ID:

dan_229

 Coordinate:

scaffold_13417:2468092-2468194 -

 Confidence:

confident

 Class:

Testes-restricted

 Genomic Locale:

intergenic

 [View on UCSC Genome Browser {Cornell Mirror}]
Legend: mature star mismatch in alignment mismatch in read

Predicted structure

Flybase annnotation

intergenic

No Repeatable elements found

Sense Strand Reads

TTCCCCGCACTGAGACAGCTCCTGTGCGACAACCACGGGGTGCGGGGAGTACCTGGTATTATGGCAGCGAGTTTCCGGGATCTCGTACTGTATGAAGTTTTCTATATACAATTCGAAAACTCAGAAACTTCCTGCCGTGAGCTACCATTGATCAACGGCTGAGTATGCGACCGGAAAGGGGACGCGAATGCGAGGACTAAAGG

******************************************************(((((((((((((.(((((((.(((...(((...((((((.((....)).))))))...)))...))).))))))).)))))))))..))))..******************************************************* 		Read size # Mismatch Hit Count Total Norm Total V106

head

 V105

male body		 V055

head

 M044

female body

 M058

embryo
..............................................................................................................ATTCGAAAACTCAGAAACTTCCT...................................................................... 23 0 1 46.00 46 29 8 5 3 1
.............................................................................................................AATTCGAAAACTCAGAAACTTC........................................................................ 22 0 1 20.00 20 7 4 4 4 1
.....................................................................AGTTTCCGGGATCTCGTACTG................................................................................................................. 21 0 1 17.00 17 1 13 0 3 0
.....................................................................AGTTTCCGGGATCTCGTACTGT................................................................................................................ 22 0 1 14.00 14 0 8 1 5 0
.....................................................................AGTTTCCGGGATCTCGTACTGTA............................................................................................................... 23 0 1 11.00 11 1 4 2 4 0
............................................................................................................CAATTCGAAAACTCAGAAACTTC........................................................................ 23 0 1 10.00 10 3 2 4 0 1
...............................................................................................................TTCGAAAACTCAGAAACTTCCT...................................................................... 22 0 1 6.00 6 4 1 1 0 0
............................................................................................................CAATTCGAAAACTCAGAAACTT......................................................................... 22 0 1 4.00 4 2 2 0 0 0
.....................................................................AGTTTCCGGGATCTCGTACT.................................................................................................................. 20 0 1 3.00 3 2 1 0 0 0
.............................................................................................................AATTCGAAAACTCAGAAACTTCC....................................................................... 23 0 1 3.00 3 1 1 0 1 0
..............................................................................................................ATTCGAAAACTCAGAAGCTTCCT...................................................................... 23 1 1 2.00 2 2 0 0 0 0
..............................................................................................................ATTCGAAAACTCAGAAACTTCCTT..................................................................... 24 1 1 2.00 2 1 0 0 1 0
..............................................................................................................ATTCGAAAGCTGAGAAACTTCCT...................................................................... 23 2 1 1.00 1 0 0 1 0 0
.....................................................................AGTTTCCCGGATCTCGTACTGT................................................................................................................ 22 1 1 1.00 1 0 0 1 0 0
.....................................................................AGTTTCCGGGAACTCGTACT.................................................................................................................. 20 1 1 1.00 1 0 1 0 0 0
..............................................................................................................ATGCGAAAACTCGGAAACTTCCT...................................................................... 23 2 1 1.00 1 1 0 0 0 0
..............................................................................................................ATTCGAAAACTCAGAAACTTC........................................................................ 21 0 1 1.00 1 0 1 0 0 0
...................................................................CGAGTTTCCGGGATCTCGTACTGTATGA............................................................................................................ 28 0 1 1.00 1 0 0 0 1 0
.......................................................................TTTCCGGGATCTCGTACTGTAT.............................................................................................................. 22 0 1 1.00 1 0 1 0 0 0
..............................................................................................................ATTCGAAAACTCAGAAACTTCCC...................................................................... 23 1 1 1.00 1 1 0 0 0 0
..............................................................................................................ATTCGAGAGCTCGGAAACTTCCT...................................................................... 23 3 1 1.00 1 0 0 1 0 0
...............................................................................................................TTCGAGAGCTCAGAAACTTCCT...................................................................... 22 2 1 1.00 1 1 0 0 0 0
...............................................................................................................TTAGAAAACTCAGAAACTGCCT...................................................................... 22 2 1 1.00 1 0 0 1 0 0
.............................................................................................................AATTCAAAAACTCAGAAACTTC........................................................................ 22 1 1 1.00 1 1 0 0 0 0
..............................................................................................................ATTCGAAAACTCGGAAACTTCCT...................................................................... 23 1 1 1.00 1 0 0 1 0 0
.....................................................................AGTTTCCGGGATCTCGTACTT................................................................................................................. 21 1 1 1.00 1 0 1 0 0 0
.............................................................................................................AATTCGAAAACTCAGAAACTTT........................................................................ 22 1 1 1.00 1 0 0 0 1 0
.....................................................................AGTTTCCGAGATCTCGTACTGT................................................................................................................ 22 1 1 1.00 1 0 0 0 1 0
.....................................................................AGTTTCCGGGATCTCGTACTGTAAA............................................................................................................. 25 2 1 1.00 1 0 0 1 0 0
.............................................................................................................AATTCGAAAACTCAGAAACTTCA....................................................................... 23 1 1 1.00 1 0 0 0 1 0
..............................................................................................................ATTCGAAAACTCAGAAACTTCC....................................................................... 22 0 1 1.00 1 1 0 0 0 0
............................................................................................................CAATTCGAAAACTCGGAAACTT......................................................................... 22 1 1 1.00 1 0 0 1 0 0
....................................................................GAGTTTCCGGGATCTCGTACT.................................................................................................................. 21 0 1 1.00 1 0 1 0 0 0
.....................................................................AGTTTCCGCGATCTCGTACTGTAA.............................................................................................................. 24 2 1 1.00 1 0 0 0 1 0
.....................................................................AGTTTCCGGGCTCTCGTACTG................................................................................................................. 21 1 1 1.00 1 0 1 0 0 0
.....................................................................AGTTTCCGGGATCTCGTACTA................................................................................................................. 21 1 1 1.00 1 0 1 0 0 0
......................................................................GTTTCCGGGATCTCGTACTG................................................................................................................. 20 0 1 1.00 1 0 0 1 0 0
.............................................................................................................AATGCGAAAACTCAGAAACTTC........................................................................ 22 1 1 1.00 1 0 0 1 0 0
.....................................................................AGTTTCCGGGATATCGTACTG................................................................................................................. 21 1 1 1.00 1 0 1 0 0 0
....................................................................GAGTTTCCGGGATCTCGTACTG................................................................................................................. 22 0 1 1.00 1 0 1 0 0 0
..............................................................................................................ATTCGAAAGCTCAGAAACTTCCT...................................................................... 23 1 1 1.00 1 1 0 0 0 0
.............................................................................................................AATTCGAAGACTCAGAAACTTC........................................................................ 22 1 1 1.00 1 0 0 0 1 0
.....................................................................AGTTTCCGGGATATCGTACTGT................................................................................................................ 22 1 1 1.00 1 0 1 0 0 0
.....................................................................AGTTTCCGGGATCTCGTACTGTAA.............................................................................................................. 24 1 1 1.00 1 0 1 0 0 0
............................................................................................................CAATTCGAAAACTCAGAACCTTC........................................................................ 23 1 1 1.00 1 0 0 1 0 0
..............................................................................................................GTTCGAAAACTCAGAAACTTCCT...................................................................... 23 1 1 1.00 1 1 0 0 0 0
..............................................................................................................ATTAGAAAACTCAGAAACTTCCT...................................................................... 23 1 1 1.00 1 1 0 0 0 0
.......................................................................TTTCCGGGATCTCGTACTGTATG............................................................................................................. 23 0 1 1.00 1 0 0 0 1 0
...........................................................................CGGGATCTCGTACTGTATGAAG.......................................................................................................... 22 0 1 1.00 1 0 1 0 0 0
..............................................................................................................ATTCGAAAACTCGGAGGCTTCCT...................................................................... 23 3 1 1.00 1 0 0 1 0 0
.......................................................................................................ATATACAATTCGAAAACTCAGA.............................................................................. 22 0 1 1.00 1 0 1 0 0 0
......................................................................GTTTCCGGGATCTCGTACTGTT............................................................................................................... 22 1 1 1.00 1 0 0 0 1 0
..............................................................................................................ATTCGAAAACTCAGAAACTCCCT...................................................................... 23 1 1 1.00 1 1 0 0 0 0
.............................................................................................................AATTCGAAAACTCTGAAACTTC........................................................................ 22 1 1 1.00 1 0 1 0 0 0
...................................................................CGAGTTTCCGGGATCTCGTAC................................................................................................................... 21 0 1 1.00 1 0 1 0 0 0
....................................................................GAGTTTCCGGGATCTCGTACTGA................................................................................................................ 23 1 1 1.00 1 0 1 0 0 0
..............................................................................................................ATTCGAAACCTCAGAAACTTCCT...................................................................... 23 1 1 1.00 1 0 0 0 1 0
..............................................................................................................ATTCGAAGACTCGGAAACTTCCT...................................................................... 23 2 1 1.00 1 0 0 1 0 0
..............................................................................................................ATTCGAGAGCTCAGAAACTTCCT...................................................................... 23 2 1 1.00 1 1 0 0 0 0
....................................................................GAGTTTCCGGGATCTCGTACAG................................................................................................................. 22 1 1 1.00 1 0 1 0 0 0
.............................................................................................................ATTACGAAAACTCAGAGACTTC........................................................................ 22 3 1 1.00 1 0 0 1 0 0
.........................................................................................................................TAGAAACTTCCTACCGTGCGCT............................................................ 22 3 2 0.50 1 0 0 1 0 0
.........................................................................................................................TAGCAACTTCCTACCGTGAG.............................................................. 20 3 2 0.50 1 0 0 1 0 0
.....................................................................AGATTCCGGGAACTCATACTG................................................................................................................. 21 3 2 0.50 1 0 0 1 0 0
.................................AACGGGTTGCGGGGAGTA........................................................................................................................................................ 18 2 2 0.50 1 0 0 1 0 0
................................CAACGGGGAGCGGGGAGTA........................................................................................................................................................ 19 2 2 0.50 1 0 0 1 0 0
.........................................................................................................................CAGGAACTTCATACCGTGAGCT............................................................ 22 3 3 0.33 1 0 0 1 0 0
...............................................................................................................TTCGAGAGCTAAGAAACTTCCT...................................................................... 22 3 3 0.33 1 1 0 0 0 0
..............................................................................................................ATTCGAGAACTCAGAAGCTTCCT...................................................................... 23 2 4 0.25 1 1 0 0 0 0
.................................CAAGGGGCGCGGTGAGTACC...................................................................................................................................................... 20 3 4 0.25 1 0 0 1 0 0
.......................................................................................................................................................................CGGCCGGTAAGGGGACG................... 17 2 5 0.20 1 0 0 1 0 0
...................................CGTGGTGCGGGGGGTACCG..................................................................................................................................................... 19 3 9 0.11 1 0 0 1 0 0
..................................ACGGGGAACGGGGAGTA........................................................................................................................................................ 17 2 20 0.10 2 0 0 2 0 0
...........................................................................................................................................................................CGGAAAGGGGACCCGAC............... 17 2 13 0.08 1 0 0 1 0 0
........................................................................................................................TCAGAAACTTAATGTCGTGA............................................................... 20 3 15 0.07 1 0 0 1 0 0
.......................................................GTATAATGTCAGCGAGTTTCT............................................................................................................................... 21 3 19 0.05 1 1 0 0 0 0
.....................................................................................................................................................................TGCGACCGGTAACGGGGC.................... 18 3 20 0.05 1 0 0 1 0 0

Anti-sense strand reads

AAGGGGCGTGACTCTGTCGAGGACACGCTGTTGGTGCCCCACGCCCCTCATGGACCATAATACCGTCGCTCAAAGGCCCTAGAGCATGACATACTTCAAAAGATATATGTTAAGCTTTTGAGTCTTTGAAGGACGGCACTCGATGGTAACTAGTTGCCGACTCATACGCTGGCCTTTCCCCTGCGCTTACGCTCCTGATTTCC

*******************************************************(((((((((((((.(((((((.(((...(((...((((((.((....)).))))))...)))...))).))))))).)))))))))..))))..****************************************************** 		Read size # Mismatch Hit Count Total Norm Total M044

female body

 V105

male body		 M058

embryo

 V039

embryo

 V106

head
............................................................................................................................................AGATGGTAACTCGTTGGCGA........................................... 20 3 9 1.11 10 8 2 0 0 0
............................................................................................................................................AGATGGTAACTGGTTGGCGA........................................... 20 3 8 0.13 1 1 0 0 0 0
...................................................................TCTCAAAGCCCCTAGCGCAT.................................................................................................................... 20 3 8 0.13 1 0 0 0 1 0
............................................................................................................................................CGATGGCAACGAGTTGCCGC........................................... 20 3 9 0.11 1 0 0 1 0 0
.........................................................................................................TATGTAAAGCTTTTGAGAC............................................................................... 19 2 12 0.08 1 0 0 1 0 0
............................................................................................................................................AGATGGTAACTCGTTGGCG............................................ 19 3 13 0.08 1 1 0 0 0 0
..................................................................................................................................................TGACTAGTTGCCGACTCTG...................................... 19 3 15 0.07 1 0 0 0 0 1
.............................................................................................................................................GATGGTAACTCGCTGGCGA........................................... 19 3 18 0.06 1 1 0 0 0 0

Re-alignment of all predicted orthologs

Species Coordinate ID Type Alignment
droAna3 scaffold_13417:2468042-2468244 - dan_229 confident TTCC---------------------------------------CCGCACTGAGACAGCTCCTGTGCGACAACCACGGGGTGCGGGGAGTACCTGGTATTATGGCAGCGAGTTTCCGGGATCTCGTACTGTATGAA-G---TTTTCTATAT----------ACAATTCGAAAACTCAGAAACTTCCTGCCGTGAGCTACCATTGATCAACG-GCTGAGTATGCGACCGGAAAGGGGACGCGAATGC------------------------GAGGACTAAAGG
droBip1 scf7180000395874:40400-40532 - AT----------------------------TG------------------------------------------CGGGGTGCGGGGAGTGCCTGGTATTATGGCAGCGAGTTTCCGGGATCTCGTAGTGTATGAA-G---TTTTATAAAT----------ACAATTCGAAAACTCAGAAACTTTCTGCCTTGAAGTACATTCATCAA-CG-GCCGAGTA--------------------------------------------------------------
droKik1 scf7180000302517:1183443-1183539 + ------------------------------------------------------------------------------------------CCTGGTATAGCCGCAGAAAGTTTCCGAG-TTTCGTAATGTATGGTTA---TATTTGAAAT----------ACAGTACGAGACATCAGAAATTTTCGGCAGTTAGCTACCGT--------------------------------------------------------------------------------
droFic1 scf7180000454073:1733615-1733717 + ------------------------------------------------------------------------------------------CTCGGTATTATCGCAGCAAGTTTCCGGGACTTCGTACTGTATGAA-G---AATTCTATAT----------ACAATACGAAACCTCAGAAATTTATTGCAATGAACCACCTTTAACTA--------------------------------------------------------------------------
droEle1 scf7180000490751:1118488-1118609 + ATAT--------------------AG----TG----------CTCGAACAC-AA------------------------------CAACTCCTTGGTATTATCGCAGCAAGTTTCCGGGATTTCGTACTGTATGAC-A---AATTCTATAT----------ACAATACGAAACCTTAGAAATTTTCTGAAGTTAGCTACCAT--------------------------------------------------------------------------------
droRho1 scf7180000761121:190389-190517 - AC----------------------------CA------------------------------------------TTCGGGCCGGAGACATCTTGGTATTATCGCAGCAAGTTTCCGGGATTTCGTACTGTATGAC-A---AATTCTATAT----------ACAATACGAAACCTTAGAAATTTTCTGCAGTTATCTACCATTAACTA-CCAGTT-------------------------------------------------------------------
droBia1 scf7180000302069:1151358-1151516 - TTCCGACTGTTT----GTATGCAT-CCATACACGTGGTTATTTCCAC--AT-GA------------------------------AGACATCTTGGTATTATCGCAACAAGTTTCCGGGATTTTGTATTGTATGACTA---GATTCTATAT----------ACAATACGAAACCTCAGAAATTTTCTGCAGTTAACTACCATAAATCG-CCG----------------------------------------------------------------------
droTak1 scf7180000415169:845145-845295 - TTCCGAATGCGTATGCGTATGCATAGCACACATATG---------AG--AG-GA------------------------------CGACACCTTGGTATTATCGCAACAAGTTTCCGGGATTTCGTACTGTATGCT-G---AATTCTATAT----------ACAATACGAAAGCTCAGAAATTTTCTGCAGTTAACTACCATTAACTA--------------------------------------------------------------------------
droEug1 scf7180000409230:879977-880113 - AA----------------------------TA----------CCCTGATAGAGG------------------------------CGACATCTTGGTATTATCGCAATAAGTTCCTGGGATTTCGCACTGTATTAC-G---ATTTTTACAT----------ACAATACGAAAGCTCAGAAACTAACTGCAATTAACTACCGTAAACTA-CG-GATGAGAACG------------------------------------------------------------
dm3 chrX:19452586-19452627 + ----------------------------------------------------GG------------------------------AGAAGTCTTGGTATTATGGCAAAAAGTTTCCAGGACATTG-------------------------------------------------------------------------------------------------------------------------------------------------------------
droSim2 x:18341755-18341798 + ------------------------------------------------------------------------------------------CTTGGTATTATGGCAACAAGTTTCCAGGACATCGAGCTGTGTGA---------------------------------------------------------------------------------------------------------------------------------------------------
droSec2 scaffold_8:1734625-1734668 + ------------------------------------------------------------------------------------------CTTGGTATTATGGCAACAAGTTTCCAGGACATCGAGCTGTGTGA---------------------------------------------------------------------------------------------------------------------------------------------------
droYak3 X:11886147-11886242 - dya_51 novel ------------------------------------------------------------------------------------------CTTGGTATTATGGCAACAAGTTTCCGGGACTTCGTACTGTATGAC-A---GACTATATAT----------ACAATACGAAGCCTCTGAAATTTTCTGCGCTCAAGTACCA---------------------------------------------------------------------------------
droEre2 scaffold_4690:9688638-9688681 + ------------------------------------------------------------------------------------------CTTGGTATTAAGGCAACAAGTTTCAGGGACTTCGCACTGTATGA---------------------------------------------------------------------------------------------------------------------------------------------------
droWil2 scf2_1100000004909:7956429-7956567 + --------------------------------------------------------------------------------------------TGGTATTATCGCAGCAAGTTTCCGGGATATCGTACTGTATTTC-TAAACATTTCATAT----------ACAATACGAAACCTCAGAAATTTGCTGCGGTTAGTTACCGTTAACAA-CT-CATAAGAAAG-----------GAGA---GAATAAA-----------------------AATGATCAATAT
droGri2 scaffold_15081:2044827-2044998 - dgr_10 confident ------------------------------------------------------------------------------------------CCTGGTATTGCTGCTGCAAATTTCCGCGGTGTCGTATTGTATTAT-C---AAAATGGTATACTCTGAACCACAATACGATTCCTCAGAAATTCGCTGCTGTAAGTTACCGTTTTCAA-CCGTATAGCAACT-----------GTGC---CGATAAACCTATCCCAGTCTATCGATAGACAACGATTGTCAG

Re-alignment of all predicted orthologs with sRNA reads

Species Read alignment
droAna3
TTCC---------------------------------------CCGCACTGAGACAGCTCCTGTGCGACAACCACGGGGTGCGGGGAGTACCTGGTATTATGGCAGCGAGTTTCCGGGATCTCGTACTGTATGAA-G---TTTTCTATAT----------ACAATTCGAAAACTCAGAAACTTCCTGCCGTGAGCTACCATTGATCAACG-GCTGAGTATGCGACCGGAAAGGGGACGCGAATGC------------------------GAGGACTAAAGGSizeHit CountTotal NormTotalM044

Female-body		M058

Embryo		V039

Embryo		V055

Head		V105

Male-body		V106

Head
...................................................................................................................................................................ATTCGAAAACTCAGAAACTTCCT...............................................................................................23146.00463105829
..................................................................................................................................................................AATTCGAAAACTCAGAAACTTC.................................................................................................22120.0020410447
............................................................................................................AGTTTCCGGGATCTCGTACTG........................................................................................................................................................21117.00173000131
............................................................................................................AGTTTCCGGGATCTCGTACTGT.......................................................................................................................................................22114.0014500180
............................................................................................................AGTTTCCGGGATCTCGTACTGTA......................................................................................................................................................23111.0011400241
.................................................................................................................................................................CAATTCGAAAACTCAGAAACTTC.................................................................................................23110.0010010423
....................................................................................................................................................................TTCGAAAACTCAGAAACTTCCT...............................................................................................2216.006000114
.................................................................................................................................................................CAATTCGAAAACTCAGAAACTT..................................................................................................2214.004000022
............................................................................................................AGTTTCCGGGATCTCGTACT.........................................................................................................................................................2013.003000012
..................................................................................................................................................................AATTCGAAAACTCAGAAACTTCC................................................................................................2313.003100011
...................................................................................................................................................................ATTCGAAAACTCAGAAACTTCCTT..............................................................................................2412.002100001
...................................................................................................................................................................ATTCGAAAACTCAGAAACTTC.................................................................................................2111.001000010
..........................................................................................................CGAGTTTCCGGGATCTCGTACTGTATGA...................................................................................................................................................2811.001100000
..............................................................................................................TTTCCGGGATCTCGTACTGTAT.....................................................................................................................................................2211.001000010
...................................................................................................................................................................ATTCGAAAACTCAGAAACTTCCC...............................................................................................2311.001000001
............................................................................................................AGTTTCCGGGATCTCGTACTT........................................................................................................................................................2111.001000010
..................................................................................................................................................................AATTCGAAAACTCAGAAACTTT.................................................................................................2211.001100000
............................................................................................................AGTTTCCGGGATCTCGTACTGTAAA....................................................................................................................................................2511.001000100
..................................................................................................................................................................AATTCGAAAACTCAGAAACTTCA................................................................................................2311.001100000
...................................................................................................................................................................ATTCGAAAACTCAGAAACTTCC................................................................................................2211.001000001
...........................................................................................................GAGTTTCCGGGATCTCGTACT.........................................................................................................................................................2111.001000010
............................................................................................................AGTTTCCGGGATCTCGTACTA........................................................................................................................................................2111.001000010
.............................................................................................................GTTTCCGGGATCTCGTACTG........................................................................................................................................................2011.001000100
...........................................................................................................GAGTTTCCGGGATCTCGTACTG........................................................................................................................................................2211.001000010
............................................................................................................AGTTTCCGGGATCTCGTACTGTAA.....................................................................................................................................................2411.001000010
..............................................................................................................TTTCCGGGATCTCGTACTGTATG....................................................................................................................................................2311.001100000
..................................................................................................................CGGGATCTCGTACTGTATGAA-G---.............................................................................................................................................2211.001000010
..................................................................................................................................................ATAT----------ACAATTCGAAAACTCAGA.......................................................................................................2211.001000010
.............................................................................................................GTTTCCGGGATCTCGTACTGTT......................................................................................................................................................2211.001100000
..........................................................................................................CGAGTTTCCGGGATCTCGTAC..........................................................................................................................................................2111.001000010
...........................................................................................................GAGTTTCCGGGATCTCGTACTGA.......................................................................................................................................................2311.001000010
droBip1
AT----------------------------TG------------------------------------------CGGGGTGCGGGGAGTGCCTGGTATTATGGCAGCGAGTTTCCGGGATCTCGTAGTGTATGAA-G---TTTTATAAAT----------ACAATTCGAAAACTCAGAAACTTTCTGCCTTGAAGTACATTCATCAA-CG-GCCGAGTA--------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droKik1
------------------------------------------------------------------------------------------CCTGGTATAGCCGCAGAAAGTTTCCGAG-TTTCGTAATGTATGGTTA---TATTTGAAAT----------ACAGTACGAGACATCAGAAATTTTCGGCAGTTAGCTACCGT--------------------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droFic1
------------------------------------------------------------------------------------------CTCGGTATTATCGCAGCAAGTTTCCGGGACTTCGTACTGTATGAA-G---AATTCTATAT----------ACAATACGAAACCTCAGAAATTTATTGCAATGAACCACCTTTAACTA--------------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droEle1
ATAT--------------------AG----TG----------CTCGAACAC-AA------------------------------CAACTCCTTGGTATTATCGCAGCAAGTTTCCGGGATTTCGTACTGTATGAC-A---AATTCTATAT----------ACAATACGAAACCTTAGAAATTTTCTGAAGTTAGCTACCAT--------------------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droRho1
AC----------------------------CA------------------------------------------TTCGGGCCGGAGACATCTTGGTATTATCGCAGCAAGTTTCCGGGATTTCGTACTGTATGAC-A---AATTCTATAT----------ACAATACGAAACCTTAGAAATTTTCTGCAGTTATCTACCATTAACTA-CCAGTT-------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droBia1
TTCCGACTGTTT----GTATGCAT-CCATACACGTGGTTATTTCCAC--AT-GA------------------------------AGACATCTTGGTATTATCGCAACAAGTTTCCGGGATTTTGTATTGTATGACTA---GATTCTATAT----------ACAATACGAAACCTCAGAAATTTTCTGCAGTTAACTACCATAAATCG-CCG----------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droTak1
TTCCGAATGCGTATGCGTATGCATAGCACACATATG---------AG--AG-GA------------------------------CGACACCTTGGTATTATCGCAACAAGTTTCCGGGATTTCGTACTGTATGCT-G---AATTCTATAT----------ACAATACGAAAGCTCAGAAATTTTCTGCAGTTAACTACCATTAACTA--------------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droEug1
AA----------------------------TA----------CCCTGATAGAGG------------------------------CGACATCTTGGTATTATCGCAATAAGTTCCTGGGATTTCGCACTGTATTAC-G---ATTTTTACAT----------ACAATACGAAAGCTCAGAAACTAACTGCAATTAACTACCGTAAACTA-CG-GATGAGAACG------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
dm3
----------------------------------------------------GG------------------------------AGAAGTCTTGGTATTATGGCAAAAAGTTTCCAGGACATTG-------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalGSM154618

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		GSM239041

Head		GSM239050

Head		GSM239051

S2		GSM239052

S2		GSM246084

Head		GSM266765

S2		GSM280082

Ovary		GSM280083

Ovary		GSM280084

Ovary		GSM280085

Testis		GSM280086

Ovary		GSM280087

S2-NP		GSM280088

S2-NP		GSM312995

Head		GSM313160

Head		GSM313161

Head		GSM313162

Head		GSM313163

Head		GSM313164

Head		GSM313165

Head		GSM343287

Embryo		GSM379050

Ovary		GSM379051

Ovary		GSM379052

Ovary		GSM379053

Ovary		GSM379054

Ovary		GSM379055

Ovary		GSM379056

Ovary		GSM379057

Ovary		GSM379058

Ovary		GSM379059

Ovary		GSM379060

Ovary		GSM379061

Ovary		GSM379062

Ovary		GSM379063

Ovary		GSM379064

Ovary		GSM379065

Ovary		GSM379066

Ovary		GSM379067

Ovary		GSM424739

S2		GSM424740

S2		GSM424741

S2		GSM467729

Female-body		GSM467730

Female-body		GSM467731

Female-body		M002

CS		M003

Male-body		M004

Male-body		M005

ML-DmD32		M006

ML-DmD32		M029

OSC		M030

OSC		M031

OSC		M032

S2-R+		M033

S2-R+		M034

S2-R+		M035

S2-R+		M036

S2-R+		M037

S2-R+		M038

S2-R+		M039

S2-R+		M048

S2-R+		OSS2

OSS		OSS6

OSS		OSS7

OSS		OSS8

OSS		S1

Head		S10

Embryo		S11

Embryo		S12

Embryo		S13

Embryo		S14

Embryo		S15

S2-GMR		S16

Kc		S17

Larvae		S18

Larvae		S19

Pupae		S2

Head		S20

Pupae		S21

Disc		S22

Head		S23

Female-body		S24

Male-body		S25

Larvae		S26

Larvae		S27

Pupae		S28

Pupae		S29

Head		S3

Male-body		S30

S2-GMR		S31

S2		S32

S2		S33

Kc		S34

Kc		S35

Kc		S4

Female-body		S5

Disc		S6

Embryo		S7

Embryo		S8

S2		S9

Embryo		SRR001337

Head		SRR001338

Head		SRR001339

Head		SRR001340

Head		SRR001341

Head		SRR001342

Head		SRR001343

Head		SRR001344

Head		SRR001345

Head		SRR001346

Head		SRR001347

Head		SRR001348

Head		SRR001349

Head		SRR001664

Head		SRR010951

Ovary		SRR010952

Ovary		SRR010953

Ovary		SRR010954

Ovary		SRR010955

Ovary		SRR010956

Ovary		SRR010957

Ovary		SRR010958

Ovary		SRR010959

Ovary		SRR010960

Ovary		SRR014268

Embryo		SRR014269

Embryo		SRR014270

Embryo		SRR014271

Embryo		SRR014272

Embryo		SRR014273

Ovary		SRR014274

Ovary		SRR014275

Ovary		SRR014276

Ovary		SRR014277

Ovary		SRR014278

Ovary		SRR014279

Ovary		SRR014280

Ovary		SRR014281

Ovary		SRR014282

Ovary		SRR023197

S2		SRR023399

S2		SRR023400

S2		SRR023402

S2		SRR023407

S2		SRR029028

S2		SRR029029

S2		SRR029030

S2		SRR029031

S2		SRR029032

S2		SRR029033

S2		SRR029608

Head		SRR029633

Head		SRR030145

gb3		SRR031692

Head		SRR031693

Head		SRR031694

Head		SRR031696

Head		SRR031697

Head		SRR031698

Head		SRR031699

Head		SRR031700

Head		SRR031701

Head		SRR031702

Head		SRR031703

Head		SRR031704

Head		SRR032092

S2		SRR032093

S2		SRR032094

S2		SRR032095

S2-NP		SRR032096

S2-NP		SRR032152

Head		SRR060643

Testis		SRR060644

Ovary		SRR060645

Testis		SRR060646

Ovary		SRR060647

Ovary		SRR060648

Ovary		SRR060649

Ovary		SRR060650

Testis		SRR060651

Ovary		SRR060652

Testis		SRR060653

Ovary		SRR065151

Ovary		SRR065152

Ovary		SRR065153

Ovary		SRR065154

Ovary		SRR065155

Ovary		SRR065800

Ovary		SRR065801

Ovary		SRR065802

Ovary		SRR065803

Ovary		SRR065804

Ovary		SRR065805

Ovary		SRR065806

Ovary		SRR065807

Ovary		SRR097865

S2-NP		SRR097866

S2-NP		SRR097867

S2-NP		SRR298536

Ovary		SRR298537

Ovary		SRR298711

Ovary		SRR298712

Ovary		SRR317110

Ovary		SRR317111

Ovary		SRR317112

Ovary		SRR317113

Ovary		SRR317114

Ovary		SRR317115

Ovary		SRR317116

Ovary		SRR317117

Ovary		SRR341115

S2		SRR341116

S2		SRR341117

S2		SRR341118

S2		SRR351332

Mixed-body		SRR351333

Mixed-body		T004

OSC		T005

CME-L1		V001

Embryo		V002

Embryo		V003

S2		V006

Female-body		V007

Head		V008

S2		V009

CME-L1		V010

ML-DmD20-C5		V011

Sg4		V012

Male-body		V013

Head		V014

DTT		V015

DreRFHV		V018

Kc167		V019

GM2		V020

S2-R+		V021

ML-DmD21		V022

ML-DmD32		V023

Head		V024

Kc167		V025

S2-R+		V026

1182-2H		V027

ML-DmD21		V028

CME-W1-Cl.8+		V029

ML-DmD9		V030

ML-DmD8		V031

GM2		V032

S1		V033

CME-W1-Cl.8+		V034

ML-DmD16-C3		V035

ML-DmD32		V036

ML-DmD20-C5		V037

S2		V038

S2		V063

Ovary		V0632

Ovary		V064

Ovary		V0642

Ovary		V065

Ovary		V0652

Ovary		V066

Ovary		V0662

Ovary		V067

S2-NP		V073

mbn2		V074

S3		V075

ML-DmBG1-C1		V076

ML-DmBG3-C2		V077

Head		V078

Head		V079

Head		V080

Head		V081

Embryo		V082

Embryo		V083

Male-body		V084

Female-body		V085

CME-W2		V086

Female-body		V088

Ovary		V0882

Ovary		V089

Ovary		V0892

Ovary		V090

Male-body		V091

fGS/OSS		V092

Male-body		V093

Male-body		V094

S2-R+		V095

S2-R+		V096

Ovary		V097

Ovary		V098

Ovary		V125

ML-DmD9		V126

CME-L1		V127

G2		V128

S3		V129

ML-DmBG1-C1		V130

ML-DmBG3-C2		V131

ML-DmD16-C3		V132

ML-DmD32		V133

Sg4		V134

ML-DmD8		V135

CME-W2		V136

Male-body		V137

Head		V138

Male-body		V139

Female-body		V140

Female-body		V141

Female-body		V142

Female-body		V144

OSC		V145

S2		V146

S1		V147

1182-2H		V148

mbn2		GSM1528798

follicle cells
No Reads
droSim2
------------------------------------------------------------------------------------------CTTGGTATTATGGCAACAAGTTTCCAGGACATCGAGCTGTGTGA---------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalM023

Head		M024

Male-body		M025

Embryo		M053

Female-body		O001

Testis		O002

Head		SRR553485

Ovary		SRR553486

Ovary		SRR553487

Ovary		SRR553488

Ovary		SRR618934

Ovary		V044

Embryo		SRR902008

Ovary		SRR902009

Testis		SRR1275487

Male larvae		SRR1275485

Male prepupae		SRR1275483

Male prepupae
No Reads
droSec2
------------------------------------------------------------------------------------------CTTGGTATTATGGCAACAAGTTTCCAGGACATCGAGCTGTGTGA---------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalM054

Female-body		V113

Male-body		V114

Embryo		V115

Head
No Reads
droYak3
------------------------------------------------------------------------------------------CTTGGTATTATGGCAACAAGTTTCCGGGACTTCGTACTGTATGAC-A---GACTATATAT----------ACAATACGAAGCCTCTGAAATTTTCTGCGCTCAAGTACCA---------------------------------------------------------------------------------SizeHit CountTotal NormTotalM026

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
..................................................................................................................................................................AATACGAAGCCTCTGAAATTTT.................................................................................................221129.0012911211000150000
............................................................................................................AGTTTCCGGGACTTCGTACTGT.......................................................................................................................................................22184.00846031110180000
...................................................................................................................................................................ATACGAAGCCTCTGAAATTTTCT...............................................................................................23130.0030300000000000
............................................................................................................AGTTTCCGGGACTTCGTACTG........................................................................................................................................................21128.0028710000200000
..................................................................................................................................................................AATACGAAGCCTCTGAAATTT..................................................................................................21123.0023211000010000
............................................................................................................AGTTTCCGGGACTTCGTACTGG.......................................................................................................................................................22118.0018180000000000
............................................................................................................AGTTTCCGGGACTTCGTACTGC.......................................................................................................................................................22111.0011110000000000
............................................................................................................AGTTTCCGGGACTTCGTACT.........................................................................................................................................................2018.00800001160000
............................................................................................................AGTTTCCGGGACTTCGTAC..........................................................................................................................................................1916.00660000000000
............................................................................................................AGTTTCCGGGACTTCGTACTGTT......................................................................................................................................................2315.00550000000000
............................................................................................................AGTTTCCGGGACTTCGTACTGTA......................................................................................................................................................2315.00550000000000
...................................................................................................................................................................ATACGAAGCCTCTGAAATTTTCTG..............................................................................................2415.00550000000000
..................................................................................................................................................................AATACGAAGCCTCTGAAATT...................................................................................................2013.00330000000000
....................................................................................................................................................................TACGAAGCCTCTGAAATTTTCT...............................................................................................2213.00330000000000
...................................................................................................................................................................ATACGAAGCCTCTGAAATTTTC................................................................................................2212.00210000010000
....................................................................................................................................................................TACGAAGCCTCTGAAATTTTCTG..............................................................................................2312.00220000000000
.................................................................................................................CCGGGACTTCGTACTGTA......................................................................................................................................................1811.00110000000000
...................................................................................................................................................................ATACGAAGCCTCTGAAATTTTCC...............................................................................................2311.00110000000000
................................................................................................................TCCGGGACTTCGTACTGTATGA...................................................................................................................................................2211.00101000000000
.............................................................................................................GTTTCCGGGACTTCGTACTGTT......................................................................................................................................................2211.00110000000000
............................................................................................................AGTTTCCGGGACTTCGTACTT........................................................................................................................................................2111.00110000000000
...................................................................................................................................................................ATACGAAGCCTCTGAAATTTTCTGC.............................................................................................2511.00110000000000
...................................................................................................................................................................ATACGAAGCCTCTGAAATTTT.................................................................................................2111.00110000000000
....................................................................................................................................................................TACGAAGCCTCTGAAATTTTC................................................................................................2111.00110000000000
.................................................................................................................................................................CAATACGAAGCCTCTGAAATTTT.................................................................................................2311.00100000100000
droEre2
------------------------------------------------------------------------------------------CTTGGTATTAAGGCAACAAGTTTCAGGGACTTCGCACTGTATGA---------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalM055

Female-body		M057

Embryo		V060

Head		V040

Embryo		V107

Male-body		V108

Head		GSM1528801

follicle cells
No Reads
droWil2
--------------------------------------------------------------------------------------------TGGTATTATCGCAGCAAGTTTCCGGGATATCGTACTGTATTTC-TAAACATTTCATAT----------ACAATACGAAACCTCAGAAATTTGCTGCGGTTAGTTACCGTTAACAA-CT-CATAAGAAAG-----------GAGA---GAATAAA-----------------------AATGATCAATATSizeHit CountTotal NormTotalM020

Head		M045

Female-body		V117

Male-body		V118

Embryo		V119

Head
............................................................................................................AGTTTCCGGGATATCGTACTGTA......................................................................................................................................................231290.0029023605310
...................................................................................................................................................................ATACGAAACCTCAGAAATTTGCT...............................................................................................231173.00173101811566
..............................................................................................................TTTCCGGGATATCGTACTGTAT.....................................................................................................................................................221161.0016112323402
............................................................................................................AGTTTCCGGGATATCGTACTGT.......................................................................................................................................................221139.001394908901
............................................................................................................AGTTTCCGGGATATCGTACTGTAA.....................................................................................................................................................241124.0012410302100
............................................................................................................AGTTTCCGGGATATCGTAC..........................................................................................................................................................19138.0038380000
...............................................................................................................TTCCGGGATATCGTACTGTATTT...................................................................................................................................................23133.0033300300
............................................................................................................AGTTTCCGGGATATCGTACTG........................................................................................................................................................21121.0021002001
...............................................................................................................TTCCGGGATATCGTACTGTATT....................................................................................................................................................22116.0016130300
...................................................................................................................................................................ATACGAAACCTCAGAAATTTGC................................................................................................22113.001331324
..............................................................................................................TTTCCGGGATATCGTACTGTATT....................................................................................................................................................2317.00750200
............................................................................................................AGTTTCCGGGATATCGTACTGTC......................................................................................................................................................2317.00760100
....................................................................................................................................................................TACGAAACCTCAGAAATTTGCT...............................................................................................2216.00600402
............................................................................................................AGTTTCCGGGATATCGTACTGC.......................................................................................................................................................2216.00660000
............................................................................................................AGTTTCCGGGATATCGTACT.........................................................................................................................................................2016.00610500
..............................................................................................................TTTCCGGGATATCGTACTGTAC.....................................................................................................................................................2216.00660000
............................................................................................................AGTTTCCGGGATATCGTACTGTAT.....................................................................................................................................................2416.00650001
..............................................................................................................TTTCCGGGATATCGTACTGTA......................................................................................................................................................2115.00540100
..................................................................................................................................................................AATACGAAACCTCAGAAATTTG.................................................................................................2215.00530200
................................................................................................................TCCGGGATATCGTACTGTATTT...................................................................................................................................................2215.00550000
.............................................................................................................GTTTCCGGGATATCGTACTGTA......................................................................................................................................................2214.00430100
............................................................................................................AGTTTCCGGGATATCGTACTGG.......................................................................................................................................................2214.00440000
............................................................................................................AGTTTCCGGGATATCGTACTGTAC.....................................................................................................................................................2413.00330000
...................................................................................................................................................................ATACGAAACCTCAGAAATTTGCTT..............................................................................................2413.00300201
............................................................................................................AGTTTCCGGGATATCGTACTGTAAA....................................................................................................................................................2512.00210100
............................................................................................................AGTTTCCGGGATATCGTACTGTT......................................................................................................................................................2312.00200200
...................................................................................................................................................................ATACGAAACCTCAGAAATTTG.................................................................................................2112.00210100
..............................................................................................................TTTCCGGGATATCGTACTGTATAA...................................................................................................................................................2412.00220000
...................................................................................................................................................................ATACGAAACCTCAGAAATTTGCTA..............................................................................................2412.00200101
...................................................................................................................................................................ATACGAAACCTCAGAAATTTGCC...............................................................................................2312.00210100
...............................................................................................................TTCCGGGATATCGTACTGTAT.....................................................................................................................................................2112.00220000
..............................................................................................................TTTCCGGGATATCGTACTGTAA.....................................................................................................................................................2211.00110000
..........................................................................................................CAAGTTTCCGGGATATCGTACT.........................................................................................................................................................2211.00110000
............................................................................................................AGTTTCCGGGATATCGTACTGTAG.....................................................................................................................................................2411.00110000
............................................................................................................AGTTTCCGGGATATCGTA...........................................................................................................................................................1811.00100100
..................................................................................................................................................................AATACGAAACCTCAGAAATTTGT................................................................................................2311.00100001
............................................................................................................AGTTTCCGGGATATCGTACTGTCA.....................................................................................................................................................2411.00110000
.............................................................................................................GTTTCCGGGATATCGTACTGTAAA....................................................................................................................................................2411.00110000
...............................................................................................................TTCCGGGATATCGTACTGTATTA...................................................................................................................................................2311.00110000
...........................................................................................................AAGTTTCCGGGATATCGTACTA........................................................................................................................................................2211.00100100
.............................................................................................................GTTTCCGGGATATCGTACTGTAA.....................................................................................................................................................2311.00110000
...........................................................................................................AAGTTTCCGGGATATCGTACTG........................................................................................................................................................2211.00100100
...........................................................................................................AAGTTTCCGGGATATCGTACT.........................................................................................................................................................2111.00100001
............................................................................................................AGTTTCCGGGATATCGTACTGTCC.....................................................................................................................................................2411.00110000
..............................................................................................................TTTCCGGGATATCGTACTGTATTAA-.................................................................................................................................................2511.00110000
..............................................................................................................TTTCCGGGATATCGTACTGTAG.....................................................................................................................................................2211.00110000
............................................................................................................AGTTTCCGGGATATCGTACTGA.......................................................................................................................................................2211.00100100
droGri2
------------------------------------------------------------------------------------------CCTGGTATTGCTGCTGCAAATTTCCGCGGTGTCGTATTGTATTAT-C---AAAATGGTATACTCTGAACCACAATACGATTCCTCAGAAATTCGCTGCTGTAAGTTACCGTTTTCAA-CCGTATAGCAACT-----------GTGC---CGATAAACCTATCCCAGTCTATCGATAGACAACGATTGTCAGSizeHit CountTotal NormTotalM041

Female-body		V109

Male-body
...........................................................................................................AAATTTCCGCGGTGTCGTATTG........................................................................................................................................................22174.0074173
..........................................................................................................CAAATTTCCGCGGTGTCGTATT.........................................................................................................................................................22154.0054153
..........................................................................................................CAAATTTCCGCGGTGTCGTAT..........................................................................................................................................................21120.0020020
...........................................................................................................AAATTTCCGCGGTGTCGTATT.........................................................................................................................................................21116.0016115
...........................................................................................................AAATTTCCGCGGTGTCGTAT..........................................................................................................................................................2014.00404
...................................................................................................................................................................ATACGATTCCTCAGAAATTCGCT...............................................................................................2313.00303
...........................................................................................................AAATTTCCGCGGTGTCGTATTT........................................................................................................................................................2212.00202
..........................................................................................................CAAATTTCCGCGGTGTCGTATTG........................................................................................................................................................2312.00202
..........................................................................................................CAAATTTCCGCGGTGTCGTATTT........................................................................................................................................................2312.00202
...................................................................................................................................................................ATACGATTCCTCAGAAATTCG.................................................................................................2112.00202
....................................................................................................................................................................TACGATTCCTCAGAAATTCGCT...............................................................................................2211.00101
..........................................................................................................CAAATTTCCGCGGTGTCGTA...........................................................................................................................................................2011.00101
...................................................................................................................................................................ATACGATTCCTCAGAAATTCGCTT..............................................................................................2411.00101

Generated: 10/21/2015 at 11:53 AM

Re-alignment of all predicted orthologs

Species Coordinate ID Type Alignment
droAna3 scaffold_13417:2468042-2468244 - dan_229 confident TTCC---------------------------------------CCGCACTGAGACAGCTCCTGTGCGACAACCACGGGGTGCGGGGAGTACCTGGTATTATGGCAGCGAGTTTCCGGGATCTCGTACTGTATGAA-G---TTTTCTATAT----------ACAATTCGAAAACTCAGAAACTTCCTGCCGTGAGCTACCATTGATCAACG-GCTGAGTATGCGACCGGAAAGGGGACGCGAATGC------------------------GAGGACTAAAGG
droBip1 scf7180000395874:40400-40532 - AT----------------------------TG------------------------------------------CGGGGTGCGGGGAGTGCCTGGTATTATGGCAGCGAGTTTCCGGGATCTCGTAGTGTATGAA-G---TTTTATAAAT----------ACAATTCGAAAACTCAGAAACTTTCTGCCTTGAAGTACATTCATCAA-CG-GCCGAGTA--------------------------------------------------------------
droKik1 scf7180000302517:1183443-1183539 + ------------------------------------------------------------------------------------------CCTGGTATAGCCGCAGAAAGTTTCCGAG-TTTCGTAATGTATGGTTA---TATTTGAAAT----------ACAGTACGAGACATCAGAAATTTTCGGCAGTTAGCTACCGT--------------------------------------------------------------------------------
droFic1 scf7180000454073:1733615-1733717 + ------------------------------------------------------------------------------------------CTCGGTATTATCGCAGCAAGTTTCCGGGACTTCGTACTGTATGAA-G---AATTCTATAT----------ACAATACGAAACCTCAGAAATTTATTGCAATGAACCACCTTTAACTA--------------------------------------------------------------------------
droEle1 scf7180000490751:1118488-1118609 + ATAT--------------------AG----TG----------CTCGAACAC-AA------------------------------CAACTCCTTGGTATTATCGCAGCAAGTTTCCGGGATTTCGTACTGTATGAC-A---AATTCTATAT----------ACAATACGAAACCTTAGAAATTTTCTGAAGTTAGCTACCAT--------------------------------------------------------------------------------
droRho1 scf7180000761121:190389-190517 - AC----------------------------CA------------------------------------------TTCGGGCCGGAGACATCTTGGTATTATCGCAGCAAGTTTCCGGGATTTCGTACTGTATGAC-A---AATTCTATAT----------ACAATACGAAACCTTAGAAATTTTCTGCAGTTATCTACCATTAACTA-CCAGTT-------------------------------------------------------------------
droBia1 scf7180000302069:1151358-1151516 - TTCCGACTGTTT----GTATGCAT-CCATACACGTGGTTATTTCCAC--AT-GA------------------------------AGACATCTTGGTATTATCGCAACAAGTTTCCGGGATTTTGTATTGTATGACTA---GATTCTATAT----------ACAATACGAAACCTCAGAAATTTTCTGCAGTTAACTACCATAAATCG-CCG----------------------------------------------------------------------
droTak1 scf7180000415169:845145-845295 - TTCCGAATGCGTATGCGTATGCATAGCACACATATG---------AG--AG-GA------------------------------CGACACCTTGGTATTATCGCAACAAGTTTCCGGGATTTCGTACTGTATGCT-G---AATTCTATAT----------ACAATACGAAAGCTCAGAAATTTTCTGCAGTTAACTACCATTAACTA--------------------------------------------------------------------------
droEug1 scf7180000409230:879977-880113 - AA----------------------------TA----------CCCTGATAGAGG------------------------------CGACATCTTGGTATTATCGCAATAAGTTCCTGGGATTTCGCACTGTATTAC-G---ATTTTTACAT----------ACAATACGAAAGCTCAGAAACTAACTGCAATTAACTACCGTAAACTA-CG-GATGAGAACG------------------------------------------------------------
dm3 chrX:19452586-19452627 + ----------------------------------------------------GG------------------------------AGAAGTCTTGGTATTATGGCAAAAAGTTTCCAGGACATTG-------------------------------------------------------------------------------------------------------------------------------------------------------------
droSim2 x:18341755-18341798 + ------------------------------------------------------------------------------------------CTTGGTATTATGGCAACAAGTTTCCAGGACATCGAGCTGTGTGA---------------------------------------------------------------------------------------------------------------------------------------------------
droSec2 scaffold_8:1734625-1734668 + ------------------------------------------------------------------------------------------CTTGGTATTATGGCAACAAGTTTCCAGGACATCGAGCTGTGTGA---------------------------------------------------------------------------------------------------------------------------------------------------
droYak3 X:11886147-11886242 - dya_51 novel ------------------------------------------------------------------------------------------CTTGGTATTATGGCAACAAGTTTCCGGGACTTCGTACTGTATGAC-A---GACTATATAT----------ACAATACGAAGCCTCTGAAATTTTCTGCGCTCAAGTACCA---------------------------------------------------------------------------------
droEre2 scaffold_4690:9688638-9688681 + ------------------------------------------------------------------------------------------CTTGGTATTAAGGCAACAAGTTTCAGGGACTTCGCACTGTATGA---------------------------------------------------------------------------------------------------------------------------------------------------
droWil2 scf2_1100000004909:7956429-7956567 + --------------------------------------------------------------------------------------------TGGTATTATCGCAGCAAGTTTCCGGGATATCGTACTGTATTTC-TAAACATTTCATAT----------ACAATACGAAACCTCAGAAATTTGCTGCGGTTAGTTACCGTTAACAA-CT-CATAAGAAAG-----------GAGA---GAATAAA-----------------------AATGATCAATAT
droGri2 scaffold_15081:2044827-2044998 - dgr_10 confident ------------------------------------------------------------------------------------------CCTGGTATTGCTGCTGCAAATTTCCGCGGTGTCGTATTGTATTAT-C---AAAATGGTATACTCTGAACCACAATACGATTCCTCAGAAATTCGCTGCTGTAAGTTACCGTTTTCAA-CCGTATAGCAACT-----------GTGC---CGATAAACCTATCCCAGTCTATCGATAGACAACGATTGTCAG

Re-alignment of all predicted orthologs with sRNA reads

CGTATAGCAACT-----------GTGC---CGATAAACCTATCCCAGTCTATCGATAGACAACGATTGTCAG
Species Read alignment
droAna3
TTCC---------------------------------------CCGCACTGAGACAGCTCCTGTGCGACAACCACGGGGTGCGGGGAGTACCTGGTATTATGGCAGCGAGTTTCCGGGATCTCGTACTGTATGAA-G---TTTTCTATAT----------ACAATTCGAAAACTCAGAAACTTCCTGCCGTGAGCTACCATTGATCAACG-GCTGAGTATGCGACCGGAAAGGGGACGCGAATGC------------------------GAGGACTAAAGGSizeHit CountTotal NormTotalM044

Female-body		M058

Embryo		V039

Embryo		V055

Head		V105

Male-body		V106

Head
...................................................................................................................................................................ATTCGAAAACTCAGAAACTTCCT...............................................................................................23146.00463105829
..................................................................................................................................................................AATTCGAAAACTCAGAAACTTC.................................................................................................22120.0020410447
............................................................................................................AGTTTCCGGGATCTCGTACTG........................................................................................................................................................21117.00173000131
............................................................................................................AGTTTCCGGGATCTCGTACTGT.......................................................................................................................................................22114.0014500180
............................................................................................................AGTTTCCGGGATCTCGTACTGTA......................................................................................................................................................23111.0011400241
.................................................................................................................................................................CAATTCGAAAACTCAGAAACTTC.................................................................................................23110.0010010423
....................................................................................................................................................................TTCGAAAACTCAGAAACTTCCT...............................................................................................2216.006000114
.................................................................................................................................................................CAATTCGAAAACTCAGAAACTT..................................................................................................2214.004000022
............................................................................................................AGTTTCCGGGATCTCGTACT.........................................................................................................................................................2013.003000012
..................................................................................................................................................................AATTCGAAAACTCAGAAACTTCC................................................................................................2313.003100011
...................................................................................................................................................................ATTCGAAAACTCAGAAACTTCCTT..............................................................................................2412.002100001
...................................................................................................................................................................ATTCGAAAACTCAGAAACTTC.................................................................................................2111.001000010
..........................................................................................................CGAGTTTCCGGGATCTCGTACTGTATGA...................................................................................................................................................2811.001100000
..............................................................................................................TTTCCGGGATCTCGTACTGTAT.....................................................................................................................................................2211.001000010
...................................................................................................................................................................ATTCGAAAACTCAGAAACTTCCC...............................................................................................2311.001000001
............................................................................................................AGTTTCCGGGATCTCGTACTT........................................................................................................................................................2111.001000010
..................................................................................................................................................................AATTCGAAAACTCAGAAACTTT.................................................................................................2211.001100000
............................................................................................................AGTTTCCGGGATCTCGTACTGTAAA....................................................................................................................................................2511.001000100
..................................................................................................................................................................AATTCGAAAACTCAGAAACTTCA................................................................................................2311.001100000
...................................................................................................................................................................ATTCGAAAACTCAGAAACTTCC................................................................................................2211.001000001
...........................................................................................................GAGTTTCCGGGATCTCGTACT.........................................................................................................................................................2111.001000010
............................................................................................................AGTTTCCGGGATCTCGTACTA........................................................................................................................................................2111.001000010
.............................................................................................................GTTTCCGGGATCTCGTACTG........................................................................................................................................................2011.001000100
...........................................................................................................GAGTTTCCGGGATCTCGTACTG........................................................................................................................................................2211.001000010
............................................................................................................AGTTTCCGGGATCTCGTACTGTAA.....................................................................................................................................................2411.001000010
..............................................................................................................TTTCCGGGATCTCGTACTGTATG....................................................................................................................................................2311.001100000
..................................................................................................................CGGGATCTCGTACTGTATGAA-G---.............................................................................................................................................2211.001000010
..................................................................................................................................................ATAT----------ACAATTCGAAAACTCAGA.......................................................................................................2211.001000010
.............................................................................................................GTTTCCGGGATCTCGTACTGTT......................................................................................................................................................2211.001100000
..........................................................................................................CGAGTTTCCGGGATCTCGTAC..........................................................................................................................................................2111.001000010
...........................................................................................................GAGTTTCCGGGATCTCGTACTGA.......................................................................................................................................................2311.001000010
droBip1
AT----------------------------TG------------------------------------------CGGGGTGCGGGGAGTGCCTGGTATTATGGCAGCGAGTTTCCGGGATCTCGTAGTGTATGAA-G---TTTTATAAAT----------ACAATTCGAAAACTCAGAAACTTTCTGCCTTGAAGTACATTCATCAA-CG-GCCGAGTA--------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droKik1
------------------------------------------------------------------------------------------CCTGGTATAGCCGCAGAAAGTTTCCGAG-TTTCGTAATGTATGGTTA---TATTTGAAAT----------ACAGTACGAGACATCAGAAATTTTCGGCAGTTAGCTACCGT--------------------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droFic1
------------------------------------------------------------------------------------------CTCGGTATTATCGCAGCAAGTTTCCGGGACTTCGTACTGTATGAA-G---AATTCTATAT----------ACAATACGAAACCTCAGAAATTTATTGCAATGAACCACCTTTAACTA--------------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droEle1
ATAT--------------------AG----TG----------CTCGAACAC-AA------------------------------CAACTCCTTGGTATTATCGCAGCAAGTTTCCGGGATTTCGTACTGTATGAC-A---AATTCTATAT----------ACAATACGAAACCTTAGAAATTTTCTGAAGTTAGCTACCAT--------------------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droRho1
AC----------------------------CA------------------------------------------TTCGGGCCGGAGACATCTTGGTATTATCGCAGCAAGTTTCCGGGATTTCGTACTGTATGAC-A---AATTCTATAT----------ACAATACGAAACCTTAGAAATTTTCTGCAGTTATCTACCATTAACTA-CCAGTT-------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droBia1
TTCCGACTGTTT----GTATGCAT-CCATACACGTGGTTATTTCCAC--AT-GA------------------------------AGACATCTTGGTATTATCGCAACAAGTTTCCGGGATTTTGTATTGTATGACTA---GATTCTATAT----------ACAATACGAAACCTCAGAAATTTTCTGCAGTTAACTACCATAAATCG-CCG----------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droTak1
TTCCGAATGCGTATGCGTATGCATAGCACACATATG---------AG--AG-GA------------------------------CGACACCTTGGTATTATCGCAACAAGTTTCCGGGATTTCGTACTGTATGCT-G---AATTCTATAT----------ACAATACGAAAGCTCAGAAATTTTCTGCAGTTAACTACCATTAACTA--------------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droEug1
AA----------------------------TA----------CCCTGATAGAGG------------------------------CGACATCTTGGTATTATCGCAATAAGTTCCTGGGATTTCGCACTGTATTAC-G---ATTTTTACAT----------ACAATACGAAAGCTCAGAAACTAACTGCAATTAACTACCGTAAACTA-CG-GATGAGAACG------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
dm3
----------------------------------------------------GG------------------------------AGAAGTCTTGGTATTATGGCAAAAAGTTTCCAGGACATTG-------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalGSM154618

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		GSM239041

Head		GSM239050

Head		GSM239051

S2		GSM239052

S2		GSM246084

Head		GSM266765

S2		GSM280082

Ovary		GSM280083

Ovary		GSM280084

Ovary		GSM280085

Testis		GSM280086

Ovary		GSM280087

S2-NP		GSM280088

S2-NP		GSM312995

Head		GSM313160

Head		GSM313161

Head		GSM313162

Head		GSM313163

Head		GSM313164

Head		GSM313165

Head		GSM343287

Embryo		GSM379050

Ovary		GSM379051

Ovary		GSM379052

Ovary		GSM379053

Ovary		GSM379054

Ovary		GSM379055

Ovary		GSM379056

Ovary		GSM379057

Ovary		GSM379058

Ovary		GSM379059

Ovary		GSM379060

Ovary		GSM379061

Ovary		GSM379062

Ovary		GSM379063

Ovary		GSM379064

Ovary		GSM379065

Ovary		GSM379066

Ovary		GSM379067

Ovary		GSM424739

S2		GSM424740

S2		GSM424741

S2		GSM467729

Female-body		GSM467730

Female-body		GSM467731

Female-body		M002

CS		M003

Male-body		M004

Male-body		M005

ML-DmD32		M006

ML-DmD32		M029

OSC		M030

OSC		M031

OSC		M032

S2-R+		M033

S2-R+		M034

S2-R+		M035

S2-R+		M036

S2-R+		M037

S2-R+		M038

S2-R+		M039

S2-R+		M048

S2-R+		OSS2

OSS		OSS6

OSS		OSS7

OSS		OSS8

OSS		S1

Head		S10

Embryo		S11

Embryo		S12

Embryo		S13

Embryo		S14

Embryo		S15

S2-GMR		S16

Kc		S17

Larvae		S18

Larvae		S19

Pupae		S2

Head		S20

Pupae		S21

Disc		S22

Head		S23

Female-body		S24

Male-body		S25

Larvae		S26

Larvae		S27

Pupae		S28

Pupae		S29

Head		S3

Male-body		S30

S2-GMR		S31

S2		S32

S2		S33

Kc		S34

Kc		S35

Kc		S4

Female-body		S5

Disc		S6

Embryo		S7

Embryo		S8

S2		S9

Embryo		SRR001337

Head		SRR001338

Head		SRR001339

Head		SRR001340

Head		SRR001341

Head		SRR001342

Head		SRR001343

Head		SRR001344

Head		SRR001345

Head		SRR001346

Head		SRR001347

Head		SRR001348

Head		SRR001349

Head		SRR001664

Head		SRR010951

Ovary		SRR010952

Ovary		SRR010953

Ovary		SRR010954

Ovary		SRR010955

Ovary		SRR010956

Ovary		SRR010957

Ovary		SRR010958

Ovary		SRR010959

Ovary		SRR010960

Ovary		SRR014268

Embryo		SRR014269

Embryo		SRR014270

Embryo		SRR014271

Embryo		SRR014272

Embryo		SRR014273

Ovary		SRR014274

Ovary		SRR014275

Ovary		SRR014276

Ovary		SRR014277

Ovary		SRR014278

Ovary		SRR014279

Ovary		SRR014280

Ovary		SRR014281

Ovary		SRR014282

Ovary		SRR023197

S2		SRR023399

S2		SRR023400

S2		SRR023402

S2		SRR023407

S2		SRR029028

S2		SRR029029

S2		SRR029030

S2		SRR029031

S2		SRR029032

S2		SRR029033

S2		SRR029608

Head		SRR029633

Head		SRR030145

gb3		SRR031692

Head		SRR031693

Head		SRR031694

Head		SRR031696

Head		SRR031697

Head		SRR031698

Head		SRR031699

Head		SRR031700

Head		SRR031701

Head		SRR031702

Head		SRR031703

Head		SRR031704

Head		SRR032092

S2		SRR032093

S2		SRR032094

S2		SRR032095

S2-NP		SRR032096

S2-NP		SRR032152

Head		SRR060643

Testis		SRR060644

Ovary		SRR060645

Testis		SRR060646

Ovary		SRR060647

Ovary		SRR060648

Ovary		SRR060649

Ovary		SRR060650

Testis		SRR060651

Ovary		SRR060652

Testis		SRR060653

Ovary		SRR065151

Ovary		SRR065152

Ovary		SRR065153

Ovary		SRR065154

Ovary		SRR065155

Ovary		SRR065800

Ovary		SRR065801

Ovary		SRR065802

Ovary		SRR065803

Ovary		SRR065804

Ovary		SRR065805

Ovary		SRR065806

Ovary		SRR065807

Ovary		SRR097865

S2-NP		SRR097866

S2-NP		SRR097867

S2-NP		SRR298536

Ovary		SRR298537

Ovary		SRR298711

Ovary		SRR298712

Ovary		SRR317110

Ovary		SRR317111

Ovary		SRR317112

Ovary		SRR317113

Ovary		SRR317114

Ovary		SRR317115

Ovary		SRR317116

Ovary		SRR317117

Ovary		SRR341115

S2		SRR341116

S2		SRR341117

S2		SRR341118

S2		SRR351332

Mixed-body		SRR351333

Mixed-body		T004

OSC		T005

CME-L1		V001

Embryo		V002

Embryo		V003

S2		V006

Female-body		V007

Head		V008

S2		V009

CME-L1		V010

ML-DmD20-C5		V011

Sg4		V012

Male-body		V013

Head		V014

DTT		V015

DreRFHV		V018

Kc167		V019

GM2		V020

S2-R+		V021

ML-DmD21		V022

ML-DmD32		V023

Head		V024

Kc167		V025

S2-R+		V026

1182-2H		V027

ML-DmD21		V028

CME-W1-Cl.8+		V029

ML-DmD9		V030

ML-DmD8		V031

GM2		V032

S1		V033

CME-W1-Cl.8+		V034

ML-DmD16-C3		V035

ML-DmD32		V036

ML-DmD20-C5		V037

S2		V038

S2		V063

Ovary		V0632

Ovary		V064

Ovary		V0642

Ovary		V065

Ovary		V0652

Ovary		V066

Ovary		V0662

Ovary		V067

S2-NP		V073

mbn2		V074

S3		V075

ML-DmBG1-C1		V076

ML-DmBG3-C2		V077

Head		V078

Head		V079

Head		V080

Head		V081

Embryo		V082

Embryo		V083

Male-body		V084

Female-body		V085

CME-W2		V086

Female-body		V088

Ovary		V0882

Ovary		V089

Ovary		V0892

Ovary		V090

Male-body		V091

fGS/OSS		V092

Male-body		V093

Male-body		V094

S2-R+		V095

S2-R+		V096

Ovary		V097

Ovary		V098

Ovary		V125

ML-DmD9		V126

CME-L1		V127

G2		V128

S3		V129

ML-DmBG1-C1		V130

ML-DmBG3-C2		V131

ML-DmD16-C3		V132

ML-DmD32		V133

Sg4		V134

ML-DmD8		V135

CME-W2		V136

Male-body		V137

Head		V138

Male-body		V139

Female-body		V140

Female-body		V141

Female-body		V142

Female-body		V144

OSC		V145

S2		V146

S1		V147

1182-2H		V148

mbn2		GSM1528798

follicle cells
No Reads
droSim2
------------------------------------------------------------------------------------------CTTGGTATTATGGCAACAAGTTTCCAGGACATCGAGCTGTGTGA---------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalM023

Head		M024

Male-body		M025

Embryo		M053

Female-body		O001

Testis		O002

Head		SRR553485

Ovary		SRR553486

Ovary		SRR553487

Ovary		SRR553488

Ovary		SRR618934

Ovary		V044

Embryo		SRR902008

Ovary		SRR902009

Testis		SRR1275487

Male larvae		SRR1275485

Male prepupae		SRR1275483

Male prepupae
No Reads
droSec2
------------------------------------------------------------------------------------------CTTGGTATTATGGCAACAAGTTTCCAGGACATCGAGCTGTGTGA--------------------------------------------Show Alignment With Reads

Re-alignment of all predicted orthologs

Species Coordinate ID Type Alignment
droAna3 scaffold_13417:2468042-2468244 - dan_229 confident TTCC---------------------------------------CCGCACTGAGACAGCTCCTGTGCGACAACCACGGGGTGCGGGGAGTACCTGGTATTATGGCAGCGAGTTTCCGGGATCTCGTACTGTATGAA-G---TTTTCTATAT----------ACAATTCGAAAACTCAGAAACTTCCTGCCGTGAGCTACCATTGATCAACG-GCTGAGTATGCGACCGGAAAGGGGACGCGAATGC------------------------GAGGACTAAAGG
droBip1 scf7180000395874:40400-40532 - AT----------------------------TG------------------------------------------CGGGGTGCGGGGAGTGCCTGGTATTATGGCAGCGAGTTTCCGGGATCTCGTAGTGTATGAA-G---TTTTATAAAT----------ACAATTCGAAAACTCAGAAACTTTCTGCCTTGAAGTACATTCATCAA-CG-GCCGAGTA--------------------------------------------------------------
droKik1 scf7180000302517:1183443-1183539 + -------------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalM054

Female-body		V113

Male-body		V114

Embryo		V115

Head
No Reads
droYak3 Show Alignment With Reads

Re-alignment of all predicted orthologs

------------------------------------------------------------------------------------------CTTGGTATTATGGCAACAAGTTTCCGGGACTTCGTACTGTATGAC-A---GACTATATAT----------ACAATACGAAGCCTCTGAAATTTTCTGCGCTCAAGTACCA--------------------------------------------------------------------------CCTGGTATAGCCGCAGAAAGTTTCCGAG-TTTCGTAATGTATGGTTA---TATTTGAAAT----------ACAGTACGAGACATCAGAAATTTTCGGCAGTTAGCTACCGT--------------------------------------------------------------------------------
droFic1 scf7180000454073:1733615-1733717 + ------------------------------------------------------------------------------------------CTCGGTATTATCGCAGCAAGTTTCCGGGACTTCGTACTGTATGAA-G---AATTCTATAT----------ACAATACGAAACCT-------------------------------------SizeHit CountTotal NormTotalM026

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
..................................................................................................................................................................AATACGAAGCCTCTGAAATTTT.................................................................................................221129.0012911211000150000
............................................................................................................AGTTTCCGGGACTTCGTACTGT.......................................................................................................................................................22184.00846031110180000
...................................................................................................................................................................ATACGAAGCCTCTGAAATTTTCT...............................................................................................23130.0030300000000000
............................................................................................................AGTTTCCGGGACTTCGTACTG........................................................................................................................................................21128.0028710000200000
..................................................................................................................................................................AATACGAAGCCTCTGAAATTT..................................................................................................21123.0023211000010000
............................................................................................................AGTTTCCGGGACTTCGTACTGG.......................................................................................................................................................22118.0018180000000000
............................................................................................................AGTTTCCGGGACTTCGTACTGC.......................................................................................................................................................22111.0011110000000000
............................................................................................................AGTTTCCGGGACTTCGTACT.........................................................................................................................................................2018.00800001160000
............................................................................................................AGTTTCCGGGACTTCGTAC..........................................................................................................................................................1916.00660000000000
............................................................................................................AGTTTCCGGGACTTCGTACTGTT......................................................................................................................................................2315.00550000000000
............................................................................................................AGTTTCCGGGACTTCGTACTGTA......................................................................................................................................................2315.00550000000000
...................................................................................................................................................................ATACGAAGCCTCTGAAATTTTCTG..............................................................................................2415.00550000000000
..................................................................................................................................................................AATACGAAGCCTCTGAAATT...................................................................................................2013.00330000000000
....................................................................................................................................................................TACGAAGCCTCTGAAATTTTCT...............................................................................................2213.00330000000000
...................................................................................................................................................................ATACGAAGCCTCTGAAATTTTC................................................................................................2212.00210000010000
....................................................................................................................................................................TACGAAGCCTCTGAAATTTTCTG................................................>CAGAAATTTATTGCAATGAACCACCTTTAACTA--------------------------------------------------------------------------
droEle1 scf7180000490751:1118488-1118609 + ATAT--------------------AG----TG----------CTCGAACAC-AA------------------------------CAACTCCTTGGTATTATCGCAGCAAGTTTCCGGGATTTCGTACTGTATGAC-A---AATTCTATAT----------ACAATACGAAACCTTAGAAATTTTCTGAAGTTAGCTACCAT--------------------------------------------------------------------------------
droRho1 scf7180000761121:190389-190517 -
Species Coordinate ID Type Alignment
droAna3 scaffold_13417:2468042-2468244 - dan_229 confident TTCC---------------------------------------CCGCACTGAGACAGCTCCTGTGCGACAACCACGGGGTGCGGGGAGTACCTGGTATTATGGCAGCGAGTTTCCGGGATCTCGTACTGTATGAA-G---TTTTCTATAT----------ACAATTCGAAAACTCAGAAACTTCCTGCCGTGAGCTACCATTGATCAACG-GCTGAGTATGCGACCGGAAAGGGGACGCGAATGC------------------------GAGGACTAAAGG
droBip1 scf7180000395874:40400-40532 - AT----------------------------TG------------------------------------------CGGGGTGCGGGGAGTGCCTGGTATTATGGCAGCGAGTTTCCGGGATCTCGTAGTGTATGAA-G---TTTTATAAAT----------ACAATTCGAAAACTCAGAAACTTTCTGCCTTGAAGTACATTCATCAA-CG-GCCGAGTA--------------------------------------------------------------
droKik1 scf7180000302517:1183443-1183539 + ------------------------------------------------------------C...............................................................................................2311.00110000000000
................................................................................................................TCCGGGACTTCGTACTGTATGA...................................................................................................................................................2211.00101000000000
.............................................................................................................GTTTCCGGGACTTCGTACTGTT......................................................................................................................................................2211.00110000000000
............................................................................................................AGTTTCCGGGACTTCGTACTT........................................................................................................................................................2111.00110000000000
...................................................................................................................................................................ATACGAAGCCTCTGAAATTTTCTGC.............................................................................................2511.00110000000000
...................................................................................................................................................................ATACGAAGCCTCTGAAATTTT.................................................................................................2111.00110000000000
....................................................................................................................................................................TACGAAGCCTCTGAAATTTTC................................................................................................2111.00110000000000
.................................................................................................................................................................CAATACGAAGCCTCTGAAATTTT.................................................................................................2311.00100000100000
droEre2
------------------------------------------------------------------------------------------CTTGGTATTAAGGCAACAAGTTTCAGGGACTTCGCACTGTATGA------------------------------------------- AC----------------------------CA------------------------------------------TTCGGGCCGGAGACATCTTGGTATTATCGCAGCAAGTTTCCGGGATTTCGTACTGTATGAC-A---AATTCTATAT----------ACAATACGAAACCTTAGAAATTTTCTGCAGTTATCTACCATTAACTA-CCAGTT-------------------------------------------------------------------
droBia1 scf7180000302069:1151358-1151516 - TTCCGACTGTTT----GTATGCAT-CCATACACGTGGTTATTTCCAC--AT-GA------------------------------AGACATCTTGGTATTATCGCAACAAGT------------------------------CCTGGTATAGCCGCAGAAAGTTTCCGAG-TTTCGTAATGTATGGTTA---TATTTGAAAT----------ACAGTACGAGACATCAGAAATTTTCGGCAGTTAGCTACCGT--------------------------------------------------------------------------------
droFic1 scf7180000454073:1733615-1733717 + ------------------------------------------------------------------------------------------CTCGGTATTATCGCAGCAAGTTTCCGGGACTTCGTACTGTATGAA-G---AATTCTATAT----------ACAATACGAAACCT--------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalM055

Female-body		M057

Embryo		V060

Head		V040

Embryo		V107

Male-body		V108

Head		GSM1528801

follicle cells
No Reads
droWil2 AT
--------------------------------------------------------------------------------------------TGGTATTATCGCAGCAAGTTTCCGGGATATCGTACTGTATTTC-TAAACATTTCATAT----------ACAATACGAAACCTCAGAAATTTGCTGCGGTTAGTTACCGTTAACAA-CT-CATAAGAAAG-----------GAGA---GAATAAA-----------------------AATGATCAATTTCCGGGATTTTGTATTGTATGACTA---GATTCTATAT----------ACAATACGAAACCTCAGAAATTTTCTGCAGTTAACTACCATAAATCG-CCG----------------------------------------------------------------------
droTak1 scf7180000415169:845145-845295 - TTCCGAATGCGTATGCGTATGCATAGCACACATATG---------AG--AG-GA------------------------------CGACACCTTGGTATTATCGCAACAAGTTTCCGGGATTTCGTACTGTATGCT-G---AATTCTATAT----------ACAATACGAAAGCTCAGAAATTTTCTGCAGTTAACTACCATTAACTA----CAGAAATTTATTGCAATGAACCACCTTTAACTA--------------------------------------------------------------------------
droEle1 scf7180000490751:1118488-1118609 + ATAT--------------------AG----TG----------CTCGAACAC-AA------------------------------CAACTCCTTGGTATTATCGCAGCAAGTTTCCGGGATTTCGTACTGTATGAC-A---AATTCTATAT----------ACAATACGAAACCTTAGAAATTTTCTGAAGTTAGCTACCAT--------------------------------------------------------------------------------
droRho1 scf7180000761121:190389-190517 - SizeHit CountTotal NormTotalM020

Head		M045

Female-body		V117

Male-body		V118

Embryo		V119

Head
............................................................................................................AGTTTCCGGGATATCGTACTGTA......................................................................................................................................................231290.0029023605310
...................................................................................................................................................................ATACGAAACCTCAGAAATTTGCT...............................................................................................231173.00173101811566
..............................................................................................................TTTCCGGGATATCGTACTGTAT.....................................................................................................................................................221161.0016112323402
............................................................................................................AGTTTCCGGGATATCGTACTGT.......................................................................................................................................................221139.001394908901
............................................................................................................AGTTTCCGGGATATCGTACTGTAA.....................................................................................................................................................241124.0012410302100
............................................................................................................AGTTTCCGGGATATCGTAC..........................................................................................................................................................19138.0038380000
...............................................................................................................TTCCGGGATATCGTACTGTATTT...................................................................................................................................................23133.0033300300
............................................................................................................AGTTTCCGGGATATCGTACTG........................................................................................................................................................21121.0021002001
...............................................................................................................TTCCGGGATATCGTACTGTATT....................................................................................................................................................22116.0016130300
...................................................................................................................................................................ATACGAAACCTCAGAAATTTGC................................................................................................22113.001331324
..............................................................................................................TTTCCGGGATATCGTACTGTATT....................................................................................................................................................2317.00750200
............................................................................................................AGTTTCCGGGATATCGTACTGTC......................................................................................................................................................2317.00760100
....................................................................................................................................................................TACGAAACCTCAGAAATTTGCT...............................................................................................2216.00600402
............................................................................................................AGTTTCCGGGATATCGTACTGC.......................................................................................................................................................2216.00660000
............................................................................................................AGTTTCCGGGATATCGTACT.........................................................................................................................................................2016.00610500
..............................................................................................................TTTCCGGGATATCGTACTGTAC.....................................................................................................................................................2216.00660000
............................................................................................................AGTTTCCGGGATATCGTACTGTAT.....................................................................................................................................................2416.00650001
..............................................................................................................TTTCCGGGATATCGTACTGTA......................................................................................................................................................2115.00540100
..................................................................................................................................................................AATACGAAACCTCAGAAATTTG.................................................................................................2215.00530200
...........................................................................................................AN class="mismatchAny">----------------------------------------------------------------------
droEug1 scf7180000409230:879977-880113 - AA----------------------------TA----------CCCTGATAGAGG------------------------------CGACATCTTGGTATTATCGCAATAAGTTCCTGGGATTTCGCACTGTATTAC-G---ATTTTTACAT----------ACAATACGAAAGCTCAGAAACTAACTGCAATTAACTACCGTAAACTA-CG-GATGAGAACG------------------------------------------------------------
dm3 chrX:19452586-19452627 + ----------------------------------------------------GG--------------- AC----------------------------CA------------------------------------------TTCGGGCCGGAGACATCTTGGTATTATCGCAGCAAGTTTCCGGGATTTCGTACTGTATGAC-A---AATTCTATAT----------ACAATACGAAACCTTAGAAATTTTCTGCAGTTATCTACCATTAACTA-CCAGTT-------------------------------------------------------------------
droBia1 scf7180000302069:1151358-1151516 - TTCCGACTGTTT----GTATGCAT-CCATACACGTGGTTATTTCCAC--AT-GA------------------------------AGACATCTTGGTATTATCGCAACAAGTG.......................................................................................................................................................2214.00440000
............................................................................................................AGTTTCCGGGATATCGTACTGTAC.....................................................................................................................................................2413.00330000
...................................................................................................................................................................ATACGAAACCTCAGAAATTTGCTT..............................................................................................2413.00300201
............................................................................................................AGTTTCCGGGATATCGTACTGTAAA....................................................................................................................................................2512.00210100
............................................................................................................AGTTTCCGGGATATCGTACTGTT......................................................................................................................................................2312.00200200
...................................................................................................................................................................ATACGAAACCTCAGAAATTTG.................................................................................................2112.00210100
..............................................................................................................TTTCCGGGATATCGTACTGTATAA...................................................................................................................................................2412.00220000
...................................................................................................................................................................ATACGAAACCTCAGAAATTTGCTA..............................................................................................2412.00200101
...................................................................................................................................................................ATACGAAACCTCAGAAATTTGCC...............................................................................................2312.00210100
...............................................................................................................TTCCGGGATATCGTACTGTAT.....................................................................................................................................................2112.00220000
..............................................................................................................TTTCCGGGATATCGTACTGTAA.....................................................................................................................................................2211.00110000
..........................................................................................................CAAGTTTCCGGGATATCGTACT.........................................................................................................................................................2211.00110000
............................................................................................................AGTTTCCGGGATATCGTACTGTAG.....................................................................................................................................................2411.00110000
............................................................................................................AGTTTCCGGGATATCGTA...........................................................................................................................................................1811.00100100
..................................................................................................................................................................AATACGAAACCTCAGAAATTTGT................................................................................................2311.00100001
............................................................................................................AGTTTCCGGGATATCGTACTGTCA.....................................................................................................................................................2411.00110000
.............................................................................................................GTTTCCGGGATATCGTACTGTAAA....................................................................................................................................................2411.00110000
......................................................................................................lass="mismatchAny">---------------AGAAGTCTTGGTATTATGGCAAAAAGTTTCCAGGACATTG-------------------------------------------------------------------------------------------------------------------------------------------------------------
droSim2 x:18341755-18341798 + ------------------------------------------------------------------------------------------CTTGGTATTATGGCAACAAGTTTCCAGGACATCGAGCTGTGTGA--TTCCGGGATTTTGTATTGTATGACTA---GATTCTATAT----------ACAATACGAAACCTCAGAAATTTTCTGCAGTTAACTACCATAAATCG-CCG----------------------------------------------------------------------
droTak1 scf7180000415169:845145-845295 - TTCCGAATGCGTATGCGTATGCATAGCACACATATG---------AG--AG-GA------------------------------CGACACCTTGGTATTATCGCAACAAGTTTCCGGGATTTCGTACTGTATGCT-G---AATTCTATAT----------ACAATACGAAAGCTCAGAAATTTTCTGCAGTTAACTACCATTAACTA-----------------------------------------------------------------------------------------------------------------------------------------------------
droSec2 scaffold_8:1734625-1734668 + ------------------------------------------------------------------------------------------CTTGGTATTATGGCAACAAGTTTCCAGGACATCGAGCTGTGTGA---------------------------------------------------------------A...................................................................................................................................................2311.00110000
...........................................................................................................AAGTTTCCGGGATATCGTACTA........................................................................................................................................................2211.00100100
.............................................................................................................GTTTCCGGGATATCGTACTGTAA.....................................................................................................................................................2311.00110000
...........................................................................................................AAGTTTCCGGGATATCGTACTG........................................................................................................................................................2211.00100100
...........................................................................................................AAGTTTCCGGGATATCGTACT.........................................................................................................................................................2111.00100001
............................................................................................................AGTTTCCGGGATATCGTACTGTCC.....................................................................................................................................................2411.00110000
..............................................................................................................TTTCCGGGATATCGTACTGTATTAA-.................................................................................................................................................2511.00110000
..............................................................................................................TTTCCGGGATATCGTACTGTAG.....................................................................................................................................................2211.00110000
............................................................................................................AGTTTCCGGGATATCGTACTGA.......................................................................................................................................................2211.00100100
droGri2 ---------------AGAAGTCTTGGTATTATGGCAAAAAGTTTCCAGGACATTG-------------------------------------------------------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------CCTGGTATTGCTGCTGCAAATTTCCGCGGTGTCGTATTGTATTAT-C---AAAATGGTATACTCTGAACCACAATACGATTCCTCAGAAATTCGCTGCTGTAAGTTACCGTTT----------------------------------------------------------------------
droEug1 scf7180000409230:879977-880113 - AA----------------------------TA----------CCCTGATAGAGG------------------------------CGACATCTTGGTATTATCGCAATAAGTTCCTGGGATTTCGCACTGTATTAC-G---ATTTTTACAT----------ACAATACGAAAGCTCAGAAACTAACTGCAATTAACTACCGTAAACTA-CG-GATGAGAACG------------------------------------------------------------
dm3 chrX:19452586-19452627 + ----------------------------------------------------GG---------------------------------------------------------------------------------------------------
droYak3 X:11886147-11886242 - dya_51 novel ------------------------------------------------------------------------------------------CTTGGTATTATGGCAACAAGTTTCCGGGACTTCGTACTGTATGAC-A---GACTATATAT----------ACAATACGAAGCCTCTGAAATTTTCTGCGCTCAAGTACCA---------------------------------------------------------------------------------
droEre2 scaffold_4690:9688638-9688681 +
droSim2 x:18341755-18341798 + ------------------------------------------------------------------------------------------CTTGGTATTATGGCAACAAGTTTCCAGGACATCGAGCTGTGTGA--TCAA-CCGTATAGCAACT-----------GTGC---CGATAAACCTATCCCAGTCTATCGATAGACAACGATTGTCAGSizeHit CountTotal NormTotalM041

Female-body		V109

Male-body
...........................................................................................................AAATTTCCGCGGTGTCGTATTG........................................................................................................................................................22174.0074173
..........................................................................................................CAAATTTCCGCGGTGTCGTATT.........................................................................................................................................................22154.0054153
..........................................................................................................CAAATTTCCGCGGTGTCGTAT..........................................................................................................................................................21120.0020020
...........................................................................................................AAATTTCCGCGGTGTCGTATT.........................................................................................................................................................21116.0016115
...........................................................................................................AAATTTCCGCGGTGTCGTAT..........................................................................................................................................................2014.00404
...................................................................................................................................................................ATACGATTCCTCAGAAATTCGCT...............................................................................................2313.00303
...........................................................................................................AAATTTCCGCGGTGTCGTATTT........................................................................................................................................................2212.00202
..........................................................................................................CAAATTTCCGCGGTGTCGTATTG........................................................................................................................................................2312.00202
..........................................................................................................CAAATTTCCGCGGTGTCGTATTT........................................................................................................................................................2312.00202
...................................................................................................................................................................ATACGATTCCTCAGAAATTCG.................................................................................................2112.00202
....................................................................................................................................................................TACGATTCCTCAGAAATTCGCT...............................................................................................2211.00101
..........................................................................................................CAAATTTCCGCGGTGTCGTA...........................................................................................................................................................2011.00101
...................................................................................................................................................................ATACGATTCCTCAGAAATTCGCTT..............................................................................................2411.00101
td>		 ------------------------------------------------------------------------------------------CTTGGTATTAAGGCAACAAGTTTCAGGGACTTCGCACTGTATGA---------------------------------------------------------------------------------------------------------------------------------------------------
droWil2 scf2_1100000004909:7956429-7956567 + --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droSec2 scaffold_8:1734625-1734668 + ------------------------------------------------------------------------------------------CTTGGTATTATGGCAACAAGTTTCCAGGACATCGAGCTGTGTGA----------------------------------------------------------------------TGGTATTATCGCAGCAAGTTTCCGGGATATCGTACTGTATTTC-TAAACATTTCATAT----------ACAATACGAAACCTCAGAAATTTGCTGCGGTTAGTTACCGTTAACAA-CT-CATAAGAAAG-----------GAGA---GAATAAA-----------------------AATGATCAATAT
droGri2 scaffold_15081:2044827-2044998 - dgr_10 confident ------------------------------------------------------------------------------------------CCTGGTATTGCTGCTGCAAATTTCCGCGGTGTCGTATTGTATTAT-C---AAAATGGTATACTCTGAACCACAATACGATTCCTCAGAAATTCGCTGCTGTAAGTTACCGTTTTCAA-C------------------------------------------------------------------------------------
droYak3 X:11886147-11886242 - dya_51 novel ------------------------------------------------------------------------------------------CTTGGTATTATGGCAACAAGTTTCCGGGACTTCGTACTGTATGAC-A---GACTATATAT----------ACAATACGAAGCCTCTGAAATTTTCTGCGCTCAAGTACCA---------------------------------------------------------------------------------
droEre2 scaffold_4690:9688638-9688681 +

Re-alignment of all predicted orthologs with sRNA reads

Species Read alignment
droAna3
TTCC---------------------------------------CCGCACTGAGACAGCTCCTGTGCGACAACCACGGGGTGCGGGGAGTACCTGGTATTATGGCAGCGAGTTTCCGGGATCTCGTACTGTATGAA-G---TTTTCTATAT----------ACAATTCGAAAACTCAGAAACTTCCTGCCGTGAGCTACCATTGATCAACG-GCTGAGTATGCGACCGGAAAGGGGACGCGAATGC------------------------GAGGACTAAAGGSizeHit CountTotal NormTotalM044

Female-body		M058

Embryo		V039

Embryo		V055

Head		V105

Male-body		V106

Head
...................................................................................................................................................................ATTCGAAAACTCAGAAACTTCCT...............................................................................................23146.00463105829
..................................................................................................................................................................AATTCGAAAACTCAGAAACTTC.................................................................................................22120.0020410447
............................................................................................................AGTTTCCGGGATCTCGTACTG........................................................................................................................................................21117.00173000131
............................................................................................................AGTTTCCGGGATCTCGTACTGT.......................................................................................................................................................22114.0014500180
............................................................................................................AGTTTCCGGGATCTCGTACTGTA......................................................................................................................................................23111.0011400241
.................................................................................................................................................................CAATTCGAAAACTCAGAAACTTC.................................................................................................23110.0010010423
....................................................................................................................................................................TTCGAAAACTCAGAAACTTCCT...............................................................................................2216.006000114
.................................................................................................................................................................CAATTCGAAAACTCAGAAACTT..................................................................................................2214.004000022
............................................................................................................AGTTTCCGGGATCTCGTACT.........................................................................................................................................................2013.003000012
............................................................................................................................td> ------------------------------------------------------------------------------------------CTTGGTATTAAGGCAACAAGTTTCAGGGACTTCGCACTGTATGA---------------------------------------------------------------------------------------------------------------------------------------------------
droWil2 scf2_1100000004909:7956429-7956567 + -------------------------------------------------------------------------------------T..............................................................................................2412.002100001
...................................................................................................................................................................ATTCGAAAACTCAGAAACTTC.................................................................................................2111.001000010
..........................................................................................................CGAGTTTCCGGGATCTCGTACTGTATGA...................................................................................................................................................2811.001100000
..............................................................................................................TTTCCGGGATCTCGTACTGTAT.....................................................................................................................................................2211.001000010
...................................................................................................................................................................ATTCGAAAACTCAGAAACTTCCC...............................................................................................2311.001000001
............................................................................................................AGTTTCCGGGATCTCGTACTT........................................................................................................................................................2111.001000010
..................................................................................................................................................................AATTCGAAAACTCAGAAACTTT.................................................................................................2211.001100000
............................................................................................................AGTTTCCGGGATCTCGTACTGTAAA....................................................................................................................................................2511.001000100
..................................................................................................................................................................AATTCGAAAACTCAGAAACTTCA................................................................................................2311.001100000
...................................................................................................................................................................ATTCGAAAACTCAGAAACTTCC................................................................................................2211.001000001
...........................................................................................................GAGTTTCCGGGATCTCGTACT.........................................................................................................................................................2111.001000010
............................................................................................................AGTTTCCGGGATCTCGTACTA........................................................................................................................................................2111.001000010
.............................................................................................................GTTTCCGGGATCTCGTACTG........................................................................................................................................................2011.001000100
...........................................................................................................GAGTTTCCGGGATCTCGTACTG........................................................................................................................................................2211.001000010
............................................................................................................AGTTTCCGGGATCTCGTACTGTAA.....................................................................................................................................................2411.001000010
..............................................................................................................TTTCCGGGATCTCGTACTGTATG....................................................................................................................................................2311.001100000
..................................................................................................................CGGGATCTCGTACTGTATGAA-G---.............................................................................................................................................2211.001000010
..................................................................................................................................................ATAT----------ACAATTCGAAAACTCAGA.......................................................................................................2211.001000010
.............................................................................................................GTTTCCGGGATCTCGTACTGTT....................................ny">-------TGGTATTATCGCAGCAAGTTTCCGGGATATCGTACTGTATTTC-TAAACATTTCATAT----------ACAATACGAAACCTCAGAAATTTGCTGCGGTTAGTTACCGTTAACAA-CT-CATAAGAAAG-----------GAGA---GAATAAA-----------------------AATGATCAATAT
droGri2 scaffold_15081:2044827-2044998 - dgr_10 confident ------------------------------------------------------------------------------------------CCTGGTATTGCTGCTGCAAATTTCCGCGGTGTCGTATTGTATTAT-C---AAAATGGTATACTCTGAACCACAATACGATTCCTCAGAAATTCGCTGCTGTAAGTTACCGTTTTCAA-C2211.001100000
..........................................................................................................CGAGTTTCCGGGATCTCGTAC..........................................................................................................................................................2111.001000010
...........................................................................................................GAGTTTCCGGGATCTCGTACTGA.......................................................................................................................................................2311.001000010
droBip1
AT----------------------------TG------------------------------------------CGGGGTGCGGGGAGTGCCTGGTATTATGGCAGCGAGTTTCCGGGATCTCGTAGTGTATGAA-G---TTTTATAAAT----------ACAATTCGAAAACTCAGAAACTTTCTGCCTTGAAGTACATTCATCAA-CG-GCCGAGTA--------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droKik1
------------------------------------------------------------------------------------------CCTGGTATAGCCGCAGAAAGTTTCCGTATAGCAACT-----------GTGC---CGATAAACCTATCCCAGTCTATCGATAGACAACGATTGTCAG

Re-alignment of all predicted orthologs with sRNA reads

Species Read alignment
droAna3
TTCC---------------------------------------CCGCACTGAGACAGCTCCTGTGCGACAACCACGGGGTGCGGGGAGTACCTGGTATTATGGCAGCGAGTTTCCGGGATCTCGTACTGTATGAA-G---TTTTCTATAT----------ACAATTCGAAAACTCAGAAACTTCCTGCCGTGAGCTACCATTGATCAACG-GCTGAGTATGCGACCGGAAAGGGGACGCGAATGC------------------------GAGGACTAAAGGSizeHit CountTotal NormTotalM044

Female-body		M058

Embryo		V039

Embryo		V055

Head		V105

Male-body		V106

Head
...................................................................................................................................................................ATTCGAAAACTCAGAAACTTCCT...............................................................................................23146.00463105829
..................................................................................................................................................................AATTCGAAAACTCAGAAACTTC.................................................................................................22120.0020410447
............................................................................................................AGTTTCCGGGATCTCGTACTG........................................................................................................................................................21117.00173000131
............................................................................................................AGTTTCCGGGATCTCGTACTGT.......................................................................................................................................................22114.0014500180
............................................................................................................AGTTTCCGGGATCTCGTACTGTA......................................................................................................................................................23111.0011400241
.................................................................................................................................................................CAATTCGAAAACTCAGAAACTTC.................................................................................................23110.0010010423
....................................................................................................................................................................TTCGAAAACTCAGAAACTTCCT...............................................................................................2216.006000114
.................................................................................................................................................................CAATTCGAAAACTCAGAAACTT..................................................................................................2214.004000022
............................................................................................................AGTTTCCGGGATCTCGTACT.........................................................................................................................................................2013.003000012
............................................................................................................................PAN class="starAny">CGAG-TTTCGTAATGTATGGTTA---TATTTGAAAT----------ACAGTACGAGACATCAGAAATTTTCGGCAGTTAGCTACCGT--------------------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droFic1
------------------------------------------------------------------------------------------CTCGGTATTATCGCAGCAAGTTTCCGGGACTTCGTACTGTATGAA-G---AATTCTATAT----------ACAATACGAAACCTCAGAAATTTATTGCAATGAACCACCTTTAACTA----------------------T..............................................................................................2412.002100001
...................................................................................................................................................................ATTCGAAAACTCAGAAACTTC.................................................................................................2111.001000010
..........................................................................................................CGAGTTTCCGGGATCTCGTACTGTATGA...................................................................................................................................................2811.001100000
..............................................................................................................TTTCCGGGATCTCGTACTGTAT.....................................................................................................................................................2211.001000010
...................................................................................................................................................................ATTCGAAAACTCAGAAACTTCCC...............................................................................................2311.001000001
............................................................................................................AGTTTCCGGGATCTCGTACTT........................................................................................................................................................2111.001000010
..................................................................................................................................................................AATTCGAAAACTCAGAAACTTT.................................................................................................2211.001100000
............................................................................................................AGTTTCCGGGATCTCGTACTGTAAA....................................................................................................................................................2511.001000100
..................................................................................................................................................................AATTCGAAAACTCAGAAACTTCA................................................................................................2311.001100000
...................................................................................................................................................................ATTCGAAAACTCAGAAACTTCC................................................................................................2211.001000001
...........................................................................................................GAGTTTCCGGGATCTCGTACT.........................................................................................................................................................2111.001000010
............................................................................................................AGTTTCCGGGATCTCGTACTA........................................................................................................................................................2111.001000010
.............................................................................................................GTTTCCGGGATCTCGTACTG........................................................................................................................................................2011.001000100
...........................................................................................................GAGTTTCCGGGATCTCGTACTG........................................................................................................................................................2211.001000010
............................................................................................................AGTTTCCGGGATCTCGTACTGTAA.....................................................................................................................................................2411.001000010
..............................................................................................................TTTCCGGGATCTCGTACTGTATG....................................................................................................................................................2311.001100000
..................................................................................................................CGGGATCTCGTACTGTATGAA-G---.............................................................................................................................................2211.001000010
..................................................................................................................................................ATAT----------ACAATTCGAAAACTCAGA.......................................................................................................2211.001000010
.............................................................................................................GTTTCCGGGATCTCGTACTGTT....................................matchAny">----------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droEle1
ATAT--------------------AG----TG----------CTCGAACAC-AA------------------------------CAACTCCTTGGTATTATCGCAGCAAGTTTCCGGGATTTCGTACTGTATGAC-A---AATTCTATAT----------ACAATACGAAACCTTAGAAATTTTCTGAAGTTAGCTACCAT--------------------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droRho1
AC----------------------------CA------------------------------------------TTC2211.001100000
..........................................................................................................CGAGTTTCCGGGATCTCGTAC..........................................................................................................................................................2111.001000010
...........................................................................................................GAGTTTCCGGGATCTCGTACTGA.......................................................................................................................................................2311.001000010
droBip1
AT----------------------------TG------------------------------------------CGGGGTGCGGGGAGTGCCTGGTATTATGGCAGCGAGTTTCCGGGATCTCGTAGTGTATGAA-G---TTTTATAAAT----------ACAATTCGAAAACTCAGAAACTTTCTGCCTTGAAGTACATTCATCAA-CG-GCCGAGTA--------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droKik1
------------------------------------------------------------------------------------------CCTGGTATAGCCGCAGAAAGTTTCGGGCCGGAGACATCTTGGTATTATCGCAGCAAGTTTCCGGGATTTCGTACTGTATGAC-A---AATTCTATAT----------ACAATACGAAACCTTAGAAATTTTCTGCAGTTATCTACCATTAACTA-CCAGTT-------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droBia1
TTCCGACTGTTT----GTATGCAT-CCATACACGTGGTTATTTCCAC--AT-GA------------------------------AGACATCTTGGTATTATCGCAACAAGTTTCCGGGATTTTGTATTGTATGACTA---GATTCTATAT----------ACAATACGAAACCTCAGAAATTTTCGAG-TTTCGTAATGTATGGTTA---TATTTGAAAT----------ACAGTACGAGACATCAGAAATTTTCGGCAGTTAGCTACCGT--------------------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droFic1
------------------------------------------------------------------------------------------CTCGGTATTATCGCAGCAAGTTTCCGGGACTTCGTACTGTATGAA-G---AATTCTATAT----------ACAATACGAAACCTCAGAAATTTATTGCAATGAACCACCTTTAACTA----------------------CTGCAGTTAACTACCATAAATCG-CCG----------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droTak1
TTCCGAATGCGTATGCGTATGCATAGCACACATATG---------AG--AG-GA------------------------------CGACACCTTGGTATTATCGCAACAAGTTTCCGGGATTTCGTACTGTATGCT-G---AATTCTATAT----------ACAATACGAAAGCTCAGAAATTTTCTGCAGTTAACTACCATTAACTA--------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droEle1
ATAT--------------------AG----TG----------CTCGAACAC-AA------------------------------CAACTCCTTGGTATTATCGCAGCAAGTTTCCGGGATTTCGTACTGTATGAC-A---AATTCTATAT----------ACAATACGAAACCTTAGAAATTTTCTGAAGTTAGCTACCAT--------------------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droRho1
AC----------------------------CA------------------------------------------TTC----SizeHit CountTotal NormTotal
No Reads
droEug1
AA----------------------------TA----------CCCTGATAGAGG------------------------------CGACATCTTGGTATTATCGCAATAAGTTCCTGGGATTTCGCACTGTATTAC-G---ATTTTTACAT----------ACAATACGAAAGCTCAGAAACTAACTGCAATTAACTACCGTAAACTA-CG-GATGAGAACG------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
dm3
----------------------------------------------------GG------------------------------AGAAGTCTTGGTATTATGGCAAAAAGTTTCCAGGACATTG----GCCGGAGACATCTTGGTATTATCGCAGCAAGTTTCCGGGATTTCGTACTGTATGAC-A---AATTCTATAT----------ACAATACGAAACCTTAGAAATTTTCTGCAGTTATCTACCATTAACTA-CCAGTT-------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droBia1
TTCCGACTGTTT----GTATGCAT-CCATACACGTGGTTATTTCCAC--AT-GA------------------------------AGACATCTTGGTATTATCGCAACAAGTTTCCGGGATTTTGTATTGTATGACTA---GATTCTATAT----------ACAATACGAAACCTCAGAAATTTT---------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalGSM154618

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		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		SRR01427">CTGCAGTTAACTACCATAAATCG-CCG----------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droTak1
TTCCGAATGCGTATGCGTATGCATAGCACACATATG---------AG--AG-GA------------------------------CGACACCTTGGTATTATCGCAACAAGTTTCCGGGATTTCGTACTGTATGCT-G---AATTCTATAT----------ACAATACGAAAGCTCAGAAATTTTCTGCAGTTAACTACCATTAACTA----------------------------------------------------------------------<1

Embryo		SRR014272

Embryo		SRR014273

Ovary		SRR014274

Ovary		SRR014275

Ovary		SRR014276

Ovary		SRR014277

Ovary		SRR014278

Ovary		SRR014279

Ovary		SRR014280

Ovary		SRR014281

Ovary		SRR014282

Ovary		SRR023197

S2		SRR023399

S2		SRR023400

S2		SRR023402

S2		SRR023407

S2		SRR029028

S2		SRR029029

S2		SRR029030

S2		SRR029031

S2		SRR029032

S2		SRR029033

S2		SRR029608

Head		SRR029633

Head		SRR030145

gb3		SRR031692

Head		SRR031693

Head		SRR031694

Head		SRR031696

Head		SRR031697

Head		SRR031698

Head		SRR031699

Head		SRR031700

Head		SRR031701

Head		SRR031702

Head		SRR031703

Head		SRR031704

Head		SRR032092

S2		SRR032093

S2		SRR032094

S2		SRR032095

S2-NP		SRR032096

S2-NP		SRR032152

Head		SRR060643

Testis		SRR060644

Ovary		SRR060645

Testis		SRR060646

Ovary		SRR060647

Ovary		SRR060648

Ovary		SRR060649

Ovary		SRR060650

Testis		SRR060651

Ovary		SRR060652

Testis		SRR060653

Ovary		SRR065151

Ovary		SRR065152

Ovary		SRR065153

Ovary		SRR065154

Ovary		SRR065155

Ovary		SRR065800

Ovary		SRR065801

Ovary		SRR065802

Ovary		SRR065803

Ovary		SRR065804

Ovary		SRR065805

Ovary		SRR065806

Ovary		SRR065807

Ovary		SRR097865

S2-NP		SRR097866

S2-NP		SRR097867

S2-NP		SRR298536

Ovary		SRR298537

Ovary		SRR298711

Ovary		SRR298712

Ovary		SRR317110

Ovary		SRR317111

Ovary		SRR317112

Ovary		SRR317113

Ovary		SRR317114

Ovary		SRR317115

Ovary		SRR317116

Ovary		SRR317117

Ovary		SRR341115

S2		SRR341116

S2		SRR341117

S2		SRR341118

S2		SRR351332

Mixed-body		SRR351333

Mixed-body		T004

OSC		T005

CME-L1		V001

Embryo		V002

Embryo		V003

S2		V006

Female-body		V007

Head		V008

S2		V009

CME-L1		V010

ML-DmD20-C5		V011

Sg4		V012

Male-body		V013

Head		V014

DTT		V015

DreRFHV		V018

Kc167		V019

GM2		V020

S2-R+		V021

ML-DmD21		V022

ML-DmD32		V023

Head		V024

Kc167		V025

S2-R+		V026

1182-2H		V027

ML-DmD21		V028

CME-W1-Cl.8+		V029

ML-DmD9		V030

ML-DmD8		V031

GM2		V032

S1		V033

CME-W1-Cl.8+		V034

ML-DmD16-C3		V035

ML-DmD32		V036

ML-DmD20-C5		V037

S2		V038

S2		V063

Ovary		V0632

Ovary		V064

Ovary		V0642

Ovary		V065

Ovary		V0652

Ovary		V066

Ovary		V0662

Ovary		V067

S2-NP		V073

mbn2		V074

S3		V075

ML-DmBG1-C1		V076

ML-DmBG3-C2		V077

Head		V078

Head		V079

Head		V080

Head		V081

Embryo		V082

Embryo		V083

Male-body		V084

Female-body		V085

CME-W2		V086

Female-body		V088

Ovary		V0882

Ovary		V089

Ovary		V0892

Ovary		V090

Male-body		V091

fGS/OSS		V092

Male-body		V093

Male-body		V094

S2-R+		V095

S2-R+		V096

Ovary		V097

Ovary		V098

Ovary		V125

ML-DmD9		V126

CME-L1		V127

G2		V128

S3		V129

ML-DmBG1-C1		V130

ML-DmBG3-C2		V131

ML-DmD16-C3		V132

ML-DmD32		V133

Sg4		V134

ML-DmD8		V135

CME-W2		V136

Male-body		V137

Head		V138

Male-body		V139

Female-body		V140

Female-body		V141

Female-body		V142

Female-body		V144

OSC		V145

S2		V146

S1		V147

1182-2H		V148

mbn2		GSM1528798

follicle cells
No Reads
droSim2
------------------------------------------------------------------------------------------CTTGGTATTATGGCAACAAGTTTCCAGGACATCGAGCT/SPAN>----SizeHit CountTotal NormTotal
No Reads
droEug1
AA----------------------------TA----------CCCTGATAGAGG------------------------------CGACATCTTGGTATTATCGCAATAAGTTCCTGGGATTTCGCACTGTATTAC-G---ATTTTTACAT----------ACAATACGAAAGCTCAGAAACTAACTGCAATTAACTACCGTAAACTA-CG-GATGAGAACG------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
dm3
----------------------------------------------------GG------------------------------AGAAGTCTTGGTATTATGGCAAAAAGTTTCCAGGACATTG----GTGTGA---------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalM023

Head		M024

Male-body		M025

Embryo		M053

Female-body		O001

Testis		O002

Head		SRR553485

Ovary		SRR553486

Ovary		SRR553487

Ovary		SRR553488

Ovary		SRR618934

Ovary		V044

Embryo		SRR902008

Ovary		SRR902009

Testis		SRR1275487

Male larvae		SRR1275485

Male prepupae		SRR1275483

Male prepupae
No Reads
droSec2
------------------------------------------------------------------------------------------CTTGGTATTATGGCAACAAGTTTCCAGGACATCGAGCTGTGTGA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalGSM154618

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		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		SRR01427PAN class="mismatchAny">-------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalM054

Female-body		V113

Male-body		V114

Embryo		V115

Head
No Reads
droYak3
------------------------------------------------------------------------------------------CTTGGTATTATGGCAACAAGTTTCCGGGACTTCGTACTGTATGAC-A---GACTATATAT----------ACAATACGAAGCCTCTGAAATTTTCTGCGCTCAAGTACCA--------------------------------------------
Embryo		SRR014272

Embryo		SRR014273

Ovary		SRR014274

Ovary		SRR014275

Ovary		SRR014276

Ovary		SRR014277

Ovary		SRR014278

Ovary		SRR014279

Ovary		SRR014280

Ovary		SRR014281

Ovary		SRR014282

Ovary		SRR023197

S2		SRR023399

S2		SRR023400

S2		SRR023402

S2		SRR023407

S2		SRR029028

S2		SRR029029

S2		SRR029030

S2		SRR029031

S2		SRR029032

S2		SRR029033

S2		SRR029608

Head		SRR029633

Head		SRR030145

gb3		SRR031692

Head		SRR031693

Head		SRR031694

Head		SRR031696

Head		SRR031697

Head		SRR031698

Head		SRR031699

Head		SRR031700

Head		SRR031701

Head		SRR031702

Head		SRR031703

Head		SRR031704

Head		SRR032092

S2		SRR032093

S2		SRR032094

S2		SRR032095

S2-NP		SRR032096

S2-NP		SRR032152

Head		SRR060643

Testis		SRR060644

Ovary		SRR060645

Testis		SRR060646

Ovary		SRR060647

Ovary		SRR060648

Ovary		SRR060649

Ovary		SRR060650

Testis		SRR060651

Ovary		SRR060652

Testis		SRR060653

Ovary		SRR065151

Ovary		SRR065152

Ovary		SRR065153

Ovary		SRR065154

Ovary		SRR065155

Ovary		SRR065800

Ovary		SRR065801

Ovary		SRR065802

Ovary		SRR065803

Ovary		SRR065804

Ovary		SRR065805

Ovary		SRR065806

Ovary		SRR065807

Ovary		SRR097865

S2-NP		SRR097866

S2-NP		SRR097867

S2-NP		SRR298536

Ovary		SRR298537

Ovary		SRR298711

Ovary		SRR298712

Ovary		SRR317110

Ovary		SRR317111

Ovary		SRR317112

Ovary		SRR317113

Ovary		SRR317114

Ovary		SRR317115

Ovary		SRR317116

Ovary		SRR317117

Ovary		SRR341115

S2		SRR341116

S2		SRR341117

S2		SRR341118

S2		SRR351332

Mixed-body		SRR351333

Mixed-body		T004

OSC		T005

CME-L1		V001

Embryo		V002

Embryo		V003

S2		V006

Female-body		V007

Head		V008

S2		V009

CME-L1		V010

ML-DmD20-C5		V011

Sg4		V012

Male-body		V013

Head		V014

DTT		V015

DreRFHV		V018

Kc167		V019

GM2		V020

S2-R+		V021

ML-DmD21		V022

ML-DmD32		V023

Head		V024

Kc167		V025

S2-R+		V026

1182-2H		V027

ML-DmD21		V028

CME-W1-Cl.8+		V029

ML-DmD9		V030

ML-DmD8		V031

GM2		V032

S1		V033

CME-W1-Cl.8+		V034

ML-DmD16-C3		V035

ML-DmD32		V036

ML-DmD20-C5		V037

S2		V038

S2		V063

Ovary		V0632

Ovary		V064

Ovary		V0642

Ovary		V065

Ovary		V0652

Ovary		V066

Ovary		V0662

Ovary		V067

S2-NP		V073

mbn2		V074

S3		V075

ML-DmBG1-C1		V076

ML-DmBG3-C2		V077

Head		V078

Head		V079

Head		V080

Head		V081

Embryo		V082

Embryo		V083

Male-body		V084

Female-body		V085

CME-W2		V086

Female-body		V088

Ovary		V0882

Ovary		V089

Ovary		V0892

Ovary		V090

Male-body		V091

fGS/OSS		V092

Male-body		V093

Male-body		V094

S2-R+		V095

S2-R+		V096

Ovary		V097

Ovary		V098

Ovary		V125

ML-DmD9		V126

CME-L1		V127

G2		V128

S3		V129

ML-DmBG1-C1		V130

ML-DmBG3-C2		V131

ML-DmD16-C3		V132

ML-DmD32		V133

Sg4		V134

ML-DmD8		V135

CME-W2		V136

Male-body		V137

Head		V138

Male-body		V139

Female-body		V140

Female-body		V141

Female-body		V142

Female-body		V144

OSC		V145

S2		V146

S1		V147

1182-2H		V148

mbn2		GSM1528798

follicle cells
No Reads
droSim2
------------------------------------------------------------------------------------------CTTGGTATTATGGCAACAAGTTTCCAGGACATCGAGCTAN class="mismatchAny">-------------------------------------SizeHit CountTotal NormTotalM026

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
..................................................................................................................................................................AATACGAAGCCTCTGAAATTTT.................................................................................................221129.0012911211000150000
............................................................................................................AGTTTCCGGGACTTCGTACTGT.......................................................................................................................................................22184.00846031110180000
...................................................................................................................................................................ATACGAAGCCTCTGAAATTTTCT...............................................................................................23130.0030300000000000
............................................................................................................AGTTTCCGGGACTTCGTACTG........................................................................................................................................................21128.0028710000200000
..................................................................................................................................................................AATACGAAGCCTCTGAAATTT..................................................................................................21123.0023211000010000
............................................................................................................AGTTTCCGGGACTTCGTACTGG.......................................................................................................................................................22118.0018180000000000
............................................................................................................AGTTTCCGGGACTTCGTACTGC.......................................................................................................................................................22111.0011110000000000
............................................................................................................AGTTTCCGGGACTTCGTACT.........................................................................................................................................................2018.00800001160000
............................................................................................................AGTTTCCGGGACTTCGTAC..........................................................................................................................................................1916.00660000000000
............................................................................................................AGTTTCCGGGACTTCGTACTGTT......................................................................................................................................................2315.00550000000000
............................................................................................................AGTTTCCGGGACTTCGTACTGTA......................................................................................................................................................2315.00550000000000
...................................................................................................................................................................ATACGAAGCCTCTGAAATTTTCTG..............................................................................................2415.00550000000000
..................................................................................................................................................................AATACGAAGCCTCTGAAATT...................................................................................................2013.00330000000000
....................................................................................................................................................................TACGAAGCCTCTGAAATTTTCT...............................................................................................2213.00330000000000
...................................................................................................................................................................ATACGAAGCCTCTGAAATTTTC................................................................................................2212.00210000010000
....................................................................................................................................................................TACGAAGCCTCTGAAATTTTCTG................................................GTGTGA---------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalM023

Head		M024

Male-body		M025

Embryo		M053

Female-body		O001

Testis		O002

Head		SRR553485

Ovary		SRR553486

Ovary		SRR553487

Ovary		SRR553488

Ovary		SRR618934

Ovary		V044

Embryo		SRR902008

Ovary		SRR902009

Testis		SRR1275487

Male larvae		SRR1275485

Male prepupae		SRR1275483

Male prepupae
No Reads
droSec2
------------------------------------------------------------------------------------------CTTGGTATTATGGCAACAAGTTTCCAGGACATCGAGCTGTGTGA--------------------------------------------2312.00220000000000
.................................................................................................................CCGGGACTTCGTACTGTA......................................................................................................................................................1811.00110000000000
...................................................................................................................................................................ATACGAAGCCTCTGAAATTTTCC...............................................................................................2311.00110000000000
................................................................................................................TCCGGGACTTCGTACTGTATGA...................................................................................................................................................2211.00101000000000
.............................................................................................................GTTTCCGGGACTTCGTACTGTT......................................................................................................................................................2211.00110000000000
............................................................................................................AGTTTCCGGGACTTCGTACTT........................................................................................................................................................2111.00110000000000
...................................................................................................................................................................ATACGAAGCCTCTGAAATTTTCTGC.............................................................................................2511.00110000000000
...................................................................................................................................................................ATACGAAGCCTCTGAAATTTT.................................................................................................2111.00110000000000
....................................................................................................................................................................TACGAAGCCTCTGAAATTTTC................................................................................................2111.00110000000000
.................................................................................................................................................................CAATACGAAGCCTCTGAAATTTT.................................................................................................2311.00100000100000
droEre2
------------------------------------------------------------------------------------------CTTGGTATTAAGGCAACAAGTTTCAGGGACTTCGCACTGTATGA--------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalM054

Female-body		V113

Male-body		V114

Embryo		V115

Head
No Reads
droYak3
------------------------------------------------------------------------------------------CTTGGTATTATGGCAACAAGTTTCCGGGACTTCGTACTGTATGAC-A---GACTATATAT----------ACAATACGAAGCCTCTGAAATTTTCTGCGCTCAAGTACCA----------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalM055

Female-body		M057

Embryo		V060

Head		V040

Embryo		V107

Male-body		V108

Head		GSM1528801

follicle cells
No Reads
droWil2
--------------------------------------------------------------------------------------------TGGTATTATCGCAGCAAGTTTCCGGGATATCGTACTGTATTTC-TAAACATTTCATAT----------ACAATACGAAACCTCAGAAATTTGCTGCGGTTAGTTACCGTTAACAA-CT-CATAAGAAAG-----------GAGA---GAATAAA-----------------------AATGATCAAT-------------------------------------SizeHit CountTotal NormTotalM026

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
..................................................................................................................................................................AATACGAAGCCTCTGAAATTTT.................................................................................................221129.0012911211000150000
............................................................................................................AGTTTCCGGGACTTCGTACTGT.......................................................................................................................................................22184.00846031110180000
...................................................................................................................................................................ATACGAAGCCTCTGAAATTTTCT...............................................................................................23130.0030300000000000
............................................................................................................AGTTTCCGGGACTTCGTACTG........................................................................................................................................................21128.0028710000200000
..................................................................................................................................................................AATACGAAGCCTCTGAAATTT..................................................................................................21123.0023211000010000
............................................................................................................AGTTTCCGGGACTTCGTACTGG.......................................................................................................................................................22118.0018180000000000
............................................................................................................AGTTTCCGGGACTTCGTACTGC.......................................................................................................................................................22111.0011110000000000
............................................................................................................AGTTTCCGGGACTTCGTACT.........................................................................................................................................................2018.00800001160000
............................................................................................................AGTTTCCGGGACTTCGTAC..........................................................................................................................................................1916.00660000000000
............................................................................................................AGTTTCCGGGACTTCGTACTGTT......................................................................................................................................................2315.00550000000000
............................................................................................................AGTTTCCGGGACTTCGTACTGTA......................................................................................................................................................2315.00550000000000
...................................................................................................................................................................ATACGAAGCCTCTGAAATTTTCTG..............................................................................................2415.00550000000000
..................................................................................................................................................................AATACGAAGCCTCTGAAATT...................................................................................................2013.00330000000000
....................................................................................................................................................................TACGAAGCCTCTGAAATTTTCT...............................................................................................2213.00330000000000
...................................................................................................................................................................ATACGAAGCCTCTGAAATTTTC................................................................................................2212.00210000010000
....................................................................................................................................................................TACGAAGCCTCTGAAATTTTCTG................................................Any">ATSizeHit CountTotal NormTotalM020

Head		M045

Female-body		V117

Male-body		V118

Embryo		V119

Head
............................................................................................................AGTTTCCGGGATATCGTACTGTA......................................................................................................................................................231290.0029023605310
...................................................................................................................................................................ATACGAAACCTCAGAAATTTGCT...............................................................................................231173.00173101811566
..............................................................................................................TTTCCGGGATATCGTACTGTAT.....................................................................................................................................................221161.0016112323402
............................................................................................................AGTTTCCGGGATATCGTACTGT.......................................................................................................................................................221139.001394908901
............................................................................................................AGTTTCCGGGATATCGTACTGTAA.....................................................................................................................................................241124.0012410302100
............................................................................................................AGTTTCCGGGATATCGTAC..........................................................................................................................................................19138.0038380000
...............................................................................................................TTCCGGGATATCGTACTGTATTT...................................................................................................................................................23133.0033300300
............................................................................................................AGTTTCCGGGATATCGTACTG........................................................................................................................................................21121.0021002001
...............................................................................................................TTCCGGGATATCGTACTGTATT....................................................................................................................................................22116.0016130300
...................................................................................................................................................................ATACGAAACCTCAGAAATTTGC................................................................................................22113.001331324
..............................................................................................................TTTCCGGGATATCGTACTGTATT....................................................................................................................................................2317.00750200
............................................................................................................AGTTTCCGGGATATCGTACTGTC......................................................................................................................................................2317.00760100
....................................................................................................................................................................TACGAAACCTCAGAAATTTGCT...............................................................................................2216.00600402
............................................................................................................AGTTTCCGGGATATCGTACTGC.......................................................................................................................................................2216.00660000
............................................................................................................AGTTTCCGGGATATCGTACT.........................................................................................................................................................2016.00610500
..............................................................................................................TTTCCGGGATATCGTACTGTAC.....................................................................................................................................................2216.00660000
............................................................................................................AGTTTCCGGGATATCGTACTGTAT.....................................................................................................................................................2416.00650001
..............................................................................................................TTTCCGGGATATCGTACTGTA......................................................................................................................................................2115.00540100
..................................................................................................................................................................AATACGAAACCTCAGAAATTTG.................................................................................................2215.00530200
.........................................................................................................................................................2312.00220000000000
.................................................................................................................CCGGGACTTCGTACTGTA......................................................................................................................................................1811.00110000000000
...................................................................................................................................................................ATACGAAGCCTCTGAAATTTTCC...............................................................................................2311.00110000000000
................................................................................................................TCCGGGACTTCGTACTGTATGA...................................................................................................................................................2211.00101000000000
.............................................................................................................GTTTCCGGGACTTCGTACTGTT......................................................................................................................................................2211.00110000000000
............................................................................................................AGTTTCCGGGACTTCGTACTT........................................................................................................................................................2111.00110000000000
...................................................................................................................................................................ATACGAAGCCTCTGAAATTTTCTGC.............................................................................................2511.00110000000000
...................................................................................................................................................................ATACGAAGCCTCTGAAATTTT.................................................................................................2111.00110000000000
....................................................................................................................................................................TACGAAGCCTCTGAAATTTTC................................................................................................2111.00110000000000
.................................................................................................................................................................CAATACGAAGCCTCTGAAATTTT.................................................................................................2311.00100000100000
droEre2
------------------------------------------------------------------------------------------CTTGGTATTAAGGCAACAAGTTTCAGGGACTTCGCACTGTATGA-------------------------------------------2215.00550000
.............................................................................................................GTTTCCGGGATATCGTACTGTA......................................................................................................................................................2214.00430100
............................................................................................................AGTTTCCGGGATATCGTACTGG.......................................................................................................................................................2214.00440000
............................................................................................................AGTTTCCGGGATATCGTACTGTAC.....................................................................................................................................................2413.00330000
...................................................................................................................................................................ATACGAAACCTCAGAAATTTGCTT..............................................................................................2413.00300201
............................................................................................................AGTTTCCGGGATATCGTACTGTAAA....................................................................................................................................................2512.00210100
............................................................................................................AGTTTCCGGGATATCGTACTGTT......................................................................................................................................................2312.00200200
...................................................................................................................................................................ATACGAAACCTCAGAAATTTG.................................................................................................2112.00210100
..............................................................................................................TTTCCGGGATATCGTACTGTATAA...................................................................................................................................................2412.00220000
...................................................................................................................................................................ATACGAAACCTCAGAAATTTGCTA..............................................................................................2412.00200101
...................................................................................................................................................................ATACGAAACCTCAGAAATTTGCC...............................................................................................2312.00210100
...............................................................................................................TTCCGGGATATCGTACTGTAT.....................................................................................................................................................2112.00220000
..............................................................................................................TTTCCGGGATATCGTACTGTAA.....................................................................................................................................................2211.00110000
..........................................................................................................CAAGTTTCCGGGATATCGTACT.........................................................................................................................................................2211.00110000
............................................................................................................AGTTTCCGGGATATCGTACTGTAG.....................................................................................................................................................2411.00110000
............................................................................................................AGTTTCCGGGATATCGTA...........................................................................................................................................................1811.00100100
..................................................................................................................................................................AATACGAAACCTCAGAAATTTGT................................................................................................2311.00100001
............................................................................................................AGTTTCCGGGATATCGTACTGTCA.....................................................................................................................................................2411.00110000
.............................................................................................................GTTTCCGGGATATCGTACTGTAAA....................................................................................................................................................2411.00110000
......................................................................................................

Generated: 10/21/2015 at 11:53 AM

"mismatchAny">--------------------------------------------------------------------------------------------------------		SizeHit CountTotal NormTotalM055

Female-body		M057

Embryo		V060

Head		V040

Embryo		V107

Male-body		V108

Head		GSM1528801

follicle cells
No Reads
droWil2
--------------------------------------------------------------------------------------------TGGTATTATCGCAGCAAGTTTCCGGGATATCGTACTGTATTTC-TAAACATTTCATAT----------ACAATACGAAACCTCAGAAATTTGCTGCGGTTAGTTACCGTTAACAA-CT-CATAAGAAAG-----------GAGA---GAATAAA-----------------------AATGATCAATA...................................................................................................................................................2311.00110000
...........................................................................................................AAGTTTCCGGGATATCGTACTA........................................................................................................................................................2211.00100100
.............................................................................................................GTTTCCGGGATATCGTACTGTAA.....................................................................................................................................................2311.00110000
...........................................................................................................AAGTTTCCGGGATATCGTACTG........................................................................................................................................................2211.00100100
...........................................................................................................AAGTTTCCGGGATATCGTACT.........................................................................................................................................................2111.00100001
............................................................................................................AGTTTCCGGGATATCGTACTGTCC.....................................................................................................................................................2411.00110000
..............................................................................................................TTTCCGGGATATCGTACTGTATTAA-.................................................................................................................................................2511.00110000
..............................................................................................................TTTCCGGGATATCGTACTGTAG.....................................................................................................................................................2211.00110000
............................................................................................................AGTTTCCGGGATATCGTACTGA.......................................................................................................................................................2211.00100100
droGri2
------------------------------------------------------------------------------------------CCTGGTATTGCTGCTGCAAATTTCCGCGGTGTCGTATTGTATTAT-C---AAAATGGTATACTCTGAACCACAATACGATTCCTCAGAAATTCGCTGCTGTAAGTTACCGTTTATSizeHit CountTotal NormTotalM020

Head		M045

Female-body		V117

Male-body		V118

Embryo		V119

Head
............................................................................................................AGTTTCCGGGATATCGTACTGTA......................................................................................................................................................231290.0029023605310
...................................................................................................................................................................ATACGAAACCTCAGAAATTTGCT...............................................................................................231173.00173101811566
..............................................................................................................TTTCCGGGATATCGTACTGTAT.....................................................................................................................................................221161.0016112323402
............................................................................................................AGTTTCCGGGATATCGTACTGT.......................................................................................................................................................221139.001394908901
............................................................................................................AGTTTCCGGGATATCGTACTGTAA.....................................................................................................................................................241124.0012410302100
............................................................................................................AGTTTCCGGGATATCGTAC..........................................................................................................................................................19138.0038380000
...............................................................................................................TTCCGGGATATCGTACTGTATTT...................................................................................................................................................23133.0033300300
............................................................................................................AGTTTCCGGGATATCGTACTG........................................................................................................................................................21121.0021002001
...............................................................................................................TTCCGGGATATCGTACTGTATT....................................................................................................................................................22116.0016130300
...................................................................................................................................................................ATACGAAACCTCAGAAATTTGC................................................................................................22113.001331324
..............................................................................................................TTTCCGGGATATCGTACTGTATT....................................................................................................................................................2317.00750200
............................................................................................................AGTTTCCGGGATATCGTACTGTC......................................................................................................................................................2317.00760100
....................................................................................................................................................................TACGAAACCTCAGAAATTTGCT...............................................................................................2216.00600402
............................................................................................................AGTTTCCGGGATATCGTACTGC.......................................................................................................................................................2216.00660000
............................................................................................................AGTTTCCGGGATATCGTACT.........................................................................................................................................................2016.00610500
..............................................................................................................TTTCCGGGATATCGTACTGTAC.....................................................................................................................................................2216.00660000
............................................................................................................AGTTTCCGGGATATCGTACTGTAT.....................................................................................................................................................2416.00650001
..............................................................................................................TTTCCGGGATATCGTACTGTA......................................................................................................................................................2115.00540100
..................................................................................................................................................................AATACGAAACCTCAGAAATTTG.................................................................................................2215.00530200
................................................................................................................TCCGGGATATCGTACTGTATTT...................................................................................................................................................2215.00550000
.............................................................................................................GTTTCCGGGATATCGTACTGTA......................................................................................................................................................2214.00430100
............................................................................................................AGTTTCCGGGATATCGTACTGG.......................................................................................................................................................2214.00440000
............................................................................................................AGTTTCCGGGATATCGTACTGTAC.....................................................................................................................................................2413.00330000
...................................................................................................................................................................ATACGAAACCTCAGAAATTTGCTT..............................................................................................2413.00300201
............................................................................................................AGTTTCCGGGATATCGTACTGTAAA....................................................................................................................................................2512.00210100
............................................................................................................AGTTTCCGGGATATCGTACTGTT......................................................................................................................................................2312.00200200
...................................................................................................................................................................ATACGAAACCTCAGAAATTTG.................................................................................................2112.00210100
..............................................................................................................TTTCCGGGATATCGTACTGTATAA...................................................................................................................................................2412.00220000
...................................................................................................................................................................ATACGAAACCTCAGAAATTTGCTA..............................................................................................2412.00200101
...................................................................................................................................................................ATACGAAACCTCAGAAATTTGCC...............................................................................................2312.00210100
...............................................................................................................TTCCGGGATATCGTACTGTAT.....................................................................................................................................................2112.00220000
..............................................................................................................TTTCCGGGATATCGTACTGTAA.....................................................................................................................................................2211.00110000
..........................................................................................................CAAGTTTCCGGGATATCGTACT.........................................................................................................................................................2211.00110000
............................................................................................................AGTTTCCGGGATATCGTACTGTAG.....................................................................................................................................................2411.00110000
............................................................................................................AGTTTCCGGGATATCGTA...........................................................................................................................................................1811.00100100
..................................................................................................................................................................AATACGAAACCTCAGAAATTTGT................................................................................................2311.00100001
............................................................................................................AGTTTCCGGGATATCGTACTGTCA.....................................................................................................................................................2411.00110000
.............................................................................................................GTTTCCGGGATATCGTACTGTAAA....................................................................................................................................................2411.00110000
......................................................................................................tchAny">TCAA-CCGTATAGCAACT-----------GTGC---CGATAAACCTATCCCAGTCTATCGATAGACAACGATTGTCAGSizeHit CountTotal NormTotalM041

Female-body		V109

Male-body
...........................................................................................................AAATTTCCGCGGTGTCGTATTG........................................................................................................................................................22174.0074173
..........................................................................................................CAAATTTCCGCGGTGTCGTATT.........................................................................................................................................................22154.0054153
..........................................................................................................CAAATTTCCGCGGTGTCGTAT..........................................................................................................................................................21120.0020020
...........................................................................................................AAATTTCCGCGGTGTCGTATT.........................................................................................................................................................21116.0016115
...........................................................................................................AAATTTCCGCGGTGTCGTAT..........................................................................................................................................................2014.00404
...................................................................................................................................................................ATACGATTCCTCAGAAATTCGCT...............................................................................................2313.00303
...........................................................................................................AAATTTCCGCGGTGTCGTATTT........................................................................................................................................................2212.00202
..........................................................................................................CAAATTTCCGCGGTGTCGTATTG........................................................................................................................................................2312.00202
..........................................................................................................CAAATTTCCGCGGTGTCGTATTT........................................................................................................................................................2312.00202
...................................................................................................................................................................ATACGATTCCTCAGAAATTCG.................................................................................................2112.00202
....................................................................................................................................................................TACGATTCCTCAGAAATTCGCT...............................................................................................2211.00101
..........................................................................................................CAAATTTCCGCGGTGTCGTA...........................................................................................................................................................2011.00101
...................................................................................................................................................................ATACGATTCCTCAGAAATTCGCTT..............................................................................................2411.00101
.........TTCCGGGATATCGTACTGTATTA...................................................................................................................................................		2311.00110000
...........................................................................................................AAGTTTCCGGGATATCGTACTA........................................................................................................................................................2211.00100100
.............................................................................................................GTTTCCGGGATATCGTACTGTAA.....................................................................................................................................................2311.00110000
...........................................................................................................AAGTTTCCGGGATATCGTACTG........................................................................................................................................................2211.00100100
...........................................................................................................AAGTTTCCGGGATATCGTACT.........................................................................................................................................................2111.00100001
............................................................................................................AGTTTCCGGGATATCGTACTGTCC.....................................................................................................................................................2411.00110000
..............................................................................................................TTTCCGGGATATCGTACTGTATTAA-.................................................................................................................................................2511.00110000
..............................................................................................................TTTCCGGGATATCGTACTGTAG.....................................................................................................................................................2211.00110000
............................................................................................................AGTTTCCGGGATATCGTACTGA.......................................................................................................................................................2211.00100100
droGri2
------------------------------------------------------------------------------------------CCTGGTATTGCTGCTGCAAATTTCCGCGGTGTCGTATTGTATTAT-C---AAAATGGTATACTCTGAACCACAATACGATTCCTCAGAAATTCGCTGCTGTAAGTTACCGTTTTCAA-CCGTATAGCAACT-----------GTGC---CGATAAACCTATCCCAGTCTATCGATAGACAACGATTGTCAGSizeHit CountTotal NormTotalM041

Female-body		V109

Male-body
...........................................................................................................AAATTTCCGCGGTGTCGTATTG........................................................................................................................................................22174.0074173
..........................................................................................................CAAATTTCCGCGGTGTCGTATT.........................................................................................................................................................22154.0054153
..........................................................................................................CAAATTTCCGCGGTGTCGTAT..........................................................................................................................................................21120.0020020
...........................................................................................................AAATTTCCGCGGTGTCGTATT.........................................................................................................................................................21116.0016115
...........................................................................................................AAATTTCCGCGGTGTCGTAT..........................................................................................................................................................2014.00404
...................................................................................................................................................................ATACGATTCCTCAGAAATTCGCT...............................................................................................2313.00303
...........................................................................................................AAATTTCCGCGGTGTCGTATTT........................................................................................................................................................2212.00202
..........................................................................................................CAAATTTCCGCGGTGTCGTATTG........................................................................................................................................................2312.00202
..........................................................................................................CAAATTTCCGCGGTGTCGTATTT........................................................................................................................................................2312.00202
...................................................................................................................................................................ATACGATTCCTCAGAAATTCG.................................................................................................2112.00202
....................................................................................................................................................................TACGATTCCTCAGAAATTCGCT...............................................................................................2211.00101
..........................................................................................................CAAATTTCCGCGGTGTCGTA...........................................................................................................................................................2011.00101
...................................................................................................................................................................ATACGATTCCTCAGAAATTCGCTT..............................................................................................2411.00101

Generated: 10/21/2015 at 11:53 AM

Generated: 10/21/2015 at 11:53 AM