dse_339

TTGAAAAAAAAAACACAAGAATGTGATATTTCATCAAATTTGCAATAACCTAAGAATAGTAAAACGAAGGACAAAAAAAAAAATTGTATTCTTTTTGCTATTCTATAGGCTAACGAGCATTCCTTAAAATACATATGTACATAAGTGTTTAAAAAAAT *********************************.....(((..((.((((((((((((((((.(((..((((.........)))).))).)))))))))))).)))).))....)))...**********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V113 male body	V114 embryo	M054 female body
..................................................TAAGAATAGTAAAACGAAGGACA.....................................................................................	23	0	1	11.00	11	7	4	0
..................................................TAAGAATAGTAAAACGAAGGAC......................................................................................	22	0	1	2.00	2	0	2	0
......................................................................................TATTCTTTTTGCTATTCTATA...................................................	21	0	1	1.00	1	0	0	1
..................................................TAAGAATAGTAAAACGAAGGACAT....................................................................................	24	1	1	1.00	1	0	0	1
...................................................AAGAATAGCAAAAAGAAGGCC......................................................................................	21	3	13	0.08	1	0	1	0

AACTTTTTTTTTTGTGTTCTTACACTATAAAGTAGTTTAAACGTTATTGGATTCTTATCATTTTGCTTCCTGTTTTTTTTTTTAACATAAGAAAAACGATAAGATATCCGATTGCTCGTAAGGAATTTTATGTATACATGTATTCACAAATTTTTTTA **********************************.....(((..((.((((((((((((((((.(((..((((.........)))).))).)))))))))))).)))).))....)))...*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V115 head	M054 female body
..............................................................................TTTTTAACATAAGAAGAA..............................................................	18	1	6	0.17	1	1	0
....................................................................................CCATAAGACAAACGCTAAGAT.....................................................	21	3	8	0.13	1	0	1

Species	Coordinate	ID	Type	Alignment
droSec2	scaffold_1:14026248-14026405 -	dse_339	candidate-rescued	TTGAAAAA-AAAAA-CA-CAAGAATGTGATATTTC--ATCAAATT-----TGCAATAACCTAAGAATAGTAAAACGAAGGACAAAAAAAA-AAATTGTATTCTTTTTGCTATTCTA-----------------------------------------------------------------------------------------------TAGGCTAACGAGC----------ATTCCTTAAAAT----------ACATATGTACATAAGTGTT-TA-AAAAAAT
droSim2	2r:17041512-17041659 -	dsi_32435	candidate-rescued	TTGA---AAAAAAA-CA-CAAGAATGTGATATTTC--ATCAAATT-----TGCCATAACCTAAGAATAGTAAAACGAAGGGCAAAAAAAA-AAATT-TATTCTTTTTGCTATTCTA-----------------------------------------------------------------------------------------------TAGGCTAATGAGC----------ATTCCTTAAAAT------------------ACATATGTGTT-TAAAAAAAAT
dm3	chr2R:16472042-16472207 -			TTGAAAAA-AAAAA-CA-CAAAAATGTGATATTTC--ATCAC----------TCATCAACTCAAAATAGTAAATCGAAGGGCAAAAAAAT---ATGGTATTCTGTTTGCTATTATA-----------------------------------------------------------------------------------------------AAAGTTCACGAGCTAAGCTAACGATTCATTAAAAT------ATGTACATACATATTTAAGTGTT-AAAAAAAAAT
droEre2	scaffold_4845:10618664-10618918 -	der_25	confident	ATAA---ACTAA-TTGT-ACAAATTGTGATATTTT--ATCAAATC-----TGCCATAACATCCAAATACTTAACCGATGATCTAAAAACGGT----GTTTTCT----GTTATTTTACTATATAACTTATTTATGAAGAAGCTTTAGGATTTAATTTTTCCGACAATGCGATCTAGGCGTTTCTATCGCTGAGGTAGTATTGTTTGAAAGATTAAGTTAAAGCGT----------AATCATCAAAATTTTAAAATGTGAATAAGTACATAAGTGTG-CCAAAAATAT
droYak3	2R:12724006-12724252 +	dya_34	confident	AAAA---ACTAA-ATGTTAAAAATTATTATATTTT--ATCAAATG-----TACCATAACCTCAAAATACTAAACTGATGAGCTAAAAAGC-TA----TTTTCTCTTTGTTATTCTGCAATG-GATTTATTT--------GCTTTAGGATTTATTTTTTCGGACAATTCAATCTGGGCGTTGCTTTCGCTGAGGTAGTATTGTTTGGAAGACTAAGTTAACGAGC----------ATTCATCTCATTTTTGAAATTT---TGTGTTCATGAGTGTG-TTAAAAATAT
droEug1	scf7180000409474:1489651-1489666 +			AA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATGTG-TT-ACAAATT
droEle1	scf7180000491201:736783-736924 -			AATA---AAAAAAA-TT-TAAGAACATGAATTTTGCAAGCAAATTATGTGTGC-------CAATAA-----------CGGTTAAAAAAAT-------------------------------------------GAAGCATTTCAAGAATTTAATTTTTTT-ATAA---------------------------------------------------------CT----------TGTGCTATAAAG----------AAACACGTAGATAACAATTAAAGAAAAAAT

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droSec2

TTGAAAAA-AAAAA-CA-CAAGAATGTGATATTTC--ATCAAATT-----TGCAATAACCTAAGAATAGTAAAACGAAGGACAAAAAAAA-AAATTGTATTCTTTTTGCTATTCTA-----------------------------------------------------------------------------------------------TAGGCTAACGAGC----------ATTCCTTAAAAT----------ACATATGTACATAAGTGTT-TA-AAAAAAT	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
............................................................TAAGAATAGTAAAACGAAGGACA...........................................................................................................................................................................................................	23	1	11.00	11	0	7	4	0
............................................................TAAGAATAGTAAAACGAAGGAC............................................................................................................................................................................................................	22	1	2.00	2	0	0	2	0
.................................................................................................TATTCTTTTTGCTATTCTA-----------------------------------------------------------------------------------------------TA.........................................................................	21	1	1.00	1	1	0	0	0
............................................................TAAGAATAGTAAAACGAAGGACAT..........................................................................................................................................................................................................	24	1	1.00	1	1	0	0	0

droSim2

TTGA---AAAAAAA-CA-CAAGAATGTGATATTTC--ATCAAATT-----TGCCATAACCTAAGAATAGTAAAACGAAGGGCAAAAAAAA-AAATT-TATTCTTTTTGCTATTCTA-----------------------------------------------------------------------------------------------TAGGCTAATGAGC----------ATTCCTTAAAAT------------------ACATATGTGTT-TAAAAAAAAT	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
............................................................TAAGAATAGTAAAACGAAGGGCA...........................................................................................................................................................................................................	23	1	32.00	32	0	0	0	0	0	0	0	2	1	0	0	0	0	29	0	0	0
............................................................TAAGAATAGTAAAACGAAGGGC............................................................................................................................................................................................................	22	1	5.00	5	0	0	2	0	0	0	0	1	0	0	0	1	0	1	0	0	0
............................................................TAAGAATAGTAAAACGAAGGGCAA..........................................................................................................................................................................................................	24	1	2.00	2	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0
............................................................TAAGAATAGTAAAACGAAGGGCAC..........................................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
............................................................TAAGAATAGTAAAACGAAGGGCATT.........................................................................................................................................................................................................	25	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
............................................................TAAGAATAGTAAAACGAAGGGCAT..........................................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
.................................................................................................TATTCTTTTTGCTATTCTA-----------------------------------------------------------------------------------------------TAGG.......................................................................	23	1	1.00	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
............................................................................AAGGGCAAAAAAAA-A..................................................................................................................................................................................................	15	17	0.06	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0

dm3

TTGAAAAA-AAAAA-CA-CAAAAATGTGATATTTC--ATCAC----------TCATCAACTCAAAATAGTAAATCGAAGGGCAAAAAAAT---ATGGTATTCTGTTTGCTATTATA-----------------------------------------------------------------------------------------------AAAGTTCACGAGCTAAGCTAACGATTCATTAAAAT------ATGTACATACATATTTAAGTGTT-AAAAAAAAAT

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

GSM239041

Head

GSM239050

Head

GSM239051

S2

GSM239052

S2

GSM246084

Head

GSM266765

S2

GSM280082

Ovary

GSM280083

Ovary

GSM280084

Ovary

GSM280085

Testis

GSM280086

Ovary

GSM280087

S2-NP

GSM280088

S2-NP

GSM312995

Head

GSM313160

Head

GSM313161

Head

GSM313162

Head

GSM313163

Head

GSM313164

Head

GSM313165

Head

GSM343287

Embryo

GSM379050

Ovary

GSM379051

Ovary

GSM379052

Ovary

GSM379053

Ovary

GSM379054

Ovary

GSM379055

Ovary

GSM379056

Ovary

GSM379057

Ovary

GSM379058

Ovary

GSM379059

Ovary

GSM379060

Ovary

GSM379061

Ovary

GSM379062

Ovary

GSM379063

Ovary

GSM379064

Ovary

GSM379065

Ovary

GSM379066

Ovary

GSM379067

Ovary

GSM424739

S2

GSM424740

S2

GSM424741

S2

GSM467729

Female-body

GSM467730

Female-body

GSM467731

Female-body

M002

CS

M003

Male-body

M004

Male-body

M005

ML-DmD32

M006

ML-DmD32

M029

OSC

M030

OSC

M031

OSC

M032

S2-R+

M033

S2-R+

M034

S2-R+

M035

S2-R+

M036

S2-R+

M037

S2-R+

M038

S2-R+

M039

S2-R+

M048

S2-R+

OSS2

OSS

OSS6

OSS

OSS7

OSS

OSS8

OSS

S1

Head

S10

Embryo

S11

Embryo

S12

Embryo

S13

Embryo

S14

Embryo

S15

S2-GMR

S16

Kc

S17

Larvae

S18

Larvae

S19

Pupae

S2

Head

S20

Pupae

S21

Disc

S22

Head

S23

Female-body

S24

Male-body

S25

Larvae

S26

Larvae

S27

Pupae

S28

Pupae

S29

Head

S3

Male-body

S30

S2-GMR

S31

S2

S32

S2

S33

Kc

S34

Kc

S35

Kc

S4

Female-body

S5

Disc

S6

Embryo

S7

Embryo

S8

S2

S9

Embryo

SRR001337

Head

SRR001338

Head

SRR001339

Head

SRR001340

Head

SRR001341

Head

SRR001342

Head

SRR001343

Head

SRR001344

Head

SRR001345

Head

SRR001346

Head

SRR001347

Head

SRR001348

Head

SRR001349

Head

SRR001664

Head

SRR010951

Ovary

SRR010952

Ovary

SRR010953

Ovary

SRR010954

Ovary

SRR010955

Ovary

SRR010956

Ovary

SRR010957

Ovary

SRR010958

Ovary

SRR010959

Ovary

SRR010960

Ovary

SRR014268

Embryo

SRR014269

Embryo

SRR014270

Embryo

SRR014271

Embryo

SRR014272

Embryo

SRR014273

Ovary

SRR014274

Ovary

SRR014275

Ovary

SRR014276

Ovary

SRR014277

Ovary

SRR014278

Ovary

SRR014279

Ovary

SRR014280

Ovary

SRR014281

Ovary

SRR014282

Ovary

SRR023197

S2

SRR023399

S2

SRR023400

S2

SRR023402

S2

SRR023407

S2

SRR029028

S2

SRR029029

S2

SRR029030

S2

SRR029031

S2

SRR029032

S2

SRR029033

S2

SRR029608

Head

SRR029633

Head

SRR030145

gb3

SRR031692

Head

SRR031693

Head

SRR031694

Head

SRR031696

Head

SRR031697

Head

SRR031698

Head

SRR031699

Head

SRR031700

Head

SRR031701

Head

SRR031702

Head

SRR031703

Head

SRR031704

Head

SRR032092

S2

SRR032093

S2

SRR032094

S2

SRR032095

S2-NP

SRR032096

S2-NP

SRR032152

Head

SRR060643

Testis

SRR060644

Ovary

SRR060645

Testis

SRR060646

Ovary

SRR060647

Ovary

SRR060648

Ovary

SRR060649

Ovary

SRR060650

Testis

SRR060651

Ovary

SRR060652

Testis

SRR060653

Ovary

SRR065151

Ovary

SRR065152

Ovary

SRR065153

Ovary

SRR065154

Ovary

SRR065155

Ovary

SRR065800

Ovary

SRR065801

Ovary

SRR065802

Ovary

SRR065803

Ovary

SRR065804

Ovary

SRR065805

Ovary

SRR065806

Ovary

SRR065807

Ovary

SRR097865

S2-NP

SRR097866

S2-NP

SRR097867

S2-NP

SRR298536

Ovary

SRR298537

Ovary

SRR298711

Ovary

SRR298712

Ovary

SRR317110

Ovary

SRR317111

Ovary

SRR317112

Ovary

SRR317113

Ovary

SRR317114

Ovary

SRR317115

Ovary

SRR317116

Ovary

SRR317117

Ovary

SRR341115

S2

SRR341116

S2

SRR341117

S2

SRR341118

S2

SRR351332

Mixed-body

SRR351333

Mixed-body

T004

OSC

T005

CME-L1

V001

Embryo

V002

Embryo

V003

S2

V006

Female-body

V007

Head

V008

S2

V009

CME-L1

V010

ML-DmD20-C5

V011

Sg4

V012

Male-body

V013

Head

V014

DTT

V015

DreRFHV

V018

Kc167

V019

GM2

V020

S2-R+

V021

ML-DmD21

V022

ML-DmD32

V023

Head

V024

Kc167

V025

S2-R+

V026

1182-2H

V027

ML-DmD21

V028

CME-W1-Cl.8+

V029

ML-DmD9

V030

ML-DmD8

V031

GM2

V032

S1

V033

CME-W1-Cl.8+

V034

ML-DmD16-C3

V035

ML-DmD32

V036

ML-DmD20-C5

V037

S2

V038

S2

V063

Ovary

V0632

Ovary

V064

Ovary

V0642

Ovary

V065

Ovary

V0652

Ovary

V066

Ovary

V0662

Ovary

V067

S2-NP

V073

mbn2

V074

S3

V075

ML-DmBG1-C1

V076

ML-DmBG3-C2

V077

Head

V078

Head

V079

Head

V080

Head

V081

Embryo

V082

Embryo

V083

Male-body

V084

Female-body

V085

CME-W2

V086

Female-body

V088

Ovary

V0882

Ovary

V089

Ovary

V0892

Ovary

V090

Male-body

V091

fGS/OSS

V092

Male-body

V093

Male-body

V094

S2-R+

V095

S2-R+

V096

Ovary

V097

Ovary

V098

Ovary

V125

ML-DmD9

V126

CME-L1

V127

G2

V128

S3

V129

ML-DmBG1-C1

V130

ML-DmBG3-C2

V131

ML-DmD16-C3

V132

ML-DmD32

V133

Sg4

V134

ML-DmD8

V135

CME-W2

V136

Male-body

V137

Head

V138

Male-body

V139

Female-body

V140

Female-body

V141

Female-body

V142

Female-body

V144

OSC

V145

S2

V146

S1

V147

1182-2H

V148

mbn2

GSM1528798

follicle cells

No Reads

droEre2

ATAA---ACTAA-TTGT-ACAAATTGTGATATTTT--ATCAAATC-----TGCCATAACATCCAAATACTTAACCGATGATCTAAAAACGGT----GTTTTCT----GTTATTTTACTATATAACTTATTTATGAAGAAGCTTTAGGATTTAATTTTTCCGACAATGCGATCTAGGCGTTTCTATCGCTGAGGTAGTATTGTTTGAAAGATTAAGTTAAAGCGT----------AATCATCAAAATTTTAAAATGTGAATAAGTACATAAGTGTG-CCAAAAATAT	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGA............................................................................	22	1	5023.00	5023	22	0	19	5	4474	503	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAG.............................................................................	21	1	1087.00	1087	8	0	4	1	958	116	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGAA...........................................................................	23	1	725.00	725	5	0	1	0	654	65	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGAT...........................................................................	23	1	392.00	392	5	0	2	0	344	38	3
...........................................................................................................................................................TTTCCGACAATGCGATCTAGG..............................................................................................................	21	1	369.00	369	11	0	8	1	297	52	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAA..............................................................................	20	1	203.00	203	2	0	3	1	171	26	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGAAA..........................................................................	24	1	145.00	145	1	0	1	0	127	16	0
.............................................................................................................................................................................................GAGGTAGTATTGTTTGAAAGA............................................................................	21	1	133.00	133	0	0	0	0	115	18	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAA.............................................................................	21	1	55.00	55	0	0	0	1	47	7	0
...........................................................................................................................................................TTTCCGACAATGCGATCTAGGC.............................................................................................................	22	1	51.00	51	1	0	3	2	37	8	0
...........................................................................................................................................................TTTCCGACAATGCGATCTAG...............................................................................................................	20	1	40.00	40	4	0	1	0	33	2	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGT............................................................................	22	1	39.00	39	0	0	0	1	33	5	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAA...............................................................................	19	1	36.00	36	0	0	0	0	30	6	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGAC...........................................................................	23	1	22.00	22	0	0	0	0	19	3	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGATA..........................................................................	24	1	17.00	17	1	0	0	0	13	3	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGACA..........................................................................	24	1	12.00	12	0	0	0	0	10	2	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGC............................................................................	22	1	11.00	11	0	0	0	0	11	0	0
.............................................................................................................................................................................................GAGGTAGTATTGTTTGAAAGAA...........................................................................	22	1	11.00	11	0	0	1	0	10	0	0
..........................................................................................................................................................TTTTCCGACAATGCGATCTAGG..............................................................................................................	22	1	11.00	11	2	0	0	0	7	2	0
.............................................................................................................................................................................................GAGGTAGTATTGTTTGAAAG.............................................................................	20	1	10.00	10	1	0	0	0	8	1	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGATT..........................................................................	24	1	9.00	9	0	0	0	0	9	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGAG...........................................................................	23	1	8.00	8	0	0	0	0	8	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAGA.............................................................................	21	1	7.00	7	0	0	1	0	6	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGATAT.........................................................................	25	1	5.00	5	0	0	0	0	4	1	0
...........................................................................................................................................................TTTCCGACAATGCGATCTAGGCGT...........................................................................................................	24	1	5.00	5	0	0	0	0	5	0	0
...........................................................................................................................................................TTTCCGACAATGCGATCTAGGA.............................................................................................................	22	1	5.00	5	0	0	1	0	4	0	0
...........................................................................................................................................................TTTCCGACAATGCGATCTAGGT.............................................................................................................	22	1	5.00	5	0	0	0	0	4	1	0
.............................................................................................................................................................................................GAGGTAGTATTGTTTGAAAGAAA..........................................................................	23	1	4.00	4	0	0	0	0	4	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGCA...........................................................................	23	1	4.00	4	0	0	0	0	3	1	0
.............................................................................................................................................................................................GAGGTAGTATTGTTTGAAAGAT...........................................................................	22	1	4.00	4	1	0	0	0	2	1	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGTA...........................................................................	23	1	3.00	3	0	0	0	0	3	0	0
...........................................................................................................................................................TTTCCGACAATGCGATCTAGGCA............................................................................................................	23	1	3.00	3	0	0	0	0	1	2	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGTAA..........................................................................	24	1	3.00	3	0	0	0	0	3	0	0
...........................................................................................................................................................TTTCCGACAATGCGATCTAGGCT............................................................................................................	23	1	2.00	2	0	0	0	0	2	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGA................................................................................	18	1	2.00	2	0	0	0	0	2	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAT..............................................................................	20	1	2.00	2	0	0	0	0	2	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGG............................................................................	22	1	2.00	2	0	0	0	0	2	0	0
.............................................................................................................................................................................................GAGGTAGTATTGTTTGAAA..............................................................................	19	1	2.00	2	0	0	0	0	1	1	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAT.............................................................................	21	1	2.00	2	0	0	0	0	1	1	0
...........................................................................................................................................................................................CTGAGGTAGTATTGTTTGAAAGA............................................................................	23	1	2.00	2	0	0	0	0	1	1	0
............................................................................................................................................................TTCCGACAATGCGATCTAGG..............................................................................................................	20	1	2.00	2	0	0	0	0	0	2	0
...........................................................................................................................................................TTTCCGACAATGCGATCTAGGCG............................................................................................................	23	1	2.00	2	0	0	0	0	1	1	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGAAGT.........................................................................	25	1	1.00	1	0	0	0	0	1	0	0
.................................................................................................................................................................................................TAGTATTGTTTGAAAGAA...........................................................................	18	2	1.00	2	0	0	0	0	2	0	0
...........................................................................................................................................................TTTCCGACAATGCGATCTAGGCAAA..........................................................................................................	25	1	1.00	1	0	0	0	0	1	0	0
.............................................................................................................................................................................................GAGGTAGTATTGTTTGAAAT.............................................................................	20	1	1.00	1	1	0	0	0	0	0	0
...........................................................................................................................................................................................CTGAGGTAGTATTGTTTGAAAGAT...........................................................................	24	1	1.00	1	0	0	0	0	1	0	0
...........................................................................................................................................................TTTCCGACAATGCGATCTAGGCGTT..........................................................................................................	25	1	1.00	1	0	0	0	0	1	0	0
...........................................................................................................................................................TTTCCGACAATGCGATCTAGGAT............................................................................................................	23	1	1.00	1	0	0	0	0	1	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAC.............................................................................	21	1	1.00	1	0	0	0	0	1	0	0
.............................................................................................................................................................................................GAGGTAGTATTGTTTGAAAGT............................................................................	21	1	1.00	1	0	0	0	0	1	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAAT............................................................................	22	1	1.00	1	0	0	0	0	1	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGAAAT.........................................................................	25	1	1.00	1	0	0	0	0	1	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGAGA..........................................................................	24	1	1.00	1	0	0	0	0	0	1	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAT...............................................................................	19	1	1.00	1	0	0	0	0	1	0	0
...........................................................................................................................................................TTTCCGACAATGCGATCTAT...............................................................................................................	20	1	1.00	1	0	0	0	0	1	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGCC...........................................................................	23	1	1.00	1	0	0	0	0	1	0	0
...........................................................................................................................................................................................CTGAGGTAGTATTGTTTGAAAGAA...........................................................................	24	1	1.00	1	0	0	0	0	0	1	0
................................................................................................................................................................................................GTAGTATTGTTTGAAAGA............................................................................	18	1	1.00	1	0	0	0	0	1	0	0

droYak3

AAAA---ACTAA-ATGTTAAAAATTATTATATTTT--ATCAAATG-----TACCATAACCTCAAAATACTAAACTGATGAGCTAAAAAGC-TA----TTTTCTCTTTGTTATTCTGCAATG-GATTTATTT--------GCTTTAGGATTTATTTTTTCGGACAATTCAATCTGGGCGTTGCTTTCGCTGAGGTAGTATTGTTTGGAAGACTAAGTTAACGAGC----------ATTCATCTCATTTTTGAAATTT---TGTGTTCATGAGTGTG-TTAAAAATAT	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
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAG.............................................................................	21	1	348.00	348	16	14	12	2	0	2	300	0	0	2	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAGA............................................................................	22	1	333.00	333	23	13	25	8	0	0	263	0	0	1	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGGGC.............................................................................................................	22	1	81.00	81	29	8	19	8	1	0	16	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAGAT...........................................................................	23	1	53.00	53	8	2	1	0	0	0	42	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAA..............................................................................	20	1	51.00	51	1	0	1	0	0	0	49	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGGGCG............................................................................................................	23	1	43.00	43	16	9	9	1	0	0	8	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGGG..............................................................................................................	21	1	32.00	32	15	6	2	1	0	0	8	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAA.............................................................................	21	1	32.00	32	1	1	0	0	0	0	30	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGA...............................................................................	19	1	29.00	29	2	0	1	0	0	0	26	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAGAA...........................................................................	23	1	24.00	24	0	0	0	0	0	0	24	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGGGT.............................................................................................................	22	1	23.00	23	14	0	1	0	0	0	8	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGGGCGT...........................................................................................................	24	1	18.00	18	12	1	1	0	0	0	4	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAT.............................................................................	21	1	17.00	17	2	0	0	0	0	0	15	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGGGCT............................................................................................................	23	1	15.00	15	13	0	0	0	0	0	2	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAT..............................................................................	20	1	12.00	12	3	0	0	0	0	0	9	0	0	0	0
...........................................................................................................................................................................................CTGAGGTAGTATTGTTTGGAAGA............................................................................	23	1	10.00	10	0	0	1	0	0	0	9	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAGT............................................................................	22	1	10.00	10	0	0	1	0	0	2	7	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGGGTT............................................................................................................	23	1	9.00	9	7	0	0	0	0	0	2	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAGAAA..........................................................................	24	1	8.00	8	0	0	0	0	0	0	6	0	0	2	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGT...............................................................................	19	1	7.00	7	0	0	0	0	0	0	7	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGGGA.............................................................................................................	22	1	5.00	5	0	0	0	0	0	0	5	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAGTA...........................................................................	23	1	5.00	5	2	0	0	0	0	0	3	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGG...............................................................................................................	20	1	4.00	4	2	1	0	0	0	0	1	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATC..................................................................................................................	17	1	4.00	4	0	0	0	0	0	0	0	1	0	3	0
...........................................................................................................................................................................................CTGAGGTAGTATTGTTTGGA...............................................................................	20	1	4.00	4	0	0	0	0	0	0	4	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGGGCGG...........................................................................................................	24	1	3.00	3	3	0	0	0	0	0	0	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGGGCGC...........................................................................................................	24	1	3.00	3	1	0	2	0	0	0	0	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGGGCGTTT.........................................................................................................	26	1	3.00	3	0	1	0	0	0	0	1	0	0	1	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGGGCC............................................................................................................	23	1	3.00	3	3	0	0	0	0	0	0	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAGTT...........................................................................	23	1	3.00	3	0	0	0	0	0	0	3	0	0	0	0
...........................................................................................................................................................................................CTGAGGTAGTATTGTTTGGAA..............................................................................	21	1	3.00	3	0	0	0	0	0	0	3	0	0	0	0
...........................................................................................................................................................................................CTGAGGTAGTATTGTTTGGAAG.............................................................................	22	1	3.00	3	0	1	1	0	0	0	1	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGATT.............................................................................	21	1	2.00	2	0	0	0	0	0	0	2	0	0	0	0
.............................................................................................................................................................................................GAGGTAGTATTGTTTGGAAGA............................................................................	21	1	2.00	2	0	2	0	0	0	0	0	0	0	0	0
...........................................................................................................................................................................................CTGAGGTAGTATTGTTTGGAAA.............................................................................	22	1	2.00	2	0	0	0	0	0	0	2	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGGGCGTT..........................................................................................................	25	1	2.00	2	2	0	0	0	0	0	0	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGTT..............................................................................	20	1	2.00	2	0	0	0	0	0	0	2	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAGG............................................................................	22	1	2.00	2	2	0	0	0	0	0	0	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGGGTC............................................................................................................	23	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAGCA...........................................................................	23	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................TTCGGACAATTCAATCTGGGCG............................................................................................................	22	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATCT.................................................................................................................	18	1	1.00	1	0	0	0	0	0	0	0	0	0	1	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAATT...........................................................................	23	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
.............................................................................................................................................................TCGGACAATTCAATCTGGGC.............................................................................................................	20	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAAT............................................................................	22	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGATA.............................................................................	21	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAGATAT.........................................................................	25	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAGAC...........................................................................	23	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................TTCGGACAATTCAATCTGGGCGT...........................................................................................................	23	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGGGCGA...........................................................................................................	24	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0
.............................................................................................................................................................................................GAGGTAGTATTGTTTGGAAG.............................................................................	20	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0
...........................................................................................................................................................................................CTGAGGTAGTATTGTTTGGAAGAA...........................................................................	24	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGA................................................................................	18	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGT................................................................................	18	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAGAAG..........................................................................	24	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAGC............................................................................	22	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAATT............................................................................	22	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGC................................................................................	18	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................TTCGGACAATTCAATCTGGGC.............................................................................................................	21	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAATA...........................................................................	23	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGG................................................................................	18	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGATAT............................................................................	22	2	0.50	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGTTT.............................................................................	21	5	0.40	2	0	0	0	0	0	0	2	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGTT...............................................................................	19	3	0.33	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGTTA.............................................................................	21	4	0.25	1	0	0	0	0	0	0	1	0	0	0	0

droEug1

AA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATGTG-TT-ACAAATT	Size	Hit Count	Total Norm	Total
No Reads

droEle1

AATA---AAAAAAA-TT-TAAGAACATGAATTTTGCAAGCAAATTATGTGTGC-------CAATAA-----------CGGTTAAAAAAAT-------------------------------------------GAAGCATTTCAAGAATTTAATTTTTTT-ATAA---------------------------------------------------------CT----------TGTGCTATAAAG----------AAACACGTAGATAACAATTAAAGAAAAAAT	Size	Hit Count	Total Norm	Total
No Reads

Species	Coordinate	ID	Type	Alignment
droSec2	scaffold_1:14026248-14026405 -	dse_339	candidate-rescued	TTGAAAAA-AAAAA-CA-CAAGAATGTGATATTTC--ATCAAATT-----TGCAATAACCTAAGAATAGTAAAACGAAGGACAAAAAAAA-AAATTGTATTCTTTTTGCTATTCTA-----------------------------------------------------------------------------------------------TAGGCTAACGAGC----------ATTCCTTAAAAT----------ACATATGTACATAAGTGTT-TA-AAAAAAT
droSim2	2r:17041512-17041659 -	dsi_32435	candidate-rescued	TTGA---AAAAAAA-CA-CAAGAATGTGATATTTC--ATCAAATT-----TGCCATAACCTAAGAATAGTAAAACGAAGGGCAAAAAAAA-AAATT-TATTCTTTTTGCTATTCTA-----------------------------------------------------------------------------------------------TAGGCTAATGAGC----------ATTCCTTAAAAT------------------ACATATGTGTT-TAAAAAAAAT
dm3	chr2R:16472042-16472207 -			TTGAAAAA-AAAAA-CA-CAAAAATGTGATATTTC--ATCAC----------TCATCAACTCAAAATAGTAAATCGAAGGGCAAAAAAAT---ATGGTATTCTGTTTGCTATTATA-----------------------------------------------------------------------------------------------AAAGTTCACGAGCTAAGCTAACGATTCATTAAAAT------ATGTACATACATATTTAAGTGTT-AAAAAAAAAT
droEre2	scaffold_4845:10618664-10618918 -	der_25	confident	ATAA---ACTAA-TTGT-ACAAATTGTGATATTTT--ATCAAATC-----TGCCATAACATCCAAATACTTAACCGATGATCTAAAAACGGT----GTTTTCT----GTTATTTTACTATATAACTTATTTATGAAGAAGCTTTAGGATTTAATTTTTCCGACAATGCGATCTAGGCGTTTCTATCGCTGAGGTAGTATTGTTTGAAAGATTAAGTTAAAGCGT----------AATCATCAAAATTTTAAAATGTGAATAAGTACATAAGTGTG-CCAAAAATAT
droYak3	2R:12724006-12724252 +	dya_34	confident	AAAA---ACTAA-ATGTTAAAAATTATTATATTTT--ATCAAATG-----TACCATAACCTCAAAATACTAAACTGATGAGCTAAAAAGC-TA----TTTTCTCTTTGTTATTCTGCAATG-GATTTATTT--------GCTTTAGGATTTATTTTTTCGGACAATTCAATCTGGGCGTTGCTTTCGCTGAGGTAGTATTGTTTGGAAGACTAAGTTAACGAGC----------ATTCATCTCATTTTTGAAATTT---TGTGTTCATGAGTGTG-TTAAAAATAT
droEug1	scf7180000409474:1489651-1489666 +			AA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATGTG-TT-ACAAATT
droEle1	scf7180000491201:736783-736924 -			AATA---AAAAAAA-TT-TAAGAACATGAATTTTGCAAGCAAATTATGTGTGC-------CAATAA-----------CGGTTAAAAAAAT-------------------------------------------GAAGCATTTCAAGAATTTAATTTTTTT-ATAA---------------------------------------------------------CT----------TGTGCTATAAAG----------AAACACGTAGATAACAATTAAAGAAAAAAT

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droSec2

TTGAAAAA-AAAAA-CA-CAAGAATGTGATATTTC--ATCAAATT-----TGCAATAACCTAAGAATAGTAAAACGAAGGACAAAAAAAA-AAATTGTATTCTTTTTGCTATTCTA-----------------------------------------------------------------------------------------------TAGGCTAACGAGC----------ATTCCTTAAAAT----------ACATATGTACATAAGTGTT-TA-AAAAAAT	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
............................................................TAAGAATAGTAAAACGAAGGACA...........................................................................................................................................................................................................	23	1	11.00	11	0	7	4	0
............................................................TAAGAATAGTAAAACGAAGGAC............................................................................................................................................................................................................	22	1	2.00	2	0	0	2	0
.................................................................................................TATTCTTTTTGCTATTCTA-----------------------------------------------------------------------------------------------TA.........................................................................	21	1	1.00	1	1	0	0	0
............................................................TAAGAATAGTAAAACGAAGGACAT..........................................................................................................................................................................................................	24	1	1.00	1	1	0	0	0

droSim2

TTGA---AAAAAAA-CA-CAAGAATGTGATATTTC--ATCAAATT-----TGCCATAACCTAAGAATAGTAAAACGAAGGGCAAAAAAAA-AAATT-TATTCTTTTTGCTATTCTA-----------------------------------------------------------------------------------------------TAGGCTAATGAGC----------ATTCCTTAAAAT------------------ACATATGTGTT-TAAAAAAAAT	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
............................................................TAAGAATAGTAAAACGAAGGGCA...........................................................................................................................................................................................................	23	1	32.00	32	0	0	0	0	0	0	0	2	1	0	0	0	0	29	0	0	0
............................................................TAAGAATAGTAAAACGAAGGGC............................................................................................................................................................................................................	22	1	5.00	5	0	0	2	0	0	0	0	1	0	0	0	1	0	1	0	0	0
............................................................TAAGAATAGTAAAACGAAGGGCAA..........................................................................................................................................................................................................	24	1	2.00	2	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0
............................................................TAAGAATAGTAAAACGAAGGGCAC..........................................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
............................................................TAAGAATAGTAAAACGAAGGGCATT.........................................................................................................................................................................................................	25	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
............................................................TAAGAATAGTAAAACGAAGGGCAT..........................................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
.................................................................................................TATTCTTTTTGCTATTCTA-----------------------------------------------------------------------------------------------TAGG.......................................................................	23	1	1.00	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
............................................................................AAGGGCAAAAAAAA-A..................................................................................................................................................................................................	15	17	0.06	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0

dm3

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

GSM239041

Head

GSM239050

Head

GSM239051

S2

GSM239052

S2

GSM246084

Head

GSM266765

S2

GSM280082

Ovary

GSM280083

Ovary

GSM280084

Ovary

GSM280085

Testis

GSM280086

Ovary

GSM280087

S2-NP

GSM280088

S2-NP

GSM312995

Head

GSM313160

Head

GSM313161

Head

GSM313162

Head

GSM313163

Head

GSM313164

Head

GSM313165

Head

GSM343287

Embryo

GSM379050

Ovary

GSM379051

Ovary

GSM379052

Ovary

GSM379053

Ovary

GSM379054

Ovary

GSM379055

Ovary

GSM379056

Ovary

GSM379057

Ovary

GSM379058

Ovary

GSM379059

Ovary

GSM379060

Ovary

GSM379061

Ovary

GSM379062

Ovary

GSM379063

Ovary

GSM379064

Ovary

GSM379065

Ovary

GSM379066

Ovary

GSM379067

Ovary

GSM424739

S2

GSM424740

S2

GSM424741

S2

GSM467729

Female-body

GSM467730

Female-body

GSM467731

Female-body

M002

CS

M003

Male-body

M004

Male-body

M005

ML-DmD32

M006

ML-DmD32

M029

OSC

M030

OSC

M031

OSC

M032

S2-R+

M033

S2-R+

M034

S2-R+

M035

S2-R+

M036

S2-R+

M037

S2-R+

M038

S2-R+

M039

S2-R+

M048

S2-R+

OSS2

OSS

OSS6

OSS

OSS7

OSS

OSS8

OSS

S1

Head

S10

Embryo

S11

Embryo

S12

Embryo

S13

Embryo

S14

Embryo

S15

S2-GMR

S16

Kc

S17

Larvae

S18

Larvae

S19

Pupae

S2

Head

S20

Pupae

S21

Disc

S22

Head

S23

Female-body

S24

Male-body

S25

Larvae

S26

Larvae

S27

Pupae

S28

Pupae

S29

Head

S3

Male-body

S30

S2-GMR

S31

S2

S32

S2

S33

Kc

S34

Kc

S35

Kc

S4

Female-body

S5

Disc

S6

Embryo

S7

Embryo

S8

S2

S9

Embryo

SRR001337

Head

SRR001338

Head

SRR001339

Head

SRR001340

Head

SRR001341

Head

SRR001342

Head

SRR001343

Head

SRR001344

Head

SRR001345

Head

SRR001346

Head

SRR001347

Head

SRR001348

Head

SRR001349

Head

SRR001664

Head

SRR010951

Ovary

SRR010952

Ovary

SRR010953

Ovary

SRR010954

Ovary

SRR010955

Ovary

SRR010956

Ovary

SRR010957

Ovary

SRR010958

Ovary

SRR010959

Ovary

SRR010960

Ovary

SRR014268

Embryo

SRR014269

Embryo

SRR014270

Embryo

SRR014271

Embryo

SRR014272

Embryo

SRR014273

Ovary

SRR014274

Ovary

SRR014275

Ovary

SRR014276

Ovary

SRR014277

Ovary

SRR014278

Ovary

SRR014279

Ovary

SRR014280

Ovary

SRR014281

Ovary

SRR014282

Ovary

SRR023197

S2

SRR023399

S2

SRR023400

S2

SRR023402

S2

SRR023407

S2

SRR029028

S2

SRR029029

S2

SRR029030

S2

SRR029031

S2

SRR029032

S2

SRR029033

S2

SRR029608

Head

SRR029633

Head

SRR030145

gb3

SRR031692

Head

SRR031693

Head

SRR031694

Head

SRR031696

Head

SRR031697

Head

SRR031698

Head

SRR031699

Head

SRR031700

Head

SRR031701

Head

SRR031702

Head

SRR031703

Head

SRR031704

Head

SRR032092

S2

SRR032093

S2

SRR032094

S2

SRR032095

S2-NP

SRR032096

S2-NP

SRR032152

Head

SRR060643

Testis

SRR060644

Ovary

SRR060645

Testis

SRR060646

Ovary

SRR060647

Ovary

SRR060648

Ovary

SRR060649

Ovary

SRR060650

Testis

SRR060651

Ovary

SRR060652

Testis

SRR060653

Ovary

SRR065151

Ovary

SRR065152

Ovary

SRR065153

Ovary

SRR065154

Ovary

SRR065155

Ovary

SRR065800

Ovary

SRR065801

Ovary

SRR065802

Ovary

SRR065803

Ovary

SRR065804

Ovary

SRR065805

Ovary

SRR065806

Ovary

SRR065807

Ovary

SRR097865

S2-NP

SRR097866

S2-NP

SRR097867

S2-NP

SRR298536

Ovary

SRR298537

Ovary

SRR298711

Ovary

SRR298712

Ovary

SRR317110

Ovary

SRR317111

Ovary

SRR317112

Ovary

SRR317113

Ovary

SRR317114

Ovary

SRR317115

Ovary

SRR317116

Ovary

SRR317117

Ovary

SRR341115

S2

SRR341116

S2

SRR341117

S2

SRR341118

S2

SRR351332

Mixed-body

SRR351333

Mixed-body

T004

OSC

T005

CME-L1

V001

Embryo

V002

Embryo

V003

S2

V006

Female-body

V007

Head

V008

S2

V009

CME-L1

V010

ML-DmD20-C5

V011

Sg4

V012

Male-body

V013

Head

V014

DTT

V015

DreRFHV

V018

Kc167

V019

GM2

V020

S2-R+

V021

ML-DmD21

V022

ML-DmD32

V023

Head

V024

Kc167

V025

S2-R+

V026

1182-2H

V027

ML-DmD21

V028

CME-W1-Cl.8+

V029

ML-DmD9

V030

ML-DmD8

V031

GM2

V032

S1

V033

CME-W1-Cl.8+

V034

ML-DmD16-C3

V035

ML-DmD32

V036

ML-DmD20-C5

V037

S2

V038

S2

V063

Ovary

V0632

Ovary

V064

Ovary

V0642

Ovary

V065

Ovary

V0652

Ovary

V066

Ovary

V0662

Ovary

V067

S2-NP

V073

mbn2

V074

S3

V075

ML-DmBG1-C1

V076

ML-DmBG3-C2

V077

Head

V078

Head

V079

Head

V080

Head

V081

Embryo

V082

Embryo

V083

Male-body

V084

Female-body

V085

CME-W2

V086

Female-body

V088

Ovary

V0882

Ovary

V089

Ovary

V0892

Ovary

V090

Male-body

V091

fGS/OSS

V092

Male-body

V093

Male-body

V094

S2-R+

V095

S2-R+

V096

Ovary

V097

Ovary

V098

Ovary

V125

ML-DmD9

V126

CME-L1

V127

G2

V128

S3

V129

ML-DmBG1-C1

V130

ML-DmBG3-C2

V131

ML-DmD16-C3

V132

ML-DmD32

V133

Sg4

V134

ML-DmD8

V135

CME-W2

V136

Male-body

V137

Head

V138

Male-body

V139

Female-body

V140

Female-body

V141

Female-body

V142

Female-body

V144

OSC

V145

S2

V146

S1

V147

1182-2H

V148

mbn2

GSM1528798

follicle cells

No Reads

droEre2

ATAA---ACTAA-TTGT-ACAAATTGTGATATTTT--ATCAAATC-----TGCCATAACATCCAAATACTTAACCGATGATCTAAAAACGGT----GTTTTCT----GTTATTTTACTATATAACTTATTTATGAAGAAGCTTTAGGATTTAATTTTTCCGACAATGCGATCTAGGCGTTTCTATCGCTGAGGTAGTATTGTTTGAAAGATTAAGTTAAAGCGT----------AATCATCAAAATTTTAAAATGTGAATAAGTACATAAGTGTG-CCAAAAATAT	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGA............................................................................	22	1	5023.00	5023	22	0	19	5	4474	503	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAG.............................................................................	21	1	1087.00	1087	8	0	4	1	958	116	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGAA...........................................................................	23	1	725.00	725	5	0	1	0	654	65	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGAT...........................................................................	23	1	392.00	392	5	0	2	0	344	38	3
...........................................................................................................................................................TTTCCGACAATGCGATCTAGG..............................................................................................................	21	1	369.00	369	11	0	8	1	297	52	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAA..............................................................................	20	1	203.00	203	2	0	3	1	171	26	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGAAA..........................................................................	24	1	145.00	145	1	0	1	0	127	16	0
.............................................................................................................................................................................................GAGGTAGTATTGTTTGAAAGA............................................................................	21	1	133.00	133	0	0	0	0	115	18	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAA.............................................................................	21	1	55.00	55	0	0	0	1	47	7	0
...........................................................................................................................................................TTTCCGACAATGCGATCTAGGC.............................................................................................................	22	1	51.00	51	1	0	3	2	37	8	0
...........................................................................................................................................................TTTCCGACAATGCGATCTAG...............................................................................................................	20	1	40.00	40	4	0	1	0	33	2	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGT............................................................................	22	1	39.00	39	0	0	0	1	33	5	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAA...............................................................................	19	1	36.00	36	0	0	0	0	30	6	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGAC...........................................................................	23	1	22.00	22	0	0	0	0	19	3	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGATA..........................................................................	24	1	17.00	17	1	0	0	0	13	3	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGACA..........................................................................	24	1	12.00	12	0	0	0	0	10	2	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGC............................................................................	22	1	11.00	11	0	0	0	0	11	0	0
.............................................................................................................................................................................................GAGGTAGTATTGTTTGAAAGAA...........................................................................	22	1	11.00	11	0	0	1	0	10	0	0
..........................................................................................................................................................TTTTCCGACAATGCGATCTAGG..............................................................................................................	22	1	11.00	11	2	0	0	0	7	2	0
.............................................................................................................................................................................................GAGGTAGTATTGTTTGAAAG.............................................................................	20	1	10.00	10	1	0	0	0	8	1	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGATT..........................................................................	24	1	9.00	9	0	0	0	0	9	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGAG...........................................................................	23	1	8.00	8	0	0	0	0	8	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAGA.............................................................................	21	1	7.00	7	0	0	1	0	6	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGATAT.........................................................................	25	1	5.00	5	0	0	0	0	4	1	0
...........................................................................................................................................................TTTCCGACAATGCGATCTAGGCGT...........................................................................................................	24	1	5.00	5	0	0	0	0	5	0	0
...........................................................................................................................................................TTTCCGACAATGCGATCTAGGA.............................................................................................................	22	1	5.00	5	0	0	1	0	4	0	0
...........................................................................................................................................................TTTCCGACAATGCGATCTAGGT.............................................................................................................	22	1	5.00	5	0	0	0	0	4	1	0
.............................................................................................................................................................................................GAGGTAGTATTGTTTGAAAGAAA..........................................................................	23	1	4.00	4	0	0	0	0	4	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGCA...........................................................................	23	1	4.00	4	0	0	0	0	3	1	0
.............................................................................................................................................................................................GAGGTAGTATTGTTTGAAAGAT...........................................................................	22	1	4.00	4	1	0	0	0	2	1	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGTA...........................................................................	23	1	3.00	3	0	0	0	0	3	0	0
...........................................................................................................................................................TTTCCGACAATGCGATCTAGGCA............................................................................................................	23	1	3.00	3	0	0	0	0	1	2	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGTAA..........................................................................	24	1	3.00	3	0	0	0	0	3	0	0
...........................................................................................................................................................TTTCCGACAATGCGATCTAGGCT............................................................................................................	23	1	2.00	2	0	0	0	0	2	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGA................................................................................	18	1	2.00	2	0	0	0	0	2	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAT..............................................................................	20	1	2.00	2	0	0	0	0	2	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGG............................................................................	22	1	2.00	2	0	0	0	0	2	0	0
.............................................................................................................................................................................................GAGGTAGTATTGTTTGAAA..............................................................................	19	1	2.00	2	0	0	0	0	1	1	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAT.............................................................................	21	1	2.00	2	0	0	0	0	1	1	0
...........................................................................................................................................................................................CTGAGGTAGTATTGTTTGAAAGA............................................................................	23	1	2.00	2	0	0	0	0	1	1	0
............................................................................................................................................................TTCCGACAATGCGATCTAGG..............................................................................................................	20	1	2.00	2	0	0	0	0	0	2	0
...........................................................................................................................................................TTTCCGACAATGCGATCTAGGCG............................................................................................................	23	1	2.00	2	0	0	0	0	1	1	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGAAGT.........................................................................	25	1	1.00	1	0	0	0	0	1	0	0
.................................................................................................................................................................................................TAGTATTGTTTGAAAGAA...........................................................................	18	2	1.00	2	0	0	0	0	2	0	0
...........................................................................................................................................................TTTCCGACAATGCGATCTAGGCAAA..........................................................................................................	25	1	1.00	1	0	0	0	0	1	0	0
.............................................................................................................................................................................................GAGGTAGTATTGTTTGAAAT.............................................................................	20	1	1.00	1	1	0	0	0	0	0	0
...........................................................................................................................................................................................CTGAGGTAGTATTGTTTGAAAGAT...........................................................................	24	1	1.00	1	0	0	0	0	1	0	0
...........................................................................................................................................................TTTCCGACAATGCGATCTAGGCGTT..........................................................................................................	25	1	1.00	1	0	0	0	0	1	0	0
...........................................................................................................................................................TTTCCGACAATGCGATCTAGGAT............................................................................................................	23	1	1.00	1	0	0	0	0	1	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAC.............................................................................	21	1	1.00	1	0	0	0	0	1	0	0
.............................................................................................................................................................................................GAGGTAGTATTGTTTGAAAGT............................................................................	21	1	1.00	1	0	0	0	0	1	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAAT............................................................................	22	1	1.00	1	0	0	0	0	1	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGAAAT.........................................................................	25	1	1.00	1	0	0	0	0	1	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGAGA..........................................................................	24	1	1.00	1	0	0	0	0	0	1	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAT...............................................................................	19	1	1.00	1	0	0	0	0	1	0	0
...........................................................................................................................................................TTTCCGACAATGCGATCTAT...............................................................................................................	20	1	1.00	1	0	0	0	0	1	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGAAAGCC...........................................................................	23	1	1.00	1	0	0	0	0	1	0	0
...........................................................................................................................................................................................CTGAGGTAGTATTGTTTGAAAGAA...........................................................................	24	1	1.00	1	0	0	0	0	0	1	0
................................................................................................................................................................................................GTAGTATTGTTTGAAAGA............................................................................	18	1	1.00	1	0	0	0	0	1	0	0

droYak3

AAAA---ACTAA-ATGTTAAAAATTATTATATTTT--ATCAAATG-----TACCATAACCTCAAAATACTAAACTGATGAGCTAAAAAGC-TA----TTTTCTCTTTGTTATTCTGCAATG-GATTTATTT--------GCTTTAGGATTTATTTTTTCGGACAATTCAATCTGGGCGTTGCTTTCGCTGAGGTAGTATTGTTTGGAAGACTAAGTTAACGAGC----------ATTCATCTCATTTTTGAAATTT---TGTGTTCATGAGTGTG-TTAAAAATAT	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
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAG.............................................................................	21	1	348.00	348	16	14	12	2	0	2	300	0	0	2	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAGA............................................................................	22	1	333.00	333	23	13	25	8	0	0	263	0	0	1	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGGGC.............................................................................................................	22	1	81.00	81	29	8	19	8	1	0	16	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAGAT...........................................................................	23	1	53.00	53	8	2	1	0	0	0	42	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAA..............................................................................	20	1	51.00	51	1	0	1	0	0	0	49	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGGGCG............................................................................................................	23	1	43.00	43	16	9	9	1	0	0	8	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGGG..............................................................................................................	21	1	32.00	32	15	6	2	1	0	0	8	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAA.............................................................................	21	1	32.00	32	1	1	0	0	0	0	30	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGA...............................................................................	19	1	29.00	29	2	0	1	0	0	0	26	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAGAA...........................................................................	23	1	24.00	24	0	0	0	0	0	0	24	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGGGT.............................................................................................................	22	1	23.00	23	14	0	1	0	0	0	8	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGGGCGT...........................................................................................................	24	1	18.00	18	12	1	1	0	0	0	4	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAT.............................................................................	21	1	17.00	17	2	0	0	0	0	0	15	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGGGCT............................................................................................................	23	1	15.00	15	13	0	0	0	0	0	2	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAT..............................................................................	20	1	12.00	12	3	0	0	0	0	0	9	0	0	0	0
...........................................................................................................................................................................................CTGAGGTAGTATTGTTTGGAAGA............................................................................	23	1	10.00	10	0	0	1	0	0	0	9	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAGT............................................................................	22	1	10.00	10	0	0	1	0	0	2	7	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGGGTT............................................................................................................	23	1	9.00	9	7	0	0	0	0	0	2	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAGAAA..........................................................................	24	1	8.00	8	0	0	0	0	0	0	6	0	0	2	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGT...............................................................................	19	1	7.00	7	0	0	0	0	0	0	7	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGGGA.............................................................................................................	22	1	5.00	5	0	0	0	0	0	0	5	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAGTA...........................................................................	23	1	5.00	5	2	0	0	0	0	0	3	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGG...............................................................................................................	20	1	4.00	4	2	1	0	0	0	0	1	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATC..................................................................................................................	17	1	4.00	4	0	0	0	0	0	0	0	1	0	3	0
...........................................................................................................................................................................................CTGAGGTAGTATTGTTTGGA...............................................................................	20	1	4.00	4	0	0	0	0	0	0	4	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGGGCGG...........................................................................................................	24	1	3.00	3	3	0	0	0	0	0	0	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGGGCGC...........................................................................................................	24	1	3.00	3	1	0	2	0	0	0	0	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGGGCGTTT.........................................................................................................	26	1	3.00	3	0	1	0	0	0	0	1	0	0	1	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGGGCC............................................................................................................	23	1	3.00	3	3	0	0	0	0	0	0	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAGTT...........................................................................	23	1	3.00	3	0	0	0	0	0	0	3	0	0	0	0
...........................................................................................................................................................................................CTGAGGTAGTATTGTTTGGAA..............................................................................	21	1	3.00	3	0	0	0	0	0	0	3	0	0	0	0
...........................................................................................................................................................................................CTGAGGTAGTATTGTTTGGAAG.............................................................................	22	1	3.00	3	0	1	1	0	0	0	1	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGATT.............................................................................	21	1	2.00	2	0	0	0	0	0	0	2	0	0	0	0
.............................................................................................................................................................................................GAGGTAGTATTGTTTGGAAGA............................................................................	21	1	2.00	2	0	2	0	0	0	0	0	0	0	0	0
...........................................................................................................................................................................................CTGAGGTAGTATTGTTTGGAAA.............................................................................	22	1	2.00	2	0	0	0	0	0	0	2	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGGGCGTT..........................................................................................................	25	1	2.00	2	2	0	0	0	0	0	0	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGTT..............................................................................	20	1	2.00	2	0	0	0	0	0	0	2	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAGG............................................................................	22	1	2.00	2	2	0	0	0	0	0	0	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGGGTC............................................................................................................	23	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAGCA...........................................................................	23	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................TTCGGACAATTCAATCTGGGCG............................................................................................................	22	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATCT.................................................................................................................	18	1	1.00	1	0	0	0	0	0	0	0	0	0	1	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAATT...........................................................................	23	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
.............................................................................................................................................................TCGGACAATTCAATCTGGGC.............................................................................................................	20	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAAT............................................................................	22	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGATA.............................................................................	21	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAGATAT.........................................................................	25	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAGAC...........................................................................	23	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................TTCGGACAATTCAATCTGGGCGT...........................................................................................................	23	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
...........................................................................................................................................................TTTCGGACAATTCAATCTGGGCGA...........................................................................................................	24	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0
.............................................................................................................................................................................................GAGGTAGTATTGTTTGGAAG.............................................................................	20	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0
...........................................................................................................................................................................................CTGAGGTAGTATTGTTTGGAAGAA...........................................................................	24	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGA................................................................................	18	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGT................................................................................	18	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAGAAG..........................................................................	24	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAGC............................................................................	22	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAATT............................................................................	22	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGC................................................................................	18	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................TTCGGACAATTCAATCTGGGC.............................................................................................................	21	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGAAATA...........................................................................	23	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGG................................................................................	18	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGATAT............................................................................	22	2	0.50	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGTTT.............................................................................	21	5	0.40	2	0	0	0	0	0	0	2	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGTT...............................................................................	19	3	0.33	1	0	0	0	0	0	0	1	0	0	0	0
............................................................................................................................................................................................TGAGGTAGTATTGTTTGGTTA.............................................................................	21	4	0.25	1	0	0	0	0	0	0	1	0	0	0	0

droEug1

AA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATGTG-TT-ACAAATT	Size	Hit Count	Total Norm	Total
No Reads

droEle1

AATA---AAAAAAA-TT-TAAGAACATGAATTTTGCAAGCAAATTATGTGTGC-------CAATAA-----------CGGTTAAAAAAAT-------------------------------------------GAAGCATTTCAAGAATTTAATTTTTTT-ATAA---------------------------------------------------------CT----------TGTGCTATAAAG----------AAACACGTAGATAACAATTAAAGAAAAAAT	Size	Hit Count	Total Norm	Total
No Reads

dse_339

scaffold_1:14026298-14026355 -

candidate-rescued

Testes-restricted

intergenic

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

Re-alignment of all predicted orthologs

Re-alignment of all predicted orthologs with sRNA reads

-20.1	-20.0	-19.3