dsi_249

############################################################################################################################################################### TGTTGTTGCTGTTGCTCTTGTCCGTGGGCGTGGCATGGCTAGTTGTTGTCGCTGTCGCTGCTGCTGCTGCTGTGCTCGTTGTTGTTGTTGTTGTGGCAGCGGAAGTTGCTGCTGTTGTTGTGCTAGTTGCTGCTGCTGCTGCTGCTGCTGCCGCTTCGG *********************************.(((.(((.....((((((((((.((.((.((.((..........)).)).)).)).)))))))))).....))))))...........*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	O001 Testis	O002 Head	SRR618934 Ovary
..................................................GCTGTCGCTGCTGCTGCT...........................................................................................	18	0	5	6.00	30	20	10	0
TGTTGTTGCTGTTGCT...............................................................................................................................................	16	0	20	0.30	6	0	0	6
..................................................................CTGCTGAGGTCTTTGTTGTTGTT......................................................................	23	3	16	0.06	1	0	0	0
..................................................................CTGCTGAGGTCTTTGTTGTTGT.......................................................................	22	3	20	0.05	1	0	0	0

############################################################################################################################################################### CCGAAGCGGCAGCAGCAGCAGCAGCAGCAGCAACTAGCACAACAACAGCAGCAACTTCCGCTGCCACAACAACAACAACAACGAGCACAGCAGCAGCAGCAGCGACAGCGACAACAACTAGCCATGCCACGCCCACGGACAAGAGCAACAGCAACAACA *********************************...........((((((.....((((((((((.((.((.((.((..........)).)).)).)).)))))))))).....))).))).*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	O002 Head	M053 Female-body	SRR618934 Ovary
........................................AACAACAGCAGCAACTTC.....................................................................................................	18	0	1	1.00	1	1	0	0
......................................................................AACAAGAACAACGAGC.........................................................................	16	1	20	0.10	2	0	0	0
...............CAGCAGCAGCAGCAGCAAC.............................................................................................................................	19	0	20	0.05	1	0	1	0
.............................................................................................................................GCCTCGCCCACGGAC...................	15	1	20	0.05	1	0	0	0
....AGCGGCAGCAGCAGCA...........................................................................................................................................	16	0	20	0.05	1	0	0	1
............................................................................................................................................AAGAGCAACAGAAACAA..	17	1	20	0.05	1	0	0	1

Species	Coordinate	ID	Alignment
droSim3	X:4471082-4471240 -	dsi_249	TGT-TG--TTGCTGTTGC---TCTTGTC---CGTGGGCGTGGCAT--------GGCTAGTT------G----TTGTCGCTGTCGCTGC-TGCT---G---CTGCTG------TGCTCGTTGTTGTTGT-------------TGTTGTGG------------CAGCGG-AAGT---TGCTGCT---GTTGTT---G---TGCTAGTT---------GCTGCTGCTGCTGCTGCTGCTGCCGCTTCGG
droSec2	scaffold_4:1033290-1033436 +		TGT-TG--TTGCTGTTGC---TCTTGTC---CGTGGGCGTGGCAT--------GGCTAGTT------G----TTGTCGCTGTCGCTGC-TGCT---G---CTCCTG------------------TGCT-------------CGTTGTTGTTGTTGGTGTGGCAGCGG-AAGT---TGCTGCT---GTTG---------------------------TTGTGCTAGTTGCTGCTGCCGCCGCTTCGG
dm3	chrX:5732215-5732376 -		TGT-TG--TTGCTGTTGC---TCTTGTC---CGTGGGCGTGGCAT--------GGCTAGTT------G----TTGTTGCTGTCGCTGC-TGCT---G------CTGTGCTCGTTGTT------GTTGT-------TGG---TGTTT---------------CAGCGG-ATGT---TGCTACT---GTTGTTGTGCCAGTTGCTGCT---------GCTGCTGCTGCTGCTGCTGCTGCCGCTTCGA
droEre2	scaffold_4690:3079682-3079819 -		TGT-TG--TTGCTGTTGT---C---------CGTGGGCGTGGCAT--------GGGTGGTT------G----TT----------------------GCTGCTGCCG------CGCTTGTTGTTGTTGC-------------TGTGGC---------------AGCGG-CTGC---TGCTGCTG---TTGTTGTGC---TAGTTGCT---------GCTGCTGCTGCTGCCGTTGCTGCCGCTTCGG
droYak3	X:2739742-2739891 +		TGT-TG--TTGCTGTTGT---C---------CGTGGGCGTGGCAT--------GGCTAGTT------G----TTGTTGTTGTTGCTGC-TGCT---G------ATG------CTGTTGTGCTTGTTGT-------------TGTTGTTCTTGTTGTGG---CAGCGG-ATGT---TGCAGCT---GTTGTTG------------------------TGCTAGTTGCTGCTGGTGCTGCTGGTTCGC
droEug1	scf7180000409787:1172169-1172321 -		TGC-TG--CTGATGTTGC---TGGTGTA---T-TGGAAGCGGA-------------TGTCA------G----TT---GCTGCGCCGCC-TGCT---GCTGATGTTG------CAGTTGATGCTGCTGC-------------TGTTGCTGCTGCTGCTGC----------------TGT---TG---CTGCTGGTG---TTGCTGGT---------GCTGCTGCTGCAAGTGCTGTTGCTGCTGCGA
droBia1	scf7180000302428:1708426-1708577 -		TGT-TG--CTGCTGCTGC---TGTTGCA---GGT---------AT--------TGC----T---GTTG----CTGTTGCTGCCGCTGC-TGCT---GCTGCTGTGG------CCGGTGTTGCTGCCGC-------------TGCTGTTGTTGCTATTGC----------------CGC---TG---TTGTTGATT---TTGCTGCT---------GTTGCTGTTGCTGCTGCTGCTGTCGCTGCTG
droTak1	scf7180000414106:7134-7296 -		TGC-TG--TTGCTGTTGC---TGTTGCC---GTTGGTGGCGGC-------------CGTTG------G----CTGTTGCTGTTGCTGC-TGCT---G------CTGATGTTGCTGCT------GCTGCCTGGCATAGTAGTCC-CAGTGTTGCTGCTGC----------------TGT---TG---CTGCTGGTG---TTGCTGCT---------GCTGCTGGAGATGTTGCTGCTGCTGCTGCGG
droEle1	scf7180000491193:1574145-1574288 +		C-T-TG--TTGTTGTTGCTGCTGTT---------GGGC----TAC--------AGCTTGTT------G----TTGTTGCTGCTGCTGT-TGCT---G------CTGGG-CGGCCGC-----TTGTTGC----------TGTTG-GG---------------CAGCAGCTTGT---TGCTGCT---GTTGTTG---------TTGTT---------GCTGCTGTTGCT-TGGCTGCCTCCGCTGCAA
droRho1	scf7180000777386:198280-198438 +		TGC-TG--ATGATGTTGC---TCATGTT---TGTT---GCTGCTGG---T-----------GTTGATGT-TGCT---GGTGTTGCTGT-TGCT---GCTGCTGCTG------CTGTTGCTGCTGTTGC-------------TGTTGCTGTTGCTGTTGC----------------TGC---TG---TTGCTGTTG---CTGTTGCT---------GCTGCTGCTGCTGTTGCTGCTGCTGCTCCTG
droFic1	scf7180000453829:1093061-1093219 -		TGTCTG--TTGCTGCTGT---TGTTGTA---TTTGGT----GCTGT---TGT-TG-TTGTA------G----TT---GCTGCTGCTGC-TGCT---GTTGTTGTTG------TAGTTGCTGCTGTTGC-------------TGTTGTTG------------CTGCTG-CTGT---TGC---TGCTGTTG---TTG---TTGTAGTT---------GCTGCTGTTGCTGTTGCTGCTGCTGTTGTTG
droKik1	scf7180000302220:11877-12036 -		TGC-TG--CTGTTGTTGT---TGTTGTG---A-T------GCTGC-AGCTGG-----T---GCTGTTGC-TGCT---GTTGGTGCTGC-TGCT---GCTGTTGCTG------CTGCTGCTGTTGTTGC-------------TGCTGCTGCTGGTGGTGC----------------TGC---TG---CTGCTGGTG---CTGCTGCT---------GCTGGTGCTGCTGCTGCTGGTGCTGCTTCTG
droAna3	scaffold_13337:21935577-21935733 +		AGT-TAAGGGTCTTTTGC---G-TGGTT---TGTTGACGAGGCAT--------GGCTACGT------G----GTG-CACTGTAGCGGACAGCTGCGGCTGGGCTTG------T------GGCTGTTGT-------------TGTTGCTG------------CAGCTG-TTGC---TGCTG------CTG---TTG---CTGCTGCT---------GCTGCTGTTGCTGCTGCTGTTGCTGTTGTTG
droBip1	scf7180000395567:7294-7450 +		T-T-TG--CTGCTGGTGCGGCTGAA------GCT----GTTGCTGG---T-----------GCAGGTG----CTGTTGCTGTTGCTGC-TGCT---GCTGGTGTTG------TAACTGTTGCTGGTGC-------------TGTTGCAG---------------CTG-ATGTTGCTGC---TG---TTGTTGCTG---CTGGTGTT---------GCTGCTGCTGGTGCTGTTGCTGCAGCTGCTG
dp5	XR_group6:12702001-12702149 -		TGC-TG--TTGCTGCTGC---TGTTGCT---GCT-------GCTGT---TGCT--------GCTG-------CTGTTGTTGCTGTTGC-TGCT---G---CTGCTGTTGCTGC------TGCTGTTGC----------------TGCTGTTGCTGCTGC----------------TGC---TT---CTGCTGCTG---CTGCTGTT---------GCTGCTGTTGCTGCTGCTGCTTCTGCTGCTG
droPer2	scaffold_76:249930-250093 -		TGT-TG--CTGTTGTTGC---TGCTGCT---GCTGCGCCTGGCAA--------TT--G---GCCGCCGCCTGCT---GCTGCTGCTGC-TGTT---GTTGTTGTTG------TTGTTGTTGTTGTTGC-------------TGTTGCTGTTGCTGCTGC----------------TGC---TG---TTGTTGCTG---CTGTTGTT---------GCTGCTGTTGTTGCTGCTGTTGTTGCTGCTG
droWil2	scf2_1100000004776:18516-18682 +		TGC-TG--TTGCTGCTGC---TGTTGTTGCAGTT----GCTGCTGC---TGC-----T---GCT---G----TTGTTGCTGTTGCTGT-TGTT---GCTGCTGTTGTTGTTGCTGTTGCTGTTGTTGC-------------TGCTGCTGTTGTTGTTGC----------------TGC---TG---TTGTTGCTG---TTGCTGTT---------GCTGCTGCTGTTGTTGCTGTTGCTGCTGCAG
droVir3	scaffold_13049:6096733-6096887 -		TGC-TG--CTGCTGCTGC---TGTTGTT---GTT-------GCTGT---TGTT--------GCTG---C-TGTTGTTGCTGTTGTTGT-TGCT---GCTGCTGTTG------TTGTTGTTGTTGATGC----------------TGTTGTTGTTGTTGT----------------TGT---TG---CTGCTGTTG---CTGTTGTT---------GTTGTTGTTGCTGCTGCTGTTGCTGCTGCTG
droMoj3	scaffold_6496:6406680-6406837 -		TGT-TG--CTGCTGTCGC---TGCTGTT---GCT-------GCTGT---TGCT--------GCTG-------CTGTTGTTGTCGCTGC-TGCTGCTGCTGTCGCTG------CTGCTGTTGCTGCTGC-------------TGTTGCTGCTGCTGTTGC----------------TGC---TG---CTGCTGATG---CTGCTGTT---------GCTGTTGCTGTTGCTGCTGCTGCGTCTGCTG
droGri2	scaffold_14853:5617620-5617779 +		TGT-TG--TTGCTGCTGC---TGCTGCA---GTT-GTTGTTGCAG--------TT------GCTG-------CTGTTGTTGGTGTTGC-TGCT---GCTGCTGCTG---CTGCTGCT------GTTGT-------TGTTGTTGCTGCTG---------C---TGCGG-CTGC---TGC---------------TG---CTGTTGTTGTTGTTGTTGCTGCTGCTGGTGTTGCTGTTGC-GCGACAA

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droSim3

TGT-TG--TTGCTGTTGC---TCTTGTC---CGTGGGCGTGGCAT--------GGCTAGTT------G----TTGTCGCTGTCGCTGC-TGCT---G---CTGCTG------TGCTCGTTGTTGTTGT-------------TGTTGTGG------------CAGCGG-AAGT---TGCTGCT---GTTGTT---G---TGCTAGTT---------GCTGCTGCTGCTGCTGCTGCTGCCGCTTCGG	Size	Hit Count	Total Norm	Total	V044 Embryo	M023 Head	M024 Male-body	M025 Embryo	O001 Testis	O002 Head	M053 Female-body	SRR553485 Ovary	SRR553486 Ovary	SRR553487 Ovary	SRR553488 Ovary	SRR618934 Ovary
.............................................................................GCTGTCGCTGC-TGCT---G---CT................................................................................................................................................	18	5	6.00	30	0	0	0	0	20	10	0	0	0	0	0	0
TGT-TG--TTGCTGTTGC---T................................................................................................................................................................................................................................	16	20	0.30	6	0	0	0	0	0	0	0	0	0	0	0	6

droSec2

TGT-TG--TTGCTGTTGC---TCTTGTC---CGTGGGCGTGGCAT--------GGCTAGTT------G----TTGTCGCTGTCGCTGC-TGCT---G---CTCCTG------------------TGCT-------------CGTTGTTGTTGTTGGTGTGGCAGCGG-AAGT---TGCTGCT---GTTG---------------------------TTGTGCTAGTTGCTGCTGCCGCCGCTTCGG	Size	Hit Count	Total Norm	Total	V113 Male-body	V114 Embryo	V115 Head	M054 Female-body
No Reads

droEre2

TGT-TG--TTGCTGTTGT---C---------CGTGGGCGTGGCAT--------GGGTGGTT------G----TT----------------------GCTGCTGCCG------CGCTTGTTGTTGTTGC-------------TGTGGC---------------AGCGG-CTGC---TGCTGCTG---TTGTTGTGC---TAGTTGCT---------GCTGCTGCTGCTGCCGTTGCTGCCGCTTCGG	Size	Hit Count	Total Norm	Total	V040 Embryo	V060 Head	V107 Male-body	V108 Head	M055 Female-body	M057 Embryo
No Reads

droYak3

TGT-TG--TTGCTGTTGT---C---------CGTGGGCGTGGCAT--------GGCTAGTT------G----TTGTTGTTGTTGCTGC-TGCT---G------ATG------CTGTTGTGCTTGTTGT-------------TGTTGTTCTTGTTGTGG---CAGCGG-ATGT---TGCAGCT---GTTGTTG------------------------TGCTAGTTGCTGCTGGTGCTGCTGGTTCGC	Size	Hit Count	Total Norm	Total	V046 Embryo	V052 Head	V120 Male-body	V058 Head	M026 Head	M043 Female-body	M056 Embryo
No Reads

droEug1

TGC-TG--CTGATGTTGC---TGGTGTA---T-TGGAAGCGGA-------------TGTCA------G----TT---GCTGCGCCGCC-TGCT---GCTGATGTTG------CAGTTGATGCTGCTGC-------------TGTTGCTGCTGCTGCTGC----------------TGT---TG---CTGCTGGTG---TTGCTGGT---------GCTGCTGCTGCAAGTGCTGTTGCTGCTGCGA	Size	Hit Count	Total Norm	Total
No Reads

droBia1

TGT-TG--CTGCTGCTGC---TGTTGCA---GGT---------AT--------TGC----T---GTTG----CTGTTGCTGCCGCTGC-TGCT---GCTGCTGTGG------CCGGTGTTGCTGCCGC-------------TGCTGTTGTTGCTATTGC----------------CGC---TG---TTGTTGATT---TTGCTGCT---------GTTGCTGTTGCTGCTGCTGCTGTCGCTGCTG	Size	Hit Count	Total Norm	Total
No Reads

droTak1

TGC-TG--TTGCTGTTGC---TGTTGCC---GTTGGTGGCGGC-------------CGTTG------G----CTGTTGCTGTTGCTGC-TGCT---G------CTGATGTTGCTGCT------GCTGCCTGGCATAGTAGTCC-CAGTGTTGCTGCTGC----------------TGT---TG---CTGCTGGTG---TTGCTGCT---------GCTGCTGGAGATGTTGCTGCTGCTGCTGCGG	Size	Hit Count	Total Norm	Total
No Reads

droEle1

C-T-TG--TTGTTGTTGCTGCTGTT---------GGGC----TAC--------AGCTTGTT------G----TTGTTGCTGCTGCTGT-TGCT---G------CTGGG-CGGCCGC-----TTGTTGC----------TGTTG-GG---------------CAGCAGCTTGT---TGCTGCT---GTTGTTG---------TTGTT---------GCTGCTGTTGCT-TGGCTGCCTCCGCTGCAA	Size	Hit Count	Total Norm	Total
No Reads

droRho1

TGC-TG--ATGATGTTGC---TCATGTT---TGTT---GCTGCTGG---T-----------GTTGATGT-TGCT---GGTGTTGCTGT-TGCT---GCTGCTGCTG------CTGTTGCTGCTGTTGC-------------TGTTGCTGTTGCTGTTGC----------------TGC---TG---TTGCTGTTG---CTGTTGCT---------GCTGCTGCTGCTGTTGCTGCTGCTGCTCCTG	Size	Hit Count	Total Norm	Total
No Reads

droFic1

TGTCTG--TTGCTGCTGT---TGTTGTA---TTTGGT----GCTGT---TGT-TG-TTGTA------G----TT---GCTGCTGCTGC-TGCT---GTTGTTGTTG------TAGTTGCTGCTGTTGC-------------TGTTGTTG------------CTGCTG-CTGT---TGC---TGCTGTTG---TTG---TTGTAGTT---------GCTGCTGTTGCTGTTGCTGCTGCTGTTGTTG	Size	Hit Count	Total Norm	Total
No Reads

droKik1

TGC-TG--CTGTTGTTGT---TGTTGTG---A-T------GCTGC-AGCTGG-----T---GCTGTTGC-TGCT---GTTGGTGCTGC-TGCT---GCTGTTGCTG------CTGCTGCTGTTGTTGC-------------TGCTGCTGCTGGTGGTGC----------------TGC---TG---CTGCTGGTG---CTGCTGCT---------GCTGGTGCTGCTGCTGCTGGTGCTGCTTCTG	Size	Hit Count	Total Norm	Total
No Reads

droAna3

AGT-TAAGGGTCTTTTGC---G-TGGTT---TGTTGACGAGGCAT--------GGCTACGT------G----GTG-CACTGTAGCGGACAGCTGCGGCTGGGCTTG------T------GGCTGTTGT-------------TGTTGCTG------------CAGCTG-TTGC---TGCTG------CTG---TTG---CTGCTGCT---------GCTGCTGTTGCTGCTGCTGTTGCTGTTGTTG	Size	Hit Count	Total Norm	Total	V105 Male-body	V106 Head	V055 Head	V039 Embryo	M044 Female-body	M058 Embryo
.............................................................................................................................................TGTTGCTG------------CAGCTG-TTGC---TGCTG------C...........................................................	24	1	1.00	1	0	0	0	0	1	0

droBip1

T-T-TG--CTGCTGGTGCGGCTGAA------GCT----GTTGCTGG---T-----------GCAGGTG----CTGTTGCTGTTGCTGC-TGCT---GCTGGTGTTG------TAACTGTTGCTGGTGC-------------TGTTGCAG---------------CTG-ATGTTGCTGC---TG---TTGTTGCTG---CTGGTGTT---------GCTGCTGCTGGTGCTGTTGCTGCAGCTGCTG	Size	Hit Count	Total Norm	Total
No Reads

dp5

TGC-TG--TTGCTGCTGC---TGTTGCT---GCT-------GCTGT---TGCT--------GCTG-------CTGTTGTTGCTGTTGC-TGCT---G---CTGCTGTTGCTGC------TGCTGTTGC----------------TGCTGTTGCTGCTGC----------------TGC---TT---CTGCTGCTG---CTGCTGTT---------GCTGCTGTTGCTGCTGCTGCTTCTGCTGCTG	Size	Hit Count	Total Norm	Total	V112 Male-body	V043 Embryo	V051 Head	M022 Male-body	M040 Female-body	M059 Embryo	M062 Head
.............................................................................................................................TGC----------------TGCTGTTGCTGCTGC----------------TGC---T................................................................	22	20	0.05	1	0	0	0	0	1	0	0
.............................................................................................................................................................................................................T---------GCTGCTGTTGCTGCTGCTGCT..........	22	20	0.05	1	0	0	0	0	1	0	0
...........................................................................................................TGCTGC------TGCTGTTGC----------------TGCTG.................................................................................................	20	20	0.05	1	0	0	0	0	1	0	0

droPer2

TGT-TG--CTGTTGTTGC---TGCTGCT---GCTGCGCCTGGCAA--------TT--G---GCCGCCGCCTGCT---GCTGCTGCTGC-TGTT---GTTGTTGTTG------TTGTTGTTGTTGTTGC-------------TGTTGCTGTTGCTGCTGC----------------TGC---TG---TTGTTGCTG---CTGTTGTT---------GCTGCTGTTGTTGCTGCTGTTGTTGCTGCTG	Size	Hit Count	Total Norm	Total	V111 Male-body	V042 Embryo	V050 Head	V057 Head	M021 Embryo	M042 Female-body
.................................................................................................................................................................................................................................TTGCTGCTGTTGTTGCTG...	18	20	0.05	1	0	0	0	0	0	1
............................................................................................................................................................................................................TT---------GCTGCTGTTGTTGCTG...............	18	20	0.05	1	0	0	0	0	0	1
.........................................................................................................G------TTGTTGTTGTTGTTGC-------------TGTT.....................................................................................................	21	20	0.05	1	1	0	0	0	0	0
.....................................................................................................................................................TTGCTGCTGC----------------TGC---TG---TTGTT.......................................................	20	20	0.05	1	1	0	0	0	0	0

droWil2

TGC-TG--TTGCTGCTGC---TGTTGTTGCAGTT----GCTGCTGC---TGC-----T---GCT---G----TTGTTGCTGTTGCTGT-TGTT---GCTGCTGTTGTTGTTGCTGTTGCTGTTGTTGC-------------TGCTGCTGTTGTTGTTGC----------------TGC---TG---TTGTTGCTG---TTGCTGTT---------GCTGCTGCTGTTGTTGCTGTTGCTGCTGCAG	Size	Hit Count	Total Norm	Total	V117 Male-body	V118 Embryo	V119 Head	M020 Head	M045 Female-body
.......................................................................................................................................................................................................TGCTGTT---------GCTGCTGCTGTTG..................	20	20	1.45	29	0	1	0	0	28
............................................................................................................................................................TGC----------------TGC---TG---TTGTTGCTG---TTGCTG..........................................	23	20	0.65	13	0	0	0	0	13
............................................................................................................................................................................................................................TGCTGTTGTTGCTGTTGCTGCTG...	23	20	0.60	12	0	0	0	0	12
.........................................................T---GCT---G----TTGTTGCTGTTGCTGT-TG...........................................................................................................................................................	23	20	0.55	11	0	0	0	0	11
.......................................................................................................................................................................................................TGCTGTT---------GCTGCTGCTGTTGTTGC..............	24	20	0.55	11	0	0	0	0	11
...............TGC---TGTTGTTGCAGTT----GCTGCTG.........................................................................................................................................................................................................	23	12	0.50	6	0	0	0	0	6
.........................................................T---GCT---G----TTGTTGCTGTTGCTG...............................................................................................................................................................	20	20	0.40	8	0	0	0	0	8
...........................................TGC---TGC-----T---GCT---G----TTGTTGCTG.....................................................................................................................................................................	20	20	0.35	7	0	0	0	0	7
.......................................................................................................................................................................................................TGCTGTT---------GCTGCTGCTGTTGTTGCTG............	26	20	0.30	6	0	0	0	0	6
TGC-TG--TTGCTGCTGC---TGTTGTTGCAG......................................................................................................................................................................................................................	26	15	0.27	4	0	0	1	0	3
..............................................................................................................................................................................................TGCTG---TTGCTGTT---------GCTGCTGCTGTTG..................	26	20	0.20	4	0	0	0	0	4
.........TGCTGCTGC---TGTTGTTGCAGTT----G...............................................................................................................................................................................................................	23	15	0.20	3	0	0	0	0	3
.............................................................................................................................................................................................................T---------GCTGCTGCTGTTGTTGCTGTTGC........	24	20	0.20	4	0	0	0	0	4
TGC-TG--TTGCTGCTGC---TGTTGTT..........................................................................................................................................................................................................................	22	20	0.20	4	0	0	0	0	4
.................................................................................................................................................................................................TG---TTGCTGTT---------GCTGCTGCTGTTGTTG...............	26	20	0.20	4	0	0	0	0	4
............................................................................................................................................................TGC----------------TGC---TG---TTGTTGCTG---TTGC............................................	21	20	0.20	4	0	0	0	0	4
.....................TGTTGTTGCAGTT----GCTGCTGC---TG...................................................................................................................................................................................................	23	13	0.15	2	0	0	0	0	2
...........................................TGC---TGC-----T---GCT---G----TTGTTGCTGT....................................................................................................................................................................	21	20	0.15	3	0	0	0	0	3
...........................................................................................................................................................................................TGTTGCTG---TTGCTGTT---------GCTGCTG........................	23	20	0.15	3	0	0	0	0	3
...............................................................................................................................................................................................GCTG---TTGCTGTT---------GCTGCTGCTGTTG..................	25	20	0.15	3	0	0	0	0	3
..........................................................................................................................................................................................................TGTT---------GCTGCTGCTGTTGTTGCTGTT..........	25	20	0.15	3	0	0	0	0	3
.................................................TGC-----T---GCT---G----TTGTTGCTGTTGCTGT-TG...........................................................................................................................................................	26	20	0.15	3	0	0	0	0	3
...............................................................................................................................................................................TGC---TG---TTGTTGCTG---TTGCT...........................................	19	20	0.15	3	0	0	0	0	3
............................................................................................................................................................TGC----------------TGC---TG---TTGTTGCTG---TTGCTGTT---------G..............................	26	20	0.15	3	0	0	0	0	3
....TG--TTGCTGCTGC---TGTTGTTGCAG......................................................................................................................................................................................................................	23	15	0.13	2	0	1	0	0	1
...........................TGCAGTT----GCTGCTGC---TGC-----T---GCT---G----TTG...........................................................................................................................................................................	26	9	0.11	1	0	0	0	0	1
.....................TGTTGTTGCAGTT----GCTGCTGC---TGC-----T---G........................................................................................................................................................................................	26	10	0.10	1	0	0	0	0	1
.........................................................................................................................................................TGTTGC----------------TGC---TG---TTGTTGCTG---TTGC............................................	24	20	0.10	2	0	0	0	0	2
................................................................................................................................................TGCTGTTGTTGTTGC----------------TGC---TG---TTG.........................................................	23	20	0.10	2	0	0	0	0	2
...............................................................................................................................................................................TGC---TG---TTGTTGCTG---TTGCTGTT---------GC.............................	24	20	0.10	2	0	0	0	0	2
...............................................................T---G----TTGTTGCTGTTGCTGT-TGTT---GC....................................................................................................................................................	24	20	0.10	2	0	0	0	0	2
..................................................................................................................................................................................................G---TTGCTGTT---------GCTGCTGCTGTTGT.................	23	20	0.10	2	0	0	0	0	2
...............................................................................................................................................................................TGC---TG---TTGTTGCTG---TTGC............................................	18	20	0.10	2	0	0	0	0	2
...............................................................................................................................................................................TGC---TG---TTGTTGCTG---TTGCTGTT---------...............................	22	20	0.10	2	0	0	0	0	2
.GC-TG--TTGCTGCTGC---TGTTGTTGC........................................................................................................................................................................................................................	23	20	0.10	2	0	0	0	0	2
.........................................................................................................................................................................................................................TGCTGCTGTTGTTGCTGTTGCTGCTG...	26	20	0.10	2	0	0	0	0	2
.............................................................................................................................................................................................................................GCTGTTGTTGCTGTTGCTGCT....	21	20	0.10	2	0	0	0	0	2
....................................................................................................................TGCTGTTGTTGC-------------TGCTGCTGT................................................................................................	21	20	0.10	2	0	0	0	0	2
TGC-TG--TTGCTGCTGC---TGTTGTTG.........................................................................................................................................................................................................................	23	20	0.10	2	0	2	0	0	0
............................................................................TGCTGTTGCTGT-TGTT---GCTGCTG...............................................................................................................................................	23	20	0.10	2	0	0	0	0	2
..................................................................................................TGCTGTTGTTGTTGCTGTTGCTGT............................................................................................................................	24	20	0.10	2	1	0	0	0	1
..................................................GC-----T---GCT---G----TTGTTGCTGTTGC.................................................................................................................................................................	20	20	0.10	2	0	0	0	0	2
.............................................................................................................................TGC-------------TGCTGCTGTTGTTGTTGC----------------TGC---.................................................................	24	20	0.10	2	0	0	0	0	2
........................................................................................................TGTTGTTGCTGTTGCTGTTGTTGC-------------.........................................................................................................	24	20	0.10	2	0	0	0	0	2
..............................................................................................................................................................................................TGCTG---TTGCTGTT---------GCTGCTGCTG.....................	23	20	0.10	2	0	0	0	0	2
...............TGC---TGTTGTTGCAGTT----GCTGCTGC---.....................................................................................................................................................................................................	24	12	0.08	1	0	0	0	0	1
.................C---TGTTGTTGCAGTT----GCTGCTGC---TG...................................................................................................................................................................................................	24	12	0.08	1	0	0	0	0	1
.....................TGTTGTTGCAGTT----GCTGCTG.........................................................................................................................................................................................................	20	13	0.08	1	0	0	0	0	1
.........................................................T---GCT---G----TTGTTGCTGTTGCTGT-TGT..........................................................................................................................................................	24	13	0.08	1	0	0	0	0	1
.....................TGTTGTTGCAGTT----GCTGCTGC---T....................................................................................................................................................................................................	22	13	0.08	1	0	0	0	0	1
...............................................................................................................................................................................TGC---TG---TTGTTGCTG---TTGCTGTT---------GCTGC..........................	27	13	0.08	1	0	0	0	0	1
...............TGC---TGTTGTTGCAGTT----GCTG............................................................................................................................................................................................................	20	14	0.07	1	0	0	0	0	1
....TG--TTGCTGCTGC---TGTTGTTGCAGTT----G...............................................................................................................................................................................................................	26	15	0.07	1	0	0	0	0	1
....TG--TTGCTGCTGC---TGTTGTTGCAGTT----................................................................................................................................................................................................................	25	15	0.07	1	0	0	0	0	1
........................TGTTGCAGTT----GCTGCTGC---TG...................................................................................................................................................................................................	20	16	0.06	1	0	0	0	0	1
..............................................................................................................................................................C----------------TGC---TG---TTGTTGCTG---TTGCTGTT---------GC.............................	25	17	0.06	1	0	0	0	0	1
....................................................................................................................TGCTGTTGTTGC-------------TGCTGCTGTTGT.............................................................................................	24	20	0.05	1	0	0	0	0	1
............................................................................................T---GCTGCTGTTGTTGTTGCTGTTG................................................................................................................................	23	20	0.05	1	0	0	0	0	1
.......................................................................................................TTGTTGTTGCTGTTGCTGTTGTTG.......................................................................................................................	24	20	0.05	1	0	0	1	0	0
..........................................................................................................................................................................................TTGTTGCTG---TTGCTGTT---------GC.............................	19	20	0.05	1	0	0	0	0	1
..................................................................................................................................................................................................G---TTGCTGTT---------GCTGCTGCTGTTG..................	22	20	0.05	1	0	1	0	0	0
...........................................TGC---TGC-----T---GCT---G----TTGTTGCTGTT...................................................................................................................................................................	22	20	0.05	1	0	0	0	1	0
....................................................................................................................TGCTGTTGTTGC-------------TGCTGCTGTTGTT............................................................................................	25	20	0.05	1	0	0	0	0	1
...........................................................................................................................................................................................TGTTGCTG---TTGCTGTT---------GCTGCTGC.......................	24	20	0.05	1	0	0	0	0	1
..........................................................................................................................................................................................................TGTT---------GCTGCTGCTGTTGTTGCTGT...........	24	20	0.05	1	0	0	1	0	0
.....................................................................................................................................................................................TG---TTGTTGCTG---TTGCTGTT---------GCTG...........................	23	20	0.05	1	0	0	0	0	1
..............................................................................................................................................................C----------------TGC---TG---TTGTTGCTG---TTGCT...........................................	20	20	0.05	1	0	0	0	0	1
.....................................................................................................TGTTGTTGTTGCTGTTGCTGTTG..........................................................................................................................	23	20	0.05	1	0	0	0	0	1
........................................................................................................TGTTGTTGCTGTTGCTGT............................................................................................................................	18	20	0.05	1	0	1	0	0	0
.........................................................................................................................................................TGTTGC----------------TGC---TG---TTGTTGCTG---TTGCTG..........................................	26	20	0.05	1	0	0	0	0	1
...................................................................G----TTGTTGCTGTTGCTGT-TGTT---GC....................................................................................................................................................	23	20	0.05	1	0	0	0	0	1
.........................................................................................................................TTGTTGC-------------TGCTGCTGTTGTTGTTG........................................................................................	24	20	0.05	1	0	0	0	0	1
........................................TGCTGC---TGC-----T---GCT---G----TTGTTGCTGT....................................................................................................................................................................	24	20	0.05	1	0	0	0	0	1
.........................................................................................TGTT---GCTGCTGTTGTTGTTGCTG...................................................................................................................................	23	20	0.05	1	0	0	0	0	1
............................................................................................................................TTGC-------------TGCTGCTGTTGTTGTTGC----------------TG.....................................................................	24	20	0.05	1	0	0	0	0	1
.......................................CTGCTGC---TGC-----T---GCT---G----TTGTTGCTGT....................................................................................................................................................................	25	20	0.05	1	0	0	0	0	1
......................................................................................................GTTGTTGTTGCTGTTGCTGTTGT.........................................................................................................................	23	20	0.05	1	0	0	1	0	0
...........................................................................................................................................................TTGC----------------TGC---TG---TTGTTGCTG---................................................	18	20	0.05	1	0	1	0	0	0
....................................................................................................................TGCTGTTGTTGC-------------TGCTGCTGTTGTTG...........................................................................................	26	20	0.05	1	0	0	0	0	1
.....G--TTGCTGCTGC---TGTTGTTG.........................................................................................................................................................................................................................	19	20	0.05	1	0	0	0	0	1
..........................................................................................................................................................GTTGC----------------TGC---TG---TTGTTGCTG---TTG.............................................	22	20	0.05	1	0	0	0	0	1
.............................................................................................................TTGCTGTTGCTGTTGTTG.......................................................................................................................	18	20	0.05	1	0	1	0	0	0
.........................................................................................................................................................TGTTGC----------------TGC---TG---TTGTTGCTG---TTGCT...........................................	25	20	0.05	1	0	0	0	0	1
.................................T----GCTGCTGC---TGC-----T---GCT---G----TTGTTGCTG.....................................................................................................................................................................	26	20	0.05	1	0	0	0	0	1
...........................................................................................................................GTTGC-------------TGCTGCTGTTGTTGTTGC----------------.......................................................................	23	20	0.05	1	0	0	1	0	0
...................................................................................................GCTGTTGTTGTTGCTGTTGCTGTT...........................................................................................................................	24	20	0.05	1	0	0	0	0	1
.............................................................GCT---G----TTGTTGCTGTTGCTG...............................................................................................................................................................	19	20	0.05	1	0	0	0	0	1
...................................................................................................................TTGCTGTTGTTGC-------------TGCTGCTGTTGT.............................................................................................	25	20	0.05	1	0	0	0	0	1
......................................................................................GT-TGTT---GCTGCTGTTGTTGT........................................................................................................................................	20	20	0.05	1	0	0	0	0	1
..........................................................................................................................TGTTGC-------------TGCTGCTGTTGTTGTTGC----------------T......................................................................	25	20	0.05	1	1	0	0	0	0
.........................................................................................................GTTGTTGCTGTTGCTGTTGTTGC-------------.........................................................................................................	23	20	0.05	1	0	0	0	0	1
..........................................................................................................................................................................................................TGTT---------GCTGCTGCTGTTGTTGCTGTTG.........	26	20	0.05	1	0	0	0	0	1
.GC-TG--TTGCTGCTGC---TGTTGTTG.........................................................................................................................................................................................................................	22	20	0.05	1	0	0	0	0	1
...........................................................................................................TGTTGCTGTTGCTGTTGTTGC-------------TG.......................................................................................................	23	20	0.05	1	0	0	0	0	1
......................................................................................................................................................................................G---TTGTTGCTG---TTGCTGTT---------GCTGCTGCT......................	27	20	0.05	1	0	0	0	0	1
.................................T----GCTGCTGC---TGC-----T---GCT---G----TTGTTGCT......................................................................................................................................................................	25	20	0.05	1	0	0	0	0	1

droVir3

TGC-TG--CTGCTGCTGC---TGTTGTT---GTT-------GCTGT---TGTT--------GCTG---C-TGTTGTTGCTGTTGTTGT-TGCT---GCTGCTGTTG------TTGTTGTTGTTGATGC----------------TGTTGTTGTTGTTGT----------------TGT---TG---CTGCTGTTG---CTGTTGTT---------GTTGTTGTTGCTGCTGCTGTTGCTGCTGCTG	Size	Hit Count	Total Norm	Total	V116 Male-body	V053 Head	V047 Embryo	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
..................................................................................................................GTTGTTGTTGATGC----------------TGTTGT................................................................................................	20	5	0.20	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
..............................................................................................................................................................................................................................TTGCTGCTGCTGTTGCTG......	18	20	0.10	2	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
.......................................................................................................TTG------TTGTTGTTGTTGATGC----------------T.....................................................................................................	20	20	0.10	2	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
.........................................................................................................G------TTGTTGTTGTTGATGC----------------T.....................................................................................................	18	20	0.05	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	0	0	0	0	0	0	0	0	0	0
...................................................................................................GCTGTTG------TTGTTGTTGTT...........................................................................................................................	18	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.........TGCTGCTGC---TGTTGTT---GTT-------GC...........................................................................................................................................................................................................	21	20	0.05	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

droMoj3

TGT-TG--CTGCTGTCGC---TGCTGTT---GCT-------GCTGT---TGCT--------GCTG-------CTGTTGTTGTCGCTGC-TGCTGCTGCTGTCGCTG------CTGCTGTTGCTGCTGC-------------TGTTGCTGCTGCTGTTGC----------------TGC---TG---CTGCTGATG---CTGCTGTT---------GCTGTTGCTGTTGCTGCTGCTGCGTCTGCTG	Size	Hit Count	Total Norm	Total	V110 Male-body	V056 Head	V049 Head	V041 Embryo	M046 Female-body	M060 Embryo
...........................................................................................CTGCTGCTGTCGCTG------CTGCTG................................................................................................................................	21	20	0.05	1	0	0	0	0	1	0

droGri2

TGT-TG--TTGCTGCTGC---TGCTGCA---GTT-GTTGTTGCAG--------TT------GCTG-------CTGTTGTTGGTGTTGC-TGCT---GCTGCTGCTG---CTGCTGCT------GTTGT-------TGTTGTTGCTGCTG---------C---TGCGG-CTGC---TGC---------------TG---CTGTTGTTGTTGTTGTTGCTGCTGCTGGTGTTGCTGTTGC-GCGACAA	Size	Hit Count	Total Norm	Total	V109 Male-body	M041 Female-body
..............................................................................................................................................GCTGCTG---------C---TGCGG-CTGC---TGC---------------T....................................................	21	20	0.05	1	0	1
...............................................................................................................................................................................TGC---------------TG---CTGTTGTTGTTGTT..................................	19	20	0.05	1	1	0

dsi_249

X:4471132-4471190 -

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

-25.9	-25.8