dmo_2602

Name	Class	Family	Strand
AT_rich	Low_complexity	Low_complexity	+
Homo6	DNA	hAT-Pegasus	-

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------################################################## TTATGCGTGCTTGCCTATGGCTGTGTGTGTGCGTGTGTGTTTGCATGTGCGAATATTTATTGAATTATCAGTTGCTCGAAGGGTTCAGGGGATCTCGTAGTCGAGCAGTCTCTACTAGAGCTTTCTTACTTATTTCAATTAAAAACGTCTTAATTGGGTTTTGTTTATATATTTTATTCTACTTATATTTTAATTTTACAGATGGCAGAGTTATCTCATAGTGTAGTATCACCCACATCATTCCGTGTGGA ************************************************........((((((.(((.((((((((((.((((((...)))))).....)))))))..((((...)))).......((....(((((((((.......)))))))))....))................))).))).)))))).......************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V049 head	M060 embryo	V110 male body	M046 female body
..............................................................................................................................TAATGATGTCAATTAAAAACGTCT.....................................................................................................	24	3	1	1.00	1	1	0	0	0
..................................................................................GTTCAGGGGATCTCGTAGTCGAGCAGT..............................................................................................................................................	27	0	20	0.20	4	0	0	4	0
...................................................AATAGTTACAGAATTATCAGT...................................................................................................................................................................................	21	3	10	0.20	2	0	0	2	0
...............................................................................................CGTAGTCGAGCAGTCTCTACTAGAGC..................................................................................................................................	26	0	6	0.17	1	0	1	0	0
......................................................................................AGGGGATCTCGTAGTCGAGCAGT..............................................................................................................................................	23	0	20	0.15	3	0	0	0	3
.................................................................................................TAGTCGAGCAGTCTCTACTAGAGCT.................................................................................................................................	25	0	7	0.14	1	0	1	0	0
.............................................................GAATTATCAGTTGCTGGAAGGGT.......................................................................................................................................................................	23	1	8	0.13	1	0	1	0	0
................................................................................................GTAGTCGACCAGTCTCTACTAGAGC..................................................................................................................................	25	1	11	0.09	1	0	1	0	0
............................................................................................TCTCGTAGTCGAGCAGTCTCTA.........................................................................................................................................	22	0	11	0.09	1	0	1	0	0
.........................................................................................GGATCTCGTAGTCGAGCAGT..............................................................................................................................................	20	0	20	0.05	1	0	0	0	1

AATACGCACGAACGGATACCGACACACACACGCACACACAAACGTACACGCTTATAAATAACTTAATAGTCAACGAGCTTCCCAAGTCCCCTAGAGCATCAGCTCGTCAGAGATGATCTCGAAAGAATGAATAAAGTTAATTTTTGCAGAATTAACCCAAAACAAATATATAAAATAAGATGAATATAAAATTAAAATGTCTACCGTCTCAATAGAGTATCACATCATAGTGGGTGTAGTAAGGCACACCT ************************************************........((((((.(((.((((((((((.((((((...)))))).....)))))))..((((...)))).......((....(((((((((.......)))))))))....))................))).))).)))))).......************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V056 head	M046 female body	M060 embryo
......................................................................................................................................................................................................GTCGACCGTCTTAATAGAGT.................................	20	2	1	1.00	1	1	0	0
..........................................................................................CTAGAGCATCAGCTCGTCAGAGATGATCT....................................................................................................................................	29	0	5	0.20	1	0	0	1
............................................................................................AGAGCATCAGCTCGTCAGAGATGATC.....................................................................................................................................	26	0	6	0.17	1	0	1	0
.................................................................................................ATCAGCTCGTCAGAGATGATCTCGA.................................................................................................................................	25	0	7	0.14	1	0	1	0
.................................................................ATAGTCAACGAGCTTCCCAAGTCCCCT...............................................................................................................................................................	27	0	20	0.10	2	0	2	0
...........................................................................AGCTTCCCAAGTCCCCTAGAGCATC.......................................................................................................................................................	25	0	20	0.10	2	0	2	0
...................................................................................................CAGCTCGTCAGAGATGATCTC...................................................................................................................................	21	0	20	0.05	1	0	0	1
.........................................................................CGAGCTTCCCAAGTCCCCTAGAGCATCAG.....................................................................................................................................................	29	0	20	0.05	1	0	1	0
.....................................................................TCAACGAGCTTCCCAAGTCCCCTA..............................................................................................................................................................	24	0	20	0.05	1	0	0	1
......................................................................CAACGAGCTTCCCAAGTCCC.................................................................................................................................................................	20	0	20	0.05	1	0	1	0
........................................................................ACGAGCTTCCCAAGTCCCCT...............................................................................................................................................................	20	0	20	0.05	1	0	1	0

Species	Coordinate	ID	Alignment
droMoj3	scaffold_6680:24161177-24161427 -	dmo_2602	TTATGCG-TG--CTTGCCTATGGCTGTGTGTGT----GCGT----GTGTGTTTGCATGTGCGAATA----------------TTTA---TTGAATT------------ATCAGTTG---------------------------------CTC-GAAGGGTTCAGGGGATCTCGTAGTCGAGC-AGTCTCTACTAGAGCTTTCTTACTTAT-----TTCAATTAAAA---------------------------------A---------------------------CGTCTTAATTGGGTT-----------------------------------------------------------T------------------------------------------------------TGTTT--A----------TATATTTTATTCT----------------A---------------------------------------CTTA-------TATTTTAATTTTACAGATGGCAGAGTTATCTCATAGTGTAGTATCACCCACATCATTCCGTGTG--GA-----------
droVir3	scaffold_12954:1239767-1239956 +		GAACTTT-TT--TTTAAATTTATTTGA-TGTTT----GAATAAGA---------------------------------------------------------------------------------------------------------------GGGTTCAGGGTATCCCCTATTCGGG-AGCTCTCGACTAAAACC-TCTTACTTGT-----TTTC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTTTTTTTTTTTTACTTTATTTTAAAAACTTATATTGTT-AGC-----------------------------------------------------AAATCTACTGCTAGCTTGTCTATTACTAAGTTTAATTTCTCCCC------TCCTTGTG--AA-----------
droGri2	scaffold_14853:7628482-7628688 +		TCATACA-TA--TATATATATGTATGTGTGTGT----GTGTGTGT----G------AGTATGTGTGTATGCGC------ACATATATA---------------------------------------------------------------------------------GTTGTGTATGTA-TGCATTTGTTTGTTTTC-TCTTGTTTG--------------------------TATAT--------------------------------------------------TTTGTTTAAGGT-----------------------------------------------------------T------------------------------------------------------TTAAC--A----------TT----------------------------TAATTTAATTTCATTACTTTCGTC--------------------------------------ATATAAATAAAAATAAATACATTTTGTTTTTGTTTTTTTTTCTTTTTTTGTT--TT-----------
droWil2	scf2_1100000004943:14246234-14246452 -		GTGTGTG-TG--TGTGTGTGTGCGTGTGTGTGT----GCGT----GTGTGTGTGTTTGTGTGGGTG----------------TGTC---GTGCGCC------------AACAAACATGTGGGAGCTTCTAAATATGAGGTTCAGTAACCTT--------------------------------------------------------------------TTTA----------T-----------------------------------GCCAAACATTATTCTAAAGCTTTTATGTTTCG--------------------------------------------------------------------------------------------TTTTCT-------TTTC------AGTTG--G----------TT------------------------------------------------------------------------------TTTTTTCCTTTTTCGTA------------------------TTTTGTATTCTTTATTTTGAGTTGACAGATTAGCAGAG
dp5	Unknown_group_745:7205-7364 +		TGTGTCC--GTGT--GTGCGTGTGTGTGCGTGT----------------------------GTGTGTTTCTGCTTATTTATTT-------------AATCTCTGTTTT-----TGT---------------------------------TTT-ATTGCGA---------------------------------------------------------------------------CGCA--TTTGGCAACTGGTTATGAA----------------------------------------GT---------------CTCATTTTCGTATT--------------------------------------------------------------------TCTCTTA------------------------------------------------------------------------------------------------------------------------ATTAAAAACTGCACTAATTTTTAATTAGGCTTTTTT------------------CA-----------
droPer2	scaffold_38:54783-54995 +		ATGCTTG-TG--TGTGTGTGTGTGTGTGTGTAC----GTCT----GT--------------GT----------------ATATATATCTTT-----GATTT-------AGCAGTTA-------------------------------------G--------------------------------------------------------------------------------------------CAGAGGATTATAGG----------------------------------------TTCTATATGAAGGTCATCTAA--------T-GGGCAGGAATTGAGTACAGTTGTGTGGTGTTTTTTTTTCGCTAAGAAGGTACAGTACTTTTGTTTTTT-------GTTT------TGTTT--G----------TTTGTTT-TTTTT----------------T---------------------------------------GTTG-------TTTTTTGTTTTTGTAT--------------------------------------------------AT-----------
droAna3	scaffold_13248:4510561-4510659 +		AGCAATC-TT--TTTTG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGTGACCTTT-----CTTACCGCAATGG------------------------------------------------------------ACACACTTTTAATTGGATT---------------TA-------------------------------------------------------------------------------------------------AACTT-------------CTTCATGGGTTTG----------------C---------------------------------------CTTA-------AATTTTGATTTCA-----------------------------------------------GA----TG-----------
droBip1	scf7180000396569:143141-143246 -		TGAGTTG-GG--TTTTCATATTA-----------------------------------------------------------------------------------------------------------------------------------------------------------AAT-GGCCC-----------------T-----TGGACTATAATTC----------TAAGTA-----------------------------CT--------------------------------------------------------------------------------------------------------------------------------------TT------------------------------------------------------------------------------------------------------------------------TCAGATGGCTGAACTCTCGCATAGTGTGGTGTCTCCCACATCCTTCCGTGTC--GA-----------
droKik1	scf7180000301710:245112-245314 -		TGCTGCA-CG--CGTGCCTGCACATGGGA-AATGTAAACAA----AAGTCGTTGTCGGGGTGAAA--------------------------------------------------A---------------------------------TTT-ATT-----------------------------------------------------------------------------GAAATACATGTGTTGAAAAGCTGGGAATATGTTATTGTTAGCCATCATTAGTACATTTTTAAATGTAGT---------------TTTATTTTTGTATG--------------------------------------------------------------------TCTTTT-GATATGTATTTATTT--TGATATCAT----------ATTTT----------------A---------------------------------------CTTA-------CATGTGCATTTTAC----------------------------------------------------AG-----------
droFic1	scf7180000453495:426440-426532 +		GTATGAG-GG--TGTGGGCGTGGGTGTGGGTGT----GTGTGTGA----A------AGTGCGAGTC----------------C----TTTT-----GATGT-------GCCAAATG-------------------------------------------------------------CGAA---------------------------------------------------------------------AGG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CACG-------GGCT---------------------------------------------------TTTGTCATG--GA-----------
droEle1	scf7180000490380:63831-63949 +		TTTGGTG-CC--CGAGCT-------------------------------------------------------------------------------------------------------------GCCAATAT----TAGTAAAATATT--------------------------------------------------CTAC-----CTAA-CAAAAATG---------------------------------TATA---------------------------TTTTTTGTTTG-----------------------------------------------------------------------------------------------------TTTCTT-ATTA--------TA---TAAATATTT----------ATGTT----------------A---------------------------------------CTTA-------TATTTTAAATATTTAGAT--------------------------------------------GG--CA-----------
droRho1	scf7180000776554:84-171 -		ATATTTA-TA--TTAAGTTG---------------------------------------------------------------------------------------------------------------------------------TTTAGCTGAGT-AACGGTATCTAATAGTCGAG--GCACTCCACTATAGCGTTCTCTCTTGT-----TTAAATTAAAA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AC-----------
droBia1	scf7180000302288:34850-35061 +		GGGTATC-T------------------------------------------------------------------------------------------------------------------------------------------------------------------GATAGTCGAG--GCACTCGACTATAGCGTTCTTCCTTGT-----TTTAATTAAAAATTTATAAAACCGAATTCGTTACATGATTGTATTTTTATTA-----------------------CTTCATTCGGTT-----------------------------------------------------------T------------------------------------------------------TACAT--A-----------------------------------------------CGCCTATATTTTCTGTTACTAAAGTAATTTTATTTATATTTTATATTTAATTTTATTATATTTCAAACTTTTCTCTTAGTGCAGCATTCTGCGC---------------AT-----------
droTak1	scf7180000414106:41983-42155 +		TTGTGTG-TG--TGTGCTTGTATCTGTGTGTGT----CTGT----CTGAGT----------------------------GCTC-------------AGAGTTCAGTGG-----T-------------------------------------------------------GTTGAGGTTGGGT-GGT-------------------------------------------------------TTTTGCGAGGGGTTGGGGGCCTCT------------------------------------------------------CGCTTTAATTT-TGGCATGCATTAAGTGCGCTCCTGGGG--GT------------------------------------------------------TGTTT--C----------CCGTTATTATTCT----------------A---------------------------------------CATA-------TATTTTCCTT--------------------------------------------------------TT-----------
droEug1	scf7180000408844:651336-651423 -		ATGGATA-TT--ATTGCAATAATATATTTA--T----AT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TT--------------------------------------------------------------------------------------------------------------------------------------TT------------------------------------------------------------------------------------------------------------------------GTAGATGGCTGAACTATCTCATAGTGTGGTCTCGCCCACCTCGTTTCGGGTG--GA-----------
dm3	chr3L:15897472-15897566 -		TTGGGACTCA--TTCTCATATTA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTTCGAATATTTCTTTC--------------------------------------------------------------------------------------------------------------------------------------TT------------------------------------------------------------------------------------------------------------------------ACAGATGGCCGAACTATCTCATAGTGTGGTGTCGCCCACCTCGTTTCGGGTG--GA-----------
droSim2	3l:15524821-15524887 -		ATATTTC-TT--TC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TT------------------------------------------------------------------------------------------------------------------------ATAGATGGCCGAACTATCTCATAGTGTGGTGTCGCCCACCTCGTTTCGGGTG--GA-----------
droSec2	scaffold_374:213-302 +		AATAGTT-CG--TATTA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGATT--TTT-----TTTTTTTTAACTG------------------------------------------------------------A-------TTGATTTGGGT-----------------------------------------------------------T------------------------------------------------------TACTTCCTTATGTTTT----------GTTTC----------------A---------------------------------------CTTA-------GATTTTAATTTTT-----------------------------------------------------CA-----------
droYak3	v2_chr3L_random_067:5444-5614 +		TGCATAT--ATAC--ATATGTATGTATATGAAT----------------------------GCATA----------------TTTATT---GTTTT------------TTAAATAA---------------------------------TCT-GCTGAGTAACGGGTATCTAATAGTCGGG--GAACTCGACTATAGCGTTCTCTCTTAT-----TAAATTT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCTCTTATT-AAA------------------------------------------------------------------------TTTTCTCTTATTAATTTTTCTCTTATTAAAATTACATTC--TA-----------
droEre2	scaffold_4820:3565048-3565162 -		GGATTTTGAA--GTGGCATACTT--------------------------------------------------------------------------------------------------------CTAAATGT----TTCTGGAGCATT--------------------------------------------------------------------TCTC----------TAAATAT--------------------------------------------------CTGCATTCAAAT-----------------------------------------------------------T------------------------------------------------------TGGAA--A----------TTTATTTTTTTTT----------------A---------------------------------------ATTT-------TTTTTTAATTTTTCCGA----------------------------------------TGTTATA--GT-----------

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droMoj3

TTATGCG-TG--CTTGCCTATGGCTGTGTGTGT----GCGT----GTGTGTTTGCATGTGCGAATA----------------TTTA---TTGAATT------------ATCAGTTG---------------------------------CTC-GAAGGGTTCAGGGGATCTCGTAGTCGAGC-AGTCTCTACTAGAGCTTTCTTACTTAT-----TTCAATTAAAA---------------------------------A---------------------------CGTCTTAATTGGGTT-----------------------------------------------------------T------------------------------------------------------TGTTT--A----------TATATTTTATTCT----------------A---------------------------------------CTTA-------TATTTTAATTTTACAGATGGCAGAGTTATCTCATAGTGTAGTATCACCCACATCATTCCGTGTG--GA-----------	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
..............................................................................................................................................................GTTCAGGGGATCTCGTAGTCGAGC-AGT.......................................................................................................................................................................................................................................................................................................................................................................................................................	27	20	0.20	4	0	0	0	0	0	4
...........................................................................................................................................................................CGTAGTCGAGC-AGTCTCTACTAGAGC...........................................................................................................................................................................................................................................................................................................................................................................................................	26	6	0.17	1	0	0	0	0	1	0
..................................................................................................................................................................AGGGGATCTCGTAGTCGAGC-AGT.......................................................................................................................................................................................................................................................................................................................................................................................................................	23	20	0.15	3	3	0	0	0	0	0
.............................................................................................................................................................................TAGTCGAGC-AGTCTCTACTAGAGCT..........................................................................................................................................................................................................................................................................................................................................................................................................	25	7	0.14	1	0	0	0	0	1	0
........................................................................................................................................................................TCTCGTAGTCGAGC-AGTCTCTA..................................................................................................................................................................................................................................................................................................................................................................................................................	22	11	0.09	1	0	0	0	0	1	0
.....................................................................................................................................................................GGATCTCGTAGTCGAGC-AGT.......................................................................................................................................................................................................................................................................................................................................................................................................................	20	20	0.05	1	1	0	0	0	0	0

droVir3

GAACTTT-TT--TTTAAATTTATTTGA-TGTTT----GAATAAGA---------------------------------------------------------------------------------------------------------------GGGTTCAGGGTATCCCCTATTCGGG-AGCTCTCGACTAAAACC-TCTTACTTGT-----TTTC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTTTTTTTTTTTTACTTTATTTTAAAAACTTATATTGTT-AGC-----------------------------------------------------AAATCTACTGCTAGCTTGTCTATTACTAAGTTTAATTTCTCCCC------TCCTTGTG--AA-----------	Size	Hit Count	Total Norm	Total	M027 Male-body	M028 Head	M047 Female-body	M061 Embryo	SRR060654 Ovary	SRR060655 Testis	SRR060656 Ovary	SRR060657 Testis	SRR060658 Ovary	SRR060659 Testis	SRR060660 Ovary	SRR060661 Embryo	SRR060662 Embryo	SRR060663 Embryo	SRR060664 Male-body	SRR060665 Female-body	SRR060666 Male-body	SRR060667 Female-body	SRR060668 Male-body	SRR060669 Female-body	SRR060670 Testis	SRR060671 Male-body	SRR060672 Female-body	SRR060673 Ovary	SRR060674 Ovary	SRR060675 Ovary	SRR060676 Ovary	SRR060677 Ovary	SRR060678 Testis	SRR060679 Testis	SRR060680 Testis	SRR060681 Testis	SRR060682 Embryo	SRR060683 Testis	SRR060684 Embryo	SRR060685 Embryo	SRR060686 Embryo	SRR060687 Embryo	SRR060688 Ovary	SRR060689 Testis	SRR1106712 embryo_0-2h	SRR1106713 embryo_0-2h	SRR1106714 embryo_2-4h	SRR1106715 embryo_4-6h	SRR1106716 embryo_4-6h	SRR1106717 embryo_6-8h	SRR1106718 embryo_6-8h	SRR1106719 embryo_8-10h	SRR1106720 embryo_8-10h	SRR1106721 embryo_10-12h	SRR1106722 embryo_10-12h	SRR1106723 embryo_12-14h	SRR1106724 embryo_12-14h	SRR1106725 embryo_14-16h	SRR1106726 embryo_14-16h	SRR1106727 larvae	SRR1106728 larvae	SRR1106729 mixed whole adult body	SRR1106730 embryo_16-30h	V047 Embryo	V053 Head	V116 Male-body	GSM1528803 follicle cells
.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTGTCTATTACTAAGTTTAATTTCTCCCC------.......................	29	6	0.67	4	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTGTCTATTACTAAGTTTAATTTCTC................................	26	6	0.33	2	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................................................................................................................................................................................................................................................AACTTATATTGTT-AGC-----------------------------------------------------AAATCTACTGC..............................................................	27	5	0.20	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...........................................................................................................................................................................................................................................................................................................................................................................................................................................................TTTTAAAAACTTATATTGTT-AGC-----------------------------------------------------AAAA.....................................................................	27	5	0.20	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
......................................AATAAGA---------------------------------------------------------------------------------------------------------------GGGTTCAGGGTATCCCC....................................................................................................................................................................................................................................................................................................................................................................................................................................	24	20	0.20	4	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..............................TTT----GAATAAGA---------------------------------------------------------------------------------------------------------------GGGTTCAGGGTATCCCC....................................................................................................................................................................................................................................................................................................................................................................................................................................	28	6	0.17	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...............................................................................................................................................................TTCAGGGTATCCCCTATTCGGG-AGC........................................................................................................................................................................................................................................................................................................................................................................................................................	25	12	0.17	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTGTCTATTACTAAGTTTAATTTCT.................................	25	6	0.17	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...............................TT----GAATAAGA---------------------------------------------------------------------------------------------------------------GGGTTCAGGGTATCCCC....................................................................................................................................................................................................................................................................................................................................................................................................................................	27	8	0.13	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.........................GA-TGTTT----GAATAAGA---------------------------------------------------------------------------------------------------------------GGGTTCAGGG...........................................................................................................................................................................................................................................................................................................................................................................................................................................	25	8	0.13	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...............................TT----GAATAAGA---------------------------------------------------------------------------------------------------------------GGGTTCAGGGTATCC......................................................................................................................................................................................................................................................................................................................................................................................................................................	25	8	0.13	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..................TTTATTTGA-TGTTT----GAATAAGA---------------------------------------------------------------------------------------------------------------.....................................................................................................................................................................................................................................................................................................................................................................................................................................................	22	9	0.11	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
................................................................................................................................................................TCAGGGTATCCCCTATTCGGG-AGCT.......................................................................................................................................................................................................................................................................................................................................................................................................................	25	10	0.10	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...............................TT----GAATAAGA---------------------------------------------------------------------------------------------------------------GGGTTCAGG............................................................................................................................................................................................................................................................................................................................................................................................................................................	19	15	0.07	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................................................................................................................................................................................CGACTAAAACC-TCTTACTTGT-----..........................................................................................................................................................................................................................................................................................................................................................................................	21	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droGri2

TCATACA-TA--TATATATATGTATGTGTGTGT----GTGTGTGT----G------AGTATGTGTGTATGCGC------ACATATATA---------------------------------------------------------------------------------GTTGTGTATGTA-TGCATTTGTTTGTTTTC-TCTTGTTTG--------------------------TATAT--------------------------------------------------TTTGTTTAAGGT-----------------------------------------------------------T------------------------------------------------------TTAAC--A----------TT----------------------------TAATTTAATTTCATTACTTTCGTC--------------------------------------ATATAAATAAAAATAAATACATTTTGTTTTTGTTTTTTTTTCTTTTTTTGTT--TT-----------	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

droWil2

GTGTGTG-TG--TGTGTGTGTGCGTGTGTGTGT----GCGT----GTGTGTGTGTTTGTGTGGGTG----------------TGTC---GTGCGCC------------AACAAACATGTGGGAGCTTCTAAATATGAGGTTCAGTAACCTT--------------------------------------------------------------------TTTA----------T-----------------------------------GCCAAACATTATTCTAAAGCTTTTATGTTTCG--------------------------------------------------------------------------------------------TTTTCT-------TTTC------AGTTG--G----------TT------------------------------------------------------------------------------TTTTTTCCTTTTTCGTA------------------------TTTTGTATTCTTTATTTTGAGTTGACAGATTAGCAGAG	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
....GTG-TG--TGTGTGTGTGCGTGTGTGTG.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	25	20	0.05	1	0	0	0	0	1
.................................................GTGTGTTTGTGTGGGTG----------------T..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	20	0.05	1	0	0	0	0	1

dp5

TGTGTCC--GTGT--GTGCGTGTGTGTGCGTGT----------------------------GTGTGTTTCTGCTTATTTATTT-------------AATCTCTGTTTT-----TGT---------------------------------TTT-ATTGCGA---------------------------------------------------------------------------CGCA--TTTGGCAACTGGTTATGAA----------------------------------------GT---------------CTCATTTTCGTATT--------------------------------------------------------------------TCTCTTA------------------------------------------------------------------------------------------------------------------------ATTAAAAACTGCACTAATTTTTAATTAGGCTTTTTT------------------CA-----------	Size	Hit Count	Total Norm	Total	M022 Male-body	M040 Female-body	M059 Embryo	M062 Head	V043 Embryo	V051 Head	V112 Male-body	SRR902010 Ovary	SRR902011 Testis	SRR902012 CNS imaginal disc
TGTGTCC--GTGT--GTGCGTGTG.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	7	0.14	1	0	0	0	0	0	1	0	0	0	0

droPer2

ATGCTTG-TG--TGTGTGTGTGTGTGTGTGTAC----GTCT----GT--------------GT----------------ATATATATCTTT-----GATTT-------AGCAGTTA-------------------------------------G--------------------------------------------------------------------------------------------CAGAGGATTATAGG----------------------------------------TTCTATATGAAGGTCATCTAA--------T-GGGCAGGAATTGAGTACAGTTGTGTGGTGTTTTTTTTTCGCTAAGAAGGTACAGTACTTTTGTTTTTT-------GTTT------TGTTT--G----------TTTGTTT-TTTTT----------------T---------------------------------------GTTG-------TTTTTTGTTTTTGTAT--------------------------------------------------AT-----------	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
No Reads

droAna3

AGCAATC-TT--TTTTG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGTGACCTTT-----CTTACCGCAATGG------------------------------------------------------------ACACACTTTTAATTGGATT---------------TA-------------------------------------------------------------------------------------------------AACTT-------------CTTCATGGGTTTG----------------C---------------------------------------CTTA-------AATTTTGATTTCA-----------------------------------------------GA----TG-----------	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
.....................................................................................................................................................................................................TGACCTTT-----CTTACCGCAATGG------------------------------------------------------------ACACAC................................................................................................................................................................................................................................................................................................................	27	1	2.00	2	2	0	0	0	0	0
.....................................................................................................................................................................................................TGACCTTT-----CTTACCGCAATGG------------------------------------------------------------ACACACT...............................................................................................................................................................................................................................................................................................................	28	1	2.00	2	2	0	0	0	0	0
.......................................................................................................................................................................................................................................................................................................TTGGATT---------------TA-------------------------------------------------------------------------------------------------AACTT-------------CTTCATGGGTTT...................................................................................................................................................	26	1	1.00	1	0	1	0	0	0	0
..............................................................................................................................................................................................................................G------------------------------------------------------------ACACACTTTTAATTGGATT---------------TA-------------------------------------------------------------------------------------------------AACTT-------------C..............................................................................................................................................................	28	1	1.00	1	0	1	0	0	0	0
...........................................................................................................................................................................................................................................................................................................ATT---------------TA-------------------------------------------------------------------------------------------------AACTT-------------CTTCATGGGTTTG----------------C---------------------------------------CT........................................................................................	26	1	1.00	1	0	1	0	0	0	0
....ATC-TT--TTTTG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGTGACCTTT-----CTTACC.........................................................................................................................................................................................................................................................................................................................................................................................	27	1	1.00	1	0	1	0	0	0	0
...............TG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGTGACCTTT-----CTTACCGCAATGG------------------------------------------------------------AC....................................................................................................................................................................................................................................................................................................................	28	1	1.00	1	1	0	0	0	0	0
....................................................................................................................................................................................................................................................................................................TAATTGGATT---------------TA-------------------------------------------------------------------------------------------------AACTT-------------CTTCATGGGT.....................................................................................................................................................	27	1	1.00	1	0	1	0	0	0	0
........TT--TTTTG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGTGACCTTT-----CTTACCGC.......................................................................................................................................................................................................................................................................................................................................................................................	26	1	1.00	1	0	1	0	0	0	0
...................................................................................................................................................................................................................TTACCGCAATGG------------------------------------------------------------ACACACTTTTAATTGG......................................................................................................................................................................................................................................................................................................	28	1	1.00	1	0	1	0	0	0	0
....................................................................................................................................................................................................................................................................................................TAATTGGATT---------------TA-------------------------------------------------------------------------------------------------AACTT-------------CTTCATGGG......................................................................................................................................................	26	1	1.00	1	1	0	0	0	0	0
....................................................................................................................................................................................................................TACCGCAATGG------------------------------------------------------------ACACACTTTTAATTG.......................................................................................................................................................................................................................................................................................................	26	1	1.00	1	0	1	0	0	0	0
...........................................................................................................................................................................................................TT-----CTTACCGCAATGG------------------------------------------------------------ACACACTTTTAAT.........................................................................................................................................................................................................................................................................................................	28	1	1.00	1	0	1	0	0	0	0
..............................................................................................................................................................................................................................G------------------------------------------------------------ACACACTTTTAATTGGATT---------------TA-------------------------------------------------------------------------------------------------AAC..............................................................................................................................................................................	25	1	1.00	1	1	0	0	0	0	0
.......................................................................................................................................................................................................................................................................................................TTGGATT---------------TA-------------------------------------------------------------------------------------------------AACTT-------------CTTCATGGGT.....................................................................................................................................................	24	1	1.00	1	0	1	0	0	0	0
........TT--TTTTG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGTGACCTTT-----CTTACCGCT......................................................................................................................................................................................................................................................................................................................................................................................	27	1	1.00	1	0	1	0	0	0	0
....................................................................................................................................................................................................................................................................................................TAATTGGATT---------------TA-------------------------------------------------------------------------------------------------AACTT-------------CTTCATGGGTT....................................................................................................................................................	28	1	1.00	1	0	1	0	0	0	0
.....................................................................................................................................................................................................................ACCGCAATGG------------------------------------------------------------ACACACTTTTAATTGG......................................................................................................................................................................................................................................................................................................	26	1	1.00	1	0	1	0	0	0	0
..................................................................................................................................................................................................................................................................................................................................................................................................................................CTT-------------CTTCATGGGTTTG----------------C---------------------------------------CTTA-------AATTT..........................................................................	26	1	1.00	1	0	1	0	0	0	0
................G---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGTGACCTTT-----CTTACCGCAATGG------------------------------------------------------------ACA...................................................................................................................................................................................................................................................................................................................	28	1	1.00	1	1	0	0	0	0	0
.........T--TTTTG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGTGACCTTT-----CTTACCGC.......................................................................................................................................................................................................................................................................................................................................................................................	25	1	1.00	1	1	0	0	0	0	0
....................................................................................................................................................................................................................TACCGCAATGG------------------------------------------------------------ACACACTTTTAATTGG......................................................................................................................................................................................................................................................................................................	27	1	1.00	1	0	1	0	0	0	0
...................................................................................................................................................................................................................................................................................................TTAATTGGATT---------------TA-------------------------------------------------------------------------------------------------AACTT-------------CTTCATGG.......................................................................................................................................................	26	1	1.00	1	1	0	0	0	0	0
............................................................................................................................................................................................................................TGG------------------------------------------------------------ACACACTTTTAATTGGATT---------------TA-------------------------------------------------------------------------------------------------AACT.............................................................................................................................................................................	28	1	1.00	1	0	1	0	0	0	0
.............TTTG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGTGACCTTT-----CTTACCGCAATG...................................................................................................................................................................................................................................................................................................................................................................................	27	1	1.00	1	1	0	0	0	0	0
..........................................................................................................................................................................................................TTT-----CTTACCGCAATGG------------------------------------------------------------ACACACTTT.............................................................................................................................................................................................................................................................................................................	25	1	1.00	1	1	0	0	0	0	0
......................................................................................................................................................................................................GACCTTT-----CTTACCGCAATGG------------------------------------------------------------ACACACTT..............................................................................................................................................................................................................................................................................................................	28	1	1.00	1	1	0	0	0	0	0
..........................................................................................................................................................................................................TTT-----CTTACCGCAATGG------------------------------------------------------------ACACACTTC.............................................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	1	0	0	0	0
...................................................................................................................................................................................................................................................................................................TTAATTGGATT---------------TA-------------------------------------------------------------------------------------------------AACTT-------------CTTCATGGGT.....................................................................................................................................................	28	1	1.00	1	0	1	0	0	0	0
.............TTTG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGTGACCTTT-----CTTACCGCA......................................................................................................................................................................................................................................................................................................................................................................................	24	1	1.00	1	1	0	0	0	0	0
............................................................................................................................................................................................................................TGG------------------------------------------------------------ACACACTTTTAATTGGATT---------------TA-------------------------------------------------------------------------------------------------AA...............................................................................................................................................................................	26	1	1.00	1	0	1	0	0	0	0
..............TTG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGTGACCTTT-----CTTACCGCAATG...................................................................................................................................................................................................................................................................................................................................................................................	26	5	0.20	1	1	0	0	0	0	0
...............TG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGTGACCTTT-----CTTACCGCAATGG------------------------------------------------------------......................................................................................................................................................................................................................................................................................................................	26	5	0.20	1	1	0	0	0	0	0

droBip1

TGAGTTG-GG--TTTTCATATTA-----------------------------------------------------------------------------------------------------------------------------------------------------------AAT-GGCCC-----------------T-----TGGACTATAATTC----------TAAGTA-----------------------------CT--------------------------------------------------------------------------------------------------------------------------------------TT------------------------------------------------------------------------------------------------------------------------TCAGATGGCTGAACTCTCGCATAGTGTGGTGTCTCCCACATCCTTCCGTGTC--GA-----------	Size	Hit Count	Total Norm	Total
No Reads

droKik1

TGCTGCA-CG--CGTGCCTGCACATGGGA-AATGTAAACAA----AAGTCGTTGTCGGGGTGAAA--------------------------------------------------A---------------------------------TTT-ATT-----------------------------------------------------------------------------GAAATACATGTGTTGAAAAGCTGGGAATATGTTATTGTTAGCCATCATTAGTACATTTTTAAATGTAGT---------------TTTATTTTTGTATG--------------------------------------------------------------------TCTTTT-GATATGTATTTATTT--TGATATCAT----------ATTTT----------------A---------------------------------------CTTA-------CATGTGCATTTTAC----------------------------------------------------AG-----------	Size	Hit Count	Total Norm	Total
No Reads

droFic1

GTATGAG-GG--TGTGGGCGTGGGTGTGGGTGT----GTGTGTGA----A------AGTGCGAGTC----------------C----TTTT-----GATGT-------GCCAAATG-------------------------------------------------------------CGAA---------------------------------------------------------------------AGG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CACG-------GGCT---------------------------------------------------TTTGTCATG--GA-----------	Size	Hit Count	Total Norm	Total
No Reads

droEle1

TTTGGTG-CC--CGAGCT-------------------------------------------------------------------------------------------------------------GCCAATAT----TAGTAAAATATT--------------------------------------------------CTAC-----CTAA-CAAAAATG---------------------------------TATA---------------------------TTTTTTGTTTG-----------------------------------------------------------------------------------------------------TTTCTT-ATTA--------TA---TAAATATTT----------ATGTT----------------A---------------------------------------CTTA-------TATTTTAAATATTTAGAT--------------------------------------------GG--CA-----------	Size	Hit Count	Total Norm	Total
No Reads

droRho1

ATATTTA-TA--TTAAGTTG---------------------------------------------------------------------------------------------------------------------------------TTTAGCTGAGT-AACGGTATCTAATAGTCGAG--GCACTCCACTATAGCGTTCTCTCTTGT-----TTAAATTAAAA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AC-----------	Size	Hit Count	Total Norm	Total
No Reads

droBia1

GGGTATC-T------------------------------------------------------------------------------------------------------------------------------------------------------------------GATAGTCGAG--GCACTCGACTATAGCGTTCTTCCTTGT-----TTTAATTAAAAATTTATAAAACCGAATTCGTTACATGATTGTATTTTTATTA-----------------------CTTCATTCGGTT-----------------------------------------------------------T------------------------------------------------------TACAT--A-----------------------------------------------CGCCTATATTTTCTGTTACTAAAGTAATTTTATTTATATTTTATATTTAATTTTATTATATTTCAAACTTTTCTCTTAGTGCAGCATTCTGCGC---------------AT-----------	Size	Hit Count	Total Norm	Total
No Reads

droTak1

TTGTGTG-TG--TGTGCTTGTATCTGTGTGTGT----CTGT----CTGAGT----------------------------GCTC-------------AGAGTTCAGTGG-----T-------------------------------------------------------GTTGAGGTTGGGT-GGT-------------------------------------------------------TTTTGCGAGGGGTTGGGGGCCTCT------------------------------------------------------CGCTTTAATTT-TGGCATGCATTAAGTGCGCTCCTGGGG--GT------------------------------------------------------TGTTT--C----------CCGTTATTATTCT----------------A---------------------------------------CATA-------TATTTTCCTT--------------------------------------------------------TT-----------	Size	Hit Count	Total Norm	Total
No Reads

droEug1

ATGGATA-TT--ATTGCAATAATATATTTA--T----AT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TT--------------------------------------------------------------------------------------------------------------------------------------TT------------------------------------------------------------------------------------------------------------------------GTAGATGGCTGAACTATCTCATAGTGTGGTCTCGCCCACCTCGTTTCGGGTG--GA-----------	Size	Hit Count	Total Norm	Total
No Reads

dm3

TTGGGACTCA--TTCTCATATTA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTTCGAATATTTCTTTC--------------------------------------------------------------------------------------------------------------------------------------TT------------------------------------------------------------------------------------------------------------------------ACAGATGGCCGAACTATCTCATAGTGTGGTGTCGCCCACCTCGTTTCGGGTG--GA-----------

Size

Hit Count

Total Norm

Total

GSM154618
Ovary

GSM154620
Ovary

GSM154621
Ovary

GSM154622
Ovary

GSM180328
Head

GSM180329
Mixed-body

GSM180330
Embryo

GSM180331
Embryo

GSM180332
Embryo

GSM180333
Embryo

GSM180334
Larvae

GSM180335
Disc

GSM180336
Pupae

GSM180337
S2

GSM231091
Ovary

GSM239041
Head

GSM239050
Head

GSM239051
S2

GSM239052
S2

GSM246084
Head

GSM266765
S2

GSM280082
Ovary

GSM280083
Ovary

GSM280084
Ovary

GSM280085
Testis

GSM280086
Ovary

GSM280087
S2-NP

GSM280088
S2-NP

GSM312995
Head

GSM313160
Head

GSM313161
Head

GSM313162
Head

GSM313163
Head

GSM313164
Head

GSM313165
Head

GSM343287
Embryo

GSM379050
Ovary

GSM379051
Ovary

GSM379052
Ovary

GSM379053
Ovary

GSM379054
Ovary

GSM379055
Ovary

GSM379056
Ovary

GSM379057
Ovary

GSM379058
Ovary

GSM379059
Ovary

GSM379060
Ovary

GSM379061
Ovary

GSM379062
Ovary

GSM379063
Ovary

GSM379064
Ovary

GSM379065
Ovary

GSM379066
Ovary

GSM379067
Ovary

GSM424739
S2

GSM424740
S2

GSM424741
S2

GSM467729
Female-body

GSM467730
Female-body

GSM467731
Female-body

M002
CS

M003
Male-body

M004
Male-body

M005
ML-DmD32

M006
ML-DmD32

M029
OSC

M030
OSC

M031
OSC

M032
S2-R+

M033
S2-R+

M034
S2-R+

M035
S2-R+

M036
S2-R+

M037
S2-R+

M038
S2-R+

M039
S2-R+

M048
S2-R+

OSS2
OSS

OSS6
OSS

OSS7
OSS

OSS8
OSS

S1
Head

S10
Embryo

S11
Embryo

S12
Embryo

S13
Embryo

S14
Embryo

S15
S2-GMR

S16
Kc

S17
Larvae

S18
Larvae

S19
Pupae

S2
Head

S20
Pupae

S21
Disc

S22
Head

S23
Female-body

S24
Male-body

S25
Larvae

S26
Larvae

S27
Pupae

S28
Pupae

S29
Head

S3
Male-body

S30
S2-GMR

S31
S2

S32
S2

S33
Kc

S34
Kc

S35
Kc

S4
Female-body

S5
Disc

S6
Embryo

S7
Embryo

S8
S2

S9
Embryo

SRR001337
Head

SRR001338
Head

SRR001339
Head

SRR001340
Head

SRR001341
Head

SRR001342
Head

SRR001343
Head

SRR001344
Head

SRR001345
Head

SRR001346
Head

SRR001347
Head

SRR001348
Head

SRR001349
Head

SRR001664
Head

SRR010951
Ovary

SRR010952
Ovary

SRR010953
Ovary

SRR010954
Ovary

SRR010955
Ovary

SRR010956
Ovary

SRR010957
Ovary

SRR010958
Ovary

SRR010959
Ovary

SRR010960
Ovary

SRR014268
Embryo

SRR014269
Embryo

SRR014270
Embryo

SRR014271
Embryo

SRR014272
Embryo

SRR014273
Ovary

SRR014274
Ovary

SRR014275
Ovary

SRR014276
Ovary

SRR014277
Ovary

SRR014278
Ovary

SRR014279
Ovary

SRR014280
Ovary

SRR014281
Ovary

SRR014282
Ovary

SRR023197
S2

SRR023399
S2

SRR023400
S2

SRR023402
S2

SRR023407
S2

SRR029028
S2

SRR029029
S2

SRR029030
S2

SRR029031
S2

SRR029032
S2

SRR029033
S2

SRR029608
Head

SRR029633
Head

SRR030145
gb3

SRR031692
Head

SRR031693
Head

SRR031694
Head

SRR031696
Head

SRR031697
Head

SRR031698
Head

SRR031699
Head

SRR031700
Head

SRR031701
Head

SRR031702
Head

SRR031703
Head

SRR031704
Head

SRR032092
S2

SRR032093
S2

SRR032094
S2

SRR032095
S2-NP

SRR032096
S2-NP

SRR032152
Head

SRR060643
Testis

SRR060644
Ovary

SRR060645
Testis

SRR060646
Ovary

SRR060647
Ovary

SRR060648
Ovary

SRR060649
Ovary

SRR060650
Testis

SRR060651
Ovary

SRR060652
Testis

SRR060653
Ovary

SRR065151
Ovary

SRR065152
Ovary

SRR065153
Ovary

SRR065154
Ovary

SRR065155
Ovary

SRR065800
Ovary

SRR065801
Ovary

SRR065802
Ovary

SRR065803
Ovary

SRR065804
Ovary

SRR065805
Ovary

SRR065806
Ovary

SRR065807
Ovary

SRR097865
S2-NP

SRR097866
S2-NP

SRR097867
S2-NP

SRR298536
Ovary

SRR298537
Ovary

SRR298711
Ovary

SRR298712
Ovary

SRR317110
Ovary

SRR317111
Ovary

SRR317112
Ovary

SRR317113
Ovary

SRR317114
Ovary

SRR317115
Ovary

SRR317116
Ovary

SRR317117
Ovary

SRR341115
S2

SRR341116
S2

SRR341117
S2

SRR341118
S2

SRR351332
Mixed-body

SRR351333
Mixed-body

T004
OSC

T005
CME-L1

V001
Embryo

V002
Embryo

V003
S2

V006
Female-body

V007
Head

V008
S2

V009
CME-L1

V010
ML-DmD20-C5

V011
Sg4

V012
Male-body

V013
Head

V014
DTT

V015
DreRFHV

V018
Kc167

V019
GM2

V020
S2-R+

V021
ML-DmD21

V022
ML-DmD32

V023
Head

V024
Kc167

V025
S2-R+

V026
1182-2H

V027
ML-DmD21

V028
CME-W1-Cl.8+

V029
ML-DmD9

V030
ML-DmD8

V031
GM2

V032
S1

V033
CME-W1-Cl.8+

V034
ML-DmD16-C3

V035
ML-DmD32

V036
ML-DmD20-C5

V037
S2

V038
S2

V063
Ovary

V0632
Ovary

V064
Ovary

V0642
Ovary

V065
Ovary

V0652
Ovary

V066
Ovary

V0662
Ovary

V067
S2-NP

V073
mbn2

V074
S3

V075
ML-DmBG1-C1

V076
ML-DmBG3-C2

V077
Head

V078
Head

V079
Head

V080
Head

V081
Embryo

V082
Embryo

V083
Male-body

V084
Female-body

V085
CME-W2

V086
Female-body

V088
Ovary

V0882
Ovary

V089
Ovary

V0892
Ovary

V090
Male-body

V091
fGS/OSS

V092
Male-body

V093
Male-body

V094
S2-R+

V095
S2-R+

V096
Ovary

V097
Ovary

V098
Ovary

V125
ML-DmD9

V126
CME-L1

V127
G2

V128
S3

V129
ML-DmBG1-C1

V130
ML-DmBG3-C2

V131
ML-DmD16-C3

V132
ML-DmD32

V133
Sg4

V134
ML-DmD8

V135
CME-W2

V136
Male-body

V137
Head

V138
Male-body

V139
Female-body

V140
Female-body

V141
Female-body

V142
Female-body

V144
OSC

V145
S2

V146
S1

V147
1182-2H

V148
mbn2

GSM1528798
follicle cells

No Reads

droSim2

ATATTTC-TT--TC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TT------------------------------------------------------------------------------------------------------------------------ATAGATGGCCGAACTATCTCATAGTGTGGTGTCGCCCACCTCGTTTCGGGTG--GA-----------

Size

Hit Count

Total Norm

Total

M023
Head

M024
Male-body

M025
Embryo

M053
Female-body

O001
Testis

O002
Head

SRR553485
Ovary

SRR553486
Ovary

SRR553487
Ovary

SRR553488
Ovary

SRR618934
Ovary

V044
Embryo

SRR902008
Ovary

SRR902009
Testis

SRR1275487
Male larvae

SRR1275485
Male prepupae

SRR1275483
Male prepupae

No Reads

droSec2

AATAGTT-CG--TATTA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGATT--TTT-----TTTTTTTTAACTG------------------------------------------------------------A-------TTGATTTGGGT-----------------------------------------------------------T------------------------------------------------------TACTTCCTTATGTTTT----------GTTTC----------------A---------------------------------------CTTA-------GATTTTAATTTTT-----------------------------------------------------CA-----------	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
.........................................................................................................................................................................................................................................................................................................................................................................T------------------------------------------------------TACTTCCTTATGTTTT----------GTTTC----------------A---------------------------------------CT........................................................................................	25	20	0.25	5	5	0	0	0
........................................................................................................................................................................................................................TTAACTG------------------------------------------------------------A-------TTGATTTGGGT-----------------------------------------------------------T------------------------------------------------------TACTTC...........................................................................................................................................................................	26	16	0.13	2	2	0	0	0
..................................................................................................................................................................................................................TTTTTTTTAACTG------------------------------------------------------------A-------TTGATTTGGGT-----------------------------------------------------------........................................................................................................................................................................................................................................	25	12	0.08	1	0	0	1	0
...................................................................................................................................................................................................................TTTTTTTAACTG------------------------------------------------------------A-------TTGATTTGGGT-----------------------------------------------------------........................................................................................................................................................................................................................................	24	13	0.08	1	0	0	1	0
......................................................................................................................................................................................................................TTTTAACTG------------------------------------------------------------A-------TTGATTTGGGT-----------------------------------------------------------T------------------------------------------------------TACT.............................................................................................................................................................................	26	16	0.06	1	1	0	0	0
........................................................................................................................................................................................................................TTAACTG------------------------------------------------------------A-------TTGATTTGGGT-----------------------------------------------------------T------------------------------------------------------TACTT............................................................................................................................................................................	25	16	0.06	1	1	0	0	0
.......................................................................................................................................................................................................................TTTAACTG------------------------------------------------------------A-------TTGATTTGGGT-----------------------------------------------------------T------------------------------------------------------TACTTCC..........................................................................................................................................................................	28	16	0.06	1	1	0	0	0
........................................................................................................................................................................................................................TTAACTG------------------------------------------------------------A-------TTGATTTGGGT-----------------------------------------------------------T------------------------------------------------------TACTTCCT.........................................................................................................................................................................	28	16	0.06	1	1	0	0	0
.............................................................................................................................................................................................................................................................................................................................................................................................................................................TTT----------GTTTC----------------A---------------------------------------CTTA-------GATTTTAATTT....................................................................	24	20	0.05	1	1	0	0	0
..........................................................................................................................................................................................................................AACTG------------------------------------------------------------A-------TTGATTTGGGT-----------------------------------------------------------T------------------------------------------------------TACTTCCTTA.......................................................................................................................................................................	28	20	0.05	1	1	0	0	0
...............................................................................................................................................................................................................................................................................................................................................................................................................................................T----------GTTTC----------------A---------------------------------------CTTA-------GATTTTAATTTTT-----------------------------------------------------.............	24	20	0.05	1	1	0	0	0
..........................................................................................................................................................................................................................................................................................................................................................................................................................................TGTTTT----------GTTTC----------------A---------------------------------------CTTA-------GATTTTAAT......................................................................	25	20	0.05	1	1	0	0	0
.......................................................................................................................................................................................................................................................................................................................................................................................................................................TTATGTTTT----------GTTTC----------------A---------------------------------------CTTA-------GATTT..........................................................................	24	20	0.05	1	1	0	0	0
...................................................................................................................................................................................................................................................................................................TTGATTTGGGT-----------------------------------------------------------T------------------------------------------------------TACTTCCTTATGT....................................................................................................................................................................	25	20	0.05	1	1	0	0	0
...................................................................................................................................................................................................................................................................................................................................................................................................................................TTCCTTATGTTTT----------GTTTC----------------A---------------------------------------CTTA-------GAT............................................................................	26	20	0.05	1	1	0	0	0
................................................................................................................................................................................................................................................................................................................................................................................................................................TACTTCCTTATGTTTT----------GTTTC----------------A---------------------------------------CT........................................................................................	24	20	0.05	1	1	0	0	0
.........................................................................................................................................................................................................................................................................................................................................................................T------------------------------------------------------TACTTCCTTATGTTTT----------GTTTC----------------A---------------------------------------C.........................................................................................	24	20	0.05	1	1	0	0	0
................................................................................................................................................................................................................................................................................................................................................................................................................................TACTTCCTTATGTTTT----------GTTTC----------------A---------------------------------------C.........................................................................................	23	20	0.05	1	1	0	0	0
.........................................................................................................................................................................................................................................................................................................................................................................T------------------------------------------------------TACTTCCTTATGTTTT----------GTTTC----------------A---------------------------------------..........................................................................................	23	20	0.05	1	1	0	0	0
.........................................................................................................................................................................................................................................................................................................................................................................T------------------------------------------------------TACTTCCTTATGTTTT----------GTTTC----------------A---------------------------------------CTTA-------G..............................................................................	28	20	0.05	1	1	0	0	0
................................................................................................................................................................................................................................................................................................................................................................................................................................TACTTCCTTATGTTTT----------GTTTC----------------A---------------------------------------CTTA-------GA.............................................................................	28	20	0.05	1	1	0	0	0

droYak3

TGCATAT--ATAC--ATATGTATGTATATGAAT----------------------------GCATA----------------TTTATT---GTTTT------------TTAAATAA---------------------------------TCT-GCTGAGTAACGGGTATCTAATAGTCGGG--GAACTCGACTATAGCGTTCTCTCTTAT-----TAAATTT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCTCTTATT-AAA------------------------------------------------------------------------TTTTCTCTTATTAATTTTTCTCTTATTAAAATTACATTC--TA-----------	Size	Hit Count	Total Norm	Total	M026 Head	M043 Female-body	M056 Embryo	V046 Embryo	V052 Head	V058 Head	V120 Male-body	SRR1275488 Male larvae	SRR1275486 Male prepupae	SRR1275484 Male prepupae	GSM1528802 follicle cells
.................................................................................................................................................................................CGGG--GAACTCGACTATAGCGT.........................................................................................................................................................................................................................................................................................................................................................................................................	21	20	0.50	10	0	0	0	0	0	0	10	0	0	0	0
...........................................................................................................................................................................................TCGACTATAGCGTTCTCTCTTAT-----T.........................................................................................................................................................................................................................................................................................................................................................................................	24	20	0.10	2	0	2	0	0	0	0	0	0	0	0	0
..........................................................................................................................................................................................CTCGACTATAGCGTTCTCTCTTAT-----T.........................................................................................................................................................................................................................................................................................................................................................................................	25	20	0.10	2	0	1	0	0	0	1	0	0	0	0	0
.......................................................................................................................................................................................GAACTCGACTATAGCGTTCTCTCTTA................................................................................................................................................................................................................................................................................................................................................................................................	26	20	0.05	1	0	0	1	0	0	0	0	0	0	0	0
.............................................................................................................................................................AGTAACGGGTATCTAATAGTCGGG--..........................................................................................................................................................................................................................................................................................................................................................................................................................	24	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
............................................................................................................................................................GAGTAACGGGTATCTAATAGTCGGG--G.........................................................................................................................................................................................................................................................................................................................................................................................................................	26	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0

droEre2

GGATTTTGAA--GTGGCATACTT--------------------------------------------------------------------------------------------------------CTAAATGT----TTCTGGAGCATT--------------------------------------------------------------------TCTC----------TAAATAT--------------------------------------------------CTGCATTCAAAT-----------------------------------------------------------T------------------------------------------------------TGGAA--A----------TTTATTTTTTTTT----------------A---------------------------------------ATTT-------TTTTTTAATTTTTCCGA----------------------------------------TGTTATA--GT-----------	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
No Reads

dmo_2602

scaffold_6680:24161227-24161377 -

Candidate

Unknown

Predicted structure

Flybase annnotation

Repeatable elements

Sense Strand Reads

Anti-sense strand reads

Re-alignment of all predicted orthologs

Re-alignment of all predicted orthologs with sRNA reads

-21.7	-21.6	-21.5