dgr_375

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------################################################## GGTTCATCAGCAACTGATACTGATTAGCATTTCGCTGATGCTCGAGGCGCTTATGGTTTGTTAAGTGGGCGACAGACCCTCGAGCGGAGAAGATGTGCGACAGCCAGAGCAAATCGAGCAACGCCAGTTTGTGTGTATAAGGGAATCTGTAGATTGCCAGATTCTCGGCGCTAATCGTTTTGATTCTCGCTTTGATTGCAGAGAGGGCATCCTGGTGGGTTGCGGCAATCCACTGCTGGATATATCGGCAC *****************************************************************.((.(((....(((.....)))....)))))...................************************************************************************************************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V109 male body	M041 female body
...................................................................GGCGACAGACCCTCGAGCGGAGAAGATG............................................................................................................................................................	28	0	1	1.00	1	1	0
.....................................................................................................................................................................................................GTTTAGAGGGCATCCTGGTGGGTTGC............................	26	3	1	1.00	1	1	0
...........................................................................ACCCTCGAGCGGAGAAGATGTGCG........................................................................................................................................................	24	0	1	1.00	1	0	1
...................................................................................................ACAGCCAGAGCAAATCGA......................................................................................................................................	18	0	1	1.00	1	0	1
...................................................................................................................................................................................................................CTGGTGGGTTGCGGCAAT......................	18	0	1	1.00	1	0	1
..............................................................................CTCGAGCGGAGAAGATGTGCG........................................................................................................................................................	21	0	1	1.00	1	1	0
...................................................................................................ACAGCCAGAGCAAATCGAGCAACC................................................................................................................................	24	1	1	1.00	1	1	0
...................................................................................................ACAGCCAGAGCAAATCGAGCA...................................................................................................................................	21	0	1	1.00	1	1	0
.........................................................................................................................................................................................................AGAGGGCATCCTGGTGGGTTGCGGC.........................	25	0	1	1.00	1	1	0
................................................................................................................................................................................................................ATCCTGGTGGGTTGCGGC.........................	18	0	1	1.00	1	1	0
..........................................................................................................................................................................................................GAGGGCATCCTGGTGGGTT..............................	19	0	1	1.00	1	0	1
...................................................................GGCGACAGACCCTCGAGCGGAGAAG...............................................................................................................................................................	25	0	1	1.00	1	1	0
.......................................................................ACAGACCCTCGAGAGGAGAA................................................................................................................................................................	20	1	1	1.00	1	1	0
....................................................................................................................................................................................................................TGGTGGGTTGCGGCAATCC....................	19	0	1	1.00	1	0	1
...................................................TATGGTTTGTTAAGTGGGCGACAGA...............................................................................................................................................................................	25	0	1	1.00	1	0	1
............................................................................................ATGTGCGACAGCCAGAGCAAATCGA......................................................................................................................................	25	0	1	1.00	1	0	1
..............................................................................................GTGCGACAGCCAGAGCAAATCG.......................................................................................................................................	22	0	1	1.00	1	1	0
.........................................................................................................................................................................................................AGAGGGCATCCTGGTGGGTTGCG...........................	23	0	1	1.00	1	1	0
.........................................................................AGACCCTCGAGCGGAGAAGATGTGCG........................................................................................................................................................	26	0	1	1.00	1	1	0

Species	Coordinate	ID	Alignment
droGri2	scaffold_15121:202647-202897 +	dgr_375	GGTTCATC------AGCAACTGATACTGAT------------------------T------------AGCATT-TCG-----------CTGATGCTCGAGGCGCTTATGG-------TTT-------GTTAAGTGGGC--------G----ACAGACCCTCG------AGCG------------------GAGAAGATGTGCGACAGCCAGAGCAAATCGAGCAACGCCAGTTTGTGTGTA-------------TAAGGGAATCTGTAGATTGC---CAGATTCTCG--------------------------------GCGC---TAATCGTT----------TTG--ATT-CT-CG---------CTTTGATTGCAGAGAGGGCATCCTGGTGGGTTGCGGCAATCCACTGCTGGATATATCG-GCAC
droVir3	scaffold_13049:22491196-22491464 +	dvi_20970	GGTTCATC------GACAACTGATACTGAT------------------------TAGAA--TTTGAG----GCGGCACTCG-------TTGATGTTGGAT-------TGCGGTTTCAATT-------GCTAATTAGGC--------G----GCAAGCCCTCG------ACTG------------------GAAAGCATGTGCGACACTAAGAGCAACTCAAGCAACGTGAGGTTGCGTATCG--CTTAGGCGCTTAAGGGAACTTCTC-------------CA-------------TT----A-A--------TT--TGAGGC---TAATCGCT------TG--TCG--CTT-CT-CT---------TTTCATTTGCAGAGAAGGCATCCTAGTCGGATGCGGTAATCCGTTGCTGGATATATCG-GCGA
droMoj3	scaffold_6680:17098807-17099048 +		GGTTCATC------GGCAAATGATACTGAA------------------------TA-----TT----AACATT-AAAGCG-GCAGGCGTTGATATTGGAC-------T-CGGTTTCAATT-------G---------CTAGTTAACG----ACAAGCCCTCG------ACTA------------------GACAACATGAGCAAC---------AA---AAGCAACGCGAGGTTGCGTATCT--ATAGGGCG--------------------------CATCAT------------------CAA---------C-TGTAGCC---TAATTCTT-------T--TGA--ATT-CG-AT----------TTTATTTGCAGAGAAGGCATCCTGGTAGGATGTGGAAATCCCCTGCTGGACATTTCG-GCAC
droWil2	scf2_1100000004511:5275689-5275990 +		GGTTCATC------GCCAACTGATAATTGTGTGTGGCTGGCTGGGTCGTCGTTAGGTAG--TTCTGA----ATGGTCATTG-------TTGATTTTGATG-------TGA-------ATC-------GCCAATTGAAAGCGTTAGTA-GAGACAAGCCCTTGTCATCGAGCGGAGGCAGCAAAATTGTAGCACAAAATGAGCACA---AGC---AG---CAACAATGTTAGGTTGTTTTTCCTGGTCCGGCGGATA--AG----------------------AT------------TT----A---------AAA--TGAAACTAAAATTGA------------CCG--CTT-CT-TT----------TTTATTTGCAGAGAAGGTATCCTAGTCGGTTGCGGCAATCCGTTGCTGGATATTTCA-GCAA
dp5	XR_group6:4378211-4378481 -	dps_3036	GGTTCATCGTGATCGCCAAGCGATTGTGGTGCT--------------------AA---G--C-----AGCGTCGTCGTTG-----------AAGTTGAAT-------TGA-------ATTGCTAATTGCTAATTGGGCGCATTAGCG----ACAGGCCCTCA------AGCA------------------GGAAGCATGTGCGATCGG------AG---CAGTAACGATAGGTGGGCGGT-GTGGTGTGGCGGGGA--GGGATGTGTC---GA--GCTGATTCC------------------GGA---------G--TGAAAC---TAATCTTT----------TTG--ATT-CT-AT------------CCAATACAGAGAAGGCATCCTGGTTGGATGCGGCAATCCACTGCTGGACATTTCC-GCCA
droPer2	scaffold_9:2667392-2667662 -	dpe_2172	GGTTCATCGTGATCGCCAAGCGATTGTGGTGCT--------------------AA---G--C-----AGCGTCGTCGTTG-----------AAGTTGAAT-------TGA-------ATTGCTAATTGCTAATTGGGCGCATTAGCG----ACAGGCCCTCA------AGTA------------------GGAAGCATGTGCGATCGG------AG---CAGTAACGATAGGTGGGCGGT-GTGGTGTGGCGGGGA--GGGATGTGTC---GA--GCTGATTCC------------------GGA---------G--TGAAAC---TAATCTTT----------TTG--ATT-CT-AT------------CCAATACAGAGAAGGCATCCTGGTTGGATGCGGCAATCCACTGCTGGACATTTCC-GCCA
droAna3	scaffold_13337:4131146-4131404 +		GGTTCATC------GCCAGCTGATTGCACT------------------------CCCAG--CGCTGT----CGGGTGGCT-----------CTGCTGAAT-------GGA-------ATC-------GTTAATTGGGCACATTAGCTTCAGTCAGGCCCTCA------GGCG------------------AGCAACATGTGTGACCGCAACGGCAG---CAGCAACGTTAGGTTCTGGAC-----------GAAGAATCGAAG---------------------------------TTCTCA----TTTCGATGGT--C-TTTTCATAATCCGT----------TTG--ATT-CT-GT----------CTTCCCTGCAGAGAAGGTATCCTTGTGGGATGTGGCAATCCGCTGTTGGACATCTCC-GCCA
droBip1	scf7180000395450:264756-265014 +		GGTTCATC------GCCAGCTGATTGCAGT------------------------CCCAG--CGCTGT----CGGTTGACT-----------CTGCTGAAT-------GGA-------ATC-------GTTAATTGGGCATATTAGCTTTAGTCTGGCCCTCA------GCCG------------------AGCAACATGTGTGACCGCAACGGCAG---CAGCAACGTTAGGTTCTCTATC----------------------------------------CAACCACGATGATCGTTTTTA----TT--GATGAT--C-TCCTACTAATCCCT---------TTTG--ATT-TT-GT-------------TTCTGCAGAGAAGGTATCCTTGTGGGATGTGGCAACCCGCTGCTGGACATCTCC-GCCA
droKik1	scf7180000302272:668370-668619 -		GGTTCATC------GCCAGCTGATTGCGCT------------------------GAAAGCGCGCTGG----CTGTACTCG-----------ATGCTGAAT-------GGA-------ATC-------GTTAATTGGGCGCATTAGCG----TCAGGCCCTCA------GAAG------------------AGAAACATGTGCGACCG---------------CAACGTTAGGTCTGGGGC----------------------------T---GG---AATCTACTCG---------TTCACT----TTTAGAGGAT--AATGCTAATAATG-------------------TT-TT-CTGTGTTTCCGTTTTCCCCACAGAGAAGGCATCCTGGTGGGCTGCGGCAATCCGCTGCTGGACATCTCA-GCCA
droFic1	scf7180000454048:722983-723234 +		GGTTCATC------GCCAGCTGATTGCGCC------------------------GAAAG--CTCTGA----CCGCACTCG-----------ATGTTGAAT-------GGA-------ATC-------GTTAATTGGGCGCATTAGCA----TCGGGCCCTCA------GACG------------------AGAAACATGTGCGATCGTATC---AG---CAGCAACGTTAGGTTCGGGGC----------------------------CTCTG------TACACCCA---------TCTAAATTAAC---AGAGAT--AATGCTAGTAATTTAT----------ATA---TA-TT-CT------------TCTCCTCAGAGAAGGAATCCTGGTCGGTTGCGGCAATCCGCTGCTGGACATCTCC-GCCG
droEle1	scf7180000491255:1413329-1413585 -		GGTTCATC------GCCAGCTGATTGCTCT------------------------GAAAG--CTCTTG----CTGTTCTCAA----------AAGATGAAT-------GGA-------ATC-------GTCAATTGGGCGCATTAGCA----TCAGGCCCTCA------GGCG------------------AGCAACATGTGCGATCGTATC---AG---CAGCAACGTTAGGTTCGGCTT----------------------------TCCTA--TCTACCTACCCA---------TTGAAA----TCGAGGAGAT--AATGCTTATAATTCGT----------ATG--ATT-TA-CT------------CTACCGCAGAGAAGGAATCCTGGTGGGATGCGGCAATCCGCTGCTGGACATCTCC-GCCG
droRho1	scf7180000779739:1489-1538 +		G--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGGGAGTTCTAATGGGCTTTGGCAATCCCCTGCTGGACATCACCTGCAC
droBia1	scf7180000302193:2255169-2255423 -		GGTTCATC------GCCTGCTGATTGCGCT------------------------GAAAG--CTCTTG----CTGTGCTCG-----------ATGTTGGAC-------GGA-------ATC-------GTTAATTGGGCGCATTAGCA----TCAGGCCCTCA------GACG------------------AGCAACATGTGCGATCGTATC---AG---CAGCAACGTTAGGTTCGGGGC----------------------------TTCTACA--CATAAACCTA---------CTAAAA----TAGGGGAAAT--AACACTAATAGCTCCT----------ACG--ATT-TT-C-------------CTTTCGCAGAGAAGGAATCCTGGTGGGCTGCGGCAACCCGCTGCTGGACATCTCC-GCCG
droTak1	scf7180000415706:67648-67891 -		GGTTCATC------GCCAGCTGATTGCGCC------------------------GAAAG--CTCTTG----CTGTACTCG-----------ATGTTGAAT-------GGA-------ATC-------CGCAATTGGGCGCATTAGCA----TCAGACCCTCA------GGCG------------------AGCAACATGTGCGATCGT---------------AACGTTAGGTTCGGGCA----------------------------CTCTACACCTATA--CT-A-----GCCATCGAAA----TAAGGGAGAT--AAGACTAATA-----------------TA--ATT-TTTAT------------TTCCCACAGAGAAGGAATCCTGGTGGGTTGCGGCAATCCGCTGCTGGACATCTCC-GCCG
droEug1	scf7180000409711:6102501-6102746 -		GGTTCATC------GCATGCTGATTGCGCT------------------------GAAAG--CTCTTT----ACGTACTTG-----------GTGTTGAAT-------GGA-------ACC-------GTTAATTGGGCGCATTAGCG----TCAGGCCCTCA------GGCG------------------AGTAACATGTGCGATCGTATC---AA---TAGCAACGTTAGGTGGGGATT----------------------------TTCGACGTTTATATACCCA-------------------------AGAT--AAATATAAGAATTCCT----------CTA--ATT-TT-GT------------TCACTGCAGAGAAGGAATCCTAGTGGGTTGTGGCAATCCACTTCTGGACATCTCC-GCCG
dm3	chr3L:13014608-13014847 -		GGTTCATCG----CGCCAGCTGATTGCGCT-----------------------TAAAAG--CTCTGG----TTGAACGCA-----------ATGTTGACT-------GGT-------ATC-------GTTAATTGGGCGCATTAGCT----AGAGGCCCTCA------GACG------------------AGCAACATGTGCGATCG------------------CGTCAGGTTTGGGGC----------------------------TACTGC---TATGTACTTA---------GCGAA--------------------ACTAATAATCCAAATAATATATTTT----TT-TT-TT------------GTTCCACAGAGAAGGAATCCTGGTCGGATGCGGCAACCCGCTGCTGGACATCTCC-GCCG
droSim2	3l:12705063-12705307 -	dsi_7533	GGTTCATC------GCCAGCTGATTGCGCT-----------------------TAAAAG--CTCTGG----CTGAACGCG-----------ATGTTGAAT-------GTT-------ATC-------GTTAATTGAGCGCATTAGCT----TGAGGCCCTCA------GACG------------------AGCAACATGTGCGACCG------------------CGTCAGGTTTGGGAC----------------------------TACTGC---TATATACTTA---------GCGAAA----CAGTGAAGAT--AGCACTATTAATCCAA----------ATA--TTTTTT-TT------------GTTCCACAGAGAAGGAATCCTGGTCGGATGCGGCAACCCGCTGCTGGACATCTCC-GCCG
droSec2	scaffold_0:5186188-5186426 -	dse_435	GGTTCATC------GCCAGCTGATTGCGCT-----------------------TAAAAG--CTCTGG----CTGAACGCG-----------ATGTTGAAT-------GGT-------ATC-------GTTAATTGAGCGCATTAGCT----TGAGGCCCTCA------GACG------------------AGCAACATGTGCGACCG------------------CGTCAGGTTTGGGAC----------------------------TACTGC---TATATACTTA---------GCGAAA----CAGTG---------CACTACTAATCCAA----------ATATTTTT-TT-TT------------GTTCCACAGAGAAGGAATCCTGGTCGGATGCGGCAACCCGCTGCTGGACATCTCC-GCCG
droYak3	3L:13093662-13093920 -		GGTTCATC------GCCAGCTGATTGCGCT------------------------GAAAG--CTCTGA----CTGAACACCA-------GTATTGTTGAGT-------GGC-------ATT-------GTTAATTGATCGCATTAGCA----TCGGGCCCTCA------GACG------------------AGCAACATGTACGATCGTATC---AG---CAGTAACATTAGGTTTGGGGC----------------------------AACTGC---TATGTACTCA---------TCGAAA----CAGAGAAGAT--AGCATCAATAATCCAA----------ATG--ATT-TT-CT------------GTTCCACAGAGAAGGAATTCTGGTCGGATGCGGCAACCCGCTGCTAGACATCTCC-GCCG
droEre2	scaffold_4784:13022182-13022436 -		AGTTCATC------GCCAGCTGATTGCGCT------------------------GAAAG--CTCTGG----CTGAACACG-----------ATGTTTAGA-------GGC-------ATC-------GTTAATTGGGCGCATTAGCA----TCAGTCCCTCA------GACG------------------AGCAACATGTGCGATCCTATA---AG---CAGTAGCATTAGGTTTGGGGC----------------------------TATTAC---TATATACTCA---------TCGAAA----CAGAGAAGAT--AGCACTAATAATCCAA----------ATG--ATT-TT-CT------------GTTTCACAGAGAAGGAACCCTGGTCGGATGCGGCAACCCGCTGCTGGACATCTCC-GCCG

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droGri2

GGTTCATC------AGCAACTGATACTGAT------------------------T------------AGCATT-TCG-----------CTGATGCTCGAGGCGCTTATGG-------TTT-------GTTAAGTGGGC--------G----ACAGACCCTCG------AGCG------------------GAGAAGATGTGCGACAGCCAGAGCAAATCGAGCAACGCCAGTTTGTGTGTA-------------TAAGGGAATCTGTAGATTGC---CAGATTCTCG--------------------------------GCGC---TAATCGTT----------TTG--ATT-CT-CG---------CTTTGATTGCAGAGAGGGCATCCTGGTGGGTTGCGGCAATCCACTGCTGGATATATCG-GCAC	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
.......................................................................................................................................GGC--------G----ACAGACCCTCG------AGCG------------------GAGAAGATG.......................................................................................................................................................................................................................................	28	1	1.00	1	0	1
...........................................................................................................................................................ACCCTCG------AGCG------------------GAGAAGATGTGCG...................................................................................................................................................................................................................................	24	1	1.00	1	1	0
...........................................................................................................................................................................................................ACAGCCAGAGCAAATCGA.................................................................................................................................................................................................................	18	1	1.00	1	1	0
.....................................................................................................................................................................................................................................................................................................................................................................................................CTGGTGGGTTGCGGCAAT.......................	18	1	1.00	1	1	0
..............................................................................................................................................................CTCG------AGCG------------------GAGAAGATGTGCG...................................................................................................................................................................................................................................	21	1	1.00	1	0	1
...........................................................................................................................................................................................................ACAGCCAGAGCAAATCGAGCAACC...........................................................................................................................................................................................................	24	1	1.00	1	0	1
...........................................................................................................................................................................................................ACAGCCAGAGCAAATCGAGCA..............................................................................................................................................................................................................	21	1	1.00	1	0	1
...........................................................................................................................................................................................................................................................................................................................................................................................AGAGGGCATCCTGGTGGGTTGCGGC..........................	25	1	1.00	1	0	1
..................................................................................................................................................................................................................................................................................................................................................................................................ATCCTGGTGGGTTGCGGC..........................	18	1	1.00	1	0	1
............................................................................................................................................................................................................................................................................................................................................................................................GAGGGCATCCTGGTGGGTT...............................	19	1	1.00	1	1	0
.......................................................................................................................................GGC--------G----ACAGACCCTCG------AGCG------------------GAGAAG..........................................................................................................................................................................................................................................	25	1	1.00	1	0	1
......................................................................................................................................................................................................................................................................................................................................................................................................TGGTGGGTTGCGGCAATCC.....................	19	1	1.00	1	1	0
.........................................................................................................TATGG-------TTT-------GTTAAGTGGGC--------G----ACAGA..................................................................................................................................................................................................................................................................................	25	1	1.00	1	1	0
....................................................................................................................................................................................................ATGTGCGACAGCCAGAGCAAATCGA.................................................................................................................................................................................................................	25	1	1.00	1	1	0
......................................................................................................................................................................................................GTGCGACAGCCAGAGCAAATCG..................................................................................................................................................................................................................	22	1	1.00	1	0	1
...........................................................................................................................................................................................................................................................................................................................................................................................AGAGGGCATCCTGGTGGGTTGCG............................	23	1	1.00	1	0	1
.........................................................................................................................................................AGACCCTCG------AGCG------------------GAGAAGATGTGCG...................................................................................................................................................................................................................................	26	1	1.00	1	0	1

droVir3

GGTTCATC------GACAACTGATACTGAT------------------------TAGAA--TTTGAG----GCGGCACTCG-------TTGATGTTGGAT-------TGCGGTTTCAATT-------GCTAATTAGGC--------G----GCAAGCCCTCG------ACTG------------------GAAAGCATGTGCGACACTAAGAGCAACTCAAGCAACGTGAGGTTGCGTATCG--CTTAGGCGCTTAAGGGAACTTCTC-------------CA-------------TT----A-A--------TT--TGAGGC---TAATCGCT------TG--TCG--CTT-CT-CT---------TTTCATTTGCAGAGAAGGCATCCTAGTCGGATGCGGTAATCCGTTGCTGGATATATCG-GCGA	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
.................................................................................................................................................................................................................................................................................................................................................................................................CATCCTAGTCGGATGCGGTAATCCGTT..................	27	1	2.00	2	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	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
...............................................................................................................................................................................................................................................................................................................................................................................................................GCGGTAATCCGTTGCTGGA............	19	1	1.00	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.................................................................................................................................................................G------ACTG------------------GAAAGCATGTGCGAC.................................................................................................................................................................................................................................	20	1	1.00	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
..............................................................................................................................................................CTCG------ACTG------------------GAAAGCATGTGC....................................................................................................................................................................................................................................	20	1	1.00	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
..................................................................................................................................................................................................GCATGTGCGACACTAAGAGCAACT....................................................................................................................................................................................................................	24	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	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
..................................................................................................................................AATTAGGC--------G----GCAAGCCCTCG------ACTG------------------................................................................................................................................................................................................................................................	24	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	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
....................................................................................................................................................................................................ATGTGCGACACTAAGAGCAAC.....................................................................................................................................................................................................................	21	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	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
..........................................................................................................................................................................................................GACACTAAGAGCAACTCAA.................................................................................................................................................................................................................	19	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	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
..........................................................................................................................................................AGCCCTCG------ACTG------------------GAAAGCATGTGCGACA................................................................................................................................................................................................................................	28	1	1.00	1	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
...........................................................................................................................................................................................................ACACTAAGAGCAACTCAAG................................................................................................................................................................................................................	19	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	1	0
.............................................................................CTCG-------TTGATGTTGGAT-------TGC................................................................................................................................................................................................................................................................................................................................	19	2	1.00	2	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
........................................................................................................................................................................................................................................................................................................................................................................................................................CGTTGCTGGATATATCG-GC..	19	1	1.00	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................................................................................TTAGGCGCTTAAGGGAACTTCT...................................................................................................................................................................	22	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droMoj3

GGTTCATC------GGCAAATGATACTGAA------------------------TA-----TT----AACATT-AAAGCG-GCAGGCGTTGATATTGGAC-------T-CGGTTTCAATT-------G---------CTAGTTAACG----ACAAGCCCTCG------ACTA------------------GACAACATGAGCAAC---------AA---AAGCAACGCGAGGTTGCGTATCT--ATAGGGCG--------------------------CATCAT------------------CAA---------C-TGTAGCC---TAATTCTT-------T--TGA--ATT-CG-AT----------TTTATTTGCAGAGAAGGCATCCTGGTAGGATGTGGAAATCCCCTGCTGGACATTTCG-GCAC	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
..............................................................................................................................................................CTCG------ACTA------------------GACAACATGAGC....................................................................................................................................................................................................................................	20	1	1.00	1	0	0	0	0	1	0
...................................................................................................................................................................................................................................................................................................................................................................................................TCCTGGTAGGATGTGGAAATCCCCTGCT...............	28	1	1.00	1	1	0	0	0	0	0

droWil2

GGTTCATC------GCCAACTGATAATTGTGTGTGGCTGGCTGGGTCGTCGTTAGGTAG--TTCTGA----ATGGTCATTG-------TTGATTTTGATG-------TGA-------ATC-------GCCAATTGAAAGCGTTAGTA-GAGACAAGCCCTTGTCATCGAGCGGAGGCAGCAAAATTGTAGCACAAAATGAGCACA---AGC---AG---CAACAATGTTAGGTTGTTTTTCCTGGTCCGGCGGATA--AG----------------------AT------------TT----A---------AAA--TGAAACTAAAATTGA------------CCG--CTT-CT-TT----------TTTATTTGCAGAGAAGGTATCCTAGTCGGTTGCGGCAATCCGTTGCTGGATATTTCA-GCAA	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
...........................................................................................................................................................................................................CA---AGC---AG---CAACAATGTTAG.......................................................................................................................................................................................................	19	1	1.00	1	0	0	0	0	1
..................................................................................................................................AATTGAAAGCGTTAGTA-GA........................................................................................................................................................................................................................................................................................	19	1	1.00	1	0	0	0	1	0
..............................................CGTCGTTAGGTAG--TTCTGA----ATG....................................................................................................................................................................................................................................................................................................................................................................	22	1	1.00	1	0	0	1	0	0
..............................................................................................TTGATG-------TGA-------ATC-------GCCAATTGAAAGC..................................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	0	0	1	0
..........................................................................................................................................................................................GTAGCACAAAATGAGCACA---AGC---AG---C..................................................................................................................................................................................................................	25	1	1.00	1	1	0	0	0	0
......................................................................................................................................................GACAAGCCCTTGTCATCGAGCGGAGGC.............................................................................................................................................................................................................................................................	27	1	1.00	1	0	0	1	0	0

dp5

GGTTCATCGTGATCGCCAAGCGATTGTGGTGCT--------------------AA---G--C-----AGCGTCGTCGTTG-----------AAGTTGAAT-------TGA-------ATTGCTAATTGCTAATTGGGCGCATTAGCG----ACAGGCCCTCA------AGCA------------------GGAAGCATGTGCGATCGG------AG---CAGTAACGATAGGTGGGCGGT-GTGGTGTGGCGGGGA--GGGATGTGTC---GA--GCTGATTCC------------------GGA---------G--TGAAAC---TAATCTTT----------TTG--ATT-CT-AT------------CCAATACAGAGAAGGCATCCTGGTTGGATGCGGCAATCCACTGCTGGACATTTCC-GCCA	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
.................................................................................................................................................................................................................................................GTGGTGTGGCGGGGA--GGG.........................................................................................................................................................................	18	1	14.00	14	0	9	0	0	0	0	5	0	0	0
...........................................................................................................................................................................................................................................GCGGT-GTGGTGTGGCGGG................................................................................................................................................................................	18	1	5.00	5	0	0	0	0	0	2	3	0	0	0
...............................................................................................................................................................................................................................................T-GTGGTGTGGCGGGGA--GGG.........................................................................................................................................................................	19	1	3.00	3	0	2	0	0	0	0	1	0	0	0
.................................................................................................................................................................................................................................................GTGGTGTGGCGGGGA--GGGA........................................................................................................................................................................	19	1	2.00	2	0	1	0	0	0	0	1	0	0	0
..................................................................................................................................AATTGGGCGCATTAGCG----ACA....................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0	0	0	0	0
............................................................................................................................................ATTAGCG----ACAGGCCCTCA------AGC...................................................................................................................................................................................................................................................................	21	1	1.00	1	0	1	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................................................................................................................................................................................ATCCTGGTTGGATGCGGC..........................	18	1	1.00	1	0	1	0	0	0	0	0	0	0	0
..........................................................................................................................................................................................................GATCGG------AG---CAGTAACGATAGA......................................................................................................................................................................................................	21	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.........................................................................................................................................................................GCA------------------GGAAGCATGTGCGATCGG------AG---...................................................................................................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0	0	0	0	0
........................................................................CGTCGTTG-----------AAGTTGAAT-------TG.................................................................................................................................................................................................................................................................................................................................	19	1	1.00	1	0	1	0	0	0	0	0	0	0	0
...............................................................................................................................................................................................................................................T-GTGGTGTGGCGGGGA--GGGA........................................................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................................................................GTGGGCGGT-GTGGTGTGGCGGGG...............................................................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................................................................GTGGGCGGT-GTGGTGTGGC...................................................................................................................................................................................	19	1	1.00	1	0	0	0	0	0	1	0	0	0	0
...........................................................................................................................................................................................................................................GCGGT-GTGGTGTGGCGGGG...............................................................................................................................................................................	19	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.................................................................................................................................................................A------AGCA------------------GGAAGCATGTGCGATCGG------AG---C..................................................................................................................................................................................................................	26	1	1.00	1	0	0	0	0	0	1	0	0	0	0
.........................................................................................................................................................................................................................................................................................................................................................................................................................ACTGCTGGACATTTCC-GCC.	19	1	1.00	1	0	0	0	1	0	0	0	0	0	0
.......................................................................................................................................................................................................................................GTGGGCGGT-GTGGTGTGGCG..................................................................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0	0	0	0	0

droPer2

GGTTCATCGTGATCGCCAAGCGATTGTGGTGCT--------------------AA---G--C-----AGCGTCGTCGTTG-----------AAGTTGAAT-------TGA-------ATTGCTAATTGCTAATTGGGCGCATTAGCG----ACAGGCCCTCA------AGTA------------------GGAAGCATGTGCGATCGG------AG---CAGTAACGATAGGTGGGCGGT-GTGGTGTGGCGGGGA--GGGATGTGTC---GA--GCTGATTCC------------------GGA---------G--TGAAAC---TAATCTTT----------TTG--ATT-CT-AT------------CCAATACAGAGAAGGCATCCTGGTTGGATGCGGCAATCCACTGCTGGACATTTCC-GCCA	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
.................................................................................................................................................................................................................................................GTGGTGTGGCGGGGA--GGG.........................................................................................................................................................................	18	2	6.50	13	0	1	0	0	1	11
.................................................................................................................................................................................................................................................GTGGTGTGGCGGGGA--GGGA........................................................................................................................................................................	19	1	4.00	4	0	0	0	0	0	4
....................................................................................................................................................................................................................................................................................................................................................................................................CCTGGTTGGATGCGGCAATC......................	20	1	2.00	2	2	0	0	0	0	0
.......................................................................................................................................................................................................................................GTGGGCGGT-GTGGTGTGGCG..................................................................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0
..............................................................................................................................................................................................................GG------AG---CAGTAACGATAGGTGGGC.................................................................................................................................................................................................	22	1	1.00	1	0	0	0	0	0	1
...........................................................................................................................................................................................................................................GCGGT-GTGGTGTGGCGGG................................................................................................................................................................................	18	1	1.00	1	0	0	0	1	0	0
.......................................................................................................................................................................................................................................GTGGGCGGT-GTGGTGTGGC...................................................................................................................................................................................	19	1	1.00	1	0	0	0	0	0	1
......................................................................................................................................................................................................................................................................................................................................................................................................TGGTTGGATGCGGCAATCCACTGCTGG.............	27	1	1.00	1	0	1	0	0	0	0
.................................................................................................................................................................................................AGCATGTGCGATCGG------AG---CAGTAACG...........................................................................................................................................................................................................	25	1	1.00	1	0	1	0	0	0	0
.........................................................................................................................................................................................................................................................................................................................................................................................................TTGGATGCGGCAATCCACTGCTGGA............	25	1	1.00	1	0	1	0	0	0	0

droAna3

GGTTCATC------GCCAGCTGATTGCACT------------------------CCCAG--CGCTGT----CGGGTGGCT-----------CTGCTGAAT-------GGA-------ATC-------GTTAATTGGGCACATTAGCTTCAGTCAGGCCCTCA------GGCG------------------AGCAACATGTGTGACCGCAACGGCAG---CAGCAACGTTAGGTTCTGGAC-----------GAAGAATCGAAG---------------------------------TTCTCA----TTTCGATGGT--C-TTTTCATAATCCGT----------TTG--ATT-CT-GT----------CTTCCCTGCAGAGAAGGTATCCTTGTGGGATGTGGCAATCCGCTGTTGGACATCTCC-GCCA	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
..........................................................................................................................................................................................................................................................................................................................................................................................................GGGATGTGGCAATCCGCTGTTGGAC...........	25	1	2.00	2	0	2	0	0	0	0
............................................................................................................................................................................................................................................................................................................................................................................................................GATGTGGCAATCCGCTGT................	18	1	1.00	1	1	0	0	0	0	0
.........................................................................................................................................................................................................................................................................................................................................................................................AGAGAAGGTATCCTTGTGGGA................................	21	1	1.00	1	1	0	0	0	0	0
.......................................................................................................................................................................................................................................................................................................................................AATCCGT----------TTG--ATT-CT-GT----------CTTCCCTG......................................................	25	1	1.00	1	1	0	0	0	0	0
....................................................................................................................................................................................................................................................................................................................................................................................................................AATCCGCTGTTGGACATCTCC-GC..	23	1	1.00	1	0	1	0	0	0	0
.................................................................................................................................................................................................AACATGTGTGACCGCAACGGC........................................................................................................................................................................................................................	21	1	1.00	1	0	0	1	0	0	0
..................................................................................................................................................................................................ACATGTGTGACCGCAACGGC........................................................................................................................................................................................................................	20	1	1.00	1	0	0	1	0	0	0
..................................................................................................................................................................................................................................................................................................................................................................................................ATCCTTGTGGGATGTGGCAATCC.....................	23	1	1.00	1	0	1	0	0	0	0
...............................................................................................................................................................................................GCAACATGTGTGACCGCAACGGC........................................................................................................................................................................................................................	23	1	1.00	1	1	0	0	0	0	0

droBip1

GGTTCATC------GCCAGCTGATTGCAGT------------------------CCCAG--CGCTGT----CGGTTGACT-----------CTGCTGAAT-------GGA-------ATC-------GTTAATTGGGCATATTAGCTTTAGTCTGGCCCTCA------GCCG------------------AGCAACATGTGTGACCGCAACGGCAG---CAGCAACGTTAGGTTCTCTATC----------------------------------------CAACCACGATGATCGTTTTTA----TT--GATGAT--C-TCCTACTAATCCCT---------TTTG--ATT-TT-GT-------------TTCTGCAGAGAAGGTATCCTTGTGGGATGTGGCAACCCGCTGCTGGACATCTCC-GCCA	Size	Hit Count	Total Norm	Total
No Reads

droKik1

GGTTCATC------GCCAGCTGATTGCGCT------------------------GAAAGCGCGCTGG----CTGTACTCG-----------ATGCTGAAT-------GGA-------ATC-------GTTAATTGGGCGCATTAGCG----TCAGGCCCTCA------GAAG------------------AGAAACATGTGCGACCG---------------CAACGTTAGGTCTGGGGC----------------------------T---GG---AATCTACTCG---------TTCACT----TTTAGAGGAT--AATGCTAATAATG-------------------TT-TT-CTGTGTTTCCGTTTTCCCCACAGAGAAGGCATCCTGGTGGGCTGCGGCAATCCGCTGCTGGACATCTCA-GCCA	Size	Hit Count	Total Norm	Total
No Reads

droFic1

GGTTCATC------GCCAGCTGATTGCGCC------------------------GAAAG--CTCTGA----CCGCACTCG-----------ATGTTGAAT-------GGA-------ATC-------GTTAATTGGGCGCATTAGCA----TCGGGCCCTCA------GACG------------------AGAAACATGTGCGATCGTATC---AG---CAGCAACGTTAGGTTCGGGGC----------------------------CTCTG------TACACCCA---------TCTAAATTAAC---AGAGAT--AATGCTAGTAATTTAT----------ATA---TA-TT-CT------------TCTCCTCAGAGAAGGAATCCTGGTCGGTTGCGGCAATCCGCTGCTGGACATCTCC-GCCG	Size	Hit Count	Total Norm	Total
No Reads

droEle1

GGTTCATC------GCCAGCTGATTGCTCT------------------------GAAAG--CTCTTG----CTGTTCTCAA----------AAGATGAAT-------GGA-------ATC-------GTCAATTGGGCGCATTAGCA----TCAGGCCCTCA------GGCG------------------AGCAACATGTGCGATCGTATC---AG---CAGCAACGTTAGGTTCGGCTT----------------------------TCCTA--TCTACCTACCCA---------TTGAAA----TCGAGGAGAT--AATGCTTATAATTCGT----------ATG--ATT-TA-CT------------CTACCGCAGAGAAGGAATCCTGGTGGGATGCGGCAATCCGCTGCTGGACATCTCC-GCCG	Size	Hit Count	Total Norm	Total
No Reads

droRho1

G--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGGGAGTTCTAATGGGCTTTGGCAATCCCCTGCTGGACATCACCTGCAC	Size	Hit Count	Total Norm	Total
No Reads

droBia1

GGTTCATC------GCCTGCTGATTGCGCT------------------------GAAAG--CTCTTG----CTGTGCTCG-----------ATGTTGGAC-------GGA-------ATC-------GTTAATTGGGCGCATTAGCA----TCAGGCCCTCA------GACG------------------AGCAACATGTGCGATCGTATC---AG---CAGCAACGTTAGGTTCGGGGC----------------------------TTCTACA--CATAAACCTA---------CTAAAA----TAGGGGAAAT--AACACTAATAGCTCCT----------ACG--ATT-TT-C-------------CTTTCGCAGAGAAGGAATCCTGGTGGGCTGCGGCAACCCGCTGCTGGACATCTCC-GCCG	Size	Hit Count	Total Norm	Total
No Reads

droTak1

GGTTCATC------GCCAGCTGATTGCGCC------------------------GAAAG--CTCTTG----CTGTACTCG-----------ATGTTGAAT-------GGA-------ATC-------CGCAATTGGGCGCATTAGCA----TCAGACCCTCA------GGCG------------------AGCAACATGTGCGATCGT---------------AACGTTAGGTTCGGGCA----------------------------CTCTACACCTATA--CT-A-----GCCATCGAAA----TAAGGGAGAT--AAGACTAATA-----------------TA--ATT-TTTAT------------TTCCCACAGAGAAGGAATCCTGGTGGGTTGCGGCAATCCGCTGCTGGACATCTCC-GCCG	Size	Hit Count	Total Norm	Total
No Reads

droEug1

GGTTCATC------GCATGCTGATTGCGCT------------------------GAAAG--CTCTTT----ACGTACTTG-----------GTGTTGAAT-------GGA-------ACC-------GTTAATTGGGCGCATTAGCG----TCAGGCCCTCA------GGCG------------------AGTAACATGTGCGATCGTATC---AA---TAGCAACGTTAGGTGGGGATT----------------------------TTCGACGTTTATATACCCA-------------------------AGAT--AAATATAAGAATTCCT----------CTA--ATT-TT-GT------------TCACTGCAGAGAAGGAATCCTAGTGGGTTGTGGCAATCCACTTCTGGACATCTCC-GCCG	Size	Hit Count	Total Norm	Total
No Reads

dm3

GGTTCATCG----CGCCAGCTGATTGCGCT-----------------------TAAAAG--CTCTGG----TTGAACGCA-----------ATGTTGACT-------GGT-------ATC-------GTTAATTGGGCGCATTAGCT----AGAGGCCCTCA------GACG------------------AGCAACATGTGCGATCG------------------CGTCAGGTTTGGGGC----------------------------TACTGC---TATGTACTTA---------GCGAA--------------------ACTAATAATCCAAATAATATATTTT----TT-TT-TT------------GTTCCACAGAGAAGGAATCCTGGTCGGATGCGGCAACCCGCTGCTGGACATCTCC-GCCG	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
............................................................................................................................................................................................................................................................................................................................................................................................GAAGGAATCCTGGTCGGATGCGGCA.........................	25	1	5.00	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................................................................................................................................................TCCTGGTCGGATGCGGCAACCCGCTGC................	27	1	5.00	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
.................................................................................................................................................................................................................................................................................................................................................................................................AATCCTGGTCGGATGCGGC..........................	19	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	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	1	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
................................................................................................................................................................................................................................................................................................................................................................................................GAATCCTGGTCGGATGCGGCA.........................	21	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	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	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
..................................................................................................................................................................................................................................................................................................................................................................................................ATCCTGGTCGGATGCGGCAACCCGCT..................	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	3	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
............................................................................................................................................................................................................................................................................................................................................................................................GAAGGAATCCTGGTCGGATGCGGC..........................	24	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	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
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..............................................................................................................................................................................................................................................................................................................................................................................................AGGAATCCTGGTCGGATGCG............................	20	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	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
.............................................................................................................................................................................................................................................................................................................................................................................................AAGGAATCCTGGTCGGATGCGGCAAA.......................	26	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	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
.................................................................................................................................................................A------GACG------------------AGCAACATGTGATC..................................................................................................................................................................................................................................	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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

droSim2

GGTTCATC------GCCAGCTGATTGCGCT-----------------------TAAAAG--CTCTGG----CTGAACGCG-----------ATGTTGAAT-------GTT-------ATC-------GTTAATTGAGCGCATTAGCT----TGAGGCCCTCA------GACG------------------AGCAACATGTGCGACCG------------------CGTCAGGTTTGGGAC----------------------------TACTGC---TATATACTTA---------GCGAAA----CAGTGAAGAT--AGCACTATTAATCCAA----------ATA--TTTTTT-TT------------GTTCCACAGAGAAGGAATCCTGGTCGGATGCGGCAACCCGCTGCTGGACATCTCC-GCCG	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
...........................................................................................................................................................................................................ACCG------------------CGTCAGGTTTGGGAC----------------------------..................................................................................................................................................................	19	1	5.00	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...........................................................................................................................................................................G------------------AGCAACATGTGCGACCG------------------.............................................................................................................................................................................................................	18	1	4.00	4	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...............................................................................................................................................................TCA------GACG------------------AGCAACATGTGCGACCG------------------.............................................................................................................................................................................................................	24	1	3.00	3	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
......................................................................................................................................................................................................................................................................................................................................................................................................TGGTCGGATGCGGCAACCCGCTGC................	24	1	3.00	3	0	0	0	0	0	0	1	1	0	1	0	0	0	0	0	0	0
..........................................................................................................................................................................................................................................................................................................................................................................................GAGAAGGAATCCTGGTCGGATGC.............................	23	1	2.00	2	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0
.......................................................................................................................................................................................................TGCGACCG------------------CGTCAGGTTTGGGAC----------------------------T.................................................................................................................................................................	24	1	2.00	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................................................................AGGTTTGGGAC----------------------------TACTGC---T........................................................................................................................................................	18	1	2.00	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.............................................................................................................................................................CCTCA------GACG------------------AGCAACATGTGCGAC.................................................................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0
........................................................................................................................................................................................................................................................................................................................................................................................................................CGCTGCTGGACATCTCC-G...	18	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.................................................................................................................................................................................................................................................................................................................................................................................................AATCCTGGTCGGATGCGGCT.........................	20	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...........................................................................................................................................................................................................................................................................................................................................................................................AGAAGGAATCCTGGTCGGAT...............................	20	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..............................................................................................................................................................CTCA------GACG------------------AGCAACATGTGCGAC.................................................................................................................................................................................................................................	23	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.............................................................................................................................................................CCTCA------GACG------------------AGCAACATG.......................................................................................................................................................................................................................................	18	1	1.00	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
...............................................................................................................................................................................................GCAACATGTGCGACCG------------------CG...........................................................................................................................................................................................................	18	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
......................................................................................................................................................................................................................................................................................................................................................................................................TGGTCGGATGCGGCAACCCGCTGCT...............	25	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................CAGGTTTGGGAC----------------------------TACTGC---T........................................................................................................................................................	19	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
........................................................................................................................................................................GACG------------------AGCAACATGTGCGACCG------------------.............................................................................................................................................................................................................	21	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................................................................................................................................................................................CCTGGTCGGATGCGGCAACCCGCT..................	24	1	1.00	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0
..............................................................................................................................................................................................................G------------------CGTCAGGTTTGGGAC----------------------------TAC...............................................................................................................................................................	19	1	1.00	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................................................................................................................................................................................CCTGGTCGGATGCGGCAACCC.....................	21	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
......................................................................................................................................................................................................................................................................................................................................................................................................TGGTCGGATGCGGCAACCCGCTG.................	23	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................................................................................................................................................................................ATCCTGGTCGGATGCGGC..........................	18	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.............................................................................................................................................................................................................CG------------------CGTCAGGTTTGGGAC----------------------------T.................................................................................................................................................................	18	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...........................................................................................................................................................................................................................................................................................................................................................................................AGAAGGAATCCTGGTCGGATGCGGCAAC.......................	28	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................CGACCG------------------CGTCAGGTTTGGGAC----------------------------TACTGC---T........................................................................................................................................................	28	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................ACATGTGCGACCG------------------CGTCAG.......................................................................................................................................................................................................	19	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0
..................................................................................................................................................................................................................................................................................................................................................................................................ATCCTGGTCGGATGCGGCAACC......................	22	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..........................................................................................................................................................................................................................................................................................................................................................................................................................CTGCTGGACATCTCC-GCC.	18	1	1.00	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0
...........................................................................................................................................................................................................ACCG------------------CGTCAGGTTTGGGAC----------------------------TACTGC---.........................................................................................................................................................	25	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.................................................................................................................................................................................................................................................................................................................................................................................................AATCCTGGTCGGATGCGGC..........................	19	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droSec2

GGTTCATC------GCCAGCTGATTGCGCT-----------------------TAAAAG--CTCTGG----CTGAACGCG-----------ATGTTGAAT-------GGT-------ATC-------GTTAATTGAGCGCATTAGCT----TGAGGCCCTCA------GACG------------------AGCAACATGTGCGACCG------------------CGTCAGGTTTGGGAC----------------------------TACTGC---TATATACTTA---------GCGAAA----CAGTG---------CACTACTAATCCAA----------ATATTTTT-TT-TT------------GTTCCACAGAGAAGGAATCCTGGTCGGATGCGGCAACCCGCTGCTGGACATCTCC-GCCG	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
...........................................................................................................................................................................G------------------AGCAACATGTGCGACCG------------------CG...........................................................................................................................................................................................................	20	1	4.00	4	0	1	0	3
...........................................................................................................................................................................G------------------AGCAACATGTGCGACCG------------------.............................................................................................................................................................................................................	18	1	3.00	3	2	0	0	1
..............................................................................................................................................................................................AGCAACATGTGCGACCG------------------CG...........................................................................................................................................................................................................	19	1	2.00	2	0	0	1	1
.............................................................................................................................................................................................................CG------------------CGTCAGGTTTGGGAC----------------------------TACTG.............................................................................................................................................................	22	1	2.00	2	2	0	0	0
.............................................................................................................................................................CCTCA------GACG------------------AGCAACATGTGCG...................................................................................................................................................................................................................................	22	1	2.00	2	0	1	0	1
..............................................................................................................................................................CTCA------GACG------------------AGCAACATGTGCGACCG------------------.............................................................................................................................................................................................................	25	1	2.00	2	0	0	0	2
.............................................................................................................................................................CCTCA------GACG------------------AGCAACATGTGCGACCG------------------.............................................................................................................................................................................................................	26	1	2.00	2	1	0	0	1
...........................................................................................................GGT-------ATC-------GTTAATTGAGCG...................................................................................................................................................................................................................................................................................................	18	1	1.00	1	1	0	0	0
..................................................................................................................................................................................................................................................................................................................................................................................................ATCCTGGTCGGATGCGGC..........................	18	1	1.00	1	0	0	1	0
.....................................................................................................................................................................................................................................................................................................................................................................T------------GTTCCACAGAGAAGGAATCCTGGT....................................	25	1	1.00	1	1	0	0	0
..............................................................................................................................................................CTCA------GACG------------------AGCAACATGTGCGAC.................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	1
....................................................................................................................................................................................................................................................................................................................................................................................................CCTGGTCGGATGCGGCAACCCGC...................	23	1	1.00	1	0	0	1	0
.............................................................................................................................................................CCTCA------GACG------------------AGCAACATG.......................................................................................................................................................................................................................................	18	1	1.00	1	0	0	1	0
........................................................................................................................................................................................................................................................................................ATACTTA---------GCGAAA----CAGTG---------CA............................................................................................................	20	1	1.00	1	1	0	0	0
................................................................................................................................................................CA------GACG------------------AGCAACATGTGCGACCG------------------C............................................................................................................................................................................................................	24	1	1.00	1	0	0	1	0
...............................................................................................................................................................................................GCAACATGTGCGACCG------------------CGTCAGGTTTG..................................................................................................................................................................................................	27	1	1.00	1	0	0	0	1
..................................................................................................................................................................................................................................................................................................................................................................................................................GCAACCCGCTGCTGGACATCTC......	22	1	1.00	1	0	0	1	0
................................................................................................................................................................................................................................................................................................................................................................................................GAATCCTGGTCGGATGCGG...........................	19	1	1.00	1	0	0	1	0
...........................................................................................................................................................................G------------------AGCAACATGTGCGACCG------------------CGTCAGAGA....................................................................................................................................................................................................	27	1	1.00	1	0	0	1	0
.................................................................................................................................................................A------GACG------------------AGCAACATGTGCGAC.................................................................................................................................................................................................................................	20	1	1.00	1	0	0	0	1
..................................................................................................................................................T----TGAGGCCCTCA------GACG------------------AGC.............................................................................................................................................................................................................................................	19	1	1.00	1	0	0	1	0
............................................................................................................................................ATTAGCT----TGAGGCCCTCA------GACG------------------AGC.............................................................................................................................................................................................................................................	25	1	1.00	1	0	0	1	0
..............................................................................................................................................................................................................G------------------CGTCAGGTTTGGGAC----------------------------TACTG.............................................................................................................................................................	21	1	1.00	1	1	0	0	0
.....................................................................................................................................................................................................TGTGCGACCG------------------CGTCAGGTTTGGGA...............................................................................................................................................................................................	24	1	1.00	1	0	0	0	1
.................................................................................................................................................................................................................................CGTCAGGTTTGGGAC----------------------------TACTGC---.........................................................................................................................................................	21	1	1.00	1	0	0	0	1
...........................................................................................................................................................................G------------------AGCAACATGTGCGACCG------------------C............................................................................................................................................................................................................	19	1	1.00	1	0	0	0	1
................................................................................................................................................................................................................................................................................................................................................................................................GAATCCTGGTCGGATGCGGCA.........................	21	1	1.00	1	0	1	0	0
.............................................................................................................................................................CCTCA------GACG------------------AGCAACATGTGC....................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	1
..............................................................................................................................................................................................AGCAACATGTGCGACCG------------------C............................................................................................................................................................................................................	18	1	1.00	1	0	0	1	0
............................................................................................................................................................CCCTCA------GACG------------------AGCAACATGTGCG...................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	1
.............................................................................................................................................................................................................CG------------------CGTCAGGTTTGGGAC----------------------------TACTGC---TA.......................................................................................................................................................	25	1	1.00	1	0	1	0	0
...................................................................................................................................................................................................................................................................................................................................................................................................TCCTGGTCGGATGCGGCAACCC.....................	22	1	1.00	1	0	0	1	0

droYak3

GGTTCATC------GCCAGCTGATTGCGCT------------------------GAAAG--CTCTGA----CTGAACACCA-------GTATTGTTGAGT-------GGC-------ATT-------GTTAATTGATCGCATTAGCA----TCGGGCCCTCA------GACG------------------AGCAACATGTACGATCGTATC---AG---CAGTAACATTAGGTTTGGGGC----------------------------AACTGC---TATGTACTCA---------TCGAAA----CAGAGAAGAT--AGCATCAATAATCCAA----------ATG--ATT-TT-CT------------GTTCCACAGAGAAGGAATTCTGGTCGGATGCGGCAACCCGCTGCTAGACATCTCC-GCCG	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
..........................................................................................................................................................................................................................................................................................................................................................................................................CGGATGCGGCAACCCGCTGCTAGAC...........	25	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................................................................................................................................................................................TCTGGTCGGATGCGGCAACCCGCTG.................	25	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0
.........................................................................................................................................................................ACG------------------AGCAACATGTACGATCGTATC---AG---CA.................................................................................................................................................................................................................	28	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
...............................................................................................................................................................................................................................................................................................................................................................................................GGAATTCTGGTCGGATGC.............................	18	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
............................................................................................................................................................................................................................................................................................................................................................................................GAAGGAATTCTGGTCGGATGCGGC..........................	24	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0
.................................................................................................................................................................................................................................................................................................................................................................................................AATTCTGGTCGGATGCGGCAACCCGCT..................	27	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
........................................................................................................................................................................GACG------------------AGCAACATGTACGATCGTATC---AG---C..................................................................................................................................................................................................................	28	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
.............................................................................ACCA-------GTATTGTTGAGT-------GGC-------.........................................................................................................................................................................................................................................................................................................................	19	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
.............................................................................................................................................................................................................................................................................................................................................................................................AAGGAATTCTGGTCGGATGCGGC..........................	23	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0

droEre2

AGTTCATC------GCCAGCTGATTGCGCT------------------------GAAAG--CTCTGG----CTGAACACG-----------ATGTTTAGA-------GGC-------ATC-------GTTAATTGGGCGCATTAGCA----TCAGTCCCTCA------GACG------------------AGCAACATGTGCGATCCTATA---AG---CAGTAGCATTAGGTTTGGGGC----------------------------TATTAC---TATATACTCA---------TCGAAA----CAGAGAAGAT--AGCACTAATAATCCAA----------ATG--ATT-TT-CT------------GTTTCACAGAGAAGGAACCCTGGTCGGATGCGGCAACCCGCTGCTGGACATCTCC-GCCG	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
.........................................................................................................................................................................................................................................................................................................................................................................................................TCGGATGCGGCAACCCGCTGCTGGAC...........	26	1	1.00	1	1	0	0	0	0	0	0
.................................................................................................................................................................................................................................................................................................................................................................................................................GGCAACCCGCTGCTGGACAT.........	20	1	1.00	1	1	0	0	0	0	0	0
.......................................................................................................................................................................................................................................................................................................................................................................................................GGTCGGATGCGGCAACCCGCTGC................	23	1	1.00	1	1	0	0	0	0	0	0
...........................................................................................................................................................................................................................................................................................................................................................................................................GGATGCGGCAACCCGCTGCTGGACAT.........	26	1	1.00	1	1	0	0	0	0	0	0
..................................................................................................................................................................................................................................................................................................................................................................................................ACCCTGGTCGGATGCGGC..........................	18	1	1.00	1	0	0	0	0	0	1	0
..................................................................................................................................................................................................................................................................................................................................................................................................ACCCTGGTCGGATGCGGCAACCCGCT..................	26	1	1.00	1	0	0	0	0	1	0	0
............................................................................................................................................................................................................................................................................................................................................................................................GAAGGAACCCTGGTCGGATGCGGC..........................	24	1	1.00	1	0	0	0	0	1	0	0
...........................................................................................................................................................................................................................................................................................................................................................................................AGAAGGAACCCTGGTCGGATG..............................	21	1	1.00	1	0	0	0	0	1	0	0

dgr_375

scaffold_15121:202697-202847 +

Candidate

Unknown

Predicted structure

Flybase annnotation

Sense Strand Reads

Anti-sense strand reads

Re-alignment of all predicted orthologs

Re-alignment of all predicted orthologs with sRNA reads

-6.5	-6.4	-6.2