ID:

dsi_293

 Coordinate:

3r:4169875-4169999 -

 Confidence:

Known Ortholog

 Class:

Canonical miRNA

 Genomic Locale:

intergenic

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

Predicted structure

-30.5 -30.4 -29.9 -29.7

Sense Strand Reads

GAACCGCATCCCCCAAATACTTTCAAAAATCCCTTCCTTTTCGTACGTACAAAAAAGCATCAGGTTTTCGGGTGAGGTTTCTGATGCTTTGTCTCTTAAGTTTTCCCTAAAAATAAGACCCTATGTCGGTATTTCGAATACCATCAAAAAACCTCACCCACCAAATGTATGACCAGAGAGATAAAAATTTCAATAAAAACCAATTCGATGACTTCTACGATGACT

****************************************************.......((.(((....(((((((((((.(((((.............((.(((.....(((((.(((.....)))..))))).))).)))))))..)))))))))))............))).))************************************************ 		Read size # Mismatch Hit Count Total Norm Total M023

head

 M025

embryo

 O002

Head

 M024

male body		 SRR553485

Chicharo_3 day-old ovaries

 SRR553487

NRT_0-2 hours eggs

 SRR553486

Makindu_3 day-old ovaries

 SRR902009

testis

 M053

female body

 SRR553488

RT_0-2 hours eggs

 O001

Testis

 GSM343915

embryo

 SRR618934

dsim w501 ovaries

 SRR902008

ovaries
...................................................................TCGGGTGAGGTTTCTGATGCT......................................................................................................................................... 21 0 1 95.00 95 47 4 3 12 10 9 7 0 0 1 2 0 0 0
..................................................................TTCGGGTGAGGTTTCTGATGCT......................................................................................................................................... 22 0 1 57.00 57 34 5 0 11 1 1 4 0 0 0 1 0 0 0
............................................................................................................................................CCATCAAAAAACCTCACCCACC............................................................... 22 0 1 34.00 34 13 4 12 2 0 0 1 2 0 0 0 0 0 0
..................................................................TTCGGGTGAGGTTTCTGATG........................................................................................................................................... 20 0 1 27.00 27 14 2 0 1 3 5 2 0 0 0 0 0 0 0
............................................................................................................................................CCATCAAAAAACCTCACCCACCA.............................................................. 23 0 1 17.00 17 0 0 8 0 0 0 0 8 1 0 0 0 0 0
...................................................................TCGGGTGAGGTTTCTGATGCTT........................................................................................................................................ 22 0 1 17.00 17 7 2 0 4 2 1 1 0 0 0 0 0 0 0
..................................................................TTCGGGTGAGGTTTCTGATGC.......................................................................................................................................... 21 0 1 9.00 9 4 0 2 0 2 1 0 0 0 0 0 0 0 0
..................................................................TTCGGGTGAGGTTTCTGATGCC......................................................................................................................................... 22 1 1 8.00 8 7 1 0 0 0 0 0 0 0 0 0 0 0 0
...................................................................TCGGGTGAGGTTTCTGATGCC......................................................................................................................................... 21 1 1 7.00 7 5 0 0 2 0 0 0 0 0 0 0 0 0 0
............................................................................................................................................CCATCAAAAAACCTCACCCAC................................................................ 21 0 1 6.00 6 2 0 3 1 0 0 0 0 0 0 0 0 0 0
...................................................................TCGGGTGAGGTTTCTGATGCTTTGTC.................................................................................................................................... 26 0 1 5.00 5 4 0 0 0 0 0 0 0 0 1 0 0 0 0
...................................................................TCGGGTGAGGTTTCTGATGC.......................................................................................................................................... 20 0 1 5.00 5 2 0 1 0 2 0 0 0 0 0 0 0 0 0
..................................................................TTCGGGTGAGGTTTCTGATGCTTTGTC.................................................................................................................................... 27 0 1 4.00 4 1 0 0 0 2 0 0 0 0 1 0 0 0 0
...........................................................................................................................................ACCATCAAAAAACCTCACCCAC................................................................ 22 0 1 4.00 4 0 0 0 0 0 0 0 2 2 0 0 0 0 0
...................................................................TCGGGTGAGGTTTCTGATGCG......................................................................................................................................... 21 1 1 4.00 4 2 2 0 0 0 0 0 0 0 0 0 0 0 0
....................................................................CGGGTGAGGTTTCTGATGCTT........................................................................................................................................ 21 0 1 4.00 4 2 0 0 0 0 1 1 0 0 0 0 0 0 0
.............................................................................................................................................CATCAAAAAACCTCACCCACCA.............................................................. 22 0 1 4.00 4 0 0 1 1 0 0 0 1 0 0 1 0 0 0
..................................................................TTCGGGTGAGGTTTCTGAT............................................................................................................................................ 19 0 1 3.00 3 2 0 1 0 0 0 0 0 0 0 0 0 0 0
....................................................................CGGGTGAGGTTTCTGATGCTTTGTCT................................................................................................................................... 26 0 1 3.00 3 2 0 0 1 0 0 0 0 0 0 0 0 0 0
...............................................TACAAAAAAGCATCAGGTTTTCGGG......................................................................................................................................................... 25 0 1 3.00 3 0 0 0 0 1 1 1 0 0 0 0 0 0 0
.....................................................AAAGCATCAGGTTTTCGGGT........................................................................................................................................................ 20 0 1 3.00 3 2 0 0 1 0 0 0 0 0 0 0 0 0 0
.................................................................................................................................................................................................TAAAAACCAATTCGATGACTT........... 21 0 1 3.00 3 0 3 0 0 0 0 0 0 0 0 0 0 0 0
............................................................................................................................................CCATCAAAAAACCTCACCC.................................................................. 19 0 1 3.00 3 0 0 2 0 0 0 0 0 0 0 1 0 0 0
............................................................................................................................................CCATCAAAAAACCTCACCCACCAA............................................................. 24 0 1 2.00 2 0 0 2 0 0 0 0 0 0 0 0 0 0 0
.....................................TTTTCGTACGTACAAAAAAGCATCAGGT................................................................................................................................................................ 28 0 1 2.00 2 0 0 0 0 1 0 1 0 0 0 0 0 0 0
....................................................................CGGGTGAGGTTTCTGATGCT......................................................................................................................................... 20 0 1 2.00 2 1 0 0 0 0 1 0 0 0 0 0 0 0 0
.................................................................TTTCGGGTGAGGTTTCTGATGCT......................................................................................................................................... 23 0 1 2.00 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0
..................................................................TTCGGGTGAGGTTTCTGATGCTTTGT..................................................................................................................................... 26 0 1 2.00 2 1 0 0 0 0 0 0 0 0 1 0 0 0 0
....................................................................CGGGTGAGGTTTCTGATGCTTT....................................................................................................................................... 22 0 1 2.00 2 1 0 0 0 0 0 0 0 0 1 0 0 0 0
..................................................................TTCGGGTGAGTTTTCTGATGCT......................................................................................................................................... 22 1 1 2.00 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0
................................................ACAAAAAAGCATCAGGTTTTCGGGT........................................................................................................................................................ 25 0 1 2.00 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0
...................................................................TCGGGGGAGGTTTCTGATGCT......................................................................................................................................... 21 1 1 2.00 2 1 0 0 1 0 0 0 0 0 0 0 0 0 0
..............................................................................................................AAATAAGACCCTATGTCGGT............................................................................................... 20 0 1 2.00 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0
............................................................................................................AAAAATAAGACCCTATGTCGGT............................................................................................... 22 0 1 2.00 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0
..............................................................GGTTTTCGGGTGAGGTTTCTGATGC.......................................................................................................................................... 25 0 1 2.00 2 1 1 0 0 0 0 0 0 0 0 0 0 0 0
............................................................................................................................................CCATCAAAAAACCTCACCCA................................................................. 20 0 1 2.00 2 0 0 2 0 0 0 0 0 0 0 0 0 0 0
...................................................................TCGGGTGAGGTTTCTGAT............................................................................................................................................ 18 0 1 2.00 2 0 0 2 0 0 0 0 0 0 0 0 0 0 0
......................................................................................................................CCCTATGTCGGTATTTCGAAT...................................................................................... 21 0 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0
........TCCCCCAAATACTTTCAAAAATC.................................................................................................................................................................................................. 23 0 1 1.00 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1
..........CCCCAAATACTTTCAAAAATCCC................................................................................................................................................................................................ 23 0 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0
..................................................................TTCGGGTGAGGTTTCTGA............................................................................................................................................. 18 0 1 1.00 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0
...........................................................................................................................................ACCATCAAAAAACCTCAC.................................................................... 18 0 1 1.00 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0
...............................................................GTTTTCGGGTGAGGTTTCTGATGCT......................................................................................................................................... 25 0 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0
............................................................................GTTTCTGATGCTTTGTCTCTTAAGTT........................................................................................................................... 26 0 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0
...........................................................................................................................................ACCATCAAAAAACCTCACCCA................................................................. 21 0 1 1.00 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0
............................ATCCCTTCCTTTTCGTACGTA................................................................................................................................................................................ 21 0 1 1.00 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0
.....................................................................GGGTGAGGTTTCTGATGCT......................................................................................................................................... 19 0 1 1.00 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0
......................................................................................................................CCCTATGTCGGTATTTCGAATACC................................................................................... 24 0 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0
...........................................................................................................................................ACCATCAAAAAACCTCACCCACA............................................................... 23 1 1 1.00 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0
............................................................................................................................................CCATCAAAAAACCTCACTTACC............................................................... 22 2 1 1.00 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0
..................................................................TTCGGGGGAGGTTTCTGATGCT......................................................................................................................................... 22 1 1 1.00 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
................................CTTCCTTTTCGTACGTACAAAAAAG........................................................................................................................................................................ 25 0 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0
........................................................................................................................CTATGTCGGTATTTCGAATACCATC................................................................................ 25 0 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0
...................................................AAAAAGCATCAGGTTTTCGGGTGA...................................................................................................................................................... 24 0 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0
.........................................................................GAGGTTTCTGATGCT......................................................................................................................................... 15 0 1 1.00 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0
..........................AAATCCCTTCCTTTTCGTACGTAC............................................................................................................................................................................... 24 0 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0
..................................................................TTCGGGTGAGGTTTCTGATGCTT........................................................................................................................................ 23 0 1 1.00 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0
..............................................................GGTTTTCGGGTGAGGTTTCTGA............................................................................................................................................. 22 0 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0
..........................................................ATCAGGTTTTCGGGTGAGGTTTCTGA............................................................................................................................................. 26 0 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0
...................................................................................................GTTTTCCCTAAAAATAAGA........................................................................................................... 19 0 1 1.00 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0
..................................................................TTCGGGTGAGGTTTCTGATGCG......................................................................................................................................... 22 1 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0
...................................................................TCGGGTGAGGTTTCTGATGG.......................................................................................................................................... 20 1 1 1.00 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
................................................................................................TAAGTTTTCCCTAAAAATAAGACCCTA...................................................................................................... 27 0 1 1.00 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0
..................................................................TGCGGGTGAGGTTTCTGATG........................................................................................................................................... 20 1 1 1.00 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0
.............................................................................................................................................CATCAAAAAACCTCACCCAC................................................................ 20 0 1 1.00 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0
...........................................................................................................................................ACCATCAAAAAACCTCACC................................................................... 19 0 1 1.00 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0
......................................................................................................................................................................................................ACCAATTCGATGACTTCTACGATGAC. 26 0 1 1.00 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
.............................................................................................................................................................................................................CGATGACTTCTACGATGAC. 19 0 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0
...................................................................TCGGGTGAGGTTTCTGATGCTTTGT..................................................................................................................................... 25 0 1 1.00 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
......................................................................................................TTCCCTAAAAATAAGACCCTATGTCGGT............................................................................................... 28 0 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0
..........................................................................................GTCTCTTAAGTTTTCCCTAAAAATAAGA........................................................................................................... 28 0 1 1.00 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0
......................................................AAGCATCAGGTTTTCGGGG........................................................................................................................................................ 19 1 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0
............................................................................................................................GTCGGTATTTCGAATACC................................................................................... 18 0 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0
....................................................................CGGGTGAGGTTTCTGATGC.......................................................................................................................................... 19 0 1 1.00 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0
......................................................................................................TTCCCTAAAAATAAGACCCTATGTCGGTATT............................................................................................ 31 0 1 1.00 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0
.................................................................................................................TAAGACCCTATGTCGGTATTTCGAA....................................................................................... 25 0 1 1.00 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0
.............................................................................................................................................CATCAAAAAACCTCACCCACC............................................................... 21 0 1 1.00 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0
............................................................................................................................................CCATCAAAAAACCTCACC................................................................... 18 0 1 1.00 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0
......................................................AAGCATCAGGTTTTCGGGTGA...................................................................................................................................................... 21 0 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0
..........................................................................................................................................TACCATCAAAAAACCTCACCCA................................................................. 22 0 1 1.00 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0
............................................................................................................................................CCATCAAAAAACCTCACCCATT............................................................... 22 2 1 1.00 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0
..................................................................TTCGGGTAAGGTTTCTGATGCT......................................................................................................................................... 22 1 1 1.00 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0
...........................................................TCAGGTTTTCGGGTGAGGTTTCTGA............................................................................................................................................. 25 0 1 1.00 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0
...................................................................TCGGGTGAGGTTTCTGATG........................................................................................................................................... 19 0 1 1.00 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0
..........................................................................................................................................TACCATCAAAAAACCTCACCCAC................................................................ 23 0 1 1.00 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0
........TCCCCCAAATACTTTCAAAAA.................................................................................................................................................................................................... 21 0 1 1.00 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0
............................................................CAGGTTTTCGGGTGAGGTT.................................................................................................................................................. 19 0 1 1.00 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0
................................................................TTTTCGGGTGAGGTTTCTGATGCC......................................................................................................................................... 24 1 1 1.00 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
.............................................................................................................................................CATCAAAAAACCTCACCC.................................................................. 18 0 1 1.00 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0
..................................................................TTCGGGAGAGGTTTCTGATGCT......................................................................................................................................... 22 1 1 1.00 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
..................................................................TTCGGGTGAGGCTTCTGATGCT......................................................................................................................................... 22 1 1 1.00 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0
...................................................................TCGGGTGAGGTTTCTGATCCT......................................................................................................................................... 21 1 1 1.00 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0
....................................................................CGGGTGAGGTTTCAGATGCTTT....................................................................................................................................... 22 1 1 1.00 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0
...............................CCTTCCTTTTCGTACGTAC............................................................................................................................................................................... 19 0 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0
...................................................................................................................................TTTCGAATACCATCAAAAAACCTC...................................................................... 24 0 1 1.00 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
...................................................................TCGGGTGAGGTTTCTGATGCTTTGTCTC.................................................................................................................................. 28 0 1 1.00 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0
..................................................................TTCGGGGGAGGTTTCTGATT........................................................................................................................................... 20 2 2 0.50 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0
......................................................................................................................................................................GTATGTCCAGAGATAAAAAAA...................................... 21 3 8 0.13 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0
..........................................................................................................................ATGTCGGGAGTTCGAATCCC................................................................................... 20 3 9 0.11 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0
..........................................................................................................................ATGTCGGGAGTTCGAATCC.................................................................................... 19 3 20 0.10 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0
.....................................................................................................................................TCTAACACCATCAAAAAA.......................................................................... 18 2 11 0.09 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0
.....................................................................................................................................................................................................AATCAATTTGATGACGTCTAC....... 21 3 14 0.07 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0
........................................................GCATCAGGTTATCGGTT........................................................................................................................................................ 17 2 14 0.07 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0
......................................................AAGCATCAGGTCATCG........................................................................................................................................................... 16 2 20 0.05 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0

Anti-sense strand reads

CTTGGCGTAGGGGGTTTATGAAAGTTTTTAGGGAAGGAAAAGCATGCATGTTTTTTCGTAGTCCAAAAGCCCACTCCAAAGACTACGAAACAGAGAATTCAAAAGGGATTTTTATTCTGGGATACAGCCATAAAGCTTATGGTAGTTTTTTGGAGTGGGTGGTTTACATACTGGTCTCTCTATTTTTAAAGTTATTTTTGGTTAAGCTACTGAAGATGCTACTGA

************************************************.......((.(((....(((((((((((.(((((.............((.(((.....(((((.(((.....)))..))))).))).)))))))..)))))))))))............))).))**************************************************** 		Read size # Mismatch Hit Count Total Norm Total M024

male body		 M023

head

 SRR618934

dsim w501 ovaries

 SRR553486

Makindu_3 day-old ovaries

 O002

Head

 GSM343915

embryo

 SRR553487

NRT_0-2 hours eggs

 M053

female body

 SRR902009

testis

 M025

embryo
......CTAGGGGGTTGATGATAG......................................................................................................................................................................................................... 18 3 20 9.55 191 145 40 0 0 0 0 0 5 0 1
..........................TTTAGGGAAGGAAAAGCAT.................................................................................................................................................................................... 19 0 1 1.00 1 0 0 0 0 1 0 0 0 0 0
................................................................................................................................CAAAAAGCTTATGGTAGATT............................................................................. 20 2 1 1.00 1 0 0 1 0 0 0 0 0 0 0
.....................................................................................................................................AGCTGATGGTAGTTTTGTGAAGT..................................................................... 23 3 1 1.00 1 0 0 0 1 0 0 0 0 0 0
.........................................................................................................................................TCTGGTAGTGTTTTGGAGTGA................................................................... 21 3 2 0.50 1 0 0 0 0 0 1 0 0 0 0
......CTAGGGGGTTGATGAAAG......................................................................................................................................................................................................... 18 2 3 0.33 1 0 0 0 0 0 0 1 0 0 0
......CTAGGGGGTTTATGATAG......................................................................................................................................................................................................... 18 2 5 0.20 1 1 0 0 0 0 0 0 0 0 0
....................................................................................................................................AGGCTTATGGTAGTTTAT........................................................................... 18 2 8 0.13 1 1 0 0 0 0 0 0 0 0 0
.............................AGGGAAGGTAAAGCATGCCA................................................................................................................................................................................ 20 3 10 0.10 1 0 0 1 0 0 0 0 0 0 0
..........................TTTAGGGGAGGAAAAGAA..................................................................................................................................................................................... 18 2 16 0.06 1 0 0 0 0 0 0 0 0 1 0
...................................................................................................................................................................................CTAGTTTGAGAGTTATTTTT.......................... 20 3 20 0.05 1 0 0 0 1 0 0 0 0 0 0

Re-alignment of all predicted orthologs

Species Coordinate ID Type Alignment
droSim2 3r:4169825-4170049 - dsi_293 confident GAACCGCATCCCCCAAATACT---TTCAAAAA--------------TCC--CTTCCTTTTCGTACGTACA----------------AAAAAGCATCAGGT-TTTCGGGTGAGGTT-TCTGATGCTT--TGTCTCT-TAAGTTTT-----CCCTAA-AA----------ATAAG-AC----------------------------------------CCTATGTCGGTATTT-CGAATACCAT------CAAAAAACCTCACCCACCAAATGTATGACCAGAGAGATAAAAA--TTTCAATAAAAAC-------------------CAAT-----TCGATGACT---------TCTA--CG--------------ATGACT
droSec2 scaffold_6:4348767-4348991 - dse_369 candidate-rescued GAACCGCATCCCCCAAATACT---TTCAAAAA--------------TCC--CTTCCTTTTCGTACGTACA----------------AAAAAGCATCAGGT-TTTCGGGTGAGGTT-TCTGATGCTT--TGTCTCT-TAAGTTTT-----CCCTAA-CA----------ATTAG-AC----------------------------------------CCTATGTCGGTATTT-CGAATACCAT------CAAAAAACCTCACCCACCAAATGTATGACCAGAGAGATAAAAA--TTTCAATAAAAAC-------------------CAAT-----TCGATTATT---------TCTA--CG--------------ATGACT
dm3 chr3R:17142402-17142640 + dme-mir-4951 Known_mirbase GAACCGCATCCCCCAAATACT---TTGAAAA---------------TCC--CTTCCTTTTCGTACGTACA----------------AAAAAGCATCAGGT-TTTCGGGTGAGGTT-TCTGATGCTT--TGTCTCT-TAAGTTTT-----TCCTAA-CA----------ATTAA-AC----------------------------------------CCTATGTCGGTATTA-CGAATACCAT------CAAAAAACCTCACCCACCAAATGTATGACCAGAGAGATAAAAA--TTTCAATAAAC-AACGTGGCA---GTCTTGACCAAT-----TCAATGACT---------TCTA--CG--------------ATGATT
droEre2 scaffold_4770:4529458-4529696 - der_256 candidate-rescued AAAT----------------------------TT---------------GATTTCCTTTCCGTACGTACTATTGTACGTAAGCATTATTAAGCATCAGGT-TTTCGGGTGAGGTT-TCTGATGCTT--CGTCTCT-TAAGTTTT-----CCATAA-CA----------ATTGG-TC----------------------------------------CCTATGTTGGTATTA-CAAATACCATAC----CAAAAAACCTCACCCACCAAATGTATGAACAGAGAGATAAAAA--TTTCAATAAAAAAATGT------TG----------------TCGATGACA-----ATGTTATT--CGATGACTTTGGCAACACCAAT
droYak3 3R:5943412-5943644 + dya_177 candidate-rescued AAACCGCAACCCCCAAAGTCT---TAAAAAAATT---------------CATTTACTTTACGTGCGTACA--------------AA-AAAAGCATCAGGT-TTTCGGGTGAGGTT-TCTGATGCTT--TGTCTCT-TAAGTTTT-----TCCTAA-CA----------ACTAG-TC----------------------------------------CCTATGTTGGTACTA-CGAATACCAAAT----CAAAAAACCTCACCCACCAAAAGTATGAACAGAGAGATAAAAA--TTTCAATATAAAAACATGTCA---GTCATGA-----------------TT---------TTTT--CA--------------ATGACA
droEug1 scf7180000409760:1269917-1270154 - AAACCGCATTACCCAATAAATC-CTAAAAAGCTTCAAACCCCTTTT---CTAATCCCTTTCGTACGAAA-----------------AAAAGGCATCAGGT-TTTCGGGTGAGGTT-TCTGATGCTT--TGTCTTT-TA-GTTTC---GCGCCTTT-TT----------ATAAA-CC----------------------------------------CCTTTGTCGGTATTG-CAAATACCAT------CAAAAAACCTCACCCACCAAATATATGAACAAAGAGATACAAA--TTTCAATCAATTAACTTGGCATTGGCCACG---------------------------------------------------TTAACA
droBia1 scf7180000302155:521218-521464 + GAGTTGCGATCTCGAACA-ACC--TTAAGAACTTCACACCC--TTT---CACGTCCTTTTCGTACGAATA--------------AA-TAAAGCGTCAGGT-TTTCGGGTGAGGTT-TCTGATGCTT--TGTCTCT-TACCTTTTTACATCCCTTT-AC----------ATGAATCC----------------------------------------CCCATCTTGGTATTG-CAAATACCA-------CAAAAAACCTCACCCACCAAATATATGAACAAAGAGAAA-AAA--TTTCAATAAG-TACTGTGACAATAGTCATAT-----------------C-----AA----CAA--AG--------------ATGTCT
droTak1 scf7180000415417:230001-230242 - GAACACCTATATCCAAT-AATACT--AAAAACTTCAAACCC--TTT---CACAT-ATTTTCGTACGAACA-----------------AAAAGCATCAGGT-TTTCGGGTGAGGTT-TCTGATGCTT--TGTCCCT-TA-------------------C----------ATGAA-TT----------------------------------------CCTATATCGGTATTG-AAAATGCCAC------CTAAAAACCTCACCCACCAAATGTATATTCAAAGAGAATAAAA--TTTCAATAAACTAACGTGACATTAGTCATGT-----------------T-----AA----CAA--AGATGACTGAGGCCCGATGACT
droEle1 scf7180000491104:1675794-1676041 + GAACCGCAAACCCCTAAAAATA-T--TAAAACTTCACTCCC-CTTT---CACATTCTTATCGTTCGAACG--------------AA-TTCAGCATCAGGT-TTTCGGGTGAGGTT-TCTGATGCTA--TGTCTTT-GTACCTTC-----TCCAAA-AA----------ATGAA-TC----------------------------------------CCTACCTTGGTATTG-CAAATACCCTA-----TAAAAAACCTCACCCACCAAATGTATGAACAAAGAGATATAAA--TTTCAATAAACTAACATGACACTTGTCATGA-----------------CA-----A------------------AGTCAAGACGACT
droRho1 scf7180000767410:75249-75484 - GAACCGCAATCCCTA-TTAATC-A--TAAAACTTCTGGCCC-CATT---TACTT-CTTATCGTACGACCG--------------AA-AACAGCATCAGGT-TTTCGGGTGAGGTT-TCTGATGCTT--TGTCCTT-TTACATTC-----TCCAAT-A-----------AAATA-TC----------------------------------------CCTATTTCGGTATTT-CAAATACTTT------AAAAAAACCTCACCCACCAAATGTATGAACAAAGAGATAAAAA--TTTCAATAAAGTAAAATGGCTCTTGTCATGA-----------------C-----------------A--------------ATGGCA
droFic1 scf7180000454096:426534-426785 + GAACCGCAATACACA----ATCGC--AAAAACTTCAGACCC-TTTT---CATTTCCCTATCGTACGAA------------------AAAAAGCATCAGGT-TTTCGGGTGAGGTT-TCTGATGCTT--TGTCTCT-CGACTTTA-----CCCCTT-AT----------ACTAT-CC----------------------------------------CCTG-TTTGGCATTC-CAAATGCCAC------CTAAAAACCTCACCCACCAAATGTATGAACAAAGAGAAAAACA--TTTCAATAAGGTATTGTGGCAATAGTCACAG-----------------C-----AA----CAA--AGATGACCAAGGCGTGATGACT
droKik1 scf7180000302461:267794-268041 + AAACCGCTCTCCCAT-ATAATC-T--AAAAGCTTCAAACCC-TTTT---CCAAT-ACCATCGTACGAACA--------------TT-AAAAGCATCAGAT-TTTCGGGTGAGGTT-ACTGATGCTCTTTGTCTCT-AAAATA-----------------------------TG-TTTTTTTTTTCTAAAAAAAAAATAAAAGGAAAACAT----------------------ACACCACCTT------AAAATAACCTCACCCACCAAATGTATGAACAAAGAGAACAAAA--TTTCAATACAAACCCACGAC-----------------------GAAGCCACCCG----TTTCA--AG--------------AAGG--
droBip1 scf7180000396395:545227-545459 - TAAACACTTTCTTAATTTACT---TTCTTATA-----A--------TTA--CAATAATTTTATA---ATA----------------GATAAGCATCAGTTTTTTCGGGTGAGGTCAACTGTTGCGA--AATCATT-TCAATTGC-----CCAAAAACA----------ATTG--AA----------------------------------------TTTTAATTGGTATTTTTCAATGCCCA------AAACTAACCTCACCCACCAAATATATGAAAAAAGAGATACAAA--TTTCAATAAAATC-------------------CAAACAACCCAGATGCCGACTG-------AA--GG--------------ATGACT
droWil2 scf2_1100000004943:16135015-16135160 + dwi_5425 AA--------------------------------------------------------------------------------------AAATCATCACGG-TTTCGGGTGAGGTT-AGTGATGACT--TTTCCTT-T------------TTCAAA-CAACTAA--AATTTTAA---------TTCCAAAA------------------A-------C-CCTTTCGGTATAG-ACAATACCAA------AAAAAAACCTCACCCACCAAATATATGAACAAAGAGAAACAAA--TTT------------------------------------------------------------------------------------
droVir3 scaffold_12822:1191970-1192146 - AG---------------------------------------------------------------------------------------AAGCATCTAGT--TTCGGGTGAGGTTTTATGATGCAATTC-T-C----G-CTCTA-----TCC----CATCTTG--AACATACG---------TTCCAAAATAAATACATAATAAAAAAATCC----CCTGCTTTGGTATTT-AAGCTACCAACCA---AAAAAAACCTCACCCACCAAATGTATGAACAAAGAGATAAAAAATTTTCAATA-------------------------------------------------------------------------------
droMoj3 scaffold_6540:33813439-33813603 - dmo_3160 AG---------------------------------------------------------------------------------------ATGCATCAGAT-TTTCGGGTGAGGTTTTATGATGCAGTAC-T-CCATG------------TCC----CACTCCGAAT--ACT---------------------AAAATAAAAAGA----ATCCTTCTCCC-ATTTGGTATTA-AAGCCACCCACC----AAAAAAACCTCACCCACCAAACATATGAACAAAGAGATACAAAATATTCAATACAA----------------------------------------------------------------------------
droGri2 scaffold_15074:2653284-2653473 + -----------------------------------------------------------TCGTACGACTA--------------ATGAAATGCATCTAGT-TTTCGGGTGAGGTT-TTAGATGCGT--TTCCCC-----------------CAGA-AA----------ATAAA-AC---------------------A----------------CTC-CTTTTTGGTATTT-AAACTACAAAAAAAAAAAAAAAACCTCACCCACCAAATATATGAACAAAGAGATAAAAT--ATTCAATAAACCAACAA-----------------AC-----CCGAAGAAGTCTG-------GAGCTG--------------ATGACC

Re-alignment of all predicted orthologs with sRNA reads

Species Read alignment
droSim2
GAACCGCATCCCCCAAATACT---TTCAAAAA--------------TCC--CTTCCTTTTCGTACGTACA----------------AAAAAGCATCAGGT-TTTCGGGTGAGGTT-TCTGATGCTT--TGTCTCT-TAAGTTTT-----CCCTAA-AA----------ATAAG-AC----------------------------------------CCTATGTCGGTATTT-CGAATACCAT------CAAAAAACCTCACCCACCAAATGTATGACCAGAGAGATAAAAA--TTTCAATAAAAAC-------------------CAAT-----TCGATGACT---------TCTA--CG--------------ATGACTSizeHit 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
.......................................................................................................TCGGGTGAGGTT-TCTGATGCT...............................................................................................................................................................................................................................................................21195.009547124023107910000000
......................................................................................................TTCGGGTGAGGTT-TCTGATGCT...............................................................................................................................................................................................................................................................22157.00573411501014100000000
..............................................................................................................................................................................................................................................CCAT------CAAAAAACCTCACCCACC..................................................................................................................22134.00341324001201000002000
......................................................................................................TTCGGGTGAGGTT-TCTGATG.................................................................................................................................................................................................................................................................20127.0027141200032500000000
..............................................................................................................................................................................................................................................CCAT------CAAAAAACCTCACCCACCA.................................................................................................................23117.001700010800000008000
.......................................................................................................TCGGGTGAGGTT-TCTGATGCTT--............................................................................................................................................................................................................................................................22117.001774200021100000000
......................................................................................................TTCGGGTGAGGTT-TCTGATGC................................................................................................................................................................................................................................................................2119.00940000220100000000
......................................................................................................TTCGGGTGAGGTT-TCTGATGCC...............................................................................................................................................................................................................................................................2218.00870100000000000000
.......................................................................................................TCGGGTGAGGTT-TCTGATGCC...............................................................................................................................................................................................................................................................2117.00752000000000000000
..............................................................................................................................................................................................................................................CCAT------CAAAAAACCTCACCCAC...................................................................................................................2116.00621000300000000000
.......................................................................................................TCGGGTGAGGTT-TCTGATGCTT--TGTC........................................................................................................................................................................................................................................................2615.00540000000010000000
.......................................................................................................TCGGGTGAGGTT-TCTGATGC................................................................................................................................................................................................................................................................2015.00520000120000000000
......................................................................................................TTCGGGTGAGGTT-TCTGATGCTT--TGTC........................................................................................................................................................................................................................................................2714.00410000020010000000
.............................................................................................................................................................................................................................................ACCAT------CAAAAAACCTCACCCAC...................................................................................................................2214.00400020000000002000
.......................................................................................................TCGGGTGAGGTT-TCTGATGCG...............................................................................................................................................................................................................................................................2114.00420200000000000000
........................................................................................................CGGGTGAGGTT-TCTGATGCTT--............................................................................................................................................................................................................................................................2114.00420000001100000000
...............................................................................................................................................................................................................................................CAT------CAAAAAACCTCACCCACCA.................................................................................................................2214.00401001100000001000
......................................................................................................TTCGGGTGAGGTT-TCTGAT..................................................................................................................................................................................................................................................................1913.00320000100000000000
........................................................................................................CGGGTGAGGTT-TCTGATGCTT--TGTCT.......................................................................................................................................................................................................................................................2613.00321000000000000000
..................................................................TACA----------------AAAAAGCATCAGGT-TTTCGGG................................................................................................................................................................................................................................................................................2513.00300000011100000000
........................................................................................AAAGCATCAGGT-TTTCGGGT...............................................................................................................................................................................................................................................................................2013.00321000000000000000
...........................................................................................................................................................................................................................................................................................................TAAAAAC-------------------CAAT-----TCGATGACT---------T...........................2113.00300300000000000000
..............................................................................................................................................................................................................................................CCAT------CAAAAAACCTCACCC.....................................................................................................................1913.00300001200000000000
..............................................................................................................................................................................................................................................CCAT------CAAAAAACCTCACCCACCAA................................................................................................................2412.00200000200000000000
........................................................TTTTCGTACGTACA----------------AAAAAGCATCAGGT-.......................................................................................................................................................................................................................................................................................2812.00200000011000000000
........................................................................................................CGGGTGAGGTT-TCTGATGCT...............................................................................................................................................................................................................................................................2012.00210000000100000000
.....................................................................................................TTTCGGGTGAGGTT-TCTGATGCT...............................................................................................................................................................................................................................................................2312.00200200000000000000
......................................................................................................TTCGGGTGAGGTT-TCTGATGCTT--TGT.........................................................................................................................................................................................................................................................2612.00210000000010000000
........................................................................................................CGGGTGAGGTT-TCTGATGCTT--T...........................................................................................................................................................................................................................................................2212.00210000000010000000
...................................................................ACA----------------AAAAAGCATCAGGT-TTTCGGGT...............................................................................................................................................................................................................................................................................2512.00220000000000000000
............................................................................................................................................................AA----------ATAAG-AC----------------------------------------CCTATGTCGGT.........................................................................................................................................................2012.00200200000000000000
.........................................................................................................................................................AA-AA----------ATAAG-AC----------------------------------------CCTATGTCGGT.........................................................................................................................................................2212.00200000000000200000
.................................................................................................GGT-TTTCGGGTGAGGTT-TCTGATGC................................................................................................................................................................................................................................................................2512.00210100000000000000
..............................................................................................................................................................................................................................................CCAT------CAAAAAACCTCACCCA....................................................................................................................2012.00200000200000000000
.......................................................................................................TCGGGTGAGGTT-TCTGAT..................................................................................................................................................................................................................................................................1812.00200000200000000000
...............................................................................................................................................................................C----------------------------------------CCTATGTCGGTATTT-CGAAT...............................................................................................................................................2111.00100100000000000000
........TCCCCCAAATACT---TTCAAAAA--------------TC............................................................................................................................................................................................................................................................................................................................................2311.00100000000000010000
..........CCCCAAATACT---TTCAAAAA--------------TCC--C........................................................................................................................................................................................................................................................................................................................................2311.00100100000000000000
......................................................................................................TTCGGGTGAGGTT-TCTGA...................................................................................................................................................................................................................................................................1811.00100000100000000000
.............................................................................................................................................................................................................................................ACCAT------CAAAAAACCTCAC.......................................................................................................................1811.00100000100000000000
..................................................................................................GT-TTTCGGGTGAGGTT-TCTGATGCT...............................................................................................................................................................................................................................................................2511.00100100000000000000
................................................................................................................GTT-TCTGATGCTT--TGTCTCT-TAAGTT..............................................................................................................................................................................................................................................2611.00100100000000000000
.............................................................................................................................................................................................................................................ACCAT------CAAAAAACCTCACCCA....................................................................................................................2111.00100000100000000000
...............................A--------------TCC--CTTCCTTTTCGTACGTA........................................................................................................................................................................................................................................................................................................................2111.00100010000000000000
.........................................................................................................GGGTGAGGTT-TCTGATGCT...............................................................................................................................................................................................................................................................1911.00100000001000000000
...............................................................................................................................................................................C----------------------------------------CCTATGTCGGTATTT-CGAATACC............................................................................................................................................2411.00100100000000000000
.............................................................................................................................................................................................................................................ACCAT------CAAAAAACCTCACCCACA..................................................................................................................2311.00100000000000001000
...................................................CTTCCTTTTCGTACGTACA----------------AAAAAG................................................................................................................................................................................................................................................................................................2511.00100100000000000000
.........................................................................................................................................................................................................................CTATGTCGGTATTT-CGAATACCAT------C...................................................................................................................................2511.00100100000000000000
......................................................................................AAAAAGCATCAGGT-TTTCGGGTGA.............................................................................................................................................................................................................................................................................2411.00100100000000000000
.............................................................................................................GAGGTT-TCTGATGCT...............................................................................................................................................................................................................................................................1511.00100000000001000000
.............................AAA--------------TCC--CTTCCTTTTCGTACGTAC.......................................................................................................................................................................................................................................................................................................................2411.00100100000000000000
......................................................................................................TTCGGGTGAGGTT-TCTGATGCTT--............................................................................................................................................................................................................................................................2311.00101000000000000000
.................................................................................................GGT-TTTCGGGTGAGGTT-TCTGA...................................................................................................................................................................................................................................................................2211.00100100000000000000
.............................................................................................ATCAGGT-TTTCGGGTGAGGTT-TCTGA...................................................................................................................................................................................................................................................................2611.00100100000000000000
...........................................................................................................................................GTTTT-----CCCTAA-AA----------ATAAG-A.............................................................................................................................................................................................................1911.00100000010000000000
......................................................................................................TTCGGGTGAGGTT-TCTGATGCG...............................................................................................................................................................................................................................................................2211.00100100000000000000
.......................................................................................................TCGGGTGAGGTT-TCTGATGG................................................................................................................................................................................................................................................................2011.00110000000000000000
........................................................................................................................................TAAGTTTT-----CCCTAA-AA----------ATAAG-AC----------------------------------------CCTA................................................................................................................................................................2711.00100010000000000000
...............................................................................................................................................................................................................................................CAT------CAAAAAACCTCACCCAC...................................................................................................................2011.00100000100000000000
.............................................................................................................................................................................................................................................ACCAT------CAAAAAACCTCACC......................................................................................................................1911.00100000100000000000
................................................................................................................................................................................................................................................................................................................AC-------------------CAAT-----TCGATGACT---------TCTA--CG--------------ATGAC.2611.00110000000000000000
...............................................................................................................................................................................................................................................................................................................................................CGATGACT---------TCTA--CG--------------ATGAC.1911.00100100000000000000
.......................................................................................................TCGGGTGAGGTT-TCTGATGCTT--TGT.........................................................................................................................................................................................................................................................2511.00110000000000000000
..............................................................................................................................................TT-----CCCTAA-AA----------ATAAG-AC----------------------------------------CCTATGTCGGT.........................................................................................................................................................2811.00100100000000000000
.................................................................................................................................GTCTCT-TAAGTTTT-----CCCTAA-AA----------ATAAG-A.............................................................................................................................................................................................................2811.00100000001000000000
.........................................................................................AAGCATCAGGT-TTTCGGGG...............................................................................................................................................................................................................................................................................1911.00100100000000000000
.............................................................................................................................................................................................................................GTCGGTATTT-CGAATACC............................................................................................................................................1811.00100100000000000000
........................................................................................................CGGGTGAGGTT-TCTGATGC................................................................................................................................................................................................................................................................1911.00100010000000000000
..............................................................................................................................................TT-----CCCTAA-AA----------ATAAG-AC----------------------------------------CCTATGTCGGTATT......................................................................................................................................................3111.00100000010000000000
.........................................................................................................................................................................TAAG-AC----------------------------------------CCTATGTCGGTATTT-CGAA................................................................................................................................................2511.00100000010000000000
...............................................................................................................................................................................................................................................CAT------CAAAAAACCTCACCCACC..................................................................................................................2111.00100000000000001000
..............................................................................................................................................................................................................................................CCAT------CAAAAAACCTCACC......................................................................................................................1811.00100000100000000000
.........................................................................................AAGCATCAGGT-TTTCGGGTGA.............................................................................................................................................................................................................................................................................2111.00100100000000000000
............................................................................................................................................................................................................................................TACCAT------CAAAAAACCTCACCCA....................................................................................................................2211.00100000000000001000
..............................................................................................................................................................................................................................................CCAT------CAAAAAACCTCACCCATT..................................................................................................................2211.00100000000000001000
..............................................................................................TCAGGT-TTTCGGGTGAGGTT-TCTGA...................................................................................................................................................................................................................................................................2511.00100000010000000000
.......................................................................................................TCGGGTGAGGTT-TCTGATG.................................................................................................................................................................................................................................................................1911.00100000001000000000
............................................................................................................................................................................................................................................TACCAT------CAAAAAACCTCACCCAC...................................................................................................................2311.00100010000000000000
........TCCCCCAAATACT---TTCAAAAA--------------..............................................................................................................................................................................................................................................................................................................................................2111.00100000000000001000
...............................................................................................CAGGT-TTTCGGGTGAGGTT-........................................................................................................................................................................................................................................................................1911.00100001000000000000
...................................................................................................T-TTTCGGGTGAGGTT-TCTGATGCC...............................................................................................................................................................................................................................................................2411.00110000000000000000
...............................................................................................................................................................................................................................................CAT------CAAAAAACCTCACCC.....................................................................................................................1811.00100000100000000000
................................................C--CTTCCTTTTCGTACGTAC.......................................................................................................................................................................................................................................................................................................................1911.00100100000000000000
....................................................................................................................................................................................................................................TTT-CGAATACCAT------CAAAAAACCTC.........................................................................................................................2411.00110000000000000000
.......................................................................................................TCGGGTGAGGTT-TCTGATGCTT--TGTCTC......................................................................................................................................................................................................................................................2811.00101000000000000000
droSec2
GAACCGCATCCCCCAAATACT---TTCAAAAA--------------TCC--CTTCCTTTTCGTACGTACA----------------AAAAAGCATCAGGT-TTTCGGGTGAGGTT-TCTGATGCTT--TGTCTCT-TAAGTTTT-----CCCTAA-CA----------ATTAG-AC----------------------------------------CCTATGTCGGTATTT-CGAATACCAT------CAAAAAACCTCACCCACCAAATGTATGACCAGAGAGATAAAAA--TTTCAATAAAAAC-------------------CAAT-----TCGATTATT---------TCTA--CG--------------ATGACTSizeHit CountTotal NormTotalM054

Female-body		V113

Male-body		V114

Embryo		V115

Head
.......................................................................................................TCGGGTGAGGTT-TCTGATGCT...............................................................................................................................................................................................................................................................2116.0062202
......................................................................................................TTCGGGTGAGGTT-TCTGATGCT...............................................................................................................................................................................................................................................................2213.0031101
......................................................................................................TTCGGGTGAGGTT-TCTGATGC................................................................................................................................................................................................................................................................2113.0030300
..............................................................................................................................................................................................................................................CCAT------CAAAAAACCTCACCCACCA.................................................................................................................2312.0021001
.......................................................................................................TCGGGTGAGGTT-TCTGATGC................................................................................................................................................................................................................................................................2012.0020002
..............................................................................................................................................................................................................................................CCAT------CAAAAAACCTCACCCAC...................................................................................................................2112.0021001
..............................................................................................................................................................................................................................................CCAT------CAAAAAACCTCACCCACC..................................................................................................................2212.0021001
...............................................................................................................................................................................................................................................CAT------CAAAAAACCTCACCCACCA.................................................................................................................2212.0021001
................................................................................................................................................................................................................................................................................ATGACCAGAGAGATAAAAA--TTTCAATA...............................................................................2711.0010001
...........................................................................................................................................................................................................................................................................AATGTATGACCAGAGAGATAAAA..........................................................................................2311.0010100
......................................................................................................TTCGGGTGAGGTT-TCTGATGCTT--TGT.........................................................................................................................................................................................................................................................2611.0010100
......................................................................................................TTCGGGTGAGGTT-TCTGATGCTT--............................................................................................................................................................................................................................................................2311.0011000
.............................................................................................ATCAGGT-TTTCGGGTGAGG...........................................................................................................................................................................................................................................................................1911.0010010
........................................................................................................................................................................................................................CCTATGTCGGTATTT-CGAA................................................................................................................................................1911.0010010
...............................................................................................................................................................................................................................................CAT------CAAAAAACCTCACCCACC..................................................................................................................2111.0010010
.............................................................................................................................................................A----------ATTAG-AC----------------------------------------CCTATGTCGGT.........................................................................................................................................................1911.0010010
.............................................................................................................................................................................................................................................ACCAT------CAAAAAACCTCACCCAC...................................................................................................................2211.0011000
........................................................................................AAAGCATCAGGT-TTTCGGGT...............................................................................................................................................................................................................................................................................2011.0010010
dm3
GAACCGCATCCCCCAAATACT---TTGAAAA---------------TCC--CTTCCTTTTCGTACGTACA----------------AAAAAGCATCAGGT-TTTCGGGTGAGGTT-TCTGATGCTT--TGTCTCT-TAAGTTTT-----TCCTAA-CA----------ATTAA-AC----------------------------------------CCTATGTCGGTATTA-CGAATACCAT------CAAAAAACCTCACCCACCAAATGTATGACCAGAGAGATAAAAA--TTTCAATAAAC-AACGTGGCA---GTCTTGACCAAT-----TCAATGACT---------TCTA--CG--------------ATGATTSizeHit 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
.......................................................................................................TCGGGTGAGGTT-TCTGATGCT...............................................................................................................................................................................................................................................................211991.0099100001000000000013100010000081000000111100011011003100000123200000000000000000000010006000001201122500401200010020253040100000431004021000000000000100200204130000001000080711048104417511020930103221218010040300000001000000684334620810162627124210120000020223202163090010060031200101020003133182223901000141122114181276154031100091876290336522204351132014180401500
......................................................................................................TTCGGGTGAGGTT-TCTGATGCT...............................................................................................................................................................................................................................................................221555.005550000000001000002000011040110100000020000010001000031100033000000000000000000000000001000003000003002460101012012303030000006110100000000000000000110020000000000000006303305204126250002194190000304000000210000004302322753222223161441220000310210105002313001000001001000200024052160512202831187836023311524910051203311523211682131057050700
......................................................................................................TTCGGGTGAGGTT-TCTGATGC................................................................................................................................................................................................................................................................211241.0024100000000000000000000000000001000000100100020000000100000000000000000000000000000001000000000001000000000200000001000110003120000100000000000000002000205200000000000010001100021002002010210100001010000000200000020021122100421200200000000122000510501002200200003000200121000501010004512331120010100480005621210223300316207547011300
.......................................................................................................TCGGGTGAGGTT-TCTGATGCTT--............................................................................................................................................................................................................................................................221161.0016100000000000000000000000000200000000000000000100000010000000000000000000000000000000000100000000010000000010000000000000002020101000002000000000000001000000000000000011021022100100000010700000000030000000000000010034002423231300000000000111100300000000000100000011100007010010060000022011010100111001200241010200013002453021010500
.......................................................................................................TCGGGTGAGGTT-TCTGATGC................................................................................................................................................................................................................................................................20181.00810000000000000000000000000100000000000000000000000000000000000000000000000000000000000000000000100000000000000000000010000000000000001000000000001000000000010000000001000000000014000000100101000000000000000000000300011100022000300000000000000100010000000000000000000001000010100000100100002001001111000011113000200033113322010110
..............................................................................................................................................................................................................................................CCAT------CAAAAAACCTCACCCACC..................................................................................................................22177.0077000000000000000000000000000000000000000000000000000000001000000000000000000000001000000100010120400008100002000000011000000000100000000000000000000000000000000000000100000020200000000001000000000100000000000000000100092119286200100000000000000000000000000000000000000000000000000001000100000000000000001000000000000000000000000
..............................................................................................................................................................................................................................................CCAT------CAAAAAACCTCACCCACCA.................................................................................................................23172.00720000000000000000000000020000002200000000000000000000000012000000000000000000000020000000000100321000120000100000000200001010001100000000000000000000000000000000000000220300020201101000001000000000000000000000000000000010102012001000000000000000001000000000000000000000000000100000001000000000000000000000000000000000000000000000
......................................................................................................TTCGGGTGAGGTT-TCTGATG.................................................................................................................................................................................................................................................................20154.0054000000000000000000000000000000000000000000000000000000000000000000000000000000000100000000000000000000000000000000001100000101000000000000000000000000000000000000000130100000000110000001000000000100000000000000000020010010202000000000000000001000000001000000010000000110001000000132110000100001101100011001000000000621010000000
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........................................................................................................CGGGTGAGGTT-TCTGATGCTT--TGTCTCT-T...................................................................................................................................................................................................................................................2911.001000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
droEre2
AAAT----------------------------TT---------------GATTTCCTTTCCGTACGTACTATTGTACGTAAGCATTATTAAGCATCAGGT-TTTCGGGTGAGGTT-TCTGATGCTT--CGTCTCT-TAAGTTTT-----CCATAA-CA----------ATTGG-TC----------------------------------------CCTATGTTGGTATTA-CAAATACCATAC----CAAAAAACCTCACCCACCAAATGTATGAACAGAGAGATAAAAA--TTTCAATAAAAAAATGT------TG----------------TCGATGACA-----ATGTTATT--CGATGACTTTGGCAACACCAATSizeHit CountTotal NormTotalM055

Female-body		M057

Embryo		V060

Head		V040

Embryo		V107

Male-body		V108

Head		GSM1528801

follicle cells
................................................................................................................................................................................................................................................ATAC----CAAAAAACCTCACCCACC..................................................................................................................2213.0032100000
.AAT----------------------------TT---------------GATTTCCTTTCCGTACGTA........................................................................................................................................................................................................................................................................................................................2412.0020100100
......................................................................................ATTAAGCATCAGGT-TTTCGGGT...............................................................................................................................................................................................................................................................................2211.0011000000
.........................................................................................................................................................AA-CA----------ATTGG-TC----------------------------------------CCTATGTTGGT.........................................................................................................................................................2211.0010000100
................................................................................................................GTT-TCTGATGCTT--CGTCTCT-TAA.................................................................................................................................................................................................................................................2311.0010000100
.....................................................................................TATTAAGCATCAGGT-TTTCGGG................................................................................................................................................................................................................................................................................2211.0010000010
.............................................................................................................................................................................................................................................................................................................................................................TGTTATT--CGATGACTTTGGC.........2011.0010001000
...................................................................................................................................................................................................................................ATTA-CAAATACCATAC----CAAAAAACCTCAC.......................................................................................................................2911.0010100000
...................................................................................ATTATTAAGCATCAGGT-TTTCGGGT...............................................................................................................................................................................................................................................................................2511.0010000100
..........................................................................................................................................................................................................................................AATACCATAC----CAAAAAACCTCACCCAC...................................................................................................................2711.0010100000
...............................................................................................................................................................................................................................................CATAC----CAAAAAACCTCACCCACCAG................................................................................................................2511.0011000000
...............................................................................................................................................................................................................................................CATAC----CAAAAAACCTCACCCACC..................................................................................................................2311.0010100000
...........................................................................................................................................................................................................................................ATACCATAC----CAAAAAACCTCACCCACC..................................................................................................................2711.0010000010
.......................................................................................................TCGGGTGAGGTT-TCTGATGCTT--CG..........................................................................................................................................................................................................................................................2411.0010000010
............................................................................................CATCAGGT-TTTCGGGTGAG............................................................................................................................................................................................................................................................................1911.0010000010
..............................................................................................................................................................................................................................................................................................................................................................GTTATT--CGATGACTTTGGCAA.......2111.0010000100
.......................................................................................................TCGGGTGAGGTT-TCTGATGCTT--CGT.........................................................................................................................................................................................................................................................2511.0010000100
.................................................................................................................................................................................................................................................TAC----CAAAAAACCTCACCCACCA.................................................................................................................2211.0010100000
..................................................................................................................................................................................................................................................AC----CAAAAAACCTCACCCACC..................................................................................................................2011.0010100000
............................................................................................CATCAGGT-TTTCGGGTGAGGTT-TCTGATG.................................................................................................................................................................................................................................................................2911.0010100000
.............................................................................................................................................................................................................................................ACCATAC----CAAAAAACCTCAC.......................................................................................................................2011.0010100000
...............................................................................................................GGTT-TCTGATGCTT--CGTCTC......................................................................................................................................................................................................................................................2011.0010000100
...................................................................................ATTATTAAGCATCAGGT-TTTCGGGTGA.............................................................................................................................................................................................................................................................................2711.0010000100
..AT----------------------------TT---------------GATTTCCTTTCCGTACGTA........................................................................................................................................................................................................................................................................................................................2311.0010000100
...............................................................................................................................................................................................................................................................................TATGAACAGAGAGATAAA...........................................................................................1820.5010000010
droYak3
AAACCGCAACCCCCAAAGTCT---TAAAAAAATT---------------CATTTACTTTACGTGCGTACA--------------AA-AAAAGCATCAGGT-TTTCGGGTGAGGTT-TCTGATGCTT--TGTCTCT-TAAGTTTT-----TCCTAA-CA----------ACTAG-TC----------------------------------------CCTATGTTGGTACTA-CGAATACCAAAT----CAAAAAACCTCACCCACCAAAAGTATGAACAGAGAGATAAAAA--TTTCAATATAAAAACATGTCA---GTCATGA-----------------TT---------TTTT--CA--------------ATGACASizeHit 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
................................................................................................................................................................................................................................................AAAT----CAAAAAACCTCACCCACCA.................................................................................................................2325.0010010000000000
...............................................................................................................................................................................................................................................CAAAT----CAAAAAACCTCACCCACC..................................................................................................................2325.001002600110000
.......................................................................................................TCGGGTGAGGTT-TCTGATGCTT--............................................................................................................................................................................................................................................................2223.50751100000000
...............................................................................................................................................................................................................................................CAAAT----CAAAAAACCTCACCCACCA.................................................................................................................2423.00606000000000
...............................................................................................................................................................................................................................................CAAAT----CAAAAAACCTCACCCAC...................................................................................................................2222.00421100000000
...............................................................................................................................................................................................................................................CAAAT----CAAAAAACCTCACCCACT..................................................................................................................2321.50310200000000
................................................................................................................................................................................................................................................AAAT----CAAAAAACCTCACCCACC..................................................................................................................2221.50301200000000
.................................................................................................................................................................................................................................................AAT----CAAAAAACCTCACCCACCA.................................................................................................................2221.00202000000000
.........CCCCCAAAGTCT---TAAAAAAATT---------------CATT.......................................................................................................................................................................................................................................................................................................................................2630.67220000000000
.................................................................................................................................................................................................................................................AAT----CAAAAAACCTCACCCAC...................................................................................................................2020.50100100000000
...........................................................................................................................................................................................................................................ATACCAAAT----CAAAAAACCTCACCCACCA.................................................................................................................2820.50101000000000
..................................................................................................................................................................................................................................................AT----CAAAAAACCTCACCCACC..................................................................................................................2020.50100100000000
............................................................................................CATCAGGT-TTTCGGGTGAG............................................................................................................................................................................................................................................................................1920.50100010000000
............................................................................................CATCAGGT-TTTCGGGTGAGG...........................................................................................................................................................................................................................................................................2020.50100000010000
.......................................................................................................TCGGGTGAGGTT-TCTGATGCT...............................................................................................................................................................................................................................................................2120.50100100000000
........................................................................................................................................................................................................................................................CAAAAAACCTCACCCACC..................................................................................................................1820.50100100000000
.......................................................................................................TCGGGTGAGGTT-TCTGATGCTT--T...........................................................................................................................................................................................................................................................2320.50110000000000
........................................................................................................CGGGTGAGGTT-TCTGATGCTT--TGA.........................................................................................................................................................................................................................................................2420.50110000000000
.........................................................................................................................................................................................................................................................AAAAAACCTCACCCACCAA................................................................................................................1920.50101000000000
.......................................................................................................TCGGGTGAGGTT-TCTGATGCTT--TGTC........................................................................................................................................................................................................................................................2620.50110000000000
................................................................................................................................................................................................................................................AAAT----CAAAAAACCTCACCCA....................................................................................................................2020.50101000000000
................................................................................................................................................................................................................................................AAAT----CAAAAAACCTCACCCACT..................................................................................................................2220.50101000000000
...............................................................................................................GGTT-TCTGATGCTT--TGTCTCT-TAAGT...............................................................................................................................................................................................................................................2620.50100000010000
..............................................................................................................................................................................................................................................CCAAAT----CAAAAAACCTCACCCACCA.................................................................................................................2520.50100100000000
..................................................................................................................................................................................................................................................AT----CAAAAAACCTCACCCACCAA................................................................................................................2220.50101000000000
.....................................................................................A-AAAAGCATCAGGT-TTTCGGGTGA.............................................................................................................................................................................................................................................................................2420.50100100000000
.................................................................................................................................................................................................................................................AAT----CAAAAAACCTCACCCACC..................................................................................................................2120.50100100000000
.................................................................................................................TT-TCTGATGCTT--TGTCTCT-TAAGTTT.............................................................................................................................................................................................................................................2620.50101000000000
.......................................................................................................TCGGGTGAGGTT-TCTGATGCTT--TG..........................................................................................................................................................................................................................................................2420.50100000010000
..................................................................................................................................................................................................................................................AT----CAAAAAACCTCACCCACCA.................................................................................................................2120.50101000000000
...........................................................................................................................................................................................................................................ATACCAAAT----CAAAAAACCTCACCCACCAA................................................................................................................2920.50101000000000
..................................................................................................................................................................................................................................................AT----CAAAAAACCTCACCCAC...................................................................................................................1920.50100100000000
....................................................................................................................................................................................................................................................................................ACAGAGAGATAAAAA--TTTCAATATA.............................................................................2520.50101000000000
...................................................................................................................................................................................................................................................T----CAAAAAACCTCACCCACC..................................................................................................................1920.50100100000000
....................................................................................................................................................................................................................................................................................ACAGAGAGATAAAAA--TTTCAAT................................................................................2220.50101000000000
.............................................................................................................GAGGTT-TCTGATGCTT--TGTCTCT-TAAGT...............................................................................................................................................................................................................................................2820.50101000000000
...............................................................................................................................................................................................................................................CAAAT----CAAAAAACCTCACCCAA...................................................................................................................2220.50100100000000
.................................................................................................GGT-TTTCGGGTGAGGTT-TCTGATGCTT--............................................................................................................................................................................................................................................................2720.50101000000000
.....................................................................................................TTTCGGGTGAGGTT-TCTTC...................................................................................................................................................................................................................................................................1950.20100100000000
droEug1
AAACCGCATTACCCAATAAATC-CTAAAAAGCTTCAAACCCCTTTT---CTAATCCCTTTCGTACGAAA-----------------AAAAGGCATCAGGT-TTTCGGGTGAGGTT-TCTGATGCTT--TGTCTTT-TA-GTTTC---GCGCCTTT-TT----------ATAAA-CC----------------------------------------CCTTTGTCGGTATTG-CAAATACCAT------CAAAAAACCTCACCCACCAAATATATGAACAAAGAGATACAAA--TTTCAATCAATTAACTTGGCATTGGCCACG---------------------------------------------------TTAACASizeHit CountTotal NormTotal
No Reads
droBia1
GAGTTGCGATCTCGAACA-ACC--TTAAGAACTTCACACCC--TTT---CACGTCCTTTTCGTACGAATA--------------AA-TAAAGCGTCAGGT-TTTCGGGTGAGGTT-TCTGATGCTT--TGTCTCT-TACCTTTTTACATCCCTTT-AC----------ATGAATCC----------------------------------------CCCATCTTGGTATTG-CAAATACCA-------CAAAAAACCTCACCCACCAAATATATGAACAAAGAGAAA-AAA--TTTCAATAAG-TACTGTGACAATAGTCATAT-----------------C-----AA----CAA--AG--------------ATGTCTSizeHit CountTotal NormTotal
No Reads
droTak1
GAACACCTATATCCAAT-AATACT--AAAAACTTCAAACCC--TTT---CACAT-ATTTTCGTACGAACA-----------------AAAAGCATCAGGT-TTTCGGGTGAGGTT-TCTGATGCTT--TGTCCCT-TA-------------------C----------ATGAA-TT----------------------------------------CCTATATCGGTATTG-AAAATGCCAC------CTAAAAACCTCACCCACCAAATGTATATTCAAAGAGAATAAAA--TTTCAATAAACTAACGTGACATTAGTCATGT-----------------T-----AA----CAA--AGATGACTGAGGCCCGATGACTSizeHit CountTotal NormTotal
No Reads
droEle1
GAACCGCAAACCCCTAAAAATA-T--TAAAACTTCACTCCC-CTTT---CACATTCTTATCGTTCGAACG--------------AA-TTCAGCATCAGGT-TTTCGGGTGAGGTT-TCTGATGCTA--TGTCTTT-GTACCTTC-----TCCAAA-AA----------ATGAA-TC----------------------------------------CCTACCTTGGTATTG-CAAATACCCTA-----TAAAAAACCTCACCCACCAAATGTATGAACAAAGAGATATAAA--TTTCAATAAACTAACATGACACTTGTCATGA-----------------CA-----A------------------AGTCAAGACGACTSizeHit CountTotal NormTotal
No Reads
droRho1
GAACCGCAATCCCTA-TTAATC-A--TAAAACTTCTGGCCC-CATT---TACTT-CTTATCGTACGACCG--------------AA-AACAGCATCAGGT-TTTCGGGTGAGGTT-TCTGATGCTT--TGTCCTT-TTACATTC-----TCCAAT-A-----------AAATA-TC----------------------------------------CCTATTTCGGTATTT-CAAATACTTT------AAAAAAACCTCACCCACCAAATGTATGAACAAAGAGATAAAAA--TTTCAATAAAGTAAAATGGCTCTTGTCATGA-----------------C-----------------A--------------ATGGCASizeHit CountTotal NormTotal
No Reads
droFic1
GAACCGCAATACACA----ATCGC--AAAAACTTCAGACCC-TTTT---CATTTCCCTATCGTACGAA------------------AAAAAGCATCAGGT-TTTCGGGTGAGGTT-TCTGATGCTT--TGTCTCT-CGACTTTA-----CCCCTT-AT----------ACTAT-CC----------------------------------------CCTG-TTTGGCATTC-CAAATGCCAC------CTAAAAACCTCACCCACCAAATGTATGAACAAAGAGAAAAACA--TTTCAATAAGGTATTGTGGCAATAGTCACAG-----------------C-----AA----CAA--AGATGACCAAGGCGTGATGACTSizeHit CountTotal NormTotal
No Reads
droKik1
AAACCGCTCTCCCAT-ATAATC-T--AAAAGCTTCAAACCC-TTTT---CCAAT-ACCATCGTACGAACA--------------TT-AAAAGCATCAGAT-TTTCGGGTGAGGTT-ACTGATGCTCTTTGTCTCT-AAAATA-----------------------------TG-TTTTTTTTTTCTAAAAAAAAAATAAAAGGAAAACAT----------------------ACACCACCTT------AAAATAACCTCACCCACCAAATGTATGAACAAAGAGAACAAAA--TTTCAATACAAACCCACGAC-----------------------GAAGCCACCCG----TTTCA--AG--------------AAGG--SizeHit CountTotal NormTotal
No Reads
droBip1
TAAACACTTTCTTAATTTACT---TTCTTATA-----A--------TTA--CAATAATTTTATA---ATA----------------GATAAGCATCAGTTTTTTCGGGTGAGGTCAACTGTTGCGA--AATCATT-TCAATTGC-----CCAAAAACA----------ATTG--AA----------------------------------------TTTTAATTGGTATTTTTCAATGCCCA------AAACTAACCTCACCCACCAAATATATGAAAAAAGAGATACAAA--TTTCAATAAAATC-------------------CAAACAACCCAGATGCCGACTG-------AA--GG--------------ATGACTSizeHit CountTotal NormTotal
No Reads
droWil2
AA--------------------------------------------------------------------------------------AAATCATCACGG-TTTCGGGTGAGGTT-AGTGATGACT--TTTCCTT-T------------TTCAAA-CAACTAA--AATTTTAA---------TTCCAAAA------------------A-------C-CCTTTCGGTATAG-ACAATACCAA------AAAAAAACCTCACCCACCAAATATATGAACAAAGAGAAACAAA--TTT------------------------------------------------------------------------------------SizeHit CountTotal NormTotalM020

Head		M045

Female-body		V117

Male-body		V118

Embryo		V119

Head
........................................................................................................CGGGTGAGGTT-AGTGATGACT--TT..........................................................................................................................................................................................................................................................2311.00100010
..............................................................................................TCACGG-TTTCGGGTGAGGTT-AGTGA...................................................................................................................................................................................................................................................................2511.00100010
.......................................................................................................TCGGGTGAGGTT-AGTGATGACT--TTT.........................................................................................................................................................................................................................................................2511.00100001
.............................................................................................................................................................................................................................................ACCAA------AAAAAAACCTCACCCA....................................................................................................................2111.00100010
droVir3
AG---------------------------------------------------------------------------------------AAGCATCTAGT--TTCGGGTGAGGTTTTATGATGCAATTC-T-C----G-CTCTA-----TCC----CATCTTG--AACATACG---------TTCCAAAATAAATACATAATAAAAAAATCC----CCTGCTTTGGTATTT-AAGCTACCAACCA---AAAAAAACCTCACCCACCAAATGTATGAACAAAGAGATAAAAAATTTTCAATA-------------------------------------------------------------------------------SizeHit CountTotal NormTotalM027

Male-body		M028

Head		M047

Female-body		M061

Embryo		SRR060654

Ovary		SRR060655

Testis		SRR060656

Ovary		SRR060657

Testis		SRR060658

Ovary		SRR060659

Testis		SRR060660

Ovary		SRR060661

Embryo		SRR060662

Embryo		SRR060663

Embryo		SRR060664

Male-body		SRR060665

Female-body		SRR060666

Male-body		SRR060667

Female-body		SRR060668

Male-body		SRR060669

Female-body		SRR060670

Testis		SRR060671

Male-body		SRR060672

Female-body		SRR060673

Ovary		SRR060674

Ovary		SRR060675

Ovary		SRR060676

Ovary		SRR060677

Ovary		SRR060678

Testis		SRR060679

Testis		SRR060680

Testis		SRR060681

Testis		SRR060682

Embryo		SRR060683

Testis		SRR060684

Embryo		SRR060685

Embryo		SRR060686

Embryo		SRR060687

Embryo		SRR060688

Ovary		SRR060689

Testis		SRR1106712

embryo_0-2h		SRR1106713

embryo_0-2h		SRR1106714

embryo_2-4h		SRR1106715

embryo_4-6h		SRR1106716

embryo_4-6h		SRR1106717

embryo_6-8h		SRR1106718

embryo_6-8h		SRR1106719

embryo_8-10h		SRR1106720

embryo_8-10h		SRR1106721

embryo_10-12h		SRR1106722

embryo_10-12h		SRR1106723

embryo_12-14h		SRR1106724

embryo_12-14h		SRR1106725

embryo_14-16h		SRR1106726

embryo_14-16h		SRR1106727

larvae		SRR1106728

larvae		SRR1106729

mixed whole adult body		SRR1106730

embryo_16-30h		V047

Embryo		V053

Head		V116

Male-body		GSM1528803

follicle cells		SRR2096013

Ovary_Strain_9_oxidized		SRR2096014

Ovary_Strain_160_oxidized		SRR2096026

embryo_0-2h from 14 day old Strain 9 mothers		SRR2096038

embryo_0-2h from 14 day old Strain 9 mothers		SRR2096050

embryo_0-2h from 14 day old Strain 160 mothers		SRR2096055

Ovary_Min_43		SRR2096056

Ovary_Min_46		SRR2096057

Ovary_Min_50		SRR2096058

Ovary_Min_98		SRR2096059

Ovary_Min_164		SRR2096060

Ovary_Min_193		SRR2096061

embryo_0-2h from 14 day old Strain 160 mothers		SRR2096072

embryo_0-2h from 15to16 day old dysgenic mothers		SRR2096079

embryo_0-2h from 15to16 day old dysgenic mothers		SRR2096080

embryo_0-2h from 15to16 day old nondysgenic mothers		SRR2096081

embryo_0-2h from 15to16 day old nondysgenic mothers
.............................................................................................ATCTAGT--TTCGGGTGAGGT..........................................................................................................................................................................................................................................................................1913.0030010000000000000000010000000000000000000000000000000000000010000000000000000000
........................................................................................................................................................................................................ATAAAAAAATCC----CCTGCTTTGGT.........................................................................................................................................................2313.0030000000000000010000000000000010000100000000000000000000000000000000000000000000
.........................................................................................AAGCATCTAGT--TTCGGGT...............................................................................................................................................................................................................................................................................1813.0030000000000000000000010000000000000000000000000000000000000000000000002000000000
...............................................................................................CTAGT--TTCGGGTGAGGTTTTATGATGC................................................................................................................................................................................................................................................................2712.0020001000000000000000000000000000000000000000000000000000000010000000000000000000
.................................................................................................................TTTTATGATGCAATTC-T-C----G-CTC..............................................................................................................................................................................................................................................2212.0020000002000000000000000000000000000000000000000000000000000000000000000000000000
....................................................................................................................TATGATGCAATTC-T-C----G-CT...............................................................................................................................................................................................................................................1812.0020000020000000000000000000000000000000000000000000000000000000000000000000000000
...................................................................................................................................................................................................................................................CA---AAAAAAACCTCACCCACCA.................................................................................................................2112.0020010000000000000001000000000000000000000000000000000000000000000000000000000000
..............................................................................................................................................................................................................................TTGGTATTT-AAGCTACCAACCA---AAA.................................................................................................................................2512.0020000000000000000000000000000000000000000000000000000000000000000200000000000000
...............................................................................................................................................................................................................................................CAACCA---AAAAAAACCTCACCCACCA.................................................................................................................2512.0020001000000000001000000000000000000000000000000000000000000000000000000000000000
............................................................................................CATCTAGT--TTCGGGTGAGG...........................................................................................................................................................................................................................................................................1911.0010010000000000000000000000000000000000000000000000000000000000000000000000000000
.......................................................................................................TCGGGTGAGGTTTTATGAT..................................................................................................................................................................................................................................................................1911.0010001000000000000000000000000000000000000000000000000000000000000000000000000000
................................................................................................................................................................................................................................................................................ATGAACAAAGAGATAAAAAAT.......................................................................................2111.0010000000000000000000000000000000000000000000000000000000000000100000000000000000
................................................................................................TAGT--TTCGGGTGAGGTTTTATGAT..................................................................................................................................................................................................................................................................2411.0010000000000000000000000000000100000000000000000000000000000000000000000000000000
...........................................................................................GCATCTAGT--TTCGGGTGAGGTTTTATG....................................................................................................................................................................................................................................................................2711.0010000000000000000000000000000000000000000000000000000000000000100000000000000000
...........................................................................................GCATCTAGT--TTCGGGTGAG............................................................................................................................................................................................................................................................................1911.0010000000000000000100000000000000000000000000000000000000000000000000000000000000
......................................................................................................TTCGGGTGAGGTTTTATGATGCAATTC-..........................................................................................................................................................................................................................................................2711.0010000000000000000000000000000000000000000000000000000000000000001000000000000000
...............................................................................................................................................A-----TCC----CATCTTG--AACATACG---------TTCCA.................................................................................................................................................................................................2411.0010000000000000000000000000000000000000000000000000000000000000000000000000100000
..................................................................................................................................................................................................................................................CCA---AAAAAAACCTCACCCACCA.................................................................................................................2211.0010010000000000000000000000000000000000000000000000000000000000000000000000000000
...........................................................................................................GTGAGGTTTTATGATGCAATTC-T-C----G-CT...............................................................................................................................................................................................................................................2711.0010000000000000000000000000000000000000000000000000000000000000001000000000000000
.........................................................................................AAGCATCTAGT--TTCGGGTGAGGTTTTATGATGC................................................................................................................................................................................................................................................................3311.0010000000000000000000000000000000000000000000000000000000000100000000000000000000
....................................................................................................................................................................................................................................................A---AAAAAAACCTCACCCACCA.................................................................................................................2011.0010010000000000000000000000000000000000000000000000000000000000000000000000000000
.........................................................................................................................................................................................CAAAATAAATACATAATAAAAAAATC.........................................................................................................................................................................2611.0010000000000000000000100000000000000000000000000000000000000000000000000000000000
...............................................................................................................................................................................................................................................................................TATGAACAAAGAGATAAAAAAT.......................................................................................2211.0010000000000000000000000000000000000000000000000000000000000000100000000000000000
.......................................................................................................TCGGGTGAGGTTTTATGATGC................................................................................................................................................................................................................................................................2111.0010000000000000000000000000000000000000000000000000000000000000100000000000000000
......................................................................................................................TGATGCAATTC-T-C----G-CTCTA-----TCC----CATCT...........................................................................................................................................................................................................................2711.0010000000000000000000000000100000000000000000000000000000000000000000000000000000
.................................................................................................................TTTTATGATGCAATTC-T-C----G-CT...............................................................................................................................................................................................................................................2111.0010000000000000000000000000000000000000001000000000000000000000000000000000000000
......................................................................................................................................................................................................................................................................CACCAAATGTATGAACAAAGAG................................................................................................2211.0010010000000000000000000000000000000000000000000000000000000000000000000000000000
.......................................................................................................................................................................CATACG---------TTCCAAAATAAAT.........................................................................................................................................................................................1911.0010000000000000000000000010000000000000000000000000000000000000000000000000000000
.................................................................................................................TTTTATGATGCAATTC-T-C----G-CTCTA-----TCC----................................................................................................................................................................................................................................2711.0010000000000000000000000000000000000000010000000000000000000000000000000000000000
..............................................................................................................................................................................................................................TTGGTATTT-AAGCTACCAAC.........................................................................................................................................2011.0010010000000000000000000000000000000000000000000000000000000000000000000000000000
...............................................................................................................................................A-----TCC----CATCTTG--AACATACG---------TT....................................................................................................................................................................................................2111.0010000000000000000000000000000000000000000000000000000000000010000000000000000000
.......................................................................................................................................................................................................AATAAAAAAATCC----CCTGCTTTGGT.........................................................................................................................................................2411.0010000000000000000000000001000000000000000000000000000000000000000000000000000000
................................................................................................................................................................................................................................................AACCA---AAAAAAACCTCACCCACCA.................................................................................................................2411.0010001000000000000000000000000000000000000000000000000000000000000000000000000000
................................................................................................................GTTTTATGATGCAATTC-T-C----G-CT...............................................................................................................................................................................................................................................2211.0010000000000000000000000000000000000100000000000000000000000000000000000000000000
.......................................................................................................................................................................................................AATAAAAAAATCC----CCTGCTT.............................................................................................................................................................2011.0010001000000000000000000000000000000000000000000000000000000000000000000000000000
..................................................................................................................TTTATGATGCAATTC-T-C----G-CT...............................................................................................................................................................................................................................................2011.0010000000000000000000000000000000001000000000000000000000000000000000000000000000
............................................................................................CATCTAGT--TTCGGGTGAGGTTTTATGAT..................................................................................................................................................................................................................................................................2811.0010000000000000000000000000000000000000000000000000000000000000010000000000000000
...........................................................................................GCATCTAGT--TTCGGGTGA.............................................................................................................................................................................................................................................................................1811.0010000000000000000000000000000000000000000000000000000000000010000000000000000000
.........................................................................................AAGCATCTAGT--TTCGGGTGA.............................................................................................................................................................................................................................................................................2011.0010000000000000001000000000000000000000000000000000000000000000000000000000000000
............................................................................................................TGAGGTTTTATGATGCAATTC-T-C----G-CT...............................................................................................................................................................................................................................................2611.0010000000000000000000000000000100000000000000000000000000000000000000000000000000
......................................................................................................................................................CC----CATCTTG--AACATACG---------TTCCC.................................................................................................................................................................................................2211.0010000000000000000000000000100000000000000000000000000000000000000000000000000000
.......................................................................................................TCGGGTGAGGTTTTATGATGCAATTC-..........................................................................................................................................................................................................................................................2611.0010000000000000000000000000000000000000000000000000000000000000000000000000000100
.............................................................................................ATCTAGT--TTCGGGTGAGG...........................................................................................................................................................................................................................................................................1811.0010000000000000000000000000000000000100000000000000000000000000000000000000000000
...................................................................................................................TTATGATGCAATTC-T-C----G-CTCTA-----TCC----C...............................................................................................................................................................................................................................2611.0010001000000000000000000000000000000000000000000000000000000000000000000000000000
...........................................................................................................................................................................................................AAAAAATCC----CCTGCTTTGGT.........................................................................................................................................................2011.0010010000000000000000000000000000000000000000000000000000000000000000000000000000
.............................................................................................................................................................................................................................................ACCAACCA---AAAAAAACCTCACCCACCA.................................................................................................................2711.0010000000000000000010000000000000000000000000000000000000000000000000000000000000
.......................................................................................................TCGGGTGAGGTTTTATGATGCAAT.............................................................................................................................................................................................................................................................2411.0010000000000000000000000000000000000100000000000000000000000000000000000000000000
.............................................................................................ATCTAGT--TTCGGGTGAGGTTTTATGAT..................................................................................................................................................................................................................................................................2711.0010000000000000000000000000000000000000000000000000000000000010000000000000000000
................................................................................................TAGT--TTCGGGTGAGGTTTTATGATGC................................................................................................................................................................................................................................................................2611.0010000001000000000000000000000000000000000000000000000000000000000000000000000000
...................................................................................................T--TTCGGGTGAGGTTTTATGATG.................................................................................................................................................................................................................................................................2211.0010000000000000000000000000000000000000000000000000000000000010000000000000000000
.............................................................................................ATCTAGT--TTCGGGTGAGGTTTTATGATGC................................................................................................................................................................................................................................................................2911.0010000000000000000000000000000000000000000000000000000000000000100000000000000000
....................................................................................................................TATGATGCAATTC-T-C----G-CTCTA-----TCC----CATCT...........................................................................................................................................................................................................................2911.0010010000000000000000000000000000000000000000000000000000000000000000000000000000
.............................................................................................................................................................ATCTTG--AACATACG---------TTCCA.................................................................................................................................................................................................1911.0010010000000000000000000000000000000000000000000000000000000000000000000000000000
...................................................................................................................................................................................................................................ATTT-AAGCTACCAACCA---AAAAAA..............................................................................................................................2311.0010000000000000000000010000000000000000000000000000000000000000000000000000000000
....................................................................................................................TATGATGCAATTC-T-C----G-CTCTA-----TCC----CATC............................................................................................................................................................................................................................2811.0010000000000000000000000000000000000000000000000000000000000000001000000000000000
...................................................................................................................TTATGATGCAATTC-T-C----G-CTCTA-----TC.....................................................................................................................................................................................................................................2411.0010010000000000000000000000000000000000000000000000000000000000000000000000000000
............................................................................................................................................................................................................................................TACCAACCA---AAAAAAACCTCACCCACCA.................................................................................................................2811.0010000000000000000000000000000000000000000000000000000000000000000000000000000010
..........................................................................................AGCATCTAGT--TTCGGGTGAGGT..........................................................................................................................................................................................................................................................................2211.0010000000000000000000000000000000000000100000000000000000000000000000000000000000
................................................................................................................GTTTTATGATGCAATTC-T-C----G-CC...............................................................................................................................................................................................................................................2211.0010001000000000000000000000000000000000000000000000000000000000000000000000000000
................................................................................................................GTTTTATGATGCAATTC-T-C----G-CTCTA-----TC.....................................................................................................................................................................................................................................2711.0010000000000000001000000000000000000000000000000000000000000000000000000000000000
..............................................................................................................................................TA-----TCC----CATCTTG--AACATACG---------TTCCAAAA..............................................................................................................................................................................................2811.0010000000000000000000000000000000100000000000000000000000000000000000000000000000
..................................................................................................................................T-C----G-CTCTA-----TCC----CATC............................................................................................................................................................................................................................1520.5010000000000000000000000000000000000000000000000000000000000000010000000000000000
...............................................................................................................................................................................................................................................CAACCA---AAAAAAACCT..........................................................................................................................1620.5010000000000000000000000000000000000000000000000000000000000100000000000000000000
droMoj3
AG---------------------------------------------------------------------------------------ATGCATCAGAT-TTTCGGGTGAGGTTTTATGATGCAGTAC-T-CCATG------------TCC----CACTCCGAAT--ACT---------------------AAAATAAAAAGA----ATCCTTCTCCC-ATTTGGTATTA-AAGCCACCCACC----AAAAAAACCTCACCCACCAAACATATGAACAAAGAGATACAAAATATTCAATACAA----------------------------------------------------------------------------SizeHit CountTotal NormTotalM046

Female-body		V041

Embryo		V049

Head		V056

Head		M060

Embryo		V110

Male-body
..................................................................................................................................................................................................................................................CC----AAAAAAACCTCACCCACCA.................................................................................................................2111.001100000
................................................................................................................................................................................................................................................CACC----AAAAAAACCTCACCCACC..................................................................................................................2211.001000010
.......................................................................................................TCGGGTGAGGTTTTATGATG.................................................................................................................................................................................................................................................................2011.001100000
.......................................................................................................TCGGGTGAGGTTTTATGATGC................................................................................................................................................................................................................................................................2111.001010000
.........................................................................................ATGCATCAGAT-TTTCGGGT...............................................................................................................................................................................................................................................................................1911.001000100
.........................................................................................................................TGCAGTAC-T-CCATG------------TCC----CACTCC..........................................................................................................................................................................................................................2311.001100000
.....................................................................................................................ATGATGCAGTAC-T-CCATG------------T......................................................................................................................................................................................................................................1911.001100000
.............................................................................................................................GTAC-T-CCATG------------TCC----CACTCCGAAT--....................................................................................................................................................................................................................2311.001100000
......................................................................................................TTCGGGTGAGGTTTTATGATG.................................................................................................................................................................................................................................................................2111.001100000
droGri2
-----------------------------------------------------------TCGTACGACTA--------------ATGAAATGCATCTAGT-TTTCGGGTGAGGTT-TTAGATGCGT--TTCCCC-----------------CAGA-AA----------ATAAA-AC---------------------A----------------CTC-CTTTTTGGTATTT-AAACTACAAAAAAAAAAAAAAAACCTCACCCACCAAATATATGAACAAAGAGATAAAAT--ATTCAATAAACCAACAA-----------------AC-----CCGAAGAAGTCTG-------GAGCTG--------------ATGACCSizeHit CountTotal NormTotalM041

Female-body		V109

Male-body
............................................................CGTACGACTA--------------ATGAAATGCATC............................................................................................................................................................................................................................................................................................2211.00101
....................................................................................................................TTAGATGCGT--TTCCCC-----------------CAGA-A...............................................................................................................................................................................................................................2111.00101

Generated: 10/20/2015 at 10:31 PM