| droWil2 | 
	scf2_1100000004954:3797605-3797844 - | 
	dwi_3732 | 
	AGCCA---CGG------------TCAAGCCAAATATCAAGGATCCCC---GAGGCGGAGGGCCAGGAGGTATTTGAA--------TATTTAACTACTTTGATGTTGTGAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CA-------------------------TATTCATA--------------------------------------------------TTTTATGATTTCTTTACTTTTATTCAATATTATTTA----T--GT-------TG--TTCGTGT-------GTGTGCG-TGT-ATGTGTG--TC----CC----------CGG-----GTTAA-ACC-TTAATATTGTAACCAGGCTGTTGCGATGTCGTACTTGACCGTGAGGAATTCTTGAATGCATC---GAAG | 
	| droVir3 | 
	scaffold_12875:13381448-13381671 + | 
	dvi_6674 | 
	AGCGC---CGC------------CCAAGCCAAGCTTTAAGGATCAGCCCCAGCGCGGCGCACCTGGCGGTGAGTCTC----------------------------GA------------------------------------------------------------------------------------------------------------------------------TCTTCA----------------------------------CATTATCA--------------------------------------------------------------------------AATCGAATTGTATTATTT-----TAATTT--GATTAATTTCTT-T--------ATT--TA---TT-GAA--------TAT---TGTAC-------GTGTGCG-TGT-GTGTG----TT----TTGGTGTT-----GT-----CCTGCTCTG-AC-----------CAGGTTGTTGTGATGTCGTGCTTGACAGGGAGCAGTTCATGAACGCCTC---AAAG | 
	| droMoj3 | 
	scaffold_6496:20683281-20683505 + | 
	 | 
	CACGC---CGC------------CTAAGCCGAGCTACAAGGATCAGCCACAACGCGGCATGCCTGGCGGTGAGTCTGGAATGAAAT--------------------AGGCTA------------------------------------------------------------------------------------------------------------------------C----CT----------------------------------TTTTATTATTA------------------------------------TAATTTCATTTATT--------------------TTGA-T------------------TTAT----------------------------T--TATCTTT-GAATA-----TTGTAAACGTGT-------GTCTGTGTTGTT---------GTTG--CT----------GGT-----GTTGT---------GGTTG--ACCAGGTTGCTGCGATGTCGTGCTTGACAGGGAGCAGTTCATGAATGCTTC---GAAG | 
	| droGri2 | 
	scaffold_15245:6970925-6971158 - | 
	 | 
	AGCGCCGCCAA------------TCAAGCCAAACTTTAAGGATCAGCAACAGCGTGGCGGACCAGGCGGTGAGTGTT----------------------------GAGGCCTTC---------------------------------------------------------------------------------------------------------------------ATTTTTCACA-------------------------------TATTTATTTTTA---------------------------------------------------------TTA------------------------------------ATTTATCAAATTTATTTATTATTTAAATATTGTCTA----A--ATA---------TTGTGTAT-------GTGTGTG-TG-----------TTGG--TG----TTGTCTTGC-----TCACTGGGG-T------------CAGGTTGTTGTGATGTCGTACTTGACCGGGAAGAGTTTATGAATGCCTC---AAAG | 
	| dp5 | 
	3:17533592-17533845 + | 
	 | 
	CGC-----CGC---CGCCCCCCCAGCAGCAGAACTTAAAGGATCAGA---GGAGCGGGGCACCGGGCGGTGAGTTGA----------------------------GTGGC-------------------------------AATGTTTC----------------------------------------------------------------------------------CG---------------------------------------CAATTAGAATCG---------------------------------------------------------AAA------------------------------------ATTTATTAGTTATTTCTTTTTATTTATTATTGTCTC----T--GTGCGCCTCTGTGTCTGTGT-------GTGCGTGT----GTGTG----TGTATGTG----------TGTGTTCGCCTGTCCTGTTTGGTGTTT----TAGGCTGTTGTGATGTTGTGCTCGACAGGGAACAGTTCATGAACGCGAC---GAAG | 
	| droPer2 | 
	scaffold_31:257781-258035 - | 
	 | 
	CGC-----CGCCGCCGCCCCCCCAGCAGCAGAACTTAAAGGAGCAGA---GGAGCGGGGCACCGGGCGGTGAGTTGA----------------------------GTGGC-------------------------------AATGTTTC----------------------------------------------------------------------------------CG---------------------------------------CAATTAGAATCG---------------------------------------------------------AAA------------------------------------ATTTATTAGTTATTTCTTTTTATTTATTATTGTCTC----T--GTGCGCCTCTGTGTCTGTGT-------GTGCGTGT----GTGTGTA--TTTG--TG----------TGT--TCGCCTGTCCTGTTTGGTGTTT----TAGGCTGTTGTGATGTTGTGCTCGACAGGGAACAGTTCATGAACGCAAC---GAAG | 
	| droAna3 | 
	scaffold_13266:7063710-7063955 - | 
	 | 
	AGCGC---CGC------------CCAAGCAAAACTTGAAGGATCAGC------GGGCCGGTCCAGGCGGTAAGTCAT----------------------------CAGGTTTTCAGAAATG---------------------------------------------------------------------------------------------------------------ATTTTCACATGGGAGGGATATTTTAT---------------------------------------TATAG--------------------ATTTTATATAT---------------A-------TA-A------------------TTATTTTATAATTATTATTATT--------ATT--TTAATTT------------AATTTCCGTAT-------TTATGT-TTGCT---------TCTG--TG----------TGG-----GCTGT-------GGTGTTG----TAGGCTGTTGCGATGTGGTGCTTGACAGGGAGCACTTTATGAATGCCTC---CAAG | 
	| droBip1 | 
	scf7180000396423:600714-600995 - | 
	 | 
	AGCGC---CGC------------CCAAGCAAAACTTTAAGGATCAGA------GAGCTGCCCCAGGCGGTAAGTCAT----------------------------CAGGTTTTCAGAACTGAGTCTATTTAAAGGGGTGTCATTGTTGT----------------------------------------------------------------------------------CA---------------------------------------TTATTAT--TTGAAAAGAT---------------T--TA-ATTTTTTAAAGATT-ATGT-----ATTTA--------TTTGTATAC-A-------------------TTTTTCCTAATTATTATTATT--------ATT--TTACATT------------TATTTCCGTAT-------TTATGTTTTCT----------TTTG--TG----------TGG-----GCTGT-------GGTGTTG----TAGGCTGTTGCGATGTCGTACTTGACAGGGAGCACTTTATGAATGCCTC---TAAG | 
	| droKik1 | 
	scf7180000302476:2014911-2015097 + | 
	 | 
	TT----------------------------------AAA----------------------------------------------T----------------------ATTT-C---------------------------------------------------------------------------------------------------------------------TT----TT----------------------------------TATTCTTATAT-------------------------------------------------TAAAAACA----TTCATTTTTATTT-A-----------TTAATCATT--------ATTATTA---TT--------ATA--CTCTTTTG--TT-------TATTCCCGCATCACTTCGGTGGGTGT--------GTGCTTTTG--TG----------TTG-----GCT-----G-TTGATGTTG--TGTAGGCTGTTGTGACGTCGTTCTTGACAGGGAGCAGTTCGTGAATATCTC---GAAG | 
	| droFic1 | 
	scf7180000454044:347265-347626 + | 
	 | 
	CG--C---CGC------------CCAAGCAAAACTTCAAGGATCCAC------GAGCTGCACCCGGAGGTGAGTCTT----------------------------CAGATCTTAAA-----------------GTAAAAGCTCTGTTGTAGCGACTCCAAAAAGTTCATCCTTATAATTTATAAACTTATTTTATAGATTAACAACAAGGAAATCTAATTTTCTGTATTTCCTCCATGA-------------------TCAATGTTCAATTTTTGTTGT--TTGAAAAGAT---------------CACTA-TTTTTATTTAGTTTGATGT--TTAATTTA--------TTTGT---C-A---------------------------ATTTTTTTTTATT--------ATT--TATCTTT------------TATTTTCCTTT-------ATGGGTGTTGTT---------GTGC--TG----------TGG-----GCT-----G-TCGATGTTG----TAGGATGTTGTGACGTCGTGCTTGACAGGGAGCAGTTCATGAATGTCTC---GAAG | 
	| droEle1 | 
	scf7180000491240:127439-127582 - | 
	 | 
	AT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATT--------------------ATTTCA------------------TTATATATTAATACATTTTATT--------TTA--TTCTTTT------------GATTTCCGTAT-------GTGGGTGGTGTT---------TGTTTGTG----------T----------GTGCTA-TCGATGTTG----TAGGATGTTGTGATGTCGTGCTTGACAGAGAGCAGTTCATGAATGTTAC---GAAG | 
	| droRho1 | 
	scf7180000779378:9994-10130 + | 
	 | 
	TT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TC-A------------------TTATTTTTCAAACACATTTATA--------ATT--TAATTTT------------TATTTTCGTGT-------GTGGGTTTTGTT---------TTTATGTG----------T----------GCGCTG-TTGATGTTG----TAGGATGTTGTGACGTCGTGCTTGACAGGGAGCAGTTCATGAATGTCTC---GAAG | 
	| droBia1 | 
	scf7180000301754:606307-606498 - | 
	 | 
	A--------------------------------CTTTAATGTT--------------------------------------------------------------GCC-----CAGA--------------------------------------------------------------------------------------------------------------------ACT------------------TCAC---------------------------------------TAGTG--------------------TTTTCATGTATTATTATTA--------TTCC--TTT-A------------------TAATTTATTATTAATTGCTTTT--------ATT--TTCTTTT------------TATTTCCGTGT-------GTGGGTGGTGTT---------ATGG--TG----------TGG-----GCTGTGCTG-TCGATGTTG----TAGGATGTTGTGACGTTGTGCTTGACAGGGAGCAGTTCATGAATGTCTC---GAAG | 
	| droTak1 | 
	scf7180000415391:141365-141520 - | 
	 | 
	TAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T-TTAT-----ATTTA--------TTTC--TTC-A------------------ATATTTATAAATTAATTGTTTT--------ATT--TTCTTTT------------CATTTCCGTAT-------GTGGGTGGTGTT---------TTTT--TG----------TGG-----GCTGTGCTG-TCGATGTTG----TAGGATGTTGTGACGTTGTGCTTGACAGGGAGCAGTTTATGAATATCTC---GAAG | 
	| droEug1 | 
	scf7180000409474:1044233-1044480 - | 
	 | 
	CA-----CCAC------------CCAAACAAAACTTCAAGGATCAAC------GAGCTGCTCCTGGCGGTAAGTTCT----------------------------TATATTT-C---------------------------------------------------------------------------------------------------------------------TTTCATTG----------------------------------TAG-----TC----------TACTTTTACAAATT--TA-C--------TTTT----------------AAAATTAAT----TTTA-A------------------TTATTTAACAATTATTATTATG--------ATT--TTCTTTT------------TATTTCCGTAT-------GTGGGTGGTGTT---------GTTG--TA----------TGG-----GCTGTGCTG-TCGATGTTG----TAGGATGTTGTGATGTCGTGCTTGACAGGGAGCAGTTTATGAATGTCTCCAAGAAG | 
	| dm3 | 
	chr2R:16907038-16907294 + | 
	 | 
	AGTGCCTCCAA------------GCCAGCCAAACTTCAAGGATCCAC------GAGCAGCACCAGGCGGTAAGTCAT----------------------------CAGATTC-T---------------------------------------------------------------------------------------------------------------------ATTCACCA----------------------------------CATTAGGA-------GCTAGGGCTTATAAATGTT--GTAC-TTTACTTAATTTCATTTATC--------------------ATTT-A------------------TTATTTATGAATTATCATCATG--------ATT--TTCTTTT------------GATTTCCGTAT-------GTGGGTGTTGTT---------GTTG--T------------------------CCGG-TCGATGTTG----TAGGATGTTGTGATGTCGTCCTGGACAGGGAGCAGTTTCTGAATGCCAC---GAAG | 
	| droSim2 | 
	2r:17464521-17464760 + | 
	 | 
	AGTGCCTCCAG------------CCCAGCCAAATTTCAAGGATCCAC------GAGCAGCACCAGGCGGTAAGTCAA----------------------------CAGTTTT-C---------------------------------------------------------------------------------------------------------------------ACTCTCAA----------------------------------CATTAGGA-------GC-----------------------------TTAGTTTAATGTATT--------------------AATT-A------------------TTGTTTATGAATTATCATCATT--------ATT--TCCTTTT------------GATTTCCTTAT-------GTGGGTGTTGTT---------GTTG--TG----------TGG-----GCTGTGCGG-TCGATGTTG----TAGGATGTTGTGATGTCGTCCTGGACAGGGAGCAGTTCCTGAATGCCAC---GAAG | 
	| droSec2 | 
	scaffold_9:237733-237972 + | 
	 | 
	AGTGCCTCCAG------------CCCAGCCAAACTTTAAGGATCCAC------GAGGTGCACCAGGCGGTAAGTCAT----------------------------TGGTTTC-C---------------------------------------------------------------------------------------------------------------------ACTCTCAA----------------------------------CATAAAGA-------GC-----------------------------TTAGTTTCATGTGTT--------------------ATTT-A------------------TTATTTATCAATTATCATCATG--------ATT--TCCTTTT------------AATTTCCTTAT-------GTGGGTGTTGTT---------GTTG--TG----------TGG-----CCTGTGCGG-TCGATGTTG----TAGGATGTTGTGATGTCGTCCTGGACAGGGAGCAGTTCCTGAATGCCAC---GAAG | 
	| droYak3 | 
	2R:12289612-12289856 - | 
	dya_558 | 
	CG-----CCGA------------CCCAGCCAAACTTGAAGGATCCGC------GCGCAGCTCCAGGCGGTGAGTCCT----------------------------CAGATTT-C---------------------------------------------------------------------------------------------------------------------CTTCACTA----------------------------------AAG-----TTGCAAAGCTAGGGCTTATACACGTT--TTAC-TACATTTAATTTCATGTATT--------------------ACTT-A------------------TTAT-------------------------------TTCCATT------------GATTTCCGTAT-------GTGGGTGGTGAT---------GTTG--TG----------TGG-----GCTGTGGCG-TCGATGTTG----TAGGATGTTGTGATGTCGTGCTGGACAGGGAGCAGTTCCTGAACGCCTCCAAGAAG | 
	| droEre2 | 
	scaffold_4845:11050910-11051162 + | 
	 | 
	CG-----CCGG------------CCCAGCCAAACTTCAAGGATCCGC------GCGCAGCACCAGGCGGTGAGTCCT----------------------------CAGGTTT-C---------------------------------------------------------------------------------------------------------------------CCCCACAA----------------------------------CAG-----TT----------GGCTTATACATCTT--TAAC-TGCATTTCATTTCATGTACT--------------------ACTT-A------------------TTGTTTATGCCTTATTTTCAAC--------ATT--TTCCTTT------------AATTTCCGTAT-------GTGGGTGGTGTT---------GTTG--TG----------TGG-----GCTGTGCCG-TCGATGTTG----TAGGATGTTGTGATGTCGTGCTGGACAGGGAGCAGTTCCTGAATGCCAC---CAAG |