"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	20323731	20324408	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1032"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	20430184	20430860	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1042"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	20446501	20447177	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1043"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	20459710	20460257	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup354"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	20463595	20464152	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup355"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	20573012	20573133	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup652"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	20573134	20573546	.	-	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup244"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	20694709	20694754	.	+	.	gene_id "POGO"; transcript_id "POGO_dup68"; family_id "Pogo"; class_id "DNA";
+chrUextra	dm3_rmsk	exon	20737713	20737995	.	+	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup357"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	20784536	20785205	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1053"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	20898322	20898891	.	-	.	gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup45"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	20977865	20978433	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup363"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	20980680	20980850	.	+	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup328"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	20984041	20984712	.	+	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup676"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	21106789	21107460	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1063"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	21131266	21131362	.	+	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup364"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	21377241	21377401	.	+	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup1839"; family_id "CR1"; class_id "LINE";
+chrUextra	dm3_rmsk	exon	21461959	21462128	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup126"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	21528691	21529097	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1078"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	21631573	21631769	.	-	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup332"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	21636942	21637608	.	+	.	gene_id "IVK_DM"; transcript_id "IVK_DM_dup163"; family_id "I"; class_id "LINE";
+chrUextra	dm3_rmsk	exon	21640777	21641443	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1082"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	21664856	21665217	.	+	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup333"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	21711341	21711989	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1086"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	21758994	21759541	.	+	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup369"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	21826284	21826949	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1088"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	21882187	21882851	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1090"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	21885247	21885911	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1091"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	21912022	21912686	.	+	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup689"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	22126822	22127485	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1101"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	22131406	22131601	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup375"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	22207714	22208376	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1105"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	22239760	22240422	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1106"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	22596021	22596680	.	-	.	gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup46"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	22630198	22630856	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1112"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	22784344	22784756	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup251"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	22784757	22784859	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup668"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	22831953	22832331	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup380"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	22994621	22995276	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1122"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	23057337	23057991	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1124"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	23066397	23066815	.	-	.	gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup47"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	23173643	23174205	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1132"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	23303172	23303787	.	+	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup383"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	23336267	23336919	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1135"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	23443874	23444070	.	+	.	gene_id "DMCR1A"; transcript_id "DMCR1A_dup1862"; family_id "CR1"; class_id "LINE";
+chrUextra	dm3_rmsk	exon	23444078	23444448	.	-	.	gene_id "Gypsy12_LTR"; transcript_id "Gypsy12_LTR_dup536"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	23847780	23847903	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup385"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	23991993	23992531	.	+	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup386"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	24009236	24009433	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup128"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	24345996	24346636	.	+	.	gene_id "Gypsy12_LTR"; transcript_id "Gypsy12_LTR_dup545"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	24360836	24361477	.	+	.	gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup723"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	24576989	24577527	.	+	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup341"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	24811648	24812150	.	+	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup391"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	25197241	25197870	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1185"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	25294542	25294915	.	+	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup342"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	25304648	25305061	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup253"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	25305062	25305121	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup679"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	25319135	25319332	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup129"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	25431843	25432469	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1194"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	25722607	25722945	.	+	.	gene_id "TIRANT_I"; transcript_id "TIRANT_I_dup139"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	25919521	25919667	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup130"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	26246267	26246681	.	+	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup255"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	26246682	26246789	.	+	.	gene_id "DM297_I"; transcript_id "DM297_I_dup682"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	26305984	26306164	.	-	.	gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup396"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	26399753	26400360	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1224"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	26779758	26780354	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1237"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	26821013	26821485	.	-	.	gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup648"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	27117304	27117501	.	-	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup132"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	27229943	27230524	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1247"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	27234053	27234637	.	+	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1248"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	27886616	27886879	.	-	.	gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup350"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	27905485	27905571	.	-	.	gene_id "DM297_I"; transcript_id "DM297_I_dup690"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	27905572	27905891	.	-	.	gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup262"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	28209068	28209265	.	+	.	gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup133"; family_id "Copia"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	28715167	28715519	.	+	.	gene_id "TABOR_I"; transcript_id "TABOR_I_dup112"; family_id "Gypsy"; class_id "LTR";
+chrUextra	dm3_rmsk	exon	28866030	28866253	.	+	.	gene_id "SAR_DM"; transcript_id "SAR_DM_dup7047"; family_id "Satellite"; class_id "Satellite";
+chrUextra	dm3_rmsk	exon	28961580	28961826	.	-	.	gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1265"; family_id "Gypsy"; class_id "LTR";
diff -r 000000000000 -r 2dfbcb88d16a test-data/treatment1.bam
Binary file test-data/treatment1.bam has changed
diff -r 000000000000 -r 2dfbcb88d16a test-data/treatment2.bam
Binary file test-data/treatment2.bam has changed
diff -r 000000000000 -r 2dfbcb88d16a tetranscript.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tetranscript.xml	Wed May 13 12:57:29 2020 -0400
@@ -0,0 +1,299 @@
+<?xml version="1.0"?>
+<tool id="tetoolkit_tetranscripts" name="TEtranscripts" version="@TOOL_VERSION@+@WRAPPER_VERSION@">
+    <description>annotates reads to genes and transposable elements</description>
+    <macros>
+        <token name="@TOOL_VERSION@">2.1.4</token>
+        <token name="@WRAPPER_VERSION@">galaxy0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">tetranscripts</requirement>
+    </requirements>
+    <version_command>TEtranscripts --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        ## initialize
+        ## file extension is required
+        ln -s '$GTF' 'gene_annotation.gtf' &&
+        ln -s '$TE' 'transposable_annotation.gtf' &&
+
+        ## run
+        TEtranscripts
+            ## required
+            -t
+            #for $s in $sample_rep
+                '${s.t}'
+            #end for
+            -c
+            #for $s in $sample_rep
+                '${s.c}'
+            #end for
+            --GTF 'gene_annotation.gtf'
+            --TE 'transposable_annotation.gtf'
+            ## optional
+            --stranded '$io.stranded'
+            $io.sortByPos
+            --project 'result'
+            --mode '$ap.mode'
+            --minread $ap.minread
+            #if $ap.fragmentLength
+                --fragmentLength $ap.fragmentLength
+            #end if
+            --iteration $ap.iteration
+            --padj $ap.padj
+            --foldchange $ap.foldchange
+            #if 'log' in $ap.out
+                --verbose 3
+                |& tee log.txt
+            #end if
+        ]]></command>
+    <inputs>
+        <repeat name="sample_rep" min="2" title="Select input data">
+            <param argument="-t" type="data" format="bam" label="Treatment sample file"/>
+            <param argument="-c" type="data" format="bam" label="Control sample file"/>
+        </repeat>
+        <param argument="--GTF" type="data" format="gtf" label="Select GTF file for gene annotations"/>
+        <param argument="--TE" type="data" format="gtf" label="Select GTF file for transposable element annotations"/>
+        <section name="io" title="Input options">
+            <param argument="--stranded" type="select" label="Select library type">
+                <option value="no">Library is unstranded (no)</option>
+                <option value="forward">Second-strand cDNA library e.g. QIAseq stranded (forward)</option>
+                <option value="reverse">First-strand cDNA library e.g. Illumina TruSeq stranded (reverse)</option>
+            </param>
+            <param argument="--sortByPos" type="boolean" truevalue="--sortByPos" falsevalue="" label="Are input files sorted by chromosome position?"/>
+        </section>
+        <section name="ap" title="Advanced parameters">
+            <param argument="--mode" type="select" label="Set TE counting mode">
+                <option value="multi">Distribute among all alignments (multi)</option>
+                <option value="uniq">Unique mappers only (uniq)</option>
+            </param>
+            <param argument="--minread" type="integer" value="1" min="0" label="Set read count cutoff"/>
+            <param argument="--fragmentLength" type="integer" min="0" optional="true" label="Set average length of fragment used for single-end sequencing" help="For paired-end, estimated from the input alignment file. For single-end, ignored by default."/>
+            <param argument="--iteration" type="integer" value="100" min="0" label="Set maximum number of iterations used to optimize multi-reads assignment"/>
+            <param argument="--padj" type="float" value="0.05" min="0.0" max="1.0" label="Set FDR cutoff for significance"/>
+            <param argument="--foldchange" type="float" value="1.0" min="0.0" label="Set fold-change ratio (absolute) cutoff for differential expression"/>
+            <param name="out" type="select" multiple="true" label="Select output file(s)" help="Result files for gene TE analysis and sigDiff gene TE will be created if more than one dataset is applied.">
+                <option value="cnttable" selected="true">cntTable</option>
+                <option value="deseq2" selected="true">DESeq2.R</option>
+                <option value="gta" selected="true">Gene TE Analysis</option>
+                <option value="sgt" selected="true">SigDiff Gene TE</option>
+                <option value="log">Log</option>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="out_cnt" format="tabular" from_work_dir="result.cntTable" label="${tool.name} on ${on_string}: cntTable">
+            <filter>'cnttable' in ap['out']</filter>
+        </data>
+        <data name="out_deseq2" format="txt" from_work_dir="result_DESeq2.R" label="${tool.name} on ${on_string}: DESeq2.R">
+            <filter>'deseq2' in ap['out']</filter>
+        </data>
+        <data name="out_log" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: log">
+            <filter>'log' in ap['out']</filter>
+        </data>
+        <data name="out_gta" format="txt" from_work_dir="result_gene_TE_analysis.txt" label="${tool.name} on ${on_string}: Gene TE analysis">
+            <filter>'gta' in ap['out']</filter>
+        </data>
+        <data name="out_sgt" format="txt" from_work_dir="result_sigdiff_gene_TE.txt" label="${tool.name} on ${on_string}: SigDiff Gene TE">
+            <filter>'sgt' in ap['out']</filter>
+        </data>
+    </outputs>
+    <tests>
+        <!-- 
+            sources for test data:
+            https://github.com/mhammell-laboratory/tetoolkit-test-data 
+            https://github.com/mhammell-laboratory/TEtranscripts/issues/66
+        -->
+
+        <!-- #1: default -->
+        <test expect_num_outputs="5">
+            <repeat name="sample_rep">
+                <param name="t" value="treatment1.bam"/>
+                <param name="c" value="control1.bam"/>
+            </repeat>
+            <repeat name="sample_rep">
+                <param name="t" value="treatment2.bam"/>
+                <param name="c" value="control2.bam"/>
+            </repeat>
+            <param name="GTF" value="gtf.gtf"/>
+            <param name="TE" value="te.gtf"/>
+            <section name="ap">
+                <param name="out" value="cnttable,deseq2,gta,sgt,log"/>
+            </section>
+            <output name="out_cnt">
+                <assert_contents>
+                    <has_n_lines n="295"/>
+                    <!-- depends on sample names -->
+                    <has_text_matching expression="gene.+"/>
+                    <!-- order changes -->
+                    <has_text_matching expression="TIRANT.+"/>
+                </assert_contents>
+            </output>
+            <output name="out_deseq2">
+                <assert_contents>
+                    <has_n_lines n="14"/>
+                    <has_text_matching expression="data.+"/>
+                </assert_contents>
+            </output>
+            <output name="out_log">
+                <assert_contents>
+                    <has_text_matching expression="INFO"/>
+                    <has_text_matching expression=".+Done"/>
+                </assert_contents>
+            </output>
+            <output name="out_gta">
+                <assert_contents>
+                    <has_n_lines n="71"/>
+                    <has_line line="baseMean&#009;log2FoldChange&#009;lfcSE&#009;stat&#009;pvalue&#009;padj"/>
+                    <!-- order changes -->
+                    <has_text_matching expression="TIRANT.+"/>
+                </assert_contents>
+            </output>
+            <!-- no content, test dataset to small -->
+            <output name="out_sgt">
+                <assert_contents>
+                    <has_n_lines n="1"/>
+                    <has_line line="baseMean&#009;log2FoldChange&#009;lfcSE&#009;stat&#009;pvalue&#009;padj"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #2 -->
+        <test expect_num_outputs="5">
+            <repeat name="sample_rep">
+                <param name="t" value="treatment1.bam"/>
+                <param name="c" value="control1.bam"/>
+            </repeat>
+            <repeat name="sample_rep">
+                <param name="t" value="treatment2.bam"/>
+                <param name="c" value="control2.bam"/>
+            </repeat>
+            <param name="GTF" value="gtf.gtf"/>
+            <param name="TE" value="te.gtf"/>
+            <section name="io">
+                <param name="stranded" value="forward"/>
+                <param name="sortByPos" value="true"/>
+            </section>
+            <section name="ap">
+                <param name="mode" value="uniq"/>
+                <param name="minread" value="2"/>
+                <param name="fragmentLength" value="10"/>
+                <param name="iteration" value="90"/>
+                <param name="padj" value="0.06"/>
+                <param name="foldchange" value="2.0"/>
+                <param name="out" value="cnttable,deseq2,gta,sgt,log"/>
+            </section>
+            <output name="out_cnt">
+                <assert_contents>
+                    <has_n_lines n="295"/>
+                    <!-- depends on sample names -->
+                    <has_text_matching expression="gene.+"/>
+                    <!-- order changes -->
+                    <has_text_matching expression="TIRANT.+"/>
+                </assert_contents>
+            </output>
+            <output name="out_deseq2">
+                <assert_contents>
+                    <has_n_lines n="14"/>
+                    <has_text_matching expression="data.+"/>
+                </assert_contents>
+            </output>
+            <output name="out_log">
+                <assert_contents>
+                    <has_text_matching expression="INFO.+"/>
+                </assert_contents>
+            </output>
+            <output name="out_gta">
+                <assert_contents>
+                    <has_n_lines n="3"/>
+                    <has_line line="baseMean&#009;log2FoldChange&#009;lfcSE&#009;stat&#009;pvalue&#009;padj"/>
+                    <!-- order changes -->
+                    <has_text_matching expression="DNAREP1.+"/>
+                </assert_contents>
+            </output>
+            <!-- no content, test dataset to small -->
+            <output name="out_sgt">
+                <assert_contents>
+                    <has_n_lines n="1"/>
+                    <has_line line="baseMean&#009;log2FoldChange&#009;lfcSE&#009;stat&#009;pvalue&#009;padj"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #3 -->
+        <test expect_num_outputs="5">
+            <repeat name="sample_rep">
+                <param name="t" value="treatment1.bam"/>
+                <param name="c" value="control1.bam"/>
+            </repeat>
+            <repeat name="sample_rep">
+                <param name="t" value="treatment2.bam"/>
+                <param name="c" value="control2.bam"/>
+            </repeat>
+            <param name="GTF" value="gtf.gtf"/>
+            <param name="TE" value="te.gtf"/>
+            <section name="io">
+                <param name="stranded" value="reverse"/>
+            </section>
+            <section name="ap">
+                <param name="out" value="cnttable,deseq2,gta,sgt,log"/>
+            </section>
+            <output name="out_cnt">
+                <assert_contents>
+                    <has_n_lines n="295"/>
+                    <!-- depends on sample names -->
+                    <has_text_matching expression="gene.+"/>
+                    <!-- order changes -->
+                    <has_text_matching expression="TIRANT.+"/>
+                </assert_contents>
+            </output>
+            <output name="out_deseq2">
+                <assert_contents>
+                    <has_n_lines n="14"/>
+                    <has_text_matching expression="data.+"/>
+                </assert_contents>
+            </output>
+            <output name="out_log">
+                <assert_contents>
+                    <has_text_matching expression="INFO.+"/>
+                </assert_contents>
+            </output>
+            <output name="out_gta">
+                <assert_contents>
+                    <has_n_lines n="23"/>
+                    <has_line line="baseMean&#009;log2FoldChange&#009;lfcSE&#009;stat&#009;pvalue&#009;padj"/>
+                    <!-- order changes -->
+                    <has_text_matching expression="TART.+"/>
+                </assert_contents>
+            </output>
+            <output name="out_sgt">
+                <assert_contents>
+                    <has_n_lines n="2"/>
+                    <has_line line="baseMean&#009;log2FoldChange&#009;lfcSE&#009;stat&#009;pvalue&#009;padj"/>
+                    <has_text_matching expression="Gypsy12.+"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+TEtranscripts is a software package that utilizes both unambiguously (uniquely) and ambiguously (multi-) mapped reads to perform differential enrichment analyses from high throughput sequencing experiments. Currently, most expression analysis software packates are not optimized for handling the complexities involved in quantifying highly repetitive regions of the genome, especially transposable elements (TE), from short sequencing reads. Although transposon elements make up between 20 to 80% of many eukaryotic genomes and contribute significantly to the cellular transcriptome output, the difficulty in quantifying their abundances from high throughput sequencing experiments has led them to be largely ignored in most studies. The TEtranscripts provides a noticeable improvement in the recovery of TE transcripts from RNA-Seq experiments and identification of peaks associated with repetitive regions of the genome.
+
+**Input**
+
+GTF files for gene annotation can be obtained from `UCSC RefSeq <http://genome.ucsc.edu/cgi-bin/hgTables>`_, Ensembl, `iGenomes <http://support.illumina.com/sequencing/sequencing_software/igenome.html>`_ or other annotation databases. GTF files for TE annotations are customly generated from `UCSC RepeatMasker <http://genome.ucsc.edu/cgi-bin/hgTables>`_ or other annotation database. They contain two custom attributes, class_id and family_id, corresponding to the class (e.g. LINE) and family (e.g. L1) of the corresponding transposable element. A unique ID (e.g. L1Md_Gf_dup1) is also assigned for each TE annotation in the transcript_id attribute.
+
+**Output**
+
+TEtranscripts quantifies both gene and transposable element (TE) transcript abundances from RNA-Seq experiments, utilizing both uniquely and ambiguously mapped short read sequences. It processes the short reads alignments (BAM files) and proportionally assigns read counts to the corresponding gene or TE based on the user-provided annotation files (GTF files). In addition, TEtranscripts combines multiple libraries and perform differential analysis using DESeq2.
+
+.. class:: infomark
+
+**References**
+
+More information are available on the `project website <http://hammelllab.labsites.cshl.edu/software/#TEtranscripts>`_ and `github <https://github.com/mhammell-laboratory/TEtranscripts>`_.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btv422</citation>
+        <citation type="doi">10.1007/978-1-4939-7710-9_11</citation>
+    </citations>
+</tool>
\ No newline at end of file