dps_2947

Name	Class	Family	Strand
Hopers2	DNA	hAT-hobo	+
DNAREP1_DM	RC	Helitron	-

##################################################--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TGTCGCAGGTACAGGAGCTCGTAACACGCGAGAAAGAACTCAGAACTCAGGTATGTTATAGTCTATACTTTTGCCCGATACTCAATGAGTATAGATTTATTAGATTTGTGGGGAAAGTAGATGTGTGTAACACCCAAAAGGAAGGGTTTCCGGCCTCATAAGGTATATACATATATTCTTGTTGGTAGTCCGTCTGTCTTGTTTGACGCCAAGTCCTCAGAGACTATAAACGCTAGAGCAACCAAATTTTG ******************************************************************************************************...((...(((................((((........)))))))..))***********************************************************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M040 female body	GSM343916 embryo	SRR902012 CNS imaginal disc	SRR902011 testis	M059 embryo	SRR902010 ovaries
...........................................................................................................................................................................................................TGACGTCAAGTCCTCATGG.............................	19	3	4	3.50	14	14	0	0	0	0	0
.................................................................................................................................ACACCCAAAAGGAAGGGTTTCCGGC.................................................................................................	25	0	1	1.00	1	0	1	0	0	0	0
...............................GAAAGAACTCAGAACTCAGGCC......................................................................................................................................................................................................	22	2	1	1.00	1	0	0	1	0	0	0
............................................................................................................................GTGTAACACCCAAAAGGAAGGGT........................................................................................................	23	0	1	1.00	1	1	0	0	0	0	0
........................................CAGAACTCAGGTATGTTATAG..............................................................................................................................................................................................	21	0	1	1.00	1	1	0	0	0	0	0
........................................................................................................TTTGTGGGGAAAGTAGATGTG..............................................................................................................................	21	0	2	0.50	1	0	1	0	0	0	0
........................................................................................................TTTGTGGGGAAAGTAGAGGTGTGT...........................................................................................................................	24	1	2	0.50	1	0	1	0	0	0	0
..........................................................................................................TGTGGGGAAAGTAGATGTGTGTAA.........................................................................................................................	24	0	2	0.50	1	0	1	0	0	0	0
........................................................................................................TTTGTGGGGAAAGTAGATGTGT.............................................................................................................................	22	0	2	0.50	1	0	1	0	0	0	0
...........................................................................................................................................................................................................................GAGACTATAAACGCTAGAGCAACCA.......	25	0	2	0.50	1	0	0	0	1	0	0
........................................................................................................TTTGTGGTGAAAGTAGATGTGTGTAAAA.......................................................................................................................	28	2	20	0.30	6	6	0	0	0	0	0
...................................................................................................................................................................................................................................AAACGCTAGAGCGAGCAAACT...	21	3	4	0.25	1	1	0	0	0	0	0
...................................................................................................................................................................................TTTTGGTAATCCGTCTGT......................................................	18	2	6	0.17	1	0	1	0	0	0	0
............................................................................................................................................................................................................GACGTCAAGTCCTCATGG.............................	18	3	20	0.10	2	2	0	0	0	0	0
........................................................................................................TTTGTGGGGAAAGTCGATGTGTGT...........................................................................................................................	24	1	11	0.09	1	0	1	0	0	0	0
........................................................................................................TTTGTGGCGAAAGTAGATGTGTGT...........................................................................................................................	24	1	18	0.06	1	0	1	0	0	0	0
........................................................................................................TTTGTGGCGAAAGTAGATGTGTG............................................................................................................................	23	1	18	0.06	1	0	0	0	0	0	1
........................................................................................................TTTGTGGAGAAAGTAGATGTGTG............................................................................................................................	23	1	18	0.06	1	0	0	0	0	1	0
..........................................................................................................TGTGGCGAAAGTAGATGTGTGTA..........................................................................................................................	23	1	19	0.05	1	1	0	0	0	0	0
........................................................................................................TTTGTGGAGAAAGCAGATGTGTGT...........................................................................................................................	24	2	19	0.05	1	0	1	0	0	0	0
.........................................................................................................................................................................................TGGACCGTCTGGCTTGTTT...............................................	19	3	20	0.05	1	1	0	0	0	0	0
........................................................................................................TTTGTGGCGAAAGTAGATGTGC.............................................................................................................................	22	2	20	0.05	1	0	0	0	0	1	0

ACAGCGTCCATGTCCTCGAGCATTGTGCGCTCTTTCTTGAGTCTTGAGTCCATACAATATCAGATATGAAAACGGGCTATGAGTTACTCATATCTAAATAATCTAAACACCCCTTTCATCTACACACATTGTGGGTTTTCCTTCCCAAAGGCCGGAGTATTCCATATATGTATATAAGAACAACCATCAGGCAGACAGAACAAACTGCGGTTCAGGAGTCTCTGATATTTGCGATCTCGTTGGTTTAAAAC ***********************************************************************************************...((...(((................((((........)))))))..))******************************************************************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	GSM444067 head	SRR902010 ovaries	GSM343916 embryo
......................................................................................................................................................................................................................GGAGTCTCTGATATTCGCGAT................	21	1	5	0.20	1	1	0	0
................................................................................................................................................................................................................GGGTCAGGAGTCTCTGATATT......................	21	1	6	0.17	1	0	1	0
................................................................................................................................................................................AGAACAACCCTCAGGCGGG........................................................	19	3	16	0.06	1	0	0	1

Species	Coordinate	ID	Alignment
dp5	XR_group5:580572-580822 -	dps_2947	TGTCGCAGGTACAGGAGCTCGT--------------AACACGCGAGAAAGAACTCAGAACTCAGGTATGTTATAGT---------------------------CTATACTTTTGCCCGATACTCAATGAGTA-------TA--GATTTATTAGATTTGTGGGGAAAGTAGATGTGTGTAACACCCAAAAGGAAGGGTTTCCGGCCTCATAAGGTATATACAT----ATATTCTTGTTGGT--------------------------AGTCCGTCTGT------------C----TTGTTTGACGCCAAGTCCTCAGAGACTATAAACGCTAGAGCAACCAAATTTTG
droPer2	scaffold_67:152808-153058 +		TGTCGCAGGTACAGGAGCTCGT--------------AACACGCGAGAAAGAACTCAGAACTCAGGTATGTTATGGT---------------------------CTATACTTTTGCCCGATACTCAATGAGTA-------TA--GATTTATTAGATTTGTGGGGAAACTAGATGTGTGTAACACCCAAAAGGAAGGGTTTCCGGCCTCATAAGGTATATACAT----ATATTCTTGTTGGT--------------------------AGTCCGTCTGT------------C----TTGTTTGACGCCAAGTCCTCAGAGACTATAAACGCTAGAGCAACCAAATTTTG
droWil2	scf2_1100000004585:3948034-3948263 +		CATAACATACA----------------------------------GAAAGGAATAATTGCACATACCCTTTATAT---------------------------TTTGTTATTATACCCTT---------GCAA-------AAAGGGTATATTAATTTTGGTC-------AGAAGTGTGCAACGCATAGAAGGAAGCATTTACGACCATATAAATTATAT--------ATATTCTTGATCAT---------CAGAGTTCAAATAGCCATGTCCGTCCGT------------C----TGGATCAACGCAAACTCCTCCTAGACCGTAAGAGCTACAGAGTTGAAATTTTG
droVir3	scaffold_13050:2281995-2282256 +		TACCGTAGCTGT------------------------AACACTTTATTGGCAGCATAAAATTTGAAT---------------------------------------ATTTTTACACCCTGAATCCATAAAAAATGGGTA-AAAGGGTATATTGTATTTGTGCAAAATGCAAATATATTTAACAGGCAGAAGGAAGCATCACCGACCCCATAAAGTATAT--------ATATTCTTGATTACCATCAACAGCTGAGTCGATCTAGCAATGTCCGTCTGT------------CCGTATGTATGAACGCAAGGATCTCAGAACCTATAAGAGCTAGAGACTTGA-ATTTTA
droMoj3	scaffold_6680:24717235-24717491 +		AAAAACTT----------TA----------------------------------AAGAATTAAAATATCTA--------------------------AAAGTATTGCTTTTAGACCCTGAACCCATTGAAGATG-----GGAAGGTATAATGGTTTTGTGA-------AAAAGTATGTAACGGGCAGAAGGAGGCGTGGCAGACCTCACAAAGTATATATGT----ATATTCTTGATCAGCACGACGAGTTGAGTCGATATAGCCCTGTCCGTCTGT----CCATCCGTCCGTCCGTATGAGTGCGTCGATCTCAGAAGTTATAAGAGCTAGAGAGCTGAAATTTGG
droGri2	scaffold_15110:22745479-22745740 +		CTTGTAGTATT-------------------------------GAAAATAGCACCT-AAACTCAAATTTATATT------------------------------ACTTTACTATACCCCAAACTCATTAAAAATGGGTAAAAGGGGTATAATGGTTTTGTGC-------AAATTTATGTAACAGGCAGAAGGAAGCATCTCCGACTCCATAAAATATGT--------ATATTCTTGATAAGGGTCAACAGCCGAGTCAATATAGCCTTGTCCGTCCGC--------CCGTCCGTCTGTATGAACACGCAGATCTCAGAGACTATAAGAGCTAGAGACTTCAAGTTTGG
droAna3	scaffold_13337:22826381-22826559 +		-------------------------------------------------------------------------------------------------------------TTATACCCGGTACTCGAAGATTG-------CAAAATTA-------ATCGTGT-------AAATATGTGTAACAGGGAGAAAAAGTCATCTCCGACCCCATAAAGTATAT--------ATATTCTTGATCAGCGTCAACATACGAGTCGATTTAGTTATATCCATCTGT------------------------------GGGTCTCAGAGACTATAAGAGATTGAACTATTAAATTTTG
droBip1	scf7180000396769:439884-440131 +		AAAAAAA---------ACTCAA--------------AAATCGGAAATGACAA---------AATATATCTA--------------------------G-----ATGTTTTTATACCAAGTACTCGTAGAGAA-------CAAGGGTATATTGGTTTAGTGT-------GAATGTATGTAACATAGAGAAAGAATCATCTCCGACCCCATAAAGTATATACATATGTATATTCTCGATCAGCATCGACAGCCGAGTCGATATATCCATGTCCGACCGT--------CGGTCTGTTCGTATG---------AGCTCAGAGACTATAAGAGG-----CTTTAAGATTTTG
droKik1	scf7180000302486:1456000-1456059 +		TGTCTCAGATTCAGGAACTGGT--------------GACACGCGAAAAGGAGCTCAGAACTCAGGTGAGTAG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TA--------------
droFic1	scf7180000451564:136428-136483 -		TGTCACAAATTCAGGAACTTGT--------------GACCCGCGAAAAGGAACTCAGAACTCAGGT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGT
droEle1	scf7180000491238:330425-330645 -		TGTTTTG-------------------------------------------------------------------TTCG-------------------------AAATTTTTATACCCGTTACTCGTAGAGTG-------AATGGGTATATTGTATTCGTTA-------CAAGGTTTGTAACAGGTAGAAGGAAGCGTTTCCGACCCTATAAAGTACAT--------ACATTCTTGATCAGGATCAATAGCCGAGTCGATCTAGCCATGTCCGTCTGT------------CCGTCTGTGTGAATGTCGAGATCTCGGAAACTATATAAGCTAGAGATTTGGGACTTGG
droRho1	scf7180000764587:105-385 +		CAG-----AAACAAGAGCTAAA--------------GATTTGGGATAAATAAAACAGATTCTAGATTT-TCTTGTG--CAGC----------------GC--AAGTTTATTATACCCGTTACTCGTAGAGTA-------AAAGGGTATATTGTATTCGTGC-------AAAAGTATGTAACAGCTAGAAGGAAGCGTTTCCGACCCTATAAAGTATAT--------ATATTTTTGATCAGGGTCACTAGCCGAGTCGATATAGCCATGTCCGTCTGT----CCGTCTGTCTGTCCGTATGAACGCTGAGATCTCGGAAACTATAAAAGCTAGAAGATTGGCATTTTG
droBia1	scf7180000302494:26384-26637 -		TTGC--------AGGGACAACA--------------AATGAATGAAAAAGTATTTGAAGTTCGGATGTAAAAATAT---------------------------GAATAATTATACCCGTTACTCGTAGAGTA-------AAAGGGTATACTAGATTCGTCG-------GAAAGTATATAACAGGTAGAAGGACGCGTTTCCGACCCCATAAAGTATAT--------ATATTCTTGATC------ACTAGCCGAGTCGATCTAGCCATGTCCGTCTGT------------C----CGTATGAACGCTGTGATCTCGGAAACTAACAAAGCTAGAACCGTCAGACTTGG
droTak1	scf7180000415123:7627-7896 -		TGCGACAAATAGTGAGACCCAGAGCTCGCAATCCACAACTCCTA------AGCGTTAGATGAAAAT-------------------------------------ATCTAGTTATACCCGTTACTCGTAGAGTA-------AAAGGGTATATTGTATTCGTGC-------AAAATTATGTAACAGCTAGAAGGAAGCGTTTCCGACTCCATAAAGTATAT--------ATATTCGTGATTAGGGTCACTTGCCGAGTCGATCTAGCCATGTCCGTCTGT------------CTGTCCGTATGAACGCTGAGATTTCGGAAACTACAAAAGCTAGAAGGTTAAGATTTTC
droEug1	scf7180000409581:83761-84044 +		GATG-------CACAAGCTTGT--------------TTCGTGCAAGCAAT---------TTAACGGTTAA----CTCT--A-AACTAGGACTT-TTAAAT---GCATTTTTATACCCGTTACTCGTAGAGTA-------AAAGGGTATACAAGATTCGTTG-------AAAAGTATGTAACAGATAGAAGGAAGCGTTTCTGACCCTATAAAGTATAT--------ATATTCTTGATCAGGATCAATAGCGAATTCGATTGAGCCATGTCCGTCTGTCGGTCCGTCCGTCCGTCCGTATGAACGCTGAGATCTCAGGAACTATATCAGATACAAAATTGAGATTAAG
dm3	chr2R:2085955-2086203 -		CAGAT-----------ACCCGC--------------TACACAGATGGTAGAAATGCGAACGCAAAA--------T---------------------------TTCATTATTATACTCGTTATTCGTAGAGTA-------AAAGGGTATACTAAATTCTTTG-------AAAAGTATGTAACAGGCAGAAGGAAGCGTTTCCGACCATATGAAGTATAT--------ATATTCTTGATCGAGATCAATAGCCGAGTCGATCTGGCCATGTCCGTCTGT------------C----CGTATAAATGTGCAGATCTCAGGAACTATAAAAGCTAGGAGGTTAAAATTCAC
droSim2	2l:23532998-23533244 +		TGTCCCAAAAACTGA-CTT-----------------CACGCATGAAAAATAAATATAAATAAACATATCTG--------------------------AGG---GTGTAATTATATCCGTCACTCCTAGAATA-------AATGGGTATATTAGATTCTATG-------AAAAGTATGTAACAGACAGAAGGAAGCGTTTCCGACTATATAAAGTATAT--------ATATTCTTGATCAGGATCAATAACCAAGTCGATCTAGCCTTGTCCTTCTGT------------C----CGCATGCACGTCGA-ATCTCAGGAACTATAAAAGCTAAA--------------
droSec2	scaffold_10:40684-40931 +		CATAGG---AACAAATGTTTGT--------------AACTCA--AGCGAGGATCCACAGTTGCAGATTATTGCCGT--CAGC----------------AT--CGAGTCATTATATCCGTTACTCTTAGAGTA-------AAAGGGTATACTAGATTCGTTG-------AAAAGTATGTAACAGGCAAAAGGAAGCGTTCCCGACTATATAAAGTATAT--------ATATTCTTGTTCAGGATCAAAAGTTGAGCTGATCTAGCTATGTCC------------------------GTATAAACGTCGAGATCGCAGGAACTATAAAAACTAGA--------------
droYak3	v2_chrUn_4442:246-525 +		ATTG-CGGGCTAAGGAAATTTG--------------AACTGCAGATAAGGGGCATTAAGTTAAGGGTTGTCAAGATCC--A----------------AAC--CTACTAGTTATACCCGTTCCTCGTAGAGTA-------AAAGGGTATACTAGATTCGTTG-------AAAAGTATGTAACAGGCAGAAGGAAGGGTTTCCGACCATATAAAGTATAT--------ATATTCTTGATCAGGACCAATAGCCGAGTCGATATGACCGT--CCGTCTGT--------CTGTCCGTCCGTATGAACGCTGTGATCTCAGGAACTACAAAAGCTAGAAAGTTGAGATTAAG
droEre2	scaffold_4784:3471411-3471644 +		CACGACT-----------TTCT--------------CACACGCCAAAA----CCGAAAACACAAAA------------------CAATGACAAACTGGAA---TCGTCTTTATACCCGTTACTCGTGGAGTA-------AACGGGTATACTAGATTCGTTG-------AAAAGTATGTAACAGGCAGAAGGAAACGTTTCCGGCCATATAAAGTATAT--------ATATTCTTG-----------------AGTCGAACTGGCCATGTCC------------------------GTATGAACGCCTCGATCTCAGGAACTACAAAAGCTAGAATGTTGAGATTAAG

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

dp5

TGTCGCAGGTACAGGAGCTCGT--------------AACACGCGAGAAAGAACTCAGAACTCAGGTATGTTATAGT---------------------------CTATACTTTTGCCCGATACTCAATGAGTA-------TA--GATTTATTAGATTTGTGGGGAAAGTAGATGTGTGTAACACCCAAAAGGAAGGGTTTCCGGCCTCATAAGGTATATACAT----ATATTCTTGTTGGT--------------------------AGTCCGTCTGT------------C----TTGTTTGACGCCAAGTCCTCAGAGACTATAAACGCTAGAGCAACCAAATTTTG	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
...................................................................................................................................................................................ACACCCAAAAGGAAGGGTTTCCGGC...............................................................................................................................................	25	1	1.00	1	0	0	0	0	1	0	0	0	0	0
.............................................GAAAGAACTCAGAACTCAGGCC........................................................................................................................................................................................................................................................................................	22	1	1.00	1	0	0	0	0	0	0	0	0	0	1
..............................................................................................................................................................................GTGTAACACCCAAAAGGAAGGGT......................................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0	0	0	0	0
......................................................CAGAACTCAGGTATGTTATAG................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	1	0	0	0	0	0	0	0	0
..........................................................................................................................................................TTTGTGGGGAAAGTAGATGTG............................................................................................................................................................................	21	2	0.50	1	0	0	0	0	1	0	0	0	0	0
............................................................................................................................................................TGTGGGGAAAGTAGATGTGTGTAA.......................................................................................................................................................................	24	2	0.50	1	0	0	0	0	1	0	0	0	0	0
..........................................................................................................................................................TTTGTGGGGAAAGTAGATGTGT...........................................................................................................................................................................	22	2	0.50	1	0	0	0	0	1	0	0	0	0	0
...........................................................................................................................................................................................................................................................................................................................GAGACTATAAACGCTAGAGCAACCA.......	25	2	0.50	1	0	0	0	0	0	0	0	0	1	0

droPer2

TGTCGCAGGTACAGGAGCTCGT--------------AACACGCGAGAAAGAACTCAGAACTCAGGTATGTTATGGT---------------------------CTATACTTTTGCCCGATACTCAATGAGTA-------TA--GATTTATTAGATTTGTGGGGAAACTAGATGTGTGTAACACCCAAAAGGAAGGGTTTCCGGCCTCATAAGGTATATACAT----ATATTCTTGTTGGT--------------------------AGTCCGTCTGT------------C----TTGTTTGACGCCAAGTCCTCAGAGACTATAAACGCTAGAGCAACCAAATTTTG	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
No Reads

droWil2

CATAACATACA----------------------------------GAAAGGAATAATTGCACATACCCTTTATAT---------------------------TTTGTTATTATACCCTT---------GCAA-------AAAGGGTATATTAATTTTGGTC-------AGAAGTGTGCAACGCATAGAAGGAAGCATTTACGACCATATAAATTATAT--------ATATTCTTGATCAT---------CAGAGTTCAAATAGCCATGTCCGTCCGT------------C----TGGATCAACGCAAACTCCTCCTAGACCGTAAGAGCTACAGAGTTGAAATTTTG	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
...............................................................................................................................................................................................................................................................TCAAATAGCCATGTCCGTCCGT------------C----TG...................................................	25	20	0.25	5	0	0	0	5	0
.........................................................................................................................................................TTTTGGTC-------AGAAGTGTGCAACG.....................................................................................................................................................................	22	20	0.20	4	0	4	0	0	0
.....................................................................................................................................................................................................................................................................................................................TCCTCCTAGACCGTAAGAGCTACAGA............	26	20	0.10	2	0	2	0	0	0
........................................................................................................................................................................AGAAGTGTGCAACGCATAGAAGG............................................................................................................................................................	23	20	0.10	2	0	0	0	2	0
....................................................................................................................................................................................................................................................................TAGCCATGTCCGTCCGT------------C----TGGATC...............................................	24	20	0.10	2	0	0	0	2	0
...................................................................................................................................................TATTAATTTTGGTC-------AGAAGTGTGCAA.......................................................................................................................................................................	26	20	0.10	2	0	0	2	0	0
......................................................................................................................................................................................................................................................................................................................CCTCCTAGACCGTAAGAGCT.................	20	20	0.10	2	2	0	0	0	0
.....................................................................................................................................................TTAATTTTGGTC-------AGAAGTGTG..........................................................................................................................................................................	21	20	0.10	2	0	2	0	0	0
...........................................................................................................................................................................................................................................................................................................................TAGACCGTAAGAGCTACAGAGT..........	22	20	0.05	1	1	0	0	0	0
...................................................................................................................................................................................................................................................................................GT------------C----TGGATCAACGCAAACTC....................................	20	20	0.05	1	0	1	0	0	0
.............................................................................................................................................................................TGTGCAACGCATAGAAGGAAGCATT.....................................................................................................................................................	25	20	0.05	1	0	0	1	0	0
....................................................................................................................................................................................................................................................................TAGCCATGTCCGTCCGT------------C----TGGATCAAC............................................	27	20	0.05	1	0	1	0	0	0
................................................................................................................................................................................................................................................................CAAATAGCCATGTCCGTCCGT------------C----TG...................................................	24	20	0.05	1	0	1	0	0	0
...................................................................................................................................................................................................................................................................ATAGCCATGTCCGTCCGT------------..........................................................	18	20	0.05	1	0	1	0	0	0
.....................................................................................................................TT---------GCAA-------AAAGGGTATATTAAT.................................................................................................................................................................................................	21	20	0.05	1	0	0	0	1	0
................................................................................................................................................................................................................................................................CAAATAGCCATGTCCGTC.........................................................................	18	20	0.05	1	0	0	0	1	0
....................................................................................................................................................................................................................................................................TAGCCATGTCCGTCCGT------------C----TG...................................................	20	20	0.05	1	0	0	0	1	0
..................................................................................................................................................................................................................................................................AATAGCCATGTCCGTCCGT------------C----TG...................................................	22	20	0.05	1	0	0	0	1	0

droVir3

TACCGTAGCTGT------------------------AACACTTTATTGGCAGCATAAAATTTGAAT---------------------------------------ATTTTTACACCCTGAATCCATAAAAAATGGGTA-AAAGGGTATATTGTATTTGTGCAAAATGCAAATATATTTAACAGGCAGAAGGAAGCATCACCGACCCCATAAAGTATAT--------ATATTCTTGATTACCATCAACAGCTGAGTCGATCTAGCAATGTCCGTCTGT------------CCGTATGTATGAACGCAAGGATCTCAGAACCTATAAGAGCTAGAGACTTGA-ATTTTA	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
....................................................................................................................................................................................................................................................................................................TATGTATGAACGCAAGGATCTC.................................	22	20	0.35	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	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	0
....................................................................................................................................................................................................................................................................................................TATGTATGAACGCAAGGATCTCAGAAC............................	27	20	0.25	5	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................................................................................TATGTATGAACGCAAGGATCTCAG...............................	24	20	0.25	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................................................................................................................................ATGTATGAACGCAAGGATCT..................................	20	20	0.15	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.............................................................................................................................................................................................................................................................................................................................ACCTATAAGAGCTAGAGACTTGA-AT....	25	14	0.14	2	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	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
.......................................................................................................................................................................................GCAGAAGGAAGCATCACCGACCC.............................................................................................................................................	23	7	0.14	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
......................................................................................................................................................................................GGCAGAAGGAAGCATCACCGAC...............................................................................................................................................	22	7	0.14	1	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	0	0	0	0
.................................................................................................................................................................................TAACAGGCAGAAGGAAGCATCACCGA................................................................................................................................................	26	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	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
..........................................................................................................................................................................................GAAGGAAGCATCACCGACCCCA...........................................................................................................................................	22	9	0.11	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	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
............................................................................................................................................................................................................................................................................................................AACGCAAGGATCTCAGAACCTATAAG.....................	26	20	0.10	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	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
...........................................................................................................................................................................................................................................................................................................................GAACCTATAAGAGCTAGAGACTTGA-ATT...	28	10	0.10	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...........................................................................................................................................................................................................................................................................................................................GAACCTATAAGAGCTAGAGACTTGA-......	25	20	0.10	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	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
...................................................................................................................................................................................................................................................................................................GTATGTATGAACGCAAGGATCTCA................................	24	20	0.10	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
........................................................................................................................................................................................CAGAAGGAAGCATCACCG.................................................................................................................................................	18	11	0.09	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
..................................................................................................................................................................................AACAGGCAGAAGGAAGCATCAC...................................................................................................................................................	22	17	0.06	1	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	0	0	0	0
...........................................................................................................................................AAAGGGTATATTGTATTTG.............................................................................................................................................................................................	19	20	0.05	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
.............................................................................................................................................................................................................................................................GTCGATCTAGCAATGTCCGTA.........................................................................	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	0	0	0	0	0	0	0	0	0	0	0	0	0	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
................................................................................................................................................GTATATTGTATTTGTGCAAAATGCAAAT...............................................................................................................................................................................	28	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	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
...........................................................................................................................................................................................................................................................................................................................GAACCTATAAGAGCTAGAGACT..........	22	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	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
........................................................................................................................................................................................................................................................................................................................TCAGAACCTATAAGAGCTAGAGA............	23	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	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
.................................................................................................................................................................................................................................................................ATCTAGCAATGTCCGTCTGT------------C.........................................................	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	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
.................................................................................................................................................................................................................................................................................................CCGTATGTATGAACGCAAGGATC...................................	23	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	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
...................................................................................................................................................................................................................................................................................................GTATGTATGAACGCAAGGATCTCAGAA.............................	27	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	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
.....................................................................................................................................................................................................................................................................................................ATGTATGAACGCAAGGATC...................................	19	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	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
............................................................................................................................................................................................................................................................................TCCGTCTGT------------CCGTATGTATGAACG...........................................	24	20	0.05	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
.......................................................................................................................................................................................................................................................................................................................CTCAGAACCTATAAGAGCTAGAGACT..........	26	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	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
...........................................................................................................................................AAAGGGTATATTGTATTTGTG...........................................................................................................................................................................................	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	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
................................................................................................................................................................................................................................................................................TCTGT------------CCGTATGTATGAACGCAAGGA.....................................	26	20	0.05	1	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	0	0	0	0	0	0	0
..................................................................................................................................................................................AACAGGCAGAAGGAAGCATCA....................................................................................................................................................	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	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
......................................................................................................................................................................................................................................................................................................TGTATGAACGCAAGGATCTCAG...............................	22	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	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
..............................................................................................................................................GGGTATATTGTATTTGTGCAAAATGC...................................................................................................................................................................................	26	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	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
................................................................................................................................AAAATGGGTA-AAAGGGTATATTGTATC...............................................................................................................................................................................................	27	20	0.05	1	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	0	0
........................................................................................................................................................................................................................................................................................................TATGAACGCAAGGATCTCAGAACCTAT........................	27	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	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
....................................................................................................................................................................................................................................................................................................................................AGAGCTAGAGACTTGA-AT....	18	20	0.05	1	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	0	0	0
......................................................................................................................................................................................................................................................................................................................TCTCAGAACCTATAAGAGCTA................	21	20	0.05	1	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	0	0
..................................................................................................................................................ATATTGTATTTGTGCAAAATG....................................................................................................................................................................................	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	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

droMoj3

AAAAACTT----------TA----------------------------------AAGAATTAAAATATCTA--------------------------AAAGTATTGCTTTTAGACCCTGAACCCATTGAAGATG-----GGAAGGTATAATGGTTTTGTGA-------AAAAGTATGTAACGGGCAGAAGGAGGCGTGGCAGACCTCACAAAGTATATATGT----ATATTCTTGATCAGCACGACGAGTTGAGTCGATATAGCCCTGTCCGTCTGT----CCATCCGTCCGTCCGTATGAGTGCGTCGATCTCAGAAGTTATAAGAGCTAGAGAGCTGAAATTTGG	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
............................................................................................................................................................................................................................................................................................................................AAGTTATAAGAGCTAGAGAGC..........	21	20	0.30	6	6	0	0	0	0	0
...........................................................................................................................................................................................................................................................................................................................GAAGTTATAAGAGCTAGAGAGCTGAAA.....	27	20	0.10	2	2	0	0	0	0	0
..............................................................................................................................................................................................................................................................TCGATATAGCCCTGTCCGTCTGT----C.................................................................	24	20	0.10	2	0	0	0	0	2	0
.................................................................................................................................................................................TAACGGGCAGAAGGAGGCGTGG....................................................................................................................................................	22	20	0.10	2	0	0	0	0	0	2
.........................................................................................................................................................................................................................................................TTGAGTCGATATAGCCCTGTCCGTCTG.......................................................................	27	14	0.07	1	1	0	0	0	0	0
.............................................................................................................................................................................................................................T----ATATTCTTGATCAGCACGAC.....................................................................................................	21	20	0.05	1	1	0	0	0	0	0
..............................................................................................................................................................TGA-------AAAAGTATGTAACGGGCA.................................................................................................................................................................	21	20	0.05	1	1	0	0	0	0	0
..............................................................................................................................................................TGA-------AAAAGTATGTAACGGGCAG................................................................................................................................................................	22	20	0.05	1	1	0	0	0	0	0
...........................................................................................................................................................................AGTATGTAACGGGCAGAAGGA...........................................................................................................................................................	21	20	0.05	1	1	0	0	0	0	0
...............................................................................................................................................................................TGTAACGGGCAGAAGGAGGCG.......................................................................................................................................................	21	20	0.05	1	1	0	0	0	0	0
.............................................................................................................................................................................................................................................................................CCGTCTGT----CCATCCGTCCGTC.....................................................	21	20	0.05	1	1	0	0	0	0	0
................................................................................................................................................GTATAATGGTTTTGTGA-------AAAAGTATG..........................................................................................................................................................................	26	20	0.05	1	0	0	0	0	0	1
........................................................................................................................................................................................................................................................................................................TATGAGTGCGTCGATCTCAGAAGT...........................	24	20	0.05	1	1	0	0	0	0	0
......................................................................................................................................................TGGTTTTGTGA-------AAAAGTATGTAACGGGC..................................................................................................................................................................	28	20	0.05	1	0	0	0	0	0	1
..................................................................................................................................................ATAATGGTTTTGTGA-------AAAAGT.............................................................................................................................................................................	21	20	0.05	1	1	0	0	0	0	0
...............................................................................................................................................................................................................................................................CGATATAGCCCTGTCCGTCTGT----CC................................................................	24	20	0.05	1	1	0	0	0	0	0

droGri2

CTTGTAGTATT-------------------------------GAAAATAGCACCT-AAACTCAAATTTATATT------------------------------ACTTTACTATACCCCAAACTCATTAAAAATGGGTAAAAGGGGTATAATGGTTTTGTGC-------AAATTTATGTAACAGGCAGAAGGAAGCATCTCCGACTCCATAAAATATGT--------ATATTCTTGATAAGGGTCAACAGCCGAGTCAATATAGCCTTGTCCGTCCGC--------CCGTCCGTCTGTATGAACACGCAGATCTCAGAGACTATAAGAGCTAGAGACTTCAAGTTTGG	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

droAna3

-------------------------------------------------------------------------------------------------------------TTATACCCGGTACTCGAAGATTG-------CAAAATTA-------ATCGTGT-------AAATATGTGTAACAGGGAGAAAAAGTCATCTCCGACCCCATAAAGTATAT--------ATATTCTTGATCAGCGTCAACATACGAGTCGATTTAGTTATATCCATCTGT------------------------------GGGTCTCAGAGACTATAAGAGATTGAACTATTAAATTTTG	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
......................................................................................................................................................................................................................ATAT--------ATATTCTTGATCAGC..........................................................................................................	19	20	0.05	1	0	1	0	0	0	0

droBip1

AAAAAAA---------ACTCAA--------------AAATCGGAAATGACAA---------AATATATCTA--------------------------G-----ATGTTTTTATACCAAGTACTCGTAGAGAA-------CAAGGGTATATTGGTTTAGTGT-------GAATGTATGTAACATAGAGAAAGAATCATCTCCGACCCCATAAAGTATATACATATGTATATTCTCGATCAGCATCGACAGCCGAGTCGATATATCCATGTCCGACCGT--------CGGTCTGTTCGTATG---------AGCTCAGAGACTATAAGAGG-----CTTTAAGATTTTG	Size	Hit Count	Total Norm	Total
No Reads

droKik1

TGTCTCAGATTCAGGAACTGGT--------------GACACGCGAAAAGGAGCTCAGAACTCAGGTGAGTAG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TA--------------	Size	Hit Count	Total Norm	Total
No Reads

droFic1

TGTCACAAATTCAGGAACTTGT--------------GACCCGCGAAAAGGAACTCAGAACTCAGGT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGT	Size	Hit Count	Total Norm	Total
No Reads

droEle1

TGTTTTG-------------------------------------------------------------------TTCG-------------------------AAATTTTTATACCCGTTACTCGTAGAGTG-------AATGGGTATATTGTATTCGTTA-------CAAGGTTTGTAACAGGTAGAAGGAAGCGTTTCCGACCCTATAAAGTACAT--------ACATTCTTGATCAGGATCAATAGCCGAGTCGATCTAGCCATGTCCGTCTGT------------CCGTCTGTGTGAATGTCGAGATCTCGGAAACTATATAAGCTAGAGATTTGGGACTTGG	Size	Hit Count	Total Norm	Total
No Reads

droRho1

CAG-----AAACAAGAGCTAAA--------------GATTTGGGATAAATAAAACAGATTCTAGATTT-TCTTGTG--CAGC----------------GC--AAGTTTATTATACCCGTTACTCGTAGAGTA-------AAAGGGTATATTGTATTCGTGC-------AAAAGTATGTAACAGCTAGAAGGAAGCGTTTCCGACCCTATAAAGTATAT--------ATATTTTTGATCAGGGTCACTAGCCGAGTCGATATAGCCATGTCCGTCTGT----CCGTCTGTCTGTCCGTATGAACGCTGAGATCTCGGAAACTATAAAAGCTAGAAGATTGGCATTTTG	Size	Hit Count	Total Norm	Total
No Reads

droBia1

TTGC--------AGGGACAACA--------------AATGAATGAAAAAGTATTTGAAGTTCGGATGTAAAAATAT---------------------------GAATAATTATACCCGTTACTCGTAGAGTA-------AAAGGGTATACTAGATTCGTCG-------GAAAGTATATAACAGGTAGAAGGACGCGTTTCCGACCCCATAAAGTATAT--------ATATTCTTGATC------ACTAGCCGAGTCGATCTAGCCATGTCCGTCTGT------------C----CGTATGAACGCTGTGATCTCGGAAACTAACAAAGCTAGAACCGTCAGACTTGG	Size	Hit Count	Total Norm	Total
No Reads

droTak1

TGCGACAAATAGTGAGACCCAGAGCTCGCAATCCACAACTCCTA------AGCGTTAGATGAAAAT-------------------------------------ATCTAGTTATACCCGTTACTCGTAGAGTA-------AAAGGGTATATTGTATTCGTGC-------AAAATTATGTAACAGCTAGAAGGAAGCGTTTCCGACTCCATAAAGTATAT--------ATATTCGTGATTAGGGTCACTTGCCGAGTCGATCTAGCCATGTCCGTCTGT------------CTGTCCGTATGAACGCTGAGATTTCGGAAACTACAAAAGCTAGAAGGTTAAGATTTTC	Size	Hit Count	Total Norm	Total
No Reads

droEug1

GATG-------CACAAGCTTGT--------------TTCGTGCAAGCAAT---------TTAACGGTTAA----CTCT--A-AACTAGGACTT-TTAAAT---GCATTTTTATACCCGTTACTCGTAGAGTA-------AAAGGGTATACAAGATTCGTTG-------AAAAGTATGTAACAGATAGAAGGAAGCGTTTCTGACCCTATAAAGTATAT--------ATATTCTTGATCAGGATCAATAGCGAATTCGATTGAGCCATGTCCGTCTGTCGGTCCGTCCGTCCGTCCGTATGAACGCTGAGATCTCAGGAACTATATCAGATACAAAATTGAGATTAAG	Size	Hit Count	Total Norm	Total
No Reads

dm3

CAGAT-----------ACCCGC--------------TACACAGATGGTAGAAATGCGAACGCAAAA--------T---------------------------TTCATTATTATACTCGTTATTCGTAGAGTA-------AAAGGGTATACTAAATTCTTTG-------AAAAGTATGTAACAGGCAGAAGGAAGCGTTTCCGACCATATGAAGTATAT--------ATATTCTTGATCGAGATCAATAGCCGAGTCGATCTGGCCATGTCCGTCTGT------------C----CGTATAAATGTGCAGATCTCAGGAACTATAAAAGCTAGGAGGTTAAAATTCAC	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
........................................................................................................................................................................................................................................TTGATCGAGATCAATAGCCGAGTCGA.........................................................................................	26	1	4.00	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
................................................................................................................................................................................................................TGAAGTATAT--------ATATTCTTGATCGAGA.........................................................................................................	26	1	2.00	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.............................................................................................................................................................................................................................................................................................................................AACTATAAAAGCTAGGAGGTTAA.......	23	1	2.00	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
................................................................................................................................................................................................................TGAAGTATAT--------ATATTCTTGATCGAGAT........................................................................................................	27	1	2.00	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	0	0	0	0	0	0	0	0	0	0	0	0	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................................................................................................................................CAGGAACTATAAAAGCTAGGAGGT..........	24	3	1.33	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................................................................................................CAGATCTCAGGAACTATAAAAGC..................	23	1	1.00	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
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......................................................................................................................................................................................GGCAGAAGGAAGCGTTTC...................................................................................................................................................	18	20	0.10	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................................................................................................CCATGTCCGTCTGT------------C----CGTAT................................................	20	20	0.10	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0
.......................................................................................................................................................................................................................................................................CCATGTCCGTCTGT------------C----CGTA.................................................	19	20	0.10	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
..............................................................................................................................................................................................................................................................TCGATCTGGCCATGTCCGTCTGT------------C----.....................................................	24	20	0.10	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..........................................................................................................................................................................AAGTATGTAACAGGCAGAAGGAAGC........................................................................................................................................................	25	20	0.10	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..............................................................................................................................................................................................................................................................TCGATCTGGCCATGTCCGTCTGT------------C----CGT..................................................	27	12	0.08	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
..................................................................................................................................................................................................CGTTTCCGACCATATGAAGTA....................................................................................................................................	21	15	0.07	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................GTTTCCGACCATATGAAGTA....................................................................................................................................	20	16	0.06	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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

droSim2

TGTCCCAAAAACTGA-CTT-----------------CACGCATGAAAAATAAATATAAATAAACATATCTG--------------------------AGG---GTGTAATTATATCCGTCACTCCTAGAATA-------AATGGGTATATTAGATTCTATG-------AAAAGTATGTAACAGACAGAAGGAAGCGTTTCCGACTATATAAAGTATAT--------ATATTCTTGATCAGGATCAATAACCAAGTCGATCTAGCCTTGTCCTTCTGT------------C----CGCATGCACGTCGA-ATCTCAGGAACTATAAAAGCTAAA--------------	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
........................................................................................................................................................................AAAAGTATGTAACAGACAGAAGGAA..........................................................................................................................................................	25	10	10.20	102	0	0	0	0	0	0	39	41	17	3	2	0	0	0	0	0	0
........................................................................................................................................................................AAAAGTATGTAACAGACAGAAGGA...........................................................................................................................................................	24	10	8.90	89	0	0	0	0	0	0	37	27	17	4	2	0	1	1	0	0	0
.............................................................................................................................................................................TATGTAACAGACAGAAGGAAGCGTT.....................................................................................................................................................	25	9	4.78	43	0	0	0	2	0	0	0	3	1	1	36	0	0	0	0	0	0
.............................................................................................................................................................................TATGTAACAGACAGAAGGAAGCGT......................................................................................................................................................	24	10	3.40	34	0	0	0	1	0	8	0	0	0	0	25	0	0	0	0	0	0
..............................................................................................................TATATCCGTCACTCCTAGAATA-------AATGGG..........................................................................................................................................................................................................	28	2	2.00	4	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0
.............................................................................................................................................................TATG-------AAAAGTATGTAACAGACAGAAGGA...........................................................................................................................................................	28	2	2.00	4	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0
.............................................................................................................................................................................................................................................CAGGATCAATAACCAAGTCGATCTA.....................................................................................	25	2	1.50	3	0	0	0	0	0	0	1	2	0	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................GTATAT--------ATATTCTTGATCAGGATC.......................................................................................................	24	20	1.50	30	0	0	0	0	0	0	0	4	0	0	26	0	0	0	0	0	0
.............................................................................................................................................TGGGTATATTAGATTCTATG-------AAAAGTA............................................................................................................................................................................	27	2	1.00	2	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0
............................................................................................................................................................................................................................................................................................................CACGTCGA-ATCTCAGGAACTATAAAAGC..................	28	2	1.00	2	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0
........................................................................................................................................................................AAAAGTATGTAACAGACAGAAGGAAG.........................................................................................................................................................	26	9	1.00	9	0	0	0	0	0	0	2	2	0	0	5	0	0	0	0	0	0
..................................................................................................................................................................................................................................................................................TGT------------C----CGCATGCACGTCGA-ATCTCAGG..............................	26	2	1.00	2	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0
........................................................................................................................................................................AAAAGTATGTAACAGACAGAAGGAAA.........................................................................................................................................................	26	14	0.86	12	0	0	0	0	0	0	3	0	9	0	0	0	0	0	0	0	0
.............................................................................................................................................................................TATGTAACAGACAGAAGGAAGCG.......................................................................................................................................................	23	11	0.82	9	0	0	0	1	0	0	0	0	0	0	7	0	1	0	0	0	0
....................................................................................................................................................................................................................GTATAT--------ATATTCTTGATCAGGAT........................................................................................................	23	20	0.80	16	0	0	8	0	0	0	0	0	0	0	8	0	0	0	0	0	0
....................................................................................................................................................................................................................GTATAT--------ATATTCTTGATCAGGATCAATA...................................................................................................	28	20	0.75	15	0	0	3	0	0	0	0	0	0	0	12	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................................................................A-ATCTCAGGAACTATAAAAGCTAAA--------------	25	3	0.67	2	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................................................................A-ATCTCAGGAACTATAAAAGCTAA...............	24	3	0.67	2	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0
...........................................................................................................................................................................................................................................................AAGTCGATCTAGCCT.................................................................................	15	2	0.50	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
.......................................................TAAATAAACATATCTG--------------------------AGG---GTGTAAT.............................................................................................................................................................................................................................................	26	2	0.50	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
...........................................................TAAACATATCTG--------------------------AGG---GTGTAATTATA.........................................................................................................................................................................................................................................	26	2	0.50	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
.............................................................................................................................................TGGGTATATTAGATTCTATG-------AAAAGAC............................................................................................................................................................................	27	2	0.50	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
......................................................................................................................................................................................................................................................TAACCAAGTCGATCTAGCCTTGTCC............................................................................	25	2	0.50	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................................................................................ATAACCAAGTCGATCTAGCC..................................................................................	20	2	0.50	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0
.................................................................................................................................................................................................................................................................................................................CGA-ATCTCAGGAACTATAAAAGCTA................	25	2	0.50	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
...........................................................................................................................................................................................................................................................................GTCCTTCTGT------------C----CGCATGCACGTCGA-AT....................................	27	2	0.50	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
............................................................................................................................................................................................................................................TCAGGATCAATAACCAAGTCGAT........................................................................................	23	2	0.50	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................................................................T------------C----CGCATGCACGTCGA-ATCTCAGG..............................	24	2	0.50	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
......................................................................................................................................................................................................................................................TAACCAAGTCGATCTAGC...................................................................................	18	2	0.50	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
.....................................................................................................................................................TTAGATTCTATG-------AAAAGTATGTAACAGA...................................................................................................................................................................	28	2	0.50	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
...............................................................................................................................................................TG-------AAAAGTATGTAACAGACAGAAGGA...........................................................................................................................................................	26	8	0.50	4	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................................................................................TTGTCCTTCTGT------------C----CGCATGCACGTCGA-......................................	27	2	0.50	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
..................................................................................................................................TA-------AATGGGTATATTAGATTCTATG-------TT.................................................................................................................................................................................	26	2	0.50	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
.............................................................................................................................................TGGGTATATTAGATTCTATG-------AAAAG..............................................................................................................................................................................	25	2	0.50	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
.............................................................................................................................................TGGGTATATTAGATTCTATG-------AAAAGTATGTA........................................................................................................................................................................	31	2	0.50	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................................................................TGT------------C----CGCATGCACGTCGA-ATC...................................	21	2	0.50	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
.......................................................TAAATAAACATATCTG--------------------------AGG---GTG.................................................................................................................................................................................................................................................	22	2	0.50	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.....................................................TATAAATAAACATATCTG--------------------------AGG---GTGTAA..............................................................................................................................................................................................................................................	27	2	0.50	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
........................................................................................................................................................................................................................................................ACCAAGTCGATCTAGC...................................................................................	16	2	0.50	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
..................................................................................................................................................................................................................................................TCAATAACCAAGTCGATCTAGCCTT................................................................................	25	2	0.50	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
.....................................................TATAAATAAACATATCTG--------------------------AGG---GTGTAAT.............................................................................................................................................................................................................................................	28	2	0.50	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
..............................................................................................................TATATCCGTCACTCCTAGAATA-------AATGG...........................................................................................................................................................................................................	27	2	0.50	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
...........................................................................................................................................AATGGGTATATTAGATTCTATG-------AAAAGTA............................................................................................................................................................................	29	2	0.50	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................................GT------------C----CGCATGCACGTCGA-ATCTCAGG..............................	25	2	0.50	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
...........................................................TAAACATATCTG--------------------------AGG---GTGTAATTATAA........................................................................................................................................................................................................................................	27	2	0.50	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
........................................................................................................................................................................................................................................................ACCAAGTCGATCTAGCCTTGT..............................................................................	21	2	0.50	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
.....................................................TATAAATAAACATATCTG--------------------------AGG---GTGTA...............................................................................................................................................................................................................................................	26	2	0.50	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
................................................................................................................................................................................................................TAAAGTATAT--------ATATTCTTGATCAGGA.........................................................................................................	26	20	0.50	10	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0
................................................................................................................................................................................................................................................................................................................TCGA-ATCTCAGGAACTATAAAAGC..................	24	2	0.50	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................................................................TGT------------C----CGCATGCACGTCGA-ATCTCAGGA.............................	27	2	0.50	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
...............................................................................................................................................................................................................................................................................TTCTGT------------C----CGCATGCACGTCGA-......................................	21	2	0.50	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................................................................................TTGTCCTTCTGT------------C----CGCATGCACGTCGA-A.....................................	28	2	0.50	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
.................................................................................................................................................................................................................................................................................................C----CGCATGCACGTCGA-ATCTCAGGAAC...........................	26	2	0.50	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
.................................................................................................................................................................................................................................................................................................................CGA-ATCTCAGGAACTATA.......................	18	2	0.50	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
..........................................................................................................................................................................................................................................................................................................TGCACGTCGA-ATCTCAGGAACTATA.......................	25	2	0.50	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
..............................................................................................................TATATCCGTCACTCCTAGAATA-------AATGGGTA........................................................................................................................................................................................................	30	2	0.50	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................................................................A-ATCTCAGGAACTATA.......................	16	20	0.40	8	0	0	0	0	0	0	0	0	0	0	8	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................................................................A-ATCTCAGGAACTATAAAAGCTA................	23	17	0.35	6	0	0	0	0	0	0	0	0	1	0	5	0	0	0	0	0	0
......................................................................................................................................................................................................................ATAT--------ATATTCTTGATCAGGAT........................................................................................................	21	20	0.30	6	0	0	2	0	0	0	0	2	2	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................AAGTATAT--------ATATTCTTGATCAGGAT........................................................................................................	25	20	0.25	5	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................................................................A-ATCTCAGGAACTATAAAAGCT.................	22	17	0.24	4	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0
.................................................................................................................................................................................................................AAAGTATAT--------ATATTCTTGATCAGGA.........................................................................................................	25	20	0.20	4	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0
............................................................................................................................................................................GTATGTAACAGACAGAAGGAA..........................................................................................................................................................	21	12	0.17	2	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0
.............................................................................................................................................................................TATGTAACAGACAGAAGGAAGC........................................................................................................................................................	22	12	0.17	2	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0
.....................................................................................................................................................................................AGACAGAAGGAAGCGTT.....................................................................................................................................................	17	12	0.17	2	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0
..............................................................................................................................................................................ATGTAACAGACAGAAGGAA..........................................................................................................................................................	19	13	0.15	2	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0
.............................................................................................................................................................................TATGTAACAGACAGAAGGAA..........................................................................................................................................................	20	13	0.15	2	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0
................................................................................................................................................................................................................TAAAGTATAT--------ATATTCTTGATCAGG..........................................................................................................	25	20	0.15	3	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................................................................A-ATCTCAGGAACTATAA......................	17	20	0.15	3	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0
.............................................................................................................................................................................TATGTAACAGACAGAAGGA...........................................................................................................................................................	19	14	0.14	2	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0
........................................................................................................................................................................AAAAGTATGTAACAGACAGAAGGAT..........................................................................................................................................................	25	15	0.13	2	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0
...............................................................................................................................................................TG-------AAAAGTATGTAACAGACAGAAGGAA..........................................................................................................................................................	27	8	0.13	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
...............................................................................................................................................................................TGTAACAGACAGAAGGAAGCGTTT....................................................................................................................................................	24	8	0.13	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
..............................................................................................................................................................................ATGTAACAGACAGAAGGAAGCGTTT....................................................................................................................................................	25	8	0.13	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0
.............................................................................................................................................................................TATGTAACAGACAGAAGGAAGCGTTT....................................................................................................................................................	26	8	0.13	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
.............................................................................................................................................................................TATGTAACAGACAGAAGGAAGCGTTTC...................................................................................................................................................	27	8	0.13	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
................................................................................................................................................................G-------AAAAGTATGTAACAGACAGAAGGA...........................................................................................................................................................	25	8	0.13	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
...............................................................................................................................................................................TGTAACAGACAGAAGGAAGCGTTTCCGA................................................................................................................................................	28	8	0.13	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
................................................................................................................................................................G-------AAAAGTATGTAACAGACAGAAGGAAG.........................................................................................................................................................	27	8	0.13	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
.................................................................................................................................................................................TAACAGACAGAAGGAAGCGTTTCCGA................................................................................................................................................	26	9	0.11	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
............................................................................................................................................................................GTATGTAACAGACAGAAGGAAGCGT......................................................................................................................................................	25	10	0.10	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
.................................................................................................................................................................................TAACAGACAGAAGGAAGCGTT.....................................................................................................................................................	21	10	0.10	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
........................................................................................................................................................................................CAGAAGGAAGCGTTTCCGACT..............................................................................................................................................	21	20	0.10	2	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0
................................................................................................................................................................................GTAACAGACAGAAGGAAGCGT......................................................................................................................................................	21	10	0.10	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
..........................................................................................................................................................................AAGTATGTAACAGACAGAAGGAAGC........................................................................................................................................................	25	10	0.10	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................................................................A-ATCTCAGGAACTATAAAAG...................	20	20	0.10	2	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0
.................................................................................................................................................................................TAACAGACAGAAGGAAGCGT......................................................................................................................................................	20	11	0.09	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
........................................................................................................................................................................AAAAGTATGTAACAGACAGAAGG............................................................................................................................................................	23	11	0.09	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
......................................................................................................................................................................................GACAGAAGGAAGCGTTT....................................................................................................................................................	17	11	0.09	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
.....................................................................................................................................................................................AGACAGAAGGAAGCGT......................................................................................................................................................	16	13	0.08	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
....................................................................................................................................................................................CAGACAGAAGGAAGCGT......................................................................................................................................................	17	13	0.08	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
...................................................................................................................................................................................ACAGACAGAAGGAAGCGT......................................................................................................................................................	18	13	0.08	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
......................................................................................................................................................................................GACAGAAGGAAGCGT......................................................................................................................................................	15	14	0.07	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
.......................................................................................................................................................................................................................................................................................................................CTCAGGAACTATAAAAGCTAA...............	21	14	0.07	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
...............................................................................................................................................................................TGTAACAGACAGAAGGA...........................................................................................................................................................	17	14	0.07	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
.................................................................................................................................................................................TAACAGACAGAAGGA...........................................................................................................................................................	15	16	0.06	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
........................................................................................................................................................................AAAAGTATGTAACAGACAGA...............................................................................................................................................................	20	18	0.06	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
.........................................................................................................................................................................................................................................................................................................................CAGGAACTATAAAAGCTAA...............	19	18	0.06	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
.............................................................................................................................................................................TATGTAACAGACAGAAG.............................................................................................................................................................	17	19	0.05	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
........................................................................................................................................................................AAAAGTATGTAACAGACAGAAGGAATA........................................................................................................................................................	27	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
...............................................................................................................................................................................................AAGCGTTTCCGACTA.............................................................................................................................................	15	20	0.05	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................GTATAT--------ATATTCTTGATCAGG..........................................................................................................	21	20	0.05	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................................................TAT--------ATATTCTTGATCAGGATCAA.....................................................................................................	23	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
...............................................................................................................................................................TG-------AAAAGTATGTAACA.....................................................................................................................................................................	16	20	0.05	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
......................................................................................................................................................................................................................ATAT--------ATATTCTTGATCAGGATCAAT....................................................................................................	25	20	0.05	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
.......................................................................................................................................................................................................................TAT--------ATATTCTTGATCAGGATCAATA...................................................................................................	25	20	0.05	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
................................................................................................................................................................................................................TAAAGTATAT--------ATATTCTTGATCAGGAT........................................................................................................	27	20	0.05	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................................TTCCGACTATATAAAGTATAT--------ATA......................................................................................................................	24	20	0.05	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
...........................................................................................................................................................................................AAGGAAGCGTTTCCGA................................................................................................................................................	16	20	0.05	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................................................................A-ATCTCAGGAACTATAAA.....................	18	20	0.05	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
....................................................................................................................................................................................................TTTCCGACTATATAAAGTATAT--------ATATT....................................................................................................................	27	20	0.05	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
......................................................................................................................................................................................................................ATAT--------ATATTCTTGATCAGGATCAA.....................................................................................................	24	20	0.05	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0

droSec2

CATAGG---AACAAATGTTTGT--------------AACTCA--AGCGAGGATCCACAGTTGCAGATTATTGCCGT--CAGC----------------AT--CGAGTCATTATATCCGTTACTCTTAGAGTA-------AAAGGGTATACTAGATTCGTTG-------AAAAGTATGTAACAGGCAAAAGGAAGCGTTCCCGACTATATAAAGTATAT--------ATATTCTTGTTCAGGATCAAAAGTTGAGCTGATCTAGCTATGTCC------------------------GTATAAACGTCGAGATCGCAGGAACTATAAAAACTAGA--------------	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
..........................................................................................................................................................TTCGTTG-------AAAAGTATGTAACAGG...................................................................................................................................................................	23	20	1.40	28	28	0	0	0
..........................................................................................................................................................TTCGTTG-------AAAAGTATGTAACAGGCA.................................................................................................................................................................	25	20	0.75	15	15	0	0	0
......................................................................................................................................................................................................................ATAT--------ATATTCTTGTTCAGGATCAAAA...................................................................................................	26	2	0.50	1	1	0	0	0
....................................................................................................................................................................................................................GTATAT--------ATATTCTTGTTCAGGATCA......................................................................................................	25	5	0.40	2	2	0	0	0
....................................................................................................................................................ACTAGATTCGTTG-------AAAAGTAT...........................................................................................................................................................................	21	20	0.10	2	0	2	0	0
..........................................................................................................................................................TTCGTTG-------AAAAGTATGTAACAGGCAA................................................................................................................................................................	26	13	0.08	1	1	0	0	0
.............................................................................................................................................AGGGTATACTAGATTCGTTG-------AAAAGTA............................................................................................................................................................................	27	20	0.05	1	1	0	0	0
.................................................................................................................................................TATACTAGATTCGTTG-------AAAAG..............................................................................................................................................................................	21	20	0.05	1	0	0	0	1
...........................................................................................................................................AAAGGGTATACTAGATTCGTT...........................................................................................................................................................................................	21	20	0.05	1	0	0	0	1
..............................................................................................................................AGAGTA-------AAAGGGTATACTAGATTCGT............................................................................................................................................................................................	26	20	0.05	1	0	1	0	0
...........................................................................................................................................AAAGGGTATACTAGATTCGT............................................................................................................................................................................................	20	20	0.05	1	0	1	0	0
..................................................................................................................................TA-------AAAGGGTATACTAGATTCGT............................................................................................................................................................................................	22	20	0.05	1	1	0	0	0
..............................................................................................................................AGAGTA-------AAAGGGTATACTAGA.................................................................................................................................................................................................	21	20	0.05	1	1	0	0	0
............................................................................................................................................................CGTTG-------AAAAGTATGTAACAGG...................................................................................................................................................................	21	20	0.05	1	1	0	0	0
...................................................................................................................................................TACTAGATTCGTTG-------AAAAGT.............................................................................................................................................................................	20	20	0.05	1	0	0	0	1

droYak3

ATTG-CGGGCTAAGGAAATTTG--------------AACTGCAGATAAGGGGCATTAAGTTAAGGGTTGTCAAGATCC--A----------------AAC--CTACTAGTTATACCCGTTCCTCGTAGAGTA-------AAAGGGTATACTAGATTCGTTG-------AAAAGTATGTAACAGGCAGAAGGAAGGGTTTCCGACCATATAAAGTATAT--------ATATTCTTGATCAGGACCAATAGCCGAGTCGATATGACCGT--CCGTCTGT--------CTGTCCGTCCGTATGAACGCTGTGATCTCAGGAACTACAAAAGCTAGAAAGTTGAGATTAAG	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
.............................................................................................................................................................................TATGTAACAGGCAGAAGGAAGGGT......................................................................................................................................................	24	20	1.00	20	0	0	19	0	0	0	1	0	0	0	0
............................................................................................................................................................................GTATGTAACAGGCAGAAGGAAGGGT......................................................................................................................................................	25	20	0.30	6	0	2	4	0	0	0	0	0	0	0	0
..............................................................................................................................................................TTG-------AAAAGTATGTAACAGGCAGAAGG............................................................................................................................................................	26	20	0.30	6	0	6	0	0	0	0	0	0	0	0	0
...........................................................................................................................................................................AGTATGTAACAGGCAGAAGGAAGGGT......................................................................................................................................................	26	20	0.30	6	0	0	6	0	0	0	0	0	0	0	0
..................................................................................................................................................................................AACAGGCAGAAGGAAGGGTTTCCGAC...............................................................................................................................................	26	20	0.25	5	0	0	5	0	0	0	0	0	0	0	0
...........................................................................................................................................................................................................................................................................................................................GGAACTACAAAAGCTAGAAAGTTGAGAT....	28	20	0.25	5	0	0	5	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................AGGCAGAAGGAAGGGTTTCCGACCATA...........................................................................................................................................	27	20	0.10	2	0	0	2	0	0	0	0	0	0	0	0
..........................................................................................................................................................................AAGTATGTAACAGGCAGAAGGAAGG........................................................................................................................................................	25	20	0.10	2	0	2	0	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................................................................TTCTTGATCAGGACCAATAGCCGAGT............................................................................................	26	20	0.10	2	2	0	0	0	0	0	0	0	0	0	0
................................................................................................................................................................G-------AAAAGTATGTAACAGGCAGAAGGA...........................................................................................................................................................	25	20	0.10	2	0	2	0	0	0	0	0	0	0	0	0
................................................................................................................................................................................GTAACAGGCAGAAGGAAGGGTTTCCG.................................................................................................................................................	26	20	0.10	2	0	2	0	0	0	0	0	0	0	0	0
..............................................................................................................................................................................................................................................................................................TGTCCGTCCGTATGAACGCTGTGATCTC.................................	28	20	0.10	2	0	2	0	0	0	0	0	0	0	0	0
...................................................................................................................................................................................ACAGGCAGAAGGAAGGGTTTCCGAC...............................................................................................................................................	25	20	0.10	2	0	0	0	2	0	0	0	0	0	0	0
.........................................................................................................................................................................AAAGTATGTAACAGGCAGAAGGAAGGG.......................................................................................................................................................	27	20	0.10	2	0	2	0	0	0	0	0	0	0	0	0
...............................................................................................................................................................................TGTAACAGGCAGAAGGAAGGGG......................................................................................................................................................	22	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
.................................................................................................................................................................................................................................................................................................................................ACAAAAGCTAGAAAGTTGAGATTA..	24	20	0.05	1	0	0	1	0	0	0	0	0	0	0	0
................................................................................................................................................................................................................................................................................................................................TACAAAAGCTAGAAAGTTGAG......	21	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
........................................................................................................................................................................................................................................TTGATCAGGACCAATAGCCGAGTCG..........................................................................................	25	20	0.05	1	0	0	0	0	0	1	0	0	0	0	0
........................................................................................................................................................................................................................................................................CGT--CCGTCTGT--------CTGTCCGTCCGTATG...............................................	26	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
................................................................................................................................................................................................................................................................................................TCCGTCCGTATGAACGCTGTGATCTCAGG..............................	29	20	0.05	1	0	0	1	0	0	0	0	0	0	0	0
..........................................................................................................................................................................................................................................................................T--CCGTCTGT--------CTGTCCGTCCGTATGA..............................................	25	20	0.05	1	0	0	1	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................AGGCAGAAGGAAGGGTTTCCGACC..............................................................................................................................................	24	20	0.05	1	0	0	1	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................................................................................TCCGTATGAACGCTGTGATCTCAG...............................	24	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
................................................................................................................................................................................GTAACAGGCAGAAGGAAGGGTTT....................................................................................................................................................	23	20	0.05	1	0	0	0	1	0	0	0	0	0	0	0
......................................................................................................................................................................................GGCAGAAGGAAGGGTTTCCGACC..............................................................................................................................................	23	20	0.05	1	0	0	0	0	0	0	1	0	0	0	0
..................................................................................................................................................................................................................................................CCAATAGCCGAGTCGATATGACC..................................................................................	23	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................ATTCTTGATCAGGACCAATAGCCGAGT............................................................................................	27	20	0.05	1	1	0	0	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................GCAGAAGGAAGGGTTTCCGACCAT............................................................................................................................................	24	20	0.05	1	0	0	0	0	0	0	1	0	0	0	0
.......................................................................................................................................................................................................................TAT--------ATATTCTTGATCAGGACCAATA...................................................................................................	25	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
......................................................................................................................................................................................................................ATAT--------ATATTCTTGATCAGGACCAA.....................................................................................................	24	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................................................................................................CCGT--CCGTCTGT--------CTGTCCGTCCGTAT................................................	26	20	0.05	1	0	0	0	1	0	0	0	0	0	0	0
........................................................................................................................................................................................................................................................................CGT--CCGTCTGT--------CTGTCCGTCCGT..................................................	23	20	0.05	1	0	0	1	0	0	0	0	0	0	0	0
..................................................................................................................................TA-------AAAGGGTATACTAGATTCGTT...........................................................................................................................................................................................	23	20	0.05	1	0	0	0	0	0	0	1	0	0	0	0
...................................................................................................................................................................................................................................TATTCTTGATCAGGACCAATAGCC................................................................................................	24	20	0.05	1	0	0	0	1	0	0	0	0	0	0	0
.................................................................................................................................................................................TAACAGGCAGAAGGAAGGGTTTCCG.................................................................................................................................................	25	20	0.05	1	0	0	0	0	0	0	1	0	0	0	0
..............................................................................................................................................................................ATGTAACAGGCAGAAGGAAGGGTTTC...................................................................................................................................................	26	20	0.05	1	0	0	1	0	0	0	0	0	0	0	0
......................................................................................................................................................................................................................................TCTTGATCAGGACCAATAGCCGAG.............................................................................................	24	20	0.05	1	0	0	0	1	0	0	0	0	0	0	0

droEre2

CACGACT-----------TTCT--------------CACACGCCAAAA----CCGAAAACACAAAA------------------CAATGACAAACTGGAA---TCGTCTTTATACCCGTTACTCGTGGAGTA-------AACGGGTATACTAGATTCGTTG-------AAAAGTATGTAACAGGCAGAAGGAAACGTTTCCGGCCATATAAAGTATAT--------ATATTCTTG-----------------AGTCGAACTGGCCATGTCC------------------------GTATGAACGCCTCGATCTCAGGAACTACAAAAGCTAGAATGTTGAGATTAAG	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
..........................................................................................................................................................TTCGTTG-------AAAAGTATGTAACAGGCAGA...............................................................................................................................................................	27	20	0.15	3	0	0	0	0	0	0	3
....................................................................................................................................................................................................................................................................TGGCCATGTCC------------------------GTATGAACGCCTCGAT....................................	27	18	0.06	1	1	0	0	0	0	0	0
.......................................................................................................................................................................................................................................................................................................................CTCAGGAACTACAAAAGCTAGAAT............	24	20	0.05	1	0	0	0	0	1	0	0
..........................................................................................................................................................................................................................................................................TGTCC------------------------GTATGAACGCCTCGAT....................................	21	20	0.05	1	0	0	0	0	1	0	0
..............................................................................................................................................................................................................................................................................................................CGCCTCGATCTCAGGAACTAC........................	21	20	0.05	1	1	0	0	0	0	0	0
..................................................................................................................................................ATACTAGATTCGTTG-------AAA................................................................................................................................................................................	18	20	0.05	1	0	0	0	0	0	1	0
............................................................................................................................................................................................................................................................................................................AACGCCTCGATCTCAGGAAC...........................	20	20	0.05	1	0	0	0	1	0	0	0
................................................................................................................................................................G-------AAAAGTATGTAACAGGCAGA...............................................................................................................................................................	21	20	0.05	1	0	0	0	0	1	0	0
.................................................................................................................................................................................TAACAGGCAGAAGGAAACGTTTCC..................................................................................................................................................	24	20	0.05	1	0	0	0	0	0	1	0
......................................................................................................................................................................................GGCAGAAGGAAACGTTTCC..................................................................................................................................................	19	20	0.05	1	0	0	0	0	1	0	0

dps_2947

XR_group5:580622-580772 -

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