dsi_191

CGGCACAGTGCAAATATAGTTTTTGTTTCTAGTATATATTTATAGTCTTTGTCAACTTAATATTTTTAACATACATTTACCGAATATTTTTAAGTGAACTTAATCTTTCTAGTATATTTTTAATTTATAATATTTGATCATTTTATATATAATGTT *********************************(((((...((.....((..(((((((((((................))))))...)))))..)).....))....)))))......*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	O001 Testis	SRR553486 Ovary	SRR553488 Ovary	SRR553487 Ovary	M053 Female-body	SRR618934 Ovary	SRR553485 Ovary
.................................................TGTCAACTTAATATTTTTAACATAC..................................................................................	25	0	2	21.00	42	42	0	0	0	0	0	0
.................................................TGTCAACTTAATATTTTTAACATACA.................................................................................	26	0	2	1.50	3	2	0	0	0	1	0	0
................................................TTGTCAACTTAATATTTTTAACATAC..................................................................................	26	0	2	1.00	2	2	0	0	0	0	0	0
................TAGTTTTTGTTTCTAGTATATATTTA..................................................................................................................	26	0	5	0.40	2	0	0	1	1	0	0	0
.........................................................TAATATTTTTAACATACATTTACCGAA........................................................................	27	0	3	0.33	1	0	1	0	0	0	0	0
............................................................TATTTTTAACATACATTTACCGAATA......................................................................	26	0	3	0.33	1	0	0	0	1	0	0	0
............................................................TATTTTTAACATACATTTACCGAA........................................................................	24	0	3	0.33	1	0	1	0	0	0	0	0
..................................................................................................................................TATTTGATCATTTTATATATAATGTT	26	0	20	0.30	6	0	3	0	1	0	1	1
................TAGTTTTTGTTTCTAGTATATATT....................................................................................................................	24	0	20	0.20	4	0	0	4	0	0	0	0
.................................................................................................................................ATATTTGATCATTTTATATATAATGTT	27	0	20	0.15	3	0	1	0	2	0	0	0
...............ATAGTTTTTGTTTCTAGTATATATT....................................................................................................................	25	0	20	0.10	2	0	0	0	2	0	0	0
............................................GTCTTTGTCAACTTAATATTTTTAACATA...................................................................................	29	0	20	0.10	2	0	0	0	0	0	0	2
..........................................................................................TAAGTGAACTTAATCTTTCTAGTATA........................................	26	0	20	0.10	2	0	0	2	0	0	0	0
..................................................................................................................................TATTTGATCATTTTATATATAAT...	23	0	20	0.10	2	0	0	2	0	0	0	0
.............................................................................TACCGAATATTTTTAAGTGAACTTAAT....................................................	27	0	20	0.05	1	0	1	0	0	0	0	0
...........................................................................TTTACCGAATATTTTTAAGT.............................................................	20	0	20	0.05	1	0	0	0	0	0	1	0
...................................................................................ATATTTTTAAGTGAACT........................................................	17	0	20	0.05	1	0	0	0	0	0	1	0
.........................................................................................................................AATTTATAATATTTGATCATTTTATA.........	26	0	20	0.05	1	0	0	1	0	0	0	0
...........................................................................TTTACCGAATATTTTTAAGTGAACT........................................................	25	0	20	0.05	1	0	1	0	0	0	0	0
................................................................................................................................AATATTTGATCATTTTATATATAATGT.	27	0	20	0.05	1	0	0	0	0	0	1	0
...............................................................................CCGAATATTTTTAAGTGAACTTAATC...................................................	26	0	20	0.05	1	0	0	1	0	0	0	0
.............................................................................TACCGAATATTTTTAAGTGAACTTAATC...................................................	28	0	20	0.05	1	0	0	0	0	1	0	0
............AATATAGTTTTTGTTTCTAGTA..........................................................................................................................	22	0	20	0.05	1	0	0	1	0	0	0	0
........TGCAAATATAGTTTTTGATTCTAGTA..........................................................................................................................	26	1	20	0.05	1	0	0	0	0	0	0	1
..................................................................................................................................TATTTGATCATTTTATATATACTGTT	26	1	20	0.05	1	0	0	1	0	0	0	0
...............................................................................................................................TAATATTTGATCATTTTATATATAATGT.	28	0	20	0.05	1	0	0	1	0	0	0	0

CGGCACAGTGCAAATATAGTTTTTGTTTCTAGTATATATTTATAGTCTTTGTCAACTTAATATTTTTAACATACATTTACCGAATATTTTTAAGTGAACTTAATCTTTCTAGTATATTTTTAATTTATAATATTTGATCATTTTATATATAATGTT
***********************************(((((...((.....((..(((((((((((................))))))...)))))..)).....))....)))))......***********************************

Read size

# Mismatch

Hit Count

Total Norm

Total

O001
Testis

SRR553486
Ovary

SRR553488
Ovary

SRR553487
Ovary

M053
Female-body

SRR618934
Ovary

SRR553485
Ovary

.................................................TGTCAACTTAATATTTTTAACATAC..................................................................................

21.00

.................................................TGTCAACTTAATATTTTTAACATACA.................................................................................

1.50

................................................TTGTCAACTTAATATTTTTAACATAC..................................................................................

1.00

................TAGTTTTTGTTTCTAGTATATATTTA..................................................................................................................

0.40

.........................................................TAATATTTTTAACATACATTTACCGAA........................................................................

0.33

............................................................TATTTTTAACATACATTTACCGAATA......................................................................

0.33

............................................................TATTTTTAACATACATTTACCGAA........................................................................

0.33

..................................................................................................................................TATTTGATCATTTTATATATAATGTT

0.30

................TAGTTTTTGTTTCTAGTATATATT....................................................................................................................

0.20

.................................................................................................................................ATATTTGATCATTTTATATATAATGTT

0.15

...............ATAGTTTTTGTTTCTAGTATATATT....................................................................................................................

0.10

............................................GTCTTTGTCAACTTAATATTTTTAACATA...................................................................................

0.10

..........................................................................................TAAGTGAACTTAATCTTTCTAGTATA........................................

0.10

..................................................................................................................................TATTTGATCATTTTATATATAAT...

0.10

.............................................................................TACCGAATATTTTTAAGTGAACTTAAT....................................................

0.05

...........................................................................TTTACCGAATATTTTTAAGT.............................................................

0.05

...................................................................................ATATTTTTAAGTGAACT........................................................

0.05

.........................................................................................................................AATTTATAATATTTGATCATTTTATA.........

0.05

...........................................................................TTTACCGAATATTTTTAAGTGAACT........................................................

0.05

................................................................................................................................AATATTTGATCATTTTATATATAATGT.

0.05

...............................................................................CCGAATATTTTTAAGTGAACTTAATC...................................................

0.05

.............................................................................TACCGAATATTTTTAAGTGAACTTAATC...................................................

0.05

............AATATAGTTTTTGTTTCTAGTA..........................................................................................................................

0.05

........TGCAAATATAGTTTTTGATTCTAGTA..........................................................................................................................

0.05

..................................................................................................................................TATTTGATCATTTTATATATACTGTT

0.05

...............................................................................................................................TAATATTTGATCATTTTATATATAATGT.

0.05

AACATTATATATAAAATGATCAAATATTATAAATTAAAAATATACTAGAAAGATTAAGTTCACTTAAAAATATTCGGTAAATGTATGTTAAAAATATTAAGTTGACAAAGACTATAAATATATACTAGAAACAAAAACTATATTTGCACTGTGCCG *********************************......(((((....((.....((..(((((...((((((................)))))))))))..)).....))...)))))*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	SRR553488 Ovary	SRR553486 Ovary	SRR553487 Ovary	SRR553485 Ovary	O001 Testis	SRR618934 Ovary	M053 Female-body
......................................................................TATTCGGTAAATGTATGTTAAAAA..............................................................	24	0	3	4.33	13	5	5	1	2	0	0	0
......................................................................TATTCGGTAAATGTATGTTAAAAATA............................................................	26	0	3	3.33	10	1	5	1	3	0	0	0
........................................................................TTCGGTAAATGTATGTTAAAAATAT...........................................................	25	0	3	2.67	8	2	3	1	2	0	0	0
..........................................TACTAGAAAGATTAAGTTCACTTA..........................................................................................	24	0	20	2.65	53	0	0	0	0	53	0	0
......................................................................TATTCGGTAAATGTATGTTAAAAATAT...........................................................	27	0	3	2.00	6	3	2	1	0	0	0	0
......................................................................TATTCGGTAAATGTATGTTAAAAAT.............................................................	25	0	3	1.67	5	3	0	2	0	0	0	0
........................................................................TTCGGTAAATGTATGTTAAAAATA............................................................	24	0	3	1.67	5	0	1	4	0	0	0	0
...................................................................AAATATTCGGTAAATGTATGTTA..................................................................	23	0	3	1.33	4	0	0	0	0	3	1	0
...................................................................AAATATTCGGTAAATGTATGTTAAAA...............................................................	26	0	3	1.33	4	3	0	0	1	0	0	0
...................................................................AAATATTCGGTAAATGTATGTTAAAAAT.............................................................	28	0	3	1.33	4	4	0	0	0	0	0	0
......................................................................TATTCGGTAAATGTATGTTAAAAATATT..........................................................	28	0	3	1.33	4	0	0	3	1	0	0	0
..........................................TACTAGAAAGATTAAGTTCACTTAAAAA......................................................................................	28	0	20	1.05	21	0	21	0	0	0	0	0
...................................................................AAATATTCGGTAAATGTATGTTAAAAA..............................................................	27	0	3	0.67	2	1	1	0	0	0	0	0
........................................................................TTCGGTAAATGTATGTTAAAAA..............................................................	22	0	3	0.67	2	2	0	0	0	0	0	0
......................................................................TATTCGGTAAATGTATGTTAAAA...............................................................	23	0	3	0.67	2	1	0	1	0	0	0	0
.....................................................................ATATTCGGTAAATGTATGTTAAAAA..............................................................	25	0	3	0.67	2	1	0	1	0	0	0	0
........................................................................TTCGGTAAATGTATGTTAAAAATATT..........................................................	26	0	3	0.67	2	0	0	1	1	0	0	0
................................................................TAAAAATATTCGGTAAATGTATGTTA..................................................................	26	0	2	0.50	1	0	0	0	1	0	0	0
........................................................................TTCGGTAAATGTATGTTAAAAATATA..........................................................	26	1	4	0.50	2	0	1	0	1	0	0	0
..........................................................................................................................TACTAGAAACAAAAACT.................	17	0	20	0.45	9	0	9	0	0	0	0	0
...................................................................AAATATTCGGTAAATGTATGTT...................................................................	22	0	3	0.33	1	0	0	0	0	0	1	0
......................................................................TATTCGGTAAATGTAGGTTAAAAATA............................................................	26	1	3	0.33	1	0	1	0	0	0	0	0
.........................................................................TCGGTAAATGTATGTTAAAAATATT..........................................................	25	0	3	0.33	1	0	1	0	0	0	0	0
...................................................................AAATATTCGGTAAATGTA.......................................................................	18	0	3	0.33	1	0	0	0	0	0	1	0
...................................................................AAATATTCGGTAAATGTATGTTAAAAATA............................................................	29	0	3	0.33	1	1	0	0	0	0	0	0
...................................................................AAATATTCGGTAAATGT........................................................................	17	0	3	0.33	1	0	0	0	0	0	1	0
...................................................................AAATATTCGGTAAATGTATGTTAAA................................................................	25	0	3	0.33	1	0	0	0	0	0	1	0
.........................................................................TCGGTAAATGTATGTTAAAAATA............................................................	23	0	3	0.33	1	0	1	0	0	0	0	0
........................................................................TTCGGTAAATGTATGTTAAAAATATTA.........................................................	27	0	3	0.33	1	0	1	0	0	0	0	0
...................................................................AAATATTCGGTAAATG.........................................................................	16	0	3	0.33	1	0	0	0	0	0	1	0
.........................................................................TCGGTAAATGTATGTTAAAAATAT...........................................................	24	0	3	0.33	1	0	0	0	1	0	0	0
......................................................................TATTCGGTAAATGTATGTTAAAAATAA...........................................................	27	1	5	0.20	1	0	0	1	0	0	0	0
........................................................................TTCGGTAAATGTATGTTAAAAAAAA...........................................................	25	2	5	0.20	1	0	1	0	0	0	0	0
......................................................................TATTCGGTAAATGTATGTTAAAAAAAA...........................................................	27	2	5	0.20	1	0	0	1	0	0	0	0
..................................................................................................................TTACAATATACTAGAAACAAAAACTATA..............	28	3	6	0.17	1	0	0	1	0	0	0	0
...................................................................AAATATTCGGTAAATGTG.......................................................................	18	1	7	0.14	1	0	0	0	0	0	1	0
.................................................................................................TAAGTTGACAAAGACTATAAATATA..................................	25	0	7	0.14	1	1	0	0	0	0	0	0
......................................................................TATTCGGTAAATGTATGTTAAAAATATTT.........................................................	29	1	8	0.13	1	0	1	0	0	0	0	0
.........................................................................................................CAAAGACTATAAATATATACTAGA...........................	24	0	8	0.13	1	0	1	0	0	0	0	0
.........................................................................TCGGTAAATGTATGTTAAAAATAA...........................................................	24	1	10	0.10	1	0	1	0	0	0	0	0
................................................................................ATGTATGTTAAAGAT.............................................................	15	1	20	0.10	2	0	0	0	0	0	2	0
.................................................................................................................................AACAAAAACTATATTTGCACTGTGCC.	26	0	20	0.10	2	0	0	0	2	0	0	0
...........................................ACTAGAAAGATTAAGTTCACTTAAAAATA....................................................................................	29	0	20	0.10	2	2	0	0	0	0	0	0
...........TAAAATGATCAAATATTATAAATT.........................................................................................................................	24	0	20	0.05	1	0	1	0	0	0	0	0
............................................................................................................................CTAGAAACAAAAACTATATTTGCACTG.....	27	0	20	0.05	1	0	1	0	0	0	0	0
..........................................................................................................................TACTAGAAACAAAAACTATATGTGC.........	25	1	20	0.05	1	0	0	0	1	0	0	0
......................................AATATACTAGAAAGATTAAGTTCACT............................................................................................	26	0	20	0.05	1	0	1	0	0	0	0	0
.............................................TAGAAAGATTAAGTTCACTTAAAAAT.....................................................................................	26	0	20	0.05	1	0	0	0	0	0	1	0
.............................................TAGAAAGATTAAGTTCACTTAAAAA......................................................................................	25	0	20	0.05	1	1	0	0	0	0	0	0
..........................................TACTAGAAAGATTAAGTTCACTTAA.........................................................................................	25	0	20	0.05	1	0	0	0	0	0	0	1
..........................................TACTAGAAAGATTAAGTTCACTTAAAAAA.....................................................................................	29	1	20	0.05	1	1	0	0	0	0	0	0
........................................TATACTAGAAAGATTAAGTTCACT............................................................................................	24	0	20	0.05	1	1	0	0	0	0	0	0
.....................................................TTAAGTTCACTTAAAAATATTCGGTAA............................................................................	27	0	20	0.05	1	0	0	1	0	0	0	0
......................................................................TATTCGGTAAATGTATTTTAAAAA..............................................................	24	1	20	0.05	1	1	0	0	0	0	0	0
...........................................................................................................................ACTAGAAACAAAAACTATATTTGCACT......	27	0	20	0.05	1	0	0	0	1	0	0	0
......................................................TAAGTTCACTTAAAAATATTCGGTAA............................................................................	26	0	20	0.05	1	0	1	0	0	0	0	0
..........................................TACTTGAAAGATTAAGTTCACTTAAAAA......................................................................................	28	1	20	0.05	1	0	1	0	0	0	0	0
...........TAAAATGATCAAATATTATAAATAAA.......................................................................................................................	26	1	20	0.05	1	1	0	0	0	0	0	0
.........................................ATACTAGAAAGATTAAGTTCACTTAAAAATA....................................................................................	31	0	20	0.05	1	0	1	0	0	0	0	0
..........................................TACTAGAAAGATTAAGTTCACTTAAAA.......................................................................................	27	0	20	0.05	1	0	0	0	1	0	0	0

AACATTATATATAAAATGATCAAATATTATAAATTAAAAATATACTAGAAAGATTAAGTTCACTTAAAAATATTCGGTAAATGTATGTTAAAAATATTAAGTTGACAAAGACTATAAATATATACTAGAAACAAAAACTATATTTGCACTGTGCCG
***********************************......(((((....((.....((..(((((...((((((................)))))))))))..)).....))...)))))***********************************

Read size

# Mismatch

Hit Count

Total Norm

Total

SRR553488
Ovary

SRR553486
Ovary

SRR553487
Ovary

SRR553485
Ovary

O001
Testis

SRR618934
Ovary

M053
Female-body

......................................................................TATTCGGTAAATGTATGTTAAAAA..............................................................

4.33

......................................................................TATTCGGTAAATGTATGTTAAAAATA............................................................

3.33

........................................................................TTCGGTAAATGTATGTTAAAAATAT...........................................................

2.67

..........................................TACTAGAAAGATTAAGTTCACTTA..........................................................................................

2.65

......................................................................TATTCGGTAAATGTATGTTAAAAATAT...........................................................

2.00

......................................................................TATTCGGTAAATGTATGTTAAAAAT.............................................................

1.67

........................................................................TTCGGTAAATGTATGTTAAAAATA............................................................

1.67

...................................................................AAATATTCGGTAAATGTATGTTA..................................................................

1.33

...................................................................AAATATTCGGTAAATGTATGTTAAAA...............................................................

1.33

...................................................................AAATATTCGGTAAATGTATGTTAAAAAT.............................................................

1.33

......................................................................TATTCGGTAAATGTATGTTAAAAATATT..........................................................

1.33

..........................................TACTAGAAAGATTAAGTTCACTTAAAAA......................................................................................

1.05

...................................................................AAATATTCGGTAAATGTATGTTAAAAA..............................................................

0.67

........................................................................TTCGGTAAATGTATGTTAAAAA..............................................................

0.67

......................................................................TATTCGGTAAATGTATGTTAAAA...............................................................

0.67

.....................................................................ATATTCGGTAAATGTATGTTAAAAA..............................................................

0.67

........................................................................TTCGGTAAATGTATGTTAAAAATATT..........................................................

0.67

................................................................TAAAAATATTCGGTAAATGTATGTTA..................................................................

0.50

........................................................................TTCGGTAAATGTATGTTAAAAATATA..........................................................

0.50

..........................................................................................................................TACTAGAAACAAAAACT.................

0.45

...................................................................AAATATTCGGTAAATGTATGTT...................................................................

0.33

......................................................................TATTCGGTAAATGTAGGTTAAAAATA............................................................

0.33

.........................................................................TCGGTAAATGTATGTTAAAAATATT..........................................................

0.33

...................................................................AAATATTCGGTAAATGTA.......................................................................

0.33

...................................................................AAATATTCGGTAAATGTATGTTAAAAATA............................................................

0.33

...................................................................AAATATTCGGTAAATGT........................................................................

0.33

...................................................................AAATATTCGGTAAATGTATGTTAAA................................................................

0.33

.........................................................................TCGGTAAATGTATGTTAAAAATA............................................................

0.33

........................................................................TTCGGTAAATGTATGTTAAAAATATTA.........................................................

0.33

...................................................................AAATATTCGGTAAATG.........................................................................

0.33

.........................................................................TCGGTAAATGTATGTTAAAAATAT...........................................................

0.33

......................................................................TATTCGGTAAATGTATGTTAAAAATAA...........................................................

0.20

........................................................................TTCGGTAAATGTATGTTAAAAAAAA...........................................................

0.20

......................................................................TATTCGGTAAATGTATGTTAAAAAAAA...........................................................

0.20

..................................................................................................................TTACAATATACTAGAAACAAAAACTATA..............

0.17

...................................................................AAATATTCGGTAAATGTG.......................................................................

0.14

.................................................................................................TAAGTTGACAAAGACTATAAATATA..................................

0.14

......................................................................TATTCGGTAAATGTATGTTAAAAATATTT.........................................................

0.13

.........................................................................................................CAAAGACTATAAATATATACTAGA...........................

0.13

.........................................................................TCGGTAAATGTATGTTAAAAATAA...........................................................

0.10

................................................................................ATGTATGTTAAAGAT.............................................................

0.10

.................................................................................................................................AACAAAAACTATATTTGCACTGTGCC.

0.10

...........................................ACTAGAAAGATTAAGTTCACTTAAAAATA....................................................................................

0.10

...........TAAAATGATCAAATATTATAAATT.........................................................................................................................

0.05

............................................................................................................................CTAGAAACAAAAACTATATTTGCACTG.....

0.05

..........................................................................................................................TACTAGAAACAAAAACTATATGTGC.........

0.05

......................................AATATACTAGAAAGATTAAGTTCACT............................................................................................

0.05

.............................................TAGAAAGATTAAGTTCACTTAAAAAT.....................................................................................

0.05

.............................................TAGAAAGATTAAGTTCACTTAAAAA......................................................................................

0.05

..........................................TACTAGAAAGATTAAGTTCACTTAA.........................................................................................

0.05

..........................................TACTAGAAAGATTAAGTTCACTTAAAAAA.....................................................................................

0.05

........................................TATACTAGAAAGATTAAGTTCACT............................................................................................

0.05

.....................................................TTAAGTTCACTTAAAAATATTCGGTAA............................................................................

0.05

......................................................................TATTCGGTAAATGTATTTTAAAAA..............................................................

0.05

...........................................................................................................................ACTAGAAACAAAAACTATATTTGCACT......

0.05

......................................................TAAGTTCACTTAAAAATATTCGGTAA............................................................................

0.05

..........................................TACTTGAAAGATTAAGTTCACTTAAAAA......................................................................................

0.05

...........TAAAATGATCAAATATTATAAATAAA.......................................................................................................................

0.05

.........................................ATACTAGAAAGATTAAGTTCACTTAAAAATA....................................................................................

0.05

..........................................TACTAGAAAGATTAAGTTCACTTAAAA.......................................................................................

0.05

Species	Coordinate	ID	Alignment
droSim3	chrU_M_671:3020-3175 +	dsi_191	CGGCACAGTGCAAATATAGT-TTTTGTTTCTAGTATAT---ATTTATAGTCTTTGTCAACTTAAT-ATTTTTAACATAC--ATTTACCGAATATTTTTAAGTG----------AACTTAATCTT--TCTAGTATATTTTT--AATTTATAATATTTGATCATTTT-ATATATAATGTT
droSec2	scaffold_5162:1653-1808 +		CGGCACAGTGCAAATATAGT-TTTTGTTTCTAGTATAT---ATTTCTAGTCTTTGTCAACTTAAT-ATTTTTAACATAT--ATTTACCGAATATTTTTAAGTG----------AAATTAATCTT--TCTAGTATATTTTT--AATTTATAATATTTGATCATTTT-ATATATAATGTT
dm3	chrX:6059673-6059841 -		CGGCACGGTGCAAATATAGT-TTTTGTTCCTAGTAAAT---ATTTGTAGTATTTATCAACTTAAT-ATTTTTAATATAGAAATATACCAAATATTTTT-AGTATATACCTACATACTTTATCTT--TCTAGTATATTTTTATAATTTA-AATTTTTTTTCATTTTTTTATATAATCAT
droEre2	scaffold_4690:15038578-15038674 -		AGGCAAGGTGAAAATATACT-TCATATTTCTAGTATAT-----TTAT-----------ACTAAAT-ATTTCTGGTATAC--G---------------------------------CTTAACTTT--TCTGGTATATACTT--AATAAATAATAT------------------------
droAna3	scaffold_12916:11012025-11012177 -		CGGAAAACTGAAAATAAAATCTTTTATTTTTTGTTTATTTCGTTTCTTGTTTTTGTAATGTTTATTGTTTTTGTT-------GTTATTGTACTTTTTGTTGTA----------AATT-GCTTTTTCTATTGTAGAGTTTC--AGTTTCTATT-----GTAATTTTTTTTTTAAATGTT

Species

Coordinate

Alignment

droSim3

chrU_M_671:3020-3175 +

dsi_191

CGGCACAGTGCAAATATAGT-TTTTGTTTCTAGTATAT---ATTTATAGTCTTTGTCAACTTAAT-ATTTTTAACATAC--ATTTACCGAATATTTTTAAGTG----------AACTTAATCTT--TCTAGTATATTTTT--AATTTATAATATTTGATCATTTT-ATATATAATGTT

droSec2

scaffold_5162:1653-1808 +

CGGCACAGTGCAAATATAGT-TTTTGTTTCTAGTATAT---ATTTCTAGTCTTTGTCAACTTAAT-ATTTTTAACATAT--ATTTACCGAATATTTTTAAGTG----------AAATTAATCTT--TCTAGTATATTTTT--AATTTATAATATTTGATCATTTT-ATATATAATGTT

dm3

chrX:6059673-6059841 -

CGGCACGGTGCAAATATAGT-TTTTGTTCCTAGTAAAT---ATTTGTAGTATTTATCAACTTAAT-ATTTTTAATATAGAAATATACCAAATATTTTT-AGTATATACCTACATACTTTATCTT--TCTAGTATATTTTTATAATTTA-AATTTTTTTTCATTTTTTTATATAATCAT

droEre2

scaffold_4690:15038578-15038674 -

AGGCAAGGTGAAAATATACT-TCATATTTCTAGTATAT-----TTAT-----------ACTAAAT-ATTTCTGGTATAC--G---------------------------------CTTAACTTT--TCTGGTATATACTT--AATAAATAATAT------------------------

droAna3

scaffold_12916:11012025-11012177 -

CGGAAAACTGAAAATAAAATCTTTTATTTTTTGTTTATTTCGTTTCTTGTTTTTGTAATGTTTATTGTTTTTGTT-------GTTATTGTACTTTTTGTTGTA----------AATT-GCTTTTTCTATTGTAGAGTTTC--AGTTTCTATT-----GTAATTTTTTTTTTAAATGTT

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droSim3

CGGCACAGTGCAAATATAGT-TTTTGTTTCTAGTATAT---ATTTATAGTCTTTGTCAACTTAAT-ATTTTTAACATAC--ATTTACCGAATATTTTTAAGTG----------AACTTAATCTT--TCTAGTATATTTTT--AATTTATAATATTTGATCATTTT-ATATATAATGTT	Size	Hit Count	Total Norm	Total	V044 Embryo	M023 Head	M024 Male-body	M025 Embryo	O001 Testis	O002 Head	M053 Female-body	SRR553485 Ovary	SRR553486 Ovary	SRR553487 Ovary	SRR553488 Ovary	SRR618934 Ovary
.....................................................TGTCAACTTAAT-ATTTTTAACATAC--.................................................................................................	25	2	21.00	42	0	0	0	0	42	0	0	0	0	0	0	0
.....................................................TGTCAACTTAAT-ATTTTTAACATAC--A................................................................................................	26	2	1.50	3	0	0	0	0	2	0	1	0	0	0	0	0
....................................................TTGTCAACTTAAT-ATTTTTAACATAC--.................................................................................................	26	2	1.00	2	0	0	0	0	2	0	0	0	0	0	0	0
................TAGT-TTTTGTTTCTAGTATAT---ATTTA....................................................................................................................................	26	5	0.40	2	0	0	0	0	0	0	0	0	0	1	1	0
.............................................................TAAT-ATTTTTAACATAC--ATTTACCGAA.......................................................................................	27	3	0.33	1	0	0	0	0	0	0	0	0	1	0	0	0
................................................................T-ATTTTTAACATAC--ATTTACCGAATA.....................................................................................	26	3	0.33	1	0	0	0	0	0	0	0	0	0	1	0	0
................................................................T-ATTTTTAACATAC--ATTTACCGAA.......................................................................................	24	3	0.33	1	0	0	0	0	0	0	0	0	1	0	0	0
.......................................................................................................................................................TATTTGATCATTTT-ATATATAATGTT	26	20	0.30	6	0	0	0	0	0	0	0	1	3	1	0	1
................TAGT-TTTTGTTTCTAGTATAT---ATT......................................................................................................................................	24	20	0.20	4	0	0	0	0	0	0	0	0	0	0	4	0
......................................................................................................................................................ATATTTGATCATTTT-ATATATAATGTT	27	20	0.15	3	0	0	0	0	0	0	0	0	1	2	0	0
...............ATAGT-TTTTGTTTCTAGTATAT---ATT......................................................................................................................................	25	20	0.10	2	0	0	0	0	0	0	0	0	0	2	0	0
................................................GTCTTTGTCAACTTAAT-ATTTTTAACATA....................................................................................................	29	20	0.10	2	0	0	0	0	0	0	0	2	0	0	0	0
.................................................................................................TAAGTG----------AACTTAATCTT--TCTAGTATA...........................................	26	20	0.10	2	0	0	0	0	0	0	0	0	0	0	2	0
.......................................................................................................................................................TATTTGATCATTTT-ATATATAAT...	23	20	0.10	2	0	0	0	0	0	0	0	0	0	0	2	0
....................................................................................TACCGAATATTTTTAAGTG----------AACTTAAT.........................................................	27	20	0.05	1	0	0	0	0	0	0	0	0	1	0	0	0
..................................................................................TTTACCGAATATTTTTAAGT............................................................................	20	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	1
..........................................................................................ATATTTTTAAGTG----------AACT.............................................................	17	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	1
..............................................................................................................................................AATTTATAATATTTGATCATTTT-ATA.........	26	20	0.05	1	0	0	0	0	0	0	0	0	0	0	1	0
..................................................................................TTTACCGAATATTTTTAAGTG----------AACT.............................................................	25	20	0.05	1	0	0	0	0	0	0	0	0	1	0	0	0
.....................................................................................................................................................AATATTTGATCATTTT-ATATATAATGT.	27	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	1
......................................................................................CCGAATATTTTTAAGTG----------AACTTAATC........................................................	26	20	0.05	1	0	0	0	0	0	0	0	0	0	0	1	0
....................................................................................TACCGAATATTTTTAAGTG----------AACTTAATC........................................................	28	20	0.05	1	0	0	0	0	0	0	1	0	0	0	0	0
............AATATAGT-TTTTGTTTCTAGTA...............................................................................................................................................	22	20	0.05	1	0	0	0	0	0	0	0	0	0	0	1	0
....................................................................................................................................................TAATATTTGATCATTTT-ATATATAATGT.	28	20	0.05	1	0	0	0	0	0	0	0	0	0	0	1	0

droSec2

CGGCACAGTGCAAATATAGT-TTTTGTTTCTAGTATAT---ATTTCTAGTCTTTGTCAACTTAAT-ATTTTTAACATAT--ATTTACCGAATATTTTTAAGTG----------AAATTAATCTT--TCTAGTATATTTTT--AATTTATAATATTTGATCATTTT-ATATATAATGTT	Size	Hit Count	Total Norm	Total	V113 Male-body	V114 Embryo	V115 Head	M054 Female-body
.......................................................................TAACATAT--ATTTACCGAATATTTT.................................................................................	24	20	0.05	1	0	0	0	1

droEre2

AGGCAAGGTGAAAATATACT-TCATATTTCTAGTATAT-----TTAT-----------ACTAAAT-ATTTCTGGTATAC--G---------------------------------CTTAACTTT--TCTGGTATATACTT--AATAAATAATAT------------------------	Size	Hit Count	Total Norm	Total	V040 Embryo	V060 Head	V107 Male-body	V108 Head	M055 Female-body	M057 Embryo
No Reads

droAna3

CGGAAAACTGAAAATAAAATCTTTTATTTTTTGTTTATTTCGTTTCTTGTTTTTGTAATGTTTATTGTTTTTGTT-------GTTATTGTACTTTTTGTTGTA----------AATT-GCTTTTTCTATTGTAGAGTTTC--AGTTTCTATT-----GTAATTTTTTTTTTAAATGTT	Size	Hit Count	Total Norm	Total	V105 Male-body	V106 Head	V055 Head	V039 Embryo	M044 Female-body	M058 Embryo
No Reads

dsi_191

chrU_M_671:3070-3125 +

Candidate

Unknown

Predicted structure

Flybase annnotation

Sense Strand Reads

Anti-sense strand reads

Re-alignment of all predicted orthologs

Re-alignment of all predicted orthologs with sRNA reads

-4.5	-4.4	-4.2