dan_1973

##################################################--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CTGTCGAGTCGTCGGATATCAAGACCGAGGAGGAGGAAGATAATGCCGAGGTGAGTGTCCTTGAGCGGAAGAGGAGGAGGCACTTGGTCTTCTGAGATTAACAGCAGCAGCAGAAGCCTTTTTTTAATCCGTGGTGTGTGCTTGAAGAGTGGTTAACCATGTTGTTTGTGTATTTCGTTGTTTATTTCCATATTTGAGTTCCTTTTTTAATTGCTTTGTCCACCGGTTTGTTATTGTTCTCTTCCTTCGGT *************************************************************.(((((..((((((((((..(((..((.(((.......))).))...)))..))))))))))..)))))..............*******************************************************************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M058 embryo	M044 female body	V105 male body	V106 head	V055 head
..............GATATCAAGACCGAGGAGGA.........................................................................................................................................................................................................................	20	0	1	1.00	1	1	0	0	0	0
...............................................................AGCGGAAGAGGAGGAGGCACTT......................................................................................................................................................................	22	0	1	1.00	1	0	1	0	0	0
.............................................................................................................................AATCCGTGGTGTGTGCTTGAA.........................................................................................................	21	0	1	1.00	1	0	0	0	1	0
.................................AGGAAGATAATGCCGAGGTGA.....................................................................................................................................................................................................	21	0	1	1.00	1	0	0	1	0	0
...............ATATCAAGACCGAGGAGGAGG.......................................................................................................................................................................................................................	21	0	1	1.00	1	0	1	0	0	0
.............GTATATCAAGACCGAGGAGG..........................................................................................................................................................................................................................	20	1	1	1.00	1	1	0	0	0	0
.................AGCAAGACCGAGGAGGAGG.......................................................................................................................................................................................................................	19	1	1	1.00	1	1	0	0	0	0
.................................................................................................TTAACAGCAGCGGCAGATG.......................................................................................................................................	19	2	6	0.50	3	0	1	1	1	0
................................GAGGAAGATAATGCCGAGAT.......................................................................................................................................................................................................	20	1	2	0.50	1	1	0	0	0	0
...............................................................................................................................................GAAGAGTGGTTCATCATG..........................................................................................	18	2	4	0.25	1	0	0	0	0	1
...............................................................ATCGGAAGAGGAGGAGGC..........................................................................................................................................................................	18	1	5	0.20	1	1	0	0	0	0
......................................GATAATGCCGAGGTCAAT...................................................................................................................................................................................................	18	2	7	0.14	1	0	1	0	0	0
.......................................................................................................................................................................................................................TTGTTCACCGGATTGTTA..................	18	2	13	0.08	1	0	0	0	0	1
.............................................................................................................................................TGGAAGAGTCGTTAACCGT...........................................................................................	19	3	14	0.07	1	0	0	0	0	1

GACAGCTCAGCAGCCTATAGTTCTGGCTCCTCCTCCTTCTATTACGGCTCCACTCACAGGAACTCGCCTTCTCCTCCTCCGTGAACCAGAAGACTCTAATTGTCGTCGTCGTCTTCGGAAAAAAATTAGGCACCACACACGAACTTCTCACCAATTGGTACAACAAACACATAAAGCAACAAATAAAGGTATAAACTCAAGGAAAAAATTAACGAAACAGGTGGCCAAACAATAACAAGAGAAGGAAGCCA *******************************************************************************************************.(((((..((((((((((..(((..((.(((.......))).))...)))..))))))))))..)))))..............*************************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M044 female body	M058 embryo	V055 head
.....................................................................................................GTCGTCGTCGTCTTCGGAAAA.................................................................................................................................	21	0	1	1.00	1	1	0	0
........................................................CAGGAACTCGCCTTCTCCTCC..............................................................................................................................................................................	21	0	1	1.00	1	1	0	0
..................AGTTCTGGCTCCTCCTCCTTC....................................................................................................................................................................................................................	21	0	1	1.00	1	1	0	0
........................GGCTCCTCCTCCTTCTATTAC..............................................................................................................................................................................................................	21	0	1	1.00	1	1	0	0
...................................................................................................................................................TCACCAATTGGTACAACAAAC...................................................................................	21	0	1	1.00	1	1	0	0
................................................................................................................................................................................................................................CCAAGCAATAAAGAGAGAAGGA.....	22	3	3	0.33	1	0	1	0
...............................................................................................................................................................AGAACCAACACATAAAGCA.........................................................................	19	2	5	0.20	1	0	1	0
..........................................................................................................................................................................................................................AGGTGGCCAAACAATTAAAA.............	20	2	8	0.13	1	0	0	1
...................................................................................................................................................................................................................ACCACACATGTGGCCAAAC.....................	19	3	12	0.08	1	0	1	0
................................................................................................................................................................CAACAAGCACACAAAGCACC.......................................................................	20	3	19	0.05	1	0	1	0
...................................................................................................................................................CCACCAATAGGTCCAACAA.....................................................................................	19	3	20	0.05	1	0	1	0
.................................................................................................................................................................ACCCAACACAAAAAGCAACAA.....................................................................	21	3	20	0.05	1	0	1	0
...................................................................................................................................................................................................................................AACAAGAACAAGGGAAGAAAG...	21	3	20	0.05	1	0	1	0

Species	Coordinate	ID	Alignment
droAna3	scaffold_13266:13065668-13065918 -	dan_1973	CTG------------------------------------------TCGAGTCGTCGGATATCAAGACCGAGGAGG---AGGAAGATAATGCCGAGGTGAGTGTCCTT-G---AGC--GGAAGA-GGAGGAGGCACTTGGT------C--TTCTGA-------------------------GATTAACA------G---------CAGCAGCA--------------GAAGCCTTTTTTTAATCC--GTGGTGTGTGCTTGAAG--AGTGGTT-AACCATGTTGT-TT--GTGT---ATTT--CGTTGTTT--AT--------TTCCATATTTGAGTTCCTT------------TTTTAAT-------TGCTTTGTCCA-CCGGTTTGTTA----------------T---------TGTTCT---CTTCCT------------TCGG-T--
droBip1	scf7180000396730:861847-862080 +		CTG------------------------------------------TCGAGGCGTCCGACATAAAGACCGAGGAGG---AGGAAGATAATGCCGAGGTGAGTGTACGG-----------------------------AA-------GTGGCTACTC---------C---------------ACTGACCA------G------C--TAG-CTGA--------------GCAGCTTTT-------TT--GTGGTGTGTGCTTGAAG--AGTGGTT-GACCATGTTGT-TT--GTGT---ATTT--TGTTGTTT--AT--------TTCGAT--TTATGTTTCTTATCCTTTTTATTGTTTTTGTTTTGATTGCTT----AC-CCGGTTTGTTG----------------T------------TCT---CTTCCT------------TCGG-T--
droKik1	scf7180000302476:1217984-1218194 -		TTG------------------------------------------CGGAATCCTCTGATATCAAAACGGAGGAGGAGGAGGAAGATAATGCCGAGGTGAGTG-----------------------------------A-------GCAGCGATGA---------T---------------GAAGCTCC------G---------GAACCGGAATTGGAACCGGAACACAGCTTT--------GTGTGTGGTGTGTGCTTGAAGAGAGTGGTT-AATCATGTTGT-TTTTGTGT---ATTT--CGTTGTTC--AT--------TTCGAT--T----------------------GTTTATGTTTG-------T----CT-TTGGTTTCC------------------------------------------TGA-------------G-TTG
droFic1	scf7180000454066:830550-830756 +		TTG------------------------------------------TGGAGGCGTCCGATATCAAGACGGAGGAGG---AGGAAGATACTGCCGAGGTGAGTGTGGCT-G------------------------GCTAG-------GCAGCGATGA-------------------------GATGCTCC------G---------CAGCCGGA--------------GCAGCTTT--------GT--GTGGTGTGTGCTTGAAG--AGTGGTT-AACCATGTTGT-TT--GTGT---ATTT--CGTTGTTCT-TT--------TTCGAT--T----------------------GTTTACG-----------T----TTTTTGGTTCCCTG----------------T------------TCTTCGACTCCTGA-------------G-T--
droEle1	scf7180000491201:278724-278936 -		TTG------------------------------------------TAGAGGCGTCCGATATCAAGACGGAGGAGG---AGGAAGATACTGCCGAGGTGAGTGTGCCGTG---------------------------GC-------GCAGCGATAA---------T---------------GATGCTCC------C---------GAGCCGGA--------------GCAGCTTT--------GT--GTGGTGTGTGCTTGAAG--AGTGGTT-AACCATGTTGT-TT--GTGT---ATTT--CGTTGTTC--AT--------TTCGGT--T----------------------GTTTACG-----------T----TT-TTGGTTCCCTG----------------TTCCTGTTCCTGTTCT---TCTCCTGA-------------G-T--
droRho1	scf7180000776809:17548-17743 +		TTG------------------------------------------TAGAGGCGTCCGATATCAAGACGGAGGAGG---AGGAAGATACTGCCGAGGTGAGTGTGCCG-----------------------------AG-------GCAGCCATG---------------------------ATGCTTC------T---------GAACCGGA--------------GCAGCTTT--------GT--GTGGTGTGTGCTTGAAG--AGTGGTT-AACCATGTTGT-TT--GTGT---ATTT--CGTTGTTC--AT--------TTCGAT--T----------------------GTTTACG-----------T----TT-TTGGTTCCCTG----------------T------------TCT---TCTCCTAA-------------G-T--
droBia1	scf7180000302291:1576008-1576226 +		TTG------------------------------------------TAGAGGCGTCCGATATCAAAACGGAGGAGG---AGGAAGATACTGCCGAGGTGAGTGTTCAGCA------------GC-GA----------TG-------GCAGCCATGA-------------------------GATGCTCC------G---------GAGCCGGA--------------GCAGCTTT--------GT--GTGGTGTGTGCTTGAAG--AGTGGTT-AACCATGTTGTTTT--GTGT---ATTC--CGTTGTTA---TTTCGTTATTTCGAT--T-ACGATTAC-------------ATTTACG-----------T----TT-TTGA-TCCCAG----------------T------------TCC---ACTCATGA-------------G-T--
droTak1	scf7180000415762:695699-695899 +		TTG------------------------------------------TAGAGGCGTCCGATATCAAAACGGAGGAGG---AGGAAGATACTGCCGAGGTGAGTGCGAAG-----------------------------AG-------GCAGCGATGA-------------------------GATGCTCC------G---------GAGCCGGA--------------GCAGCTTT--------GT--GTGGTGTGTGCTTGAAG--AGTGGTT-AACCATGTTGTTTT--GTGT---ATTT--CGTTGTTC--AT--------TTCGAT--T-AC-------------------GTTTACG-----------T----TT-TTGA-TCCCAG----------------T------------TCT---ACTCATGA-------------GTT--
droEug1	scf7180000409672:4165243-4165458 +		TTG------------------------------------------TAGAGG---CCGATATCAAAACGGAGGAGG---AGGAAGATACTGCCGAGGTGAGTGTGCAG-----------------------------AA-------GCAGCGATGA-------------------------GATGCTCCGAAGCTG---------GAGCCGGA--------------GCAGCTTT--------GT--GTGGTGTGTGCTTGAAG--AGTGGTT-AACCATGTTGT-TT--GTGT---ATTT--CGTTGTTT--AT--------TTCGAT--T-AC-------------------GTTTACG-----------T----TT-TTGATTCCCTG----------------T------------TCT---ACTCATGAGTTGTGTTTTTCGG-T--
dm3	chr2R:8466478-8466683 -		TTG------------------------------------------TAGATGGGTCCGATATCAAGACGGAGGCGG---ACGAAGATACTGCCGAGGTAAGTGTCATA-----------------------------AG-------GCAGCGATGA-------------------------GATGCTCC------G---------GAGCCGGA--------------GCAGCTAT--------GT--GTGGTGTGTGCTTGAAG--AGTGGTT-AACCATGTTGT-TT--GTGT---ATTT--CGTTGTTC--AT--------TTCGAT--T-ATGTTTAC-------------GTTTACG-----------T----TT-TTGATTCCCTG----------------T------------TCT---ACTCATGA-------------G-T--
droSim2	2r:9175360-9175565 -	dsi_14500	TTG------------------------------------------TAGAGGCGTCCGATATCAAGACGGAGGCGG---ACGAAGATACTGCCGAGGTAAGTGTCGCA-----------------------------AG-------GCAGCGATGA-------------------------GATGCTCC------G---------GAGCCGGA--------------GCAGCTAT--------GT--GTGGTGTGTGCTTGAAG--AGTGGTT-AACCATGTTGT-TT--GTGT---ATTT--CGTTGTTC--AT--------TTCGAT--T-ATGTTTAC-------------GTTTACG-----------T----TT-TTGATTCCCTG----------------T------------TCT---ACTCATGA-------------G-T--
droSec2	scaffold_1:6012840-6013045 -		TTG------------------------------------------TAGAGGCGTCCGATATCAAGACGGAGGCGG---ACGAAGATACTGCCGAGGTAAGTGTCGCA-----------------------------AG-------GCAGCGATGA-------------------------GATGCTCC------G---------GAGCCGGA--------------GCAGCTAT--------GT--GTGGTGTGTGCTTGAAG--AGTGGTT-AACCATGTTGT-TA--GTGT---ATTT--CGTTGTTC--AT--------TTCGAT--T-ATGTTTAC-------------GTTTACG-----------T----TT-TTGATTCCCTG----------------T------------TCT---ACTCATGA-------------G-T--
droYak3	2R:8477549-8477759 +		TTG------------------------------------------TAGAGGCATCCGATATCAAGACGGAGGAGG---ACGAAGATACTGCCGAGGTAAGTGTGCTA-----------------------------AG-------GCAGCGATGA-------------------------GATGCTCA------G---------CAGCCGGA--------------GCAGCTAT--------GT--GTGGTGTGTGCTTGAAG--AGTGGTT-AACCATGTTGT-TT--GTGT---ATTT--CGTTGTTC--AT--------TTCGAT--T-AT-------------------GTTTACG-----------T----TT-TTGACTCCCTG----------------T------------TCT---ACTCATGATTTGTGTT--TCGG-T--
droEre2	scaffold_4845:17332811-17333022 +		TTG------------------------------------------TAGAGGCGTCCGATATCAAGACGGAGGAGG---ACGAAGATACTGCCGAGGTAAGTGTGCTA-----------------------------AG-------GCAGCGATGA-------------------------GAAGCTCC------G---------GAGCCGGA--------------GCAGCTAT--------GT--GTGGTGTGTGCTTGAAG--AGTGGTT-AACCATGTTGT-TT--GTGT---ATTT--CGTTGTTC--AT--------TTCGAT--T-AT-------------------GTTTACG-----------T----TT-TTGATTCCCTG----------------T------------TCT---ACTCATGATTTGTGTT-TTCGG-T--
dp5	3:12448113-12448317 +	dps_1191	TTG------------------------------------------TGGAAGAGTCCGACATCAAGACGGAGGAGG---AGGATGAAAATGCCGAGGTGAGTGTTGGGC------------------AGGAGGAGCTGGGCA----GCAGCAGTA---------TTTGA------------G---C--CAAAGCCA---------GAGCCAGA--------------GCCGCTTT--------GC--G---TGTGTGCTGGAAG--AGTGGTT-AACCATGTTGT-TT--GTGT---ATTC--TGTTATTC--AT--------TT--------AT-------------------------G-----------T----TT--TATTTCCCGA----------------T------------TCG---TATCCTCT-------------GTT--
droPer2	scaffold_99:99922-100129 -		TTG------------------------------------------TGGAAGAGTCCGACATCAAGACGGAGGAGG---AGGATGAAAATGCCGAGGTGAGTGTTGGGC------------------AGGAGGAGCTGGGCA----GCAGCAGTA---------TTTGA------------G---CT--AAAGCCA---------GAGCCAGA--------------GCCGCTTT--------GC--G---TGTGTGCTGGAAG--AGTGGTT-AACCATGTTGT-TT--GTGT---ATTC--TGTTATTC--AT--------TT--------AT-------------------------G-----------T----TT--TATTTCCCGA----------------T------------TCGTATCCTCCTCT-------------GTT--
droWil2	scf2_1100000004954:2083298-2083370 -		GTT-----------------------TTAAATCTTGAAA---TGCCCGAAACATCTGAAATCAAAAAGGAAGAGG---AGGAGGAAAACGCTGAGGTGAGTG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	scaffold_12875:17112045-17112283 -	dvi_7408	GCG-----------------------TCAGGCAATGACAATCTAGTGGAATCGTCCGATATCAAAACGGAGGAGG---AAGAGGAGAACGCTGAGGTGAGTGGAGGCCATTAAAA--AGAAAAAGA--------------AATAAG----CGTA---------TCTAAGCGTATCGGCTACAT------CAGCTA---------GAGC---A--------------GCAGCTTT--------G-------TGTGTGCTTGACG--AGTGGTT-AACCATGTTGT-TT--GTGTTGTATTCTCTGTTGTGTTCAT--------TT-GTT--T----------------------GTTTGTT-----------T----GT-TTGTTTTGTTG----------------T------------TGT---TC------------------------
droMoj3	scaffold_6496:10886921-10887172 +		TGG------------------------------------------TGGAAACGTCCGGCATCAAAACGGAGGAAG---CAGATGAGATCGCCGAGGTGAGTGAAGCA-A-CAAAATGAGAGAAAGA--------------TATAAGCAATGATGCGCTGGCTTACAGTGCGTATA-GCTAAAT------CAGCTAGAGCAGCAGCATCAGCA--------------GCAGCTTT--------G-------TGTGTGCTTGACG--AAAGGTTGAAACATGTTGT-TT--GTGT---ATTCTCTGTTGTGTTTAT--------T------------------------------------------------T----GT-TTGTTTTGTTGTTGTTAAGTTTACGAAT------------------TCACCT------------TTAT-T--
droGri2	scaffold_15245:16643623-16643721 -		CTGGCGGCAACAATGCAACAGCATCTTCCAACACTGACAATCTGATGGAAACGTCCGACATCAAAGCGGAGGAGG---AAGAGGAGAATGCCGAGGTGAGTG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droAna3

CTG------------------------------------------TCGAGTCGTCGGATATCAAGACCGAGGAGG---AGGAAGATAATGCCGAGGTGAGTGTCCTT-G---AGC--GGAAGA-GGAGGAGGCACTTGGT------C--TTCTGA-------------------------GATTAACA------G---------CAGCAGCA--------------GAAGCCTTTTTTTAATCC--GTGGTGTGTGCTTGAAG--AGTGGTT-AACCATGTTGT-TT--GTGT---ATTT--CGTTGTTT--AT--------TTCCATATTTGAGTTCCTT------------TTTTAAT-------TGCTTTGTCCA-CCGGTTTGTTA----------------T---------TGTTCT---CTTCCT------------TCGG-T--	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
........................................................GATATCAAGACCGAGGAGG---A....................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0
................................................................................................................AGC--GGAAGA-GGAGGAGGCACTT..........................................................................................................................................................................................................................................................................................................................	22	1	1.00	1	1	0	0	0	0	0
...............................................................................................................................................................................................................................................AATCC--GTGGTGTGTGCTTGAA.............................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	1
..............................................................................AGGAAGATAATGCCGAGGTGA................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	1	0
.........................................................ATATCAAGACCGAGGAGG---AGG..................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	1	0	0	0	0	0

droBip1

CTG------------------------------------------TCGAGGCGTCCGACATAAAGACCGAGGAGG---AGGAAGATAATGCCGAGGTGAGTGTACGG-----------------------------AA-------GTGGCTACTC---------C---------------ACTGACCA------G------C--TAG-CTGA--------------GCAGCTTTT-------TT--GTGGTGTGTGCTTGAAG--AGTGGTT-GACCATGTTGT-TT--GTGT---ATTT--TGTTGTTT--AT--------TTCGAT--TTATGTTTCTTATCCTTTTTATTGTTTTTGTTTTGATTGCTT----AC-CCGGTTTGTTG----------------T------------TCT---CTTCCT------------TCGG-T--	Size	Hit Count	Total Norm	Total
No Reads

droKik1

TTG------------------------------------------CGGAATCCTCTGATATCAAAACGGAGGAGGAGGAGGAAGATAATGCCGAGGTGAGTG-----------------------------------A-------GCAGCGATGA---------T---------------GAAGCTCC------G---------GAACCGGAATTGGAACCGGAACACAGCTTT--------GTGTGTGGTGTGTGCTTGAAGAGAGTGGTT-AATCATGTTGT-TTTTGTGT---ATTT--CGTTGTTC--AT--------TTCGAT--T----------------------GTTTATGTTTG-------T----CT-TTGGTTTCC------------------------------------------TGA-------------G-TTG	Size	Hit Count	Total Norm	Total
No Reads

droFic1

TTG------------------------------------------TGGAGGCGTCCGATATCAAGACGGAGGAGG---AGGAAGATACTGCCGAGGTGAGTGTGGCT-G------------------------GCTAG-------GCAGCGATGA-------------------------GATGCTCC------G---------CAGCCGGA--------------GCAGCTTT--------GT--GTGGTGTGTGCTTGAAG--AGTGGTT-AACCATGTTGT-TT--GTGT---ATTT--CGTTGTTCT-TT--------TTCGAT--T----------------------GTTTACG-----------T----TTTTTGGTTCCCTG----------------T------------TCTTCGACTCCTGA-------------G-T--	Size	Hit Count	Total Norm	Total
No Reads

droEle1

TTG------------------------------------------TAGAGGCGTCCGATATCAAGACGGAGGAGG---AGGAAGATACTGCCGAGGTGAGTGTGCCGTG---------------------------GC-------GCAGCGATAA---------T---------------GATGCTCC------C---------GAGCCGGA--------------GCAGCTTT--------GT--GTGGTGTGTGCTTGAAG--AGTGGTT-AACCATGTTGT-TT--GTGT---ATTT--CGTTGTTC--AT--------TTCGGT--T----------------------GTTTACG-----------T----TT-TTGGTTCCCTG----------------TTCCTGTTCCTGTTCT---TCTCCTGA-------------G-T--	Size	Hit Count	Total Norm	Total
No Reads

droRho1

TTG------------------------------------------TAGAGGCGTCCGATATCAAGACGGAGGAGG---AGGAAGATACTGCCGAGGTGAGTGTGCCG-----------------------------AG-------GCAGCCATG---------------------------ATGCTTC------T---------GAACCGGA--------------GCAGCTTT--------GT--GTGGTGTGTGCTTGAAG--AGTGGTT-AACCATGTTGT-TT--GTGT---ATTT--CGTTGTTC--AT--------TTCGAT--T----------------------GTTTACG-----------T----TT-TTGGTTCCCTG----------------T------------TCT---TCTCCTAA-------------G-T--	Size	Hit Count	Total Norm	Total
No Reads

droBia1

TTG------------------------------------------TAGAGGCGTCCGATATCAAAACGGAGGAGG---AGGAAGATACTGCCGAGGTGAGTGTTCAGCA------------GC-GA----------TG-------GCAGCCATGA-------------------------GATGCTCC------G---------GAGCCGGA--------------GCAGCTTT--------GT--GTGGTGTGTGCTTGAAG--AGTGGTT-AACCATGTTGTTTT--GTGT---ATTC--CGTTGTTA---TTTCGTTATTTCGAT--T-ACGATTAC-------------ATTTACG-----------T----TT-TTGA-TCCCAG----------------T------------TCC---ACTCATGA-------------G-T--	Size	Hit Count	Total Norm	Total
No Reads

droTak1

TTG------------------------------------------TAGAGGCGTCCGATATCAAAACGGAGGAGG---AGGAAGATACTGCCGAGGTGAGTGCGAAG-----------------------------AG-------GCAGCGATGA-------------------------GATGCTCC------G---------GAGCCGGA--------------GCAGCTTT--------GT--GTGGTGTGTGCTTGAAG--AGTGGTT-AACCATGTTGTTTT--GTGT---ATTT--CGTTGTTC--AT--------TTCGAT--T-AC-------------------GTTTACG-----------T----TT-TTGA-TCCCAG----------------T------------TCT---ACTCATGA-------------GTT--	Size	Hit Count	Total Norm	Total
No Reads

droEug1

TTG------------------------------------------TAGAGG---CCGATATCAAAACGGAGGAGG---AGGAAGATACTGCCGAGGTGAGTGTGCAG-----------------------------AA-------GCAGCGATGA-------------------------GATGCTCCGAAGCTG---------GAGCCGGA--------------GCAGCTTT--------GT--GTGGTGTGTGCTTGAAG--AGTGGTT-AACCATGTTGT-TT--GTGT---ATTT--CGTTGTTT--AT--------TTCGAT--T-AC-------------------GTTTACG-----------T----TT-TTGATTCCCTG----------------T------------TCT---ACTCATGAGTTGTGTTTTTCGG-T--	Size	Hit Count	Total Norm	Total
No Reads

dm3

TTG------------------------------------------TAGATGGGTCCGATATCAAGACGGAGGCGG---ACGAAGATACTGCCGAGGTAAGTGTCATA-----------------------------AG-------GCAGCGATGA-------------------------GATGCTCC------G---------GAGCCGGA--------------GCAGCTAT--------GT--GTGGTGTGTGCTTGAAG--AGTGGTT-AACCATGTTGT-TT--GTGT---ATTT--CGTTGTTC--AT--------TTCGAT--T-ATGTTTAC-------------GTTTACG-----------T----TT-TTGATTCCCTG----------------T------------TCT---ACTCATGA-------------G-T--	Size	Hit Count	Total Norm	Total	GSM154618 Ovary	GSM154620 Ovary	GSM154621 Ovary	GSM154622 Ovary	GSM180328 Head	GSM180329 Mixed-body	GSM180330 Embryo	GSM180331 Embryo	GSM180332 Embryo	GSM180333 Embryo	GSM180334 Larvae	GSM180335 Disc	GSM180336 Pupae	GSM180337 S2	GSM231091 Ovary	GSM239041 Head	GSM239050 Head	GSM239051 S2	GSM239052 S2	GSM246084 Head	GSM266765 S2	GSM280082 Ovary	GSM280083 Ovary	GSM280084 Ovary	GSM280085 Testis	GSM280086 Ovary	GSM280087 S2-NP	GSM280088 S2-NP	GSM312995 Head	GSM313160 Head	GSM313161 Head	GSM313162 Head	GSM313163 Head	GSM313164 Head	GSM313165 Head	GSM343287 Embryo	GSM379050 Ovary	GSM379051 Ovary	GSM379052 Ovary	GSM379053 Ovary	GSM379054 Ovary	GSM379055 Ovary	GSM379056 Ovary	GSM379057 Ovary	GSM379058 Ovary	GSM379059 Ovary	GSM379060 Ovary	GSM379061 Ovary	GSM379062 Ovary	GSM379063 Ovary	GSM379064 Ovary	GSM379065 Ovary	GSM379066 Ovary	GSM379067 Ovary	GSM424739 S2	GSM424740 S2	GSM424741 S2	GSM467729 Female-body	GSM467730 Female-body	GSM467731 Female-body	M002 CS	M003 Male-body	M004 Male-body	M005 ML-DmD32	M006 ML-DmD32	M029 OSC	M030 OSC	M031 OSC	M032 S2-R+	M033 S2-R+	M034 S2-R+	M035 S2-R+	M036 S2-R+	M037 S2-R+	M038 S2-R+	M039 S2-R+	M048 S2-R+	OSS2 OSS	OSS6 OSS	OSS7 OSS	OSS8 OSS	S1 Head	S10 Embryo	S11 Embryo	S12 Embryo	S13 Embryo	S14 Embryo	S15 S2-GMR	S16 Kc	S17 Larvae	S18 Larvae	S19 Pupae	S2 Head	S20 Pupae	S21 Disc	S22 Head	S23 Female-body	S24 Male-body	S25 Larvae	S26 Larvae	S27 Pupae	S28 Pupae	S29 Head	S3 Male-body	S30 S2-GMR	S31 S2	S32 S2	S33 Kc	S34 Kc	S35 Kc	S4 Female-body	S5 Disc	S6 Embryo	S7 Embryo	S8 S2	S9 Embryo	SRR001337 Head	SRR001338 Head	SRR001339 Head	SRR001340 Head	SRR001341 Head	SRR001342 Head	SRR001343 Head	SRR001344 Head	SRR001345 Head	SRR001346 Head	SRR001347 Head	SRR001348 Head	SRR001349 Head	SRR001664 Head	SRR010951 Ovary	SRR010952 Ovary	SRR010953 Ovary	SRR010954 Ovary	SRR010955 Ovary	SRR010956 Ovary	SRR010957 Ovary	SRR010958 Ovary	SRR010959 Ovary	SRR010960 Ovary	SRR014268 Embryo	SRR014269 Embryo	SRR014270 Embryo	SRR014271 Embryo	SRR014272 Embryo	SRR014273 Ovary	SRR014274 Ovary	SRR014275 Ovary	SRR014276 Ovary	SRR014277 Ovary	SRR014278 Ovary	SRR014279 Ovary	SRR014280 Ovary	SRR014281 Ovary	SRR014282 Ovary	SRR023197 S2	SRR023399 S2	SRR023400 S2	SRR023402 S2	SRR023407 S2	SRR029028 S2	SRR029029 S2	SRR029030 S2	SRR029031 S2	SRR029032 S2	SRR029033 S2	SRR029608 Head	SRR029633 Head	SRR030145 gb3	SRR031692 Head	SRR031693 Head	SRR031694 Head	SRR031696 Head	SRR031697 Head	SRR031698 Head	SRR031699 Head	SRR031700 Head	SRR031701 Head	SRR031702 Head	SRR031703 Head	SRR031704 Head	SRR032092 S2	SRR032093 S2	SRR032094 S2	SRR032095 S2-NP	SRR032096 S2-NP	SRR032152 Head	SRR060643 Testis	SRR060644 Ovary	SRR060645 Testis	SRR060646 Ovary	SRR060647 Ovary	SRR060648 Ovary	SRR060649 Ovary	SRR060650 Testis	SRR060651 Ovary	SRR060652 Testis	SRR060653 Ovary	SRR065151 Ovary	SRR065152 Ovary	SRR065153 Ovary	SRR065154 Ovary	SRR065155 Ovary	SRR065800 Ovary	SRR065801 Ovary	SRR065802 Ovary	SRR065803 Ovary	SRR065804 Ovary	SRR065805 Ovary	SRR065806 Ovary	SRR065807 Ovary	SRR097865 S2-NP	SRR097866 S2-NP	SRR097867 S2-NP	SRR298536 Ovary	SRR298537 Ovary	SRR298711 Ovary	SRR298712 Ovary	SRR317110 Ovary	SRR317111 Ovary	SRR317112 Ovary	SRR317113 Ovary	SRR317114 Ovary	SRR317115 Ovary	SRR317116 Ovary	SRR317117 Ovary	SRR341115 S2	SRR341116 S2	SRR341117 S2	SRR341118 S2	SRR351332 Mixed-body	SRR351333 Mixed-body	T004 OSC	T005 CME-L1	V001 Embryo	V002 Embryo	V003 S2	V006 Female-body	V007 Head	V008 S2	V009 CME-L1	V010 ML-DmD20-C5	V011 Sg4	V012 Male-body	V013 Head	V014 DTT	V015 DreRFHV	V018 Kc167	V019 GM2	V020 S2-R+	V021 ML-DmD21	V022 ML-DmD32	V023 Head	V024 Kc167	V025 S2-R+	V026 1182-2H	V027 ML-DmD21	V028 CME-W1-Cl.8+	V029 ML-DmD9	V030 ML-DmD8	V031 GM2	V032 S1	V033 CME-W1-Cl.8+	V034 ML-DmD16-C3	V035 ML-DmD32	V036 ML-DmD20-C5	V037 S2	V038 S2	V063 Ovary	V0632 Ovary	V064 Ovary	V0642 Ovary	V065 Ovary	V0652 Ovary	V066 Ovary	V0662 Ovary	V067 S2-NP	V073 mbn2	V074 S3	V075 ML-DmBG1-C1	V076 ML-DmBG3-C2	V077 Head	V078 Head	V079 Head	V080 Head	V081 Embryo	V082 Embryo	V083 Male-body	V084 Female-body	V085 CME-W2	V086 Female-body	V088 Ovary	V0882 Ovary	V089 Ovary	V0892 Ovary	V090 Male-body	V091 fGS/OSS	V092 Male-body	V093 Male-body	V094 S2-R+	V095 S2-R+	V096 Ovary	V097 Ovary	V098 Ovary	V125 ML-DmD9	V126 CME-L1	V127 G2	V128 S3	V129 ML-DmBG1-C1	V130 ML-DmBG3-C2	V131 ML-DmD16-C3	V132 ML-DmD32	V133 Sg4	V134 ML-DmD8	V135 CME-W2	V136 Male-body	V137 Head	V138 Male-body	V139 Female-body	V140 Female-body	V141 Female-body	V142 Female-body	V144 OSC	V145 S2	V146 S1	V147 1182-2H	V148 mbn2	GSM1528798 follicle cells
.............................................................................................................................................................................................................AGCCGGA--------------GCAGCTAT--------GT--GTGG.........................................................................................................................................................................................................	21	1	23.00	23	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	2	0	0	0	0	0	0	1	0	0	2	0
........................................................GATATCAAGACGGAGGCGG---AC...................................................................................................................................................................................................................................................................................................................................................................................	21	1	22.00	22	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
................................................................................................................................................................................................................CGGA--------------GCAGCTAT--------GT--GTGGTGT......................................................................................................................................................................................................	21	1	19.00	19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................................GT--GTGGTGTGTGCTTGAAG--AG........................................................................................................................................................................................	21	1	18.00	18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	1	0	0	1	1	1	0	0	0	0	0	2	0	0	0
..................................................................................AGATACTGCCGAGGTAAGTGT............................................................................................................................................................................................................................................................................................................................................................	21	1	14.00	14	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	2	0	0	0
......................................................................................................................................................GATGA-------------------------GATGCTCC------G---------GAGCCGG................................................................................................................................................................................................................................................	21	1	13.00	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	1	0	1	0	1	1	0
..........................................................................................................................................................................................................................................................................................GT-TT--GTGT---ATTT--CGTTGTTC--A..........................................................................................................................................	21	1	13.00	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................................................................................TGGTGTGTGCTTGAAG--AGTGG.....................................................................................................................................................................................	21	1	13.00	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0
.........................................................................................................................................................................................................................................................GTGTGTGCTTGAAG--AGTGGTT-..................................................................................................................................................................................	21	1	12.00	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0
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....................................................GTCCGATATCAAGACGGAGGCGG---AC...................................................................................................................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...................................................................GGAGGCGG---ACGAAGATACTGCCGAG....................................................................................................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
........................................................................................TGCCGAGGTAAGTGTCATA-----------------------------AG-------GCAGC.............................................................................................................................................................................................................................................................................................................	26	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
.................................................TGGGTCCGATATCAAGACGGAGGCG.........................................................................................................................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..........................................................................................CCGAGGTAAGTGTCATA-----------------------------AG-------GA................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droSim2

TTG------------------------------------------TAGAGGCGTCCGATATCAAGACGGAGGCGG---ACGAAGATACTGCCGAGGTAAGTGTCGCA-----------------------------AG-------GCAGCGATGA-------------------------GATGCTCC------G---------GAGCCGGA--------------GCAGCTAT--------GT--GTGGTGTGTGCTTGAAG--AGTGGTT-AACCATGTTGT-TT--GTGT---ATTT--CGTTGTTC--AT--------TTCGAT--T-ATGTTTAC-------------GTTTACG-----------T----TT-TTGATTCCCTG----------------T------------TCT---ACTCATGA-------------G-T--	Size	Hit Count	Total Norm	Total	M023 Head	M024 Male-body	M025 Embryo	M053 Female-body	O001 Testis	O002 Head	SRR553485 Ovary	SRR553486 Ovary	SRR553487 Ovary	SRR553488 Ovary	SRR618934 Ovary	V044 Embryo	SRR902008 Ovary	SRR902009 Testis	SRR1275487 Male larvae	SRR1275485 Male prepupae	SRR1275483 Male prepupae
.........................................................................................................................................................................................................................................................................................................................................................................................T-TTGATTCCCTG----------------T------------TCT---ACTCATGA-------------G-T--	26	1	2.00	2	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0
...............................................................................................................................................................................................................................................................GCTTGAAG--AGTGGTT-AACCAT............................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
...................................................................................GATACTGCCGAGGTAAGTGTC...........................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
......................................................................................................................................................................................................................................................GTGGTGTGTGCTTGAAG--AG........................................................................................................................................................................................	19	1	1.00	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
.............................................................................................................................................................................................................................................................................GTT-AACCATGTTGT-TT--GTGT---A..........................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
...........................................................................................................................................................................................................................................................................................T-TT--GTGT---ATTT--CGTTGTTC--AT--------.................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
.....................................................................................................................................................CGATGA-------------------------GATGCTCC------G---------GAGC...................................................................................................................................................................................................................................................	19	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
......................................................................................................................................................GATGA-------------------------GATGCTCC------G---------GAGCCGTT--------------T................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
.....................................................................................................................................................CGATGA-------------------------GATGCTCC------G---------GAGCC..................................................................................................................................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
......................................................................................................................................................GATGA-------------------------GATGCTCC------G---------GAGCCGG................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
..................................................GCGTCCGATATCAAGACG...............................................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
....................................................................................ATACTGCCGAGGTAAGTGTCG..........................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
...............................................................AGACGGAGGCGG---ACGAAGATACT..........................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................................................TCAAGACGGAGGCGG---ACGAAG...............................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
..........................................................TATCAAGACGGAGGCGG---ACGAAGATA............................................................................................................................................................................................................................................................................................................................................................................	26	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
.............................................................................................................................................................................................................AGCCGGA--------------GCAGCTAT--------GT--GTGG.........................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
..................................................................................................................................................CAGCGATGA-------------------------GATGCTCC------G---------GAGC...................................................................................................................................................................................................................................................	22	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.......................................................................................................................................................ATGA-------------------------GATGCTCC------G---------GAGCCG.................................................................................................................................................................................................................................................	19	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droSec2

TTG------------------------------------------TAGAGGCGTCCGATATCAAGACGGAGGCGG---ACGAAGATACTGCCGAGGTAAGTGTCGCA-----------------------------AG-------GCAGCGATGA-------------------------GATGCTCC------G---------GAGCCGGA--------------GCAGCTAT--------GT--GTGGTGTGTGCTTGAAG--AGTGGTT-AACCATGTTGT-TA--GTGT---ATTT--CGTTGTTC--AT--------TTCGAT--T-ATGTTTAC-------------GTTTACG-----------T----TT-TTGATTCCCTG----------------T------------TCT---ACTCATGA-------------G-T--	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
...............................................................................CGAAGATACTGCCGAGGTAAG...............................................................................................................................................................................................................................................................................................................................................................	21	1	2.00	2	1	0	1	0
..........................................................................................CCGAGGTAAGTGTCGCA-----------------------------AG-------GC................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	1	0	0
.......................................................................................................................................................................................................................................................TGGTGTGTGCTTGAAG--AGTGG.....................................................................................................................................................................................	21	1	1.00	1	0	0	0	1
.........................................................................................................................................................................................................................................................GTGTGTGCTTGAAG--AGTGGTT-..................................................................................................................................................................................	21	1	1.00	1	0	1	0	0
........................................................................................................................................................TGA-------------------------GATGCTCC------G---------GAGCCGGA--------------GTT..............................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	1
..........................................................................G---ACGAAGATACTGCCGAG....................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	1	0	0	1	0
...................................................................................................................................................................................................................................................T--GTGGTGTGTGCTTGAAG--AG........................................................................................................................................................................................	20	1	1.00	1	0	0	0	1
.........................................................ATATCAAGACGGAGGCGG---A....................................................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	1	0	0	0	1
......................................................CCGATATCAAGACGGAGGC..........................................................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	1	0	0	0	1
...................................................................................................................................................................................................................................CAGCTAT--------GT--GTGGTGTGTGCTT................................................................................................................................................................................................	22	1	1.00	1	0	1	0	0
......................................................................................................................................................................................................................................................GTGGTGTGTGCTTGAAG--AG........................................................................................................................................................................................	19	1	1.00	1	0	0	0	1
...............................................................................CGAAGATACTGCCGAGGTAAGT..............................................................................................................................................................................................................................................................................................................................................................	22	1	1.00	1	0	1	0	0
.................................................................................................AAGTGTCGCA-----------------------------AG-------GCAGCGATG.........................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	1	0	0

droYak3

TTG------------------------------------------TAGAGGCATCCGATATCAAGACGGAGGAGG---ACGAAGATACTGCCGAGGTAAGTGTGCTA-----------------------------AG-------GCAGCGATGA-------------------------GATGCTCA------G---------CAGCCGGA--------------GCAGCTAT--------GT--GTGGTGTGTGCTTGAAG--AGTGGTT-AACCATGTTGT-TT--GTGT---ATTT--CGTTGTTC--AT--------TTCGAT--T-AT-------------------GTTTACG-----------T----TT-TTGACTCCCTG----------------T------------TCT---ACTCATGATTTGTGTT--TCGG-T--	Size	Hit Count	Total Norm	Total	M026 Head	M043 Female-body	M056 Embryo	V046 Embryo	V052 Head	V058 Head	V120 Male-body	SRR1275488 Male larvae	SRR1275486 Male prepupae	SRR1275484 Male prepupae	GSM1528802 follicle cells
.................................................GGCATCCGATATCAAGACGGAG............................................................................................................................................................................................................................................................................................................................................................................................	22	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
........................................................................AGG---ACGAAGATACTGCCG......................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0
..G------------------------------------------TAGAGGCATCCGATATCA....................................................................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
.................................................................................................................................................................................................................................................................................................................................................................GTTTACG-----------T----TT-TTGACTCCCTG----------------T------------T...............................	23	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................................................................................TCGAT--T-AT-------------------GTTTACG-----------T----TT-TTGA....................................................................	22	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0

droEre2

TTG------------------------------------------TAGAGGCGTCCGATATCAAGACGGAGGAGG---ACGAAGATACTGCCGAGGTAAGTGTGCTA-----------------------------AG-------GCAGCGATGA-------------------------GAAGCTCC------G---------GAGCCGGA--------------GCAGCTAT--------GT--GTGGTGTGTGCTTGAAG--AGTGGTT-AACCATGTTGT-TT--GTGT---ATTT--CGTTGTTC--AT--------TTCGAT--T-AT-------------------GTTTACG-----------T----TT-TTGATTCCCTG----------------T------------TCT---ACTCATGATTTGTGTT-TTCGG-T--	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
..G------------------------------------------TAGAGGCGTCCGATATCAAGACGGA.............................................................................................................................................................................................................................................................................................................................................................................................	26	1	1.00	1	1	0	0	0	0	0	0
.....................................................................................................................................................CGATGA-------------------------GAAGCTCC------G---------GAG....................................................................................................................................................................................................................................................	18	1	1.00	1	0	0	0	0	0	1	0
.........................................................................................................TA-----------------------------AG-------GCAGCGATGA-------------------------GAAGCTC........................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	1	0

dp5

TTG------------------------------------------TGGAAGAGTCCGACATCAAGACGGAGGAGG---AGGATGAAAATGCCGAGGTGAGTGTTGGGC------------------AGGAGGAGCTGGGCA----GCAGCAGTA---------TTTGA------------G---C--CAAAGCCA---------GAGCCAGA--------------GCCGCTTT--------GC--G---TGTGTGCTGGAAG--AGTGGTT-AACCATGTTGT-TT--GTGT---ATTC--TGTTATTC--AT--------TT--------AT-------------------------G-----------T----TT--TATTTCCCGA----------------T------------TCG---TATCCTCT-------------GTT--	Size	Hit Count	Total Norm	Total	M022 Male-body	M040 Female-body	M059 Embryo	M062 Head	V043 Embryo	V051 Head	V112 Male-body	SRR902010 Ovary	SRR902011 Testis	SRR902012 CNS imaginal disc
...........................................................ATCAAGACGGAGGAGG---AGGA.................................................................................................................................................................................................................................................................................................................................................................................	20	1	2.00	2	0	1	0	0	0	0	0	0	0	1
................................................................................................TGAGTGTTGGGC------------------AGGAGGAG.............................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0	0	0	0	0
........................................................................................TGCCGAGGTGAGTGTTGGGC------------------.....................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	0	0	0	0	0	1	0	0	0
........................................................................................................................................................................................................................................TT--------GC--G---TGTGTGCTGGAAG--AGC.......................................................................................................................................................................................	21	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................................................T--------GC--G---TGTGTGCTGGAAG--AGTG......................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	1	0
...........................................................................................................................................CA----GCAGCAGTA---------TTTGA------------G---C--CAA.....................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	1	0	0	0
.........................................................ACATCAAGACGGAGGAGG---AG...................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	0	0	0	0	1	0	0	0	0
.......................................................................................ATGCCGAGGTGAGTGTTGG.........................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	1	0	0	0	0	0	0	1	0	0	0
...................................................AGTCCGACATCAAGACGGAGG...........................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	1	0	0	0	0	0	0	0	0
................................................................................................TGAGTGTTGGGC------------------AGGAGGA..............................................................................................................................................................................................................................................................................................................................	19	1	1.00	1	0	0	0	0	0	0	0	0	1	0

droPer2

TTG------------------------------------------TGGAAGAGTCCGACATCAAGACGGAGGAGG---AGGATGAAAATGCCGAGGTGAGTGTTGGGC------------------AGGAGGAGCTGGGCA----GCAGCAGTA---------TTTGA------------G---CT--AAAGCCA---------GAGCCAGA--------------GCCGCTTT--------GC--G---TGTGTGCTGGAAG--AGTGGTT-AACCATGTTGT-TT--GTGT---ATTC--TGTTATTC--AT--------TT--------AT-------------------------G-----------T----TT--TATTTCCCGA----------------T------------TCGTATCCTCCTCT-------------GTT--	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
.......................................................CGACATCAAGACGGAGGAGG---AG...................................................................................................................................................................................................................................................................................................................................................................................	22	1	1.00	1	0	1	0	0	0	0

droWil2

GTT-----------------------TTAAATCTTGAAA---TGCCCGAAACATCTGAAATCAAAAAGGAAGAGG---AGGAGGAAAACGCTGAGGTGAGTG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
...........................................................ATCAAAAAGGAAGAGG---AGGA.................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	0	0	1	0
...........................TAAATCTTGAAA---TGCCCGAAACATC............................................................................................................................................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	1	0	0	0
..........................................................AATCAAAAAGGAAGAGG---AGGA.................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	1
.......................................................TGAAATCAAAAAGGAAGAGG---A....................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	1
.............................................................CAAAAAGGAAGAGG---AGGAGG...............................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	0	0	0	1
......................................................CTGAAATCAAAAAGGAAGAGG---AGG..................................................................................................................................................................................................................................................................................................................................................................................	24	1	1.00	1	0	0	1	0	0

droVir3

GCG-----------------------TCAGGCAATGACAATCTAGTGGAATCGTCCGATATCAAAACGGAGGAGG---AAGAGGAGAACGCTGAGGTGAGTGGAGGCCATTAAAA--AGAAAAAGA--------------AATAAG----CGTA---------TCTAAGCGTATCGGCTACAT------CAGCTA---------GAGC---A--------------GCAGCTTT--------G-------TGTGTGCTTGACG--AGTGGTT-AACCATGTTGT-TT--GTGTTGTATTCTCTGTTGTGTTCAT--------TT-GTT--T----------------------GTTTGTT-----------T----GT-TTGTTTTGTTG----------------T------------TGT---TC------------------------	Size	Hit Count	Total Norm	Total	M027 Male-body	M028 Head	M047 Female-body	M061 Embryo	SRR060654 Ovary	SRR060655 Testis	SRR060656 Ovary	SRR060657 Testis	SRR060658 Ovary	SRR060659 Testis	SRR060660 Ovary	SRR060661 Embryo	SRR060662 Embryo	SRR060663 Embryo	SRR060664 Male-body	SRR060665 Female-body	SRR060666 Male-body	SRR060667 Female-body	SRR060668 Male-body	SRR060669 Female-body	SRR060670 Testis	SRR060671 Male-body	SRR060672 Female-body	SRR060673 Ovary	SRR060674 Ovary	SRR060675 Ovary	SRR060676 Ovary	SRR060677 Ovary	SRR060678 Testis	SRR060679 Testis	SRR060680 Testis	SRR060681 Testis	SRR060682 Embryo	SRR060683 Testis	SRR060684 Embryo	SRR060685 Embryo	SRR060686 Embryo	SRR060687 Embryo	SRR060688 Ovary	SRR060689 Testis	SRR1106712 embryo_0-2h	SRR1106713 embryo_0-2h	SRR1106714 embryo_2-4h	SRR1106715 embryo_4-6h	SRR1106716 embryo_4-6h	SRR1106717 embryo_6-8h	SRR1106718 embryo_6-8h	SRR1106719 embryo_8-10h	SRR1106720 embryo_8-10h	SRR1106721 embryo_10-12h	SRR1106722 embryo_10-12h	SRR1106723 embryo_12-14h	SRR1106724 embryo_12-14h	SRR1106725 embryo_14-16h	SRR1106726 embryo_14-16h	SRR1106727 larvae	SRR1106728 larvae	SRR1106729 mixed whole adult body	SRR1106730 embryo_16-30h	V047 Embryo	V053 Head	V116 Male-body	GSM1528803 follicle cells
..........................................TAGTGGAATCGTCCGAT........................................................................................................................................................................................................................................................................................................................................................................................................	17	1	3.00	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3
.................................ATGACAATCTAGTGGAATC...............................................................................................................................................................................................................................................................................................................................................................................................................	19	1	2.00	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...................................GACAATCTAGTGGAATCGTC............................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..........................................................TATCAAAACGGAGGAGG---AAGAGGA..............................................................................................................................................................................................................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..........................................................................G---AAGAGGAGAACGCTGAG....................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
......................................AATCTAGTGGAATCGTCCG..........................................................................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...........................................................ATCAAAACGGAGGAGG---AAGAGGA..............................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...............................................................................................................................................AAG----CGTA---------TCTAAGCGTATCGGC.................................................................................................................................................................................................................................................................................	22	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
........................................................GATATCAAAACGGAGGAGG---AAGAG................................................................................................................................................................................................................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.............................................................................................AGGTGAGTGGAGGCCATTAAA.................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
.........................................CTAGTGGAATCGTCCGATAT......................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1
..................................................................................................................................................................................................................................................G-------TGTGTGCTTGACG--AGTGG.....................................................................................................................................................................................	19	1	1.00	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...........................CAGGCAATGACAATCTAGTGGA..................................................................................................................................................................................................................................................................................................................................................................................................................	22	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
....................................................................GAGGAGG---AAGAGGAGAACGCT.......................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.................................ATGACAATCTAGTGGAATCGTC............................................................................................................................................................................................................................................................................................................................................................................................................	22	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..........................................................TATCAAAACGGAGGAGG---AAGAGG...............................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
.....................................CAATCTAGTGGAATCGTCCG..........................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................................................................................................................................................................GTT--T----------------------GTTTGTT-----------T----GT-TTGTTTTG................................................................	22	8	0.25	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................................................................................................................................................................GTT--T----------------------GTTTGTT-----------T----GT-TTGT....................................................................	18	20	0.05	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................................................................................T-GTT--T----------------------GTTTGTT-----------T----GT-TTGTTTT.................................................................	22	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................................................................................................................................T--------TT-GTT--T----------------------GTTTGTT-----------T----GT-TTGTT...................................................................	22	20	0.05	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droMoj3

TGG------------------------------------------TGGAAACGTCCGGCATCAAAACGGAGGAAG---CAGATGAGATCGCCGAGGTGAGTGAAGCA-A-CAAAATGAGAGAAAGA--------------TATAAGCAATGATGCGCTGGCTTACAGTGCGTATA-GCTAAAT------CAGCTAGAGCAGCAGCATCAGCA--------------GCAGCTTT--------G-------TGTGTGCTTGACG--AAAGGTTGAAACATGTTGT-TT--GTGT---ATTCTCTGTTGTGTTTAT--------T------------------------------------------------T----GT-TTGTTTTGTTGTTGTTAAGTTTACGAAT------------------TCACCT------------TTAT-T--	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
......................................................CCGGCATCAAAACGGAGGAAG---.....................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	1	0	0	0	0	0
.GG------------------------------------------TGGAAACGTCCGGCATCAAAA.................................................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	1
..............................................................AAAACGGAGGAAG---CAGATG...............................................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	1	1	0	0	0	0	0
..........................................................................G---CAGATGAGATCGCCGAG....................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	1	0	0	0	0	1	0
......................................................................................................................................................................................................CAGCAGCATCAGCA--------------GCAGCTT..........................................................................................................................................................................................................................	21	1	1.00	1	1	0	0	0	0	0

droGri2

CTGGCGGCAACAATGCAACAGCATCTTCCAACACTGACAATCTGATGGAAACGTCCGACATCAAAGCGGAGGAGG---AAGAGGAGAATGCCGAGGTGAGTG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

dan_1973

scaffold_13266:13065718-13065868 -

Candidate

Unknown

Predicted structure

Flybase annnotation

Sense Strand Reads

Anti-sense strand reads

Re-alignment of all predicted orthologs

Re-alignment of all predicted orthologs with sRNA reads

-20.8	-20.6	-20.4