dsi_156

GCACGACTCAAAAAACAATTCTCCGGCGCCACATGGCGCCCTCTCCGGCAGTCCATGTGCCCGGGCTCCGGTCCGGATGCACAGTGGGACTGGGACAACAAATGAAATTTGGGTGCAGTTCGTGAGCGCGCTTTCTTCGCGCT *********************************........(((..((((((.(((((((((((....))))))..)))))...))))))))).............*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M023 head	M024 male body	SRR553485 Ovary	M053 Female-body
...............................................................................CACATTGGGACTGAGACAC.............................................	19	3	16	181.94	2911	724	2152	0	23
...............................................................................CACATTGGGACTGAGACA..............................................	18	2	4	24.50	98	24	68	0	1
.......................................................................TCCGGATGCACAGTGGGACTG...................................................	21	0	1	6.00	6	3	3	0	0
...............................................................................CACACTGGGACTGAGACA..............................................	18	2	4	3.25	13	1	0	1	0
..........................................................GACCGGGGTCCGGTGCGGA..................................................................	19	3	7	2.57	18	0	0	0	0
.............................................................................TGCACAGTGGGACTGGGACA..............................................	20	0	1	1.00	1	0	0	1	0
.......................................................................TCCGGATGCACAGTGGGACTGT..................................................	22	1	1	1.00	1	0	1	0	0
.............................................CGGCAGTCCATGTGCCCGGGC.............................................................................	21	0	1	1.00	1	1	0	0	0
.............................................................................................................TGGGTGCAGTTCGTGAGCGCG.............	21	0	1	1.00	1	0	0	1	0
...............................................................................CACATTGGGACTGAGACAA.............................................	19	2	2	1.00	2	1	1	0	0
.........................................................................CGGATGCACAGTGGGACTG...................................................	19	0	1	1.00	1	0	1	0	0
......................................................................................................TGAAATTTGGGTGCAGTTCGTGAGCGCGC............	29	0	1	1.00	1	0	0	1	0
...............................................................................CACATTGGGACTGAGAC...............................................	17	2	7	1.00	7	0	0	0	0
........................................................................................................AAATTTGGGTGCAGTTCGTGA..................	21	0	1	1.00	1	0	0	1	0
......................................................................GTCCGGATGCACAGTGGGACT....................................................	21	0	1	1.00	1	1	0	0	0
..........................................................................................TGGGACAACAAATGAAATTTG................................	21	0	1	1.00	1	0	0	0	1
...............................................................................CACACTGGGACTGAGAC...............................................	17	2	20	0.95	19	0	0	3	0
................................................................................ACATTGGGACTGGGACAC.............................................	18	2	4	0.75	3	1	2	0	0
............................................................CCGGGGTCCGGTGCGGA..................................................................	17	2	7	0.71	5	0	0	0	0
..............................................................................CCACACTGGGACTGAGACA..............................................	19	3	20	0.55	11	0	0	1	0
...............................................................................CACATTGGGACTGGGACAC.............................................	19	2	2	0.50	1	0	1	0	0
..............................................................................GCACATTGGGACTGAGACA..............................................	19	2	2	0.50	1	0	0	0	0
............................................................................ATCCACATTGGGACTGAGACA..............................................	21	3	3	0.33	1	0	0	0	0
........................................CTGTCCGTCAGTCCATGTGC...................................................................................	20	2	3	0.33	1	0	0	0	0
...............................................................................CACATTGGGACTGAGACACC............................................	20	3	4	0.25	1	0	1	0	0
.........................................................GGACCGGGGTCCGGTCCGGA..................................................................	20	3	5	0.20	1	0	0	0	0
.............................................CGTCCGTCCATGTGCCCGCG..............................................................................	20	3	6	0.17	1	0	0	0	0
.....................................................................................................GTGGAATTTGGGTGCAGT........................	18	2	12	0.08	1	0	0	0	0
...............................................................................CACATTGGGACTGAGACAT.............................................	19	3	18	0.06	1	0	1	0	0
...........................................................ACCGGGGTCCGGTGCGGA..................................................................	18	3	20	0.05	1	0	0	0	0
..............................................................................CCACATTGGGACTGTGACA..............................................	19	3	20	0.05	1	0	0	0	0
..............................................................................CCACACTGGGACTGCGACA..............................................	19	3	20	0.05	1	0	0	0	0

GCACGACTCAAAAAACAATTCTCCGGCGCCACATGGCGCCCTCTCCGGCAGTCCATGTGCCCGGGCTCCGGTCCGGATGCACAGTGGGACTGGGACAACAAATGAAATTTGGGTGCAGTTCGTGAGCGCGCTTTCTTCGCGCT
***********************************........(((..((((((.(((((((((((....))))))..)))))...))))))))).............***********************************

Read size

# Mismatch

Hit Count

Total Norm

Total

M023
head

M024
male body

SRR553485
Ovary

M053
Female-body

...............................................................................CACATTGGGACTGAGACAC.............................................

181.94

2911

724

2152

...............................................................................CACATTGGGACTGAGACA..............................................

24.50

.......................................................................TCCGGATGCACAGTGGGACTG...................................................

6.00

...............................................................................CACACTGGGACTGAGACA..............................................

3.25

..........................................................GACCGGGGTCCGGTGCGGA..................................................................

2.57

.............................................................................TGCACAGTGGGACTGGGACA..............................................

1.00

.......................................................................TCCGGATGCACAGTGGGACTGT..................................................

1.00

.............................................CGGCAGTCCATGTGCCCGGGC.............................................................................

1.00

.............................................................................................................TGGGTGCAGTTCGTGAGCGCG.............

1.00

...............................................................................CACATTGGGACTGAGACAA.............................................

1.00

.........................................................................CGGATGCACAGTGGGACTG...................................................

1.00

......................................................................................................TGAAATTTGGGTGCAGTTCGTGAGCGCGC............

1.00

...............................................................................CACATTGGGACTGAGAC...............................................

1.00

........................................................................................................AAATTTGGGTGCAGTTCGTGA..................

1.00

......................................................................GTCCGGATGCACAGTGGGACT....................................................

1.00

..........................................................................................TGGGACAACAAATGAAATTTG................................

1.00

...............................................................................CACACTGGGACTGAGAC...............................................

0.95

................................................................................ACATTGGGACTGGGACAC.............................................

0.75

............................................................CCGGGGTCCGGTGCGGA..................................................................

0.71

..............................................................................CCACACTGGGACTGAGACA..............................................

0.55

...............................................................................CACATTGGGACTGGGACAC.............................................

0.50

..............................................................................GCACATTGGGACTGAGACA..............................................

0.50

............................................................................ATCCACATTGGGACTGAGACA..............................................

0.33

........................................CTGTCCGTCAGTCCATGTGC...................................................................................

0.33

...............................................................................CACATTGGGACTGAGACACC............................................

0.25

.........................................................GGACCGGGGTCCGGTCCGGA..................................................................

0.20

.............................................CGTCCGTCCATGTGCCCGCG..............................................................................

0.17

.....................................................................................................GTGGAATTTGGGTGCAGT........................

0.08

...............................................................................CACATTGGGACTGAGACAT.............................................

0.06

...........................................................ACCGGGGTCCGGTGCGGA..................................................................

0.05

..............................................................................CCACATTGGGACTGTGACA..............................................

0.05

..............................................................................CCACACTGGGACTGCGACA..............................................

0.05

AGCGCGAAGAAAGCGCGCTCACGAACTGCACCCAAATTTCATTTGTTGTCCCAGTCCCACTGTGCATCCGGACCGGAGCCCGGGCACATGGACTGCCGGAGAGGGCGCCATGTGGCGCCGGAGAATTGTTTTTTGAGTCGTGC *********************************.............(((((((((...(((((..((((((....))))))))))).))))))..)))........*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	SRR618934 Ovary	SRR553485 Ovary	SRR553486 Ovary	M024 male body	M023 head	M025 embryo	M053 Female-body	SRR553487 Ovary
.............................................................................................TGCCGGAGAGGGCGCCATGTGGCGC.........................	25	0	1	14.00	14	14	0	0	0	0	0	0	0
......................................................TCCCACTGTGCATCCGGACCGGAGCC...............................................................	26	0	1	5.00	5	1	1	3	0	0	0	0	0
....................................................................................................GAGGGCGCCATGTGGCGCAA.......................	20	2	1	2.00	2	2	0	0	0	0	0	0	0
................................................................................CGGGCACATGGACTGCCGGAGAGGGCGCCA.................................	30	0	1	2.00	2	0	2	0	0	0	0	0	0
..............................................................................CGCGGGCACATGGACGGACGGA...........................................	22	3	1	2.00	2	0	0	2	0	0	0	0	0
.............................................TTGTCCCAGTCCCACTGTGCA.............................................................................	21	0	1	2.00	2	0	0	0	2	0	0	0	0
............................................................................................CTGCCGGAGAGGGCGCCATGTGGCGCA........................	27	1	1	2.00	2	2	0	0	0	0	0	0	0
..................................................................TCCGGACCGGAGCCCGGGCACATGGAC..................................................	27	0	1	2.00	2	1	1	0	0	0	0	0	0
..........................................................................GGAGCCCGGGCACATGGACTGCCGGA...........................................	26	0	1	2.00	2	0	0	2	0	0	0	0	0
..................TCACGAACTGCACCCAAATTTCATT....................................................................................................	25	0	1	2.00	2	0	2	0	0	0	0	0	0
.........................................TTTGTTGTCCCAGTCCCACTG.................................................................................	21	0	1	2.00	2	0	0	0	0	2	0	0	0
.............................................................................................TGCCGGAGAGGGCGCCATGTGGCGCA........................	26	1	1	2.00	2	2	0	0	0	0	0	0	0
..............................................................................CGCGGGCACATGGACGGACG.............................................	20	3	6	1.50	9	0	0	9	0	0	0	0	0
..............................................................................CGCGGGCACATGGACGGACGG............................................	21	3	3	1.33	4	0	0	4	0	0	0	0	0
.....................................TTCATTTGTTGTCCCAGTCCCACTG.................................................................................	25	0	1	1.00	1	0	0	0	0	0	1	0	0
..........................TGCACCCAAATTTCATTTGTTGTC.............................................................................................	24	0	1	1.00	1	0	0	0	0	0	0	0	1
......................................................TCCCACTGTGCATCCGGACCGGAGCCCG.............................................................	28	0	1	1.00	1	0	0	1	0	0	0	0	0
.........................................................................CGGAGCCCGGGCACATGGACTGCCGGA...........................................	27	0	1	1.00	1	0	0	1	0	0	0	0	0
........................................................................................TGGACTGCCGGAGAGGGCGCCATGTGGC...........................	28	0	1	1.00	1	1	0	0	0	0	0	0	0
...............................................................GCATCCGGACCGGAGCC...............................................................	17	0	1	1.00	1	1	0	0	0	0	0	0	0
.............................................TTGTCCCAGTCCCACTGTGCATCCGGACC.....................................................................	29	0	1	1.00	1	0	0	1	0	0	0	0	0
...................................................................................GCACATGGACTGCCGGAGAGG.......................................	21	0	1	1.00	1	0	0	0	1	0	0	0	0
........................................................................................TGGACTGCCGGAGAGGGCG....................................	19	0	1	1.00	1	0	1	0	0	0	0	0	0
................................................................................CGGGCACATGGACTGCCGGAGAGGGCGC...................................	28	0	1	1.00	1	0	1	0	0	0	0	0	0
..............................................TGTCCCAGTCCCACTGTGCATCCGGA.......................................................................	26	0	1	1.00	1	0	0	1	0	0	0	0	0
........................................................................................TGGACTGCCGGAGAGGGCGCCATGTG.............................	26	0	1	1.00	1	1	0	0	0	0	0	0	0
..............GCGCTCACGAACTGCACC...............................................................................................................	18	0	1	1.00	1	0	0	0	0	1	0	0	0
................................................................................CGGGCACATGGACTGCCGGAGAGGGCG....................................	27	0	1	1.00	1	0	0	1	0	0	0	0	0
......................................................TCCCACTGTGCATCCGGACCGGAGC................................................................	25	0	1	1.00	1	0	1	0	0	0	0	0	0
.................................................CCCAGTCCCACTGTGCATCCGGA.......................................................................	23	0	1	1.00	1	0	0	0	0	0	1	0	0
.............................................................................................TGCCGGAGAGGGCGCCATGTGGCGCAA.......................	27	2	1	1.00	1	1	0	0	0	0	0	0	0
.............................................................................................TGCCGGAGAGGGCGCCATGTGGCGA.........................	25	1	1	1.00	1	1	0	0	0	0	0	0	0
.............CGCGCTCACGAACTGCACCCA.............................................................................................................	21	0	1	1.00	1	0	0	0	1	0	0	0	0
.....................................................GTCCCACTGTGCATCCGGACCGGAGC................................................................	26	0	1	1.00	1	1	0	0	0	0	0	0	0
........................................................................................TGGACTGCCGGAGAGGGCGCC..................................	21	0	1	1.00	1	1	0	0	0	0	0	0	0
........................................................CCACTGTGCATCCGGACCGG...................................................................	20	0	1	1.00	1	0	0	0	1	0	0	0	0
........................................................................CCGGAGCCCGGGCACATGGACTGCCGGAG..........................................	29	0	1	1.00	1	1	0	0	0	0	0	0	0
.....GAAGAAAGCGCGCTCACGAACTGCA.................................................................................................................	25	0	1	1.00	1	0	1	0	0	0	0	0	0
.........................................TTTGTTGTCCCAGTCCCACTGTGCATC...........................................................................	27	0	1	1.00	1	1	0	0	0	0	0	0	0
..............................................................TGCATCCGGACCGGAGCCCGGGCAC........................................................	25	0	1	1.00	1	0	0	0	0	0	0	1	0
.......................................................CCCACTGTGCATCCGGACC.....................................................................	19	0	1	1.00	1	1	0	0	0	0	0	0	0
........................................................................................TGGACTGCCGGAGAGGGC.....................................	18	0	1	1.00	1	1	0	0	0	0	0	0	0
........................................................................................TGGACTGCCGGAGAGGGCGCCATGGG.............................	26	1	1	1.00	1	1	0	0	0	0	0	0	0
.............................................................................................TGCCGGAGAGGGCGCCATGTGGCG..........................	24	0	1	1.00	1	1	0	0	0	0	0	0	0
..................................................CCAGTCCCACTGTGCATCCGGACCGGAGCC...............................................................	30	0	1	1.00	1	1	0	0	0	0	0	0	0
..............................................................................................GCCGGAGAGGGCGCCATGTGGCGC.........................	24	0	1	1.00	1	1	0	0	0	0	0	0	0
.............................................................................................TGCCGGAGAGGGCGCCATGTGGCGCCGGA.....................	29	0	1	1.00	1	0	1	0	0	0	0	0	0
....................................................................................CACATGGACCGTCGGCGAGG.......................................	20	3	5	0.80	4	0	0	0	2	0	1	1	0
....................................................................................CACATGGACCGTCGGCGAG........................................	19	3	15	0.53	8	0	0	0	2	0	5	1	0
................................................................................CGGGCACATGGACGGACGGA...........................................	20	2	6	0.50	3	0	0	3	0	0	0	0	0
....................................................................................CACATGGACCGTCGGCGAGGG......................................	21	3	2	0.50	1	0	0	0	1	0	0	0	0
.....................................................................................ACATGGACCGTCGGCGAGG.......................................	19	3	17	0.18	3	0	0	0	0	0	3	0	0
.............................................................................................................ATGGGGCGCCGGAGA...................	15	1	8	0.13	1	0	1	0	0	0	0	0	0
.........AAGGCGCCCTGACGAACTGC..................................................................................................................	20	3	9	0.11	1	0	0	0	0	0	0	0	0
...............................................................................GCGGGCACATGGACGGACGGA...........................................	21	3	10	0.10	1	0	0	1	0	0	0	0	0
.................................................................................................TGAGAGCGCGCCATGTG.............................	17	2	10	0.10	1	1	0	0	0	0	0	0	0
........................................................................CCGGAGCCGGGGCAC........................................................	15	1	11	0.09	1	1	0	0	0	0	0	0	0
................................................................TATCGGAACCGGAGCCCGG............................................................	19	3	16	0.06	1	0	0	1	0	0	0	0	0
...........................................................................................................CGATGTGGGGACGGAGAAT.................	19	3	17	0.06	1	0	0	0	0	0	0	0	0
................................................................................CTGGCACATGGACGGACGGA...........................................	20	3	18	0.06	1	0	0	1	0	0	0	0	0

AGCGCGAAGAAAGCGCGCTCACGAACTGCACCCAAATTTCATTTGTTGTCCCAGTCCCACTGTGCATCCGGACCGGAGCCCGGGCACATGGACTGCCGGAGAGGGCGCCATGTGGCGCCGGAGAATTGTTTTTTGAGTCGTGC
***********************************.............(((((((((...(((((..((((((....))))))))))).))))))..)))........***********************************

Read size

# Mismatch

Hit Count

Total Norm

Total

SRR618934
Ovary

SRR553485
Ovary

SRR553486
Ovary

M024
male body

M023
head

M025
embryo

M053
Female-body

SRR553487
Ovary

.............................................................................................TGCCGGAGAGGGCGCCATGTGGCGC.........................

14.00

......................................................TCCCACTGTGCATCCGGACCGGAGCC...............................................................

5.00

....................................................................................................GAGGGCGCCATGTGGCGCAA.......................

2.00

................................................................................CGGGCACATGGACTGCCGGAGAGGGCGCCA.................................

2.00

..............................................................................CGCGGGCACATGGACGGACGGA...........................................

2.00

.............................................TTGTCCCAGTCCCACTGTGCA.............................................................................

2.00

............................................................................................CTGCCGGAGAGGGCGCCATGTGGCGCA........................

2.00

..................................................................TCCGGACCGGAGCCCGGGCACATGGAC..................................................

2.00

..........................................................................GGAGCCCGGGCACATGGACTGCCGGA...........................................

2.00

..................TCACGAACTGCACCCAAATTTCATT....................................................................................................

2.00

.........................................TTTGTTGTCCCAGTCCCACTG.................................................................................

2.00

.............................................................................................TGCCGGAGAGGGCGCCATGTGGCGCA........................

2.00

..............................................................................CGCGGGCACATGGACGGACG.............................................

1.50

..............................................................................CGCGGGCACATGGACGGACGG............................................

1.33

.....................................TTCATTTGTTGTCCCAGTCCCACTG.................................................................................

1.00

..........................TGCACCCAAATTTCATTTGTTGTC.............................................................................................

1.00

......................................................TCCCACTGTGCATCCGGACCGGAGCCCG.............................................................

1.00

.........................................................................CGGAGCCCGGGCACATGGACTGCCGGA...........................................

1.00

........................................................................................TGGACTGCCGGAGAGGGCGCCATGTGGC...........................

1.00

...............................................................GCATCCGGACCGGAGCC...............................................................

1.00

.............................................TTGTCCCAGTCCCACTGTGCATCCGGACC.....................................................................

1.00

...................................................................................GCACATGGACTGCCGGAGAGG.......................................

1.00

........................................................................................TGGACTGCCGGAGAGGGCG....................................

1.00

................................................................................CGGGCACATGGACTGCCGGAGAGGGCGC...................................

1.00

..............................................TGTCCCAGTCCCACTGTGCATCCGGA.......................................................................

1.00

........................................................................................TGGACTGCCGGAGAGGGCGCCATGTG.............................

1.00

..............GCGCTCACGAACTGCACC...............................................................................................................

1.00

................................................................................CGGGCACATGGACTGCCGGAGAGGGCG....................................

1.00

......................................................TCCCACTGTGCATCCGGACCGGAGC................................................................

1.00

.................................................CCCAGTCCCACTGTGCATCCGGA.......................................................................

1.00

.............................................................................................TGCCGGAGAGGGCGCCATGTGGCGCAA.......................

1.00

.............................................................................................TGCCGGAGAGGGCGCCATGTGGCGA.........................

1.00

.............CGCGCTCACGAACTGCACCCA.............................................................................................................

1.00

.....................................................GTCCCACTGTGCATCCGGACCGGAGC................................................................

1.00

........................................................................................TGGACTGCCGGAGAGGGCGCC..................................

1.00

........................................................CCACTGTGCATCCGGACCGG...................................................................

1.00

........................................................................CCGGAGCCCGGGCACATGGACTGCCGGAG..........................................

1.00

.....GAAGAAAGCGCGCTCACGAACTGCA.................................................................................................................

1.00

.........................................TTTGTTGTCCCAGTCCCACTGTGCATC...........................................................................

1.00

..............................................................TGCATCCGGACCGGAGCCCGGGCAC........................................................

1.00

.......................................................CCCACTGTGCATCCGGACC.....................................................................

1.00

........................................................................................TGGACTGCCGGAGAGGGC.....................................

1.00

........................................................................................TGGACTGCCGGAGAGGGCGCCATGGG.............................

1.00

.............................................................................................TGCCGGAGAGGGCGCCATGTGGCG..........................

1.00

..................................................CCAGTCCCACTGTGCATCCGGACCGGAGCC...............................................................

1.00

..............................................................................................GCCGGAGAGGGCGCCATGTGGCGC.........................

1.00

.............................................................................................TGCCGGAGAGGGCGCCATGTGGCGCCGGA.....................

1.00

....................................................................................CACATGGACCGTCGGCGAGG.......................................

0.80

....................................................................................CACATGGACCGTCGGCGAG........................................

0.53

................................................................................CGGGCACATGGACGGACGGA...........................................

0.50

....................................................................................CACATGGACCGTCGGCGAGGG......................................

0.50

.....................................................................................ACATGGACCGTCGGCGAGG.......................................

0.18

.............................................................................................................ATGGGGCGCCGGAGA...................

0.13

.........AAGGCGCCCTGACGAACTGC..................................................................................................................

0.11

...............................................................................GCGGGCACATGGACGGACGGA...........................................

0.10

.................................................................................................TGAGAGCGCGCCATGTG.............................

0.10

........................................................................CCGGAGCCGGGGCAC........................................................

0.09

................................................................TATCGGAACCGGAGCCCGG............................................................

0.06

...........................................................................................................CGATGTGGGGACGGAGAAT.................

0.06

................................................................................CTGGCACATGGACGGACGGA...........................................

0.06

Re-alignment of all predicted orthologs

Species	Coordinate	ID	Alignment
droSim3	3L:2686034-2686176 -	dsi_156	GCACGACTCAAAAAACAATTCTCCGGCGCCAC--AT--GGCGCCC-T--------------------CTCCG-GCAGT----CCATGTGCCCGG-GCTCC--------G--------GTCCGGAT--GCACAGTGGGACT-----GGGACAACAAATGAA-ATTTGG---GTGCAGTTCG---TG-AGCGCGCTTTC---TTCGCGCT-----
droSec2	scaffold_2:3151366-3151509 -		GCACGACTCAAAAAACAATTCTCCGGCGCCAC--AT--GGCGCCC-T--------------------CTCCA-GCAGT----GCATGTGCCCGG-GCTCC--------G--------GTCCGGAT--GCACAGTGGGACT-----GGGACAACAAATGAAAATTTGG---GTGCAGTTCG---TG-AGTGCGCTTTC---TTCGCGCT-----
dm3	chr3L:3157748-3157891 -		GCACGGCTCAAAAAACAATTCTCTGGCGCCAC--CT--GGCGCCC-T--------------------CTCTC-GCAGT----CCATGTGCCCGG-ACTCC--------G--------GGCCGGAT--GCACAGTGGGACT-----GGGACAACAAATGAAAATTTGG---GTGCAGTTCG---TG-AGCGCGCGTTT---TTCGCGCT-----
droEre2	scaffold_4784:3166784-3166931 -		GCACGGCTCAAAAAACAAATCTCCGGCGCCAC--AT--GGCGCCC-T--------------------CTCCG-GCAGTCCGTCCGTGTGCCCGG-GCTCC--------G--------GGCCGGAT--GCACAGTGGGACT-----GGGACAACAAATGAAAACTTTG---GTGCAGGTCG---TG-AGCGCGTGTTT---TTCGCGCT-----
droYak3	3L:8784050-8784197 +		GCACGGCTCAAAAAACAAATCTCCGGCGCCAC--AT--GGCGCCC-T--------------------CTCCG-GCAGTCCGTCCATGTGCCCGG-ACTCC--------G--------GGCCGGAT--GCACAGTGGGACT-----GGGACAACAAATGAAAATTTTG---GTGCAGGTCG---TG-AGCGCGCGTTT---TTCGCGCT-----
droEug1	scf7180000409466:881424-881567 -		GCATGGCTCTAAAAACAAATCTTCCGCGCCAC--TT--AGCGCCC-T--------------------TTCTG-GCAGT----CCATGTGC-CGG-GCTCT--------G--------GGCCGGAT--GCACATTGGAACT-----GGGACAACAAATGAAAATTTCG---ATGCAGGTTG---TAAAATACGCGATT---TACACGCA-----
droBia1	scf7180000302428:2505496-2505644 -		GCACGGCTCAAAAAACAAATCTCCGGGGCCTA--GT--GGCGCCCAT--------------------CTCCG-GCAGT----CCATGTGCCCGG-TCACC--------G--------GGCCGGAT--GCACAATGGGACT-----GGGACAACAAATGAAAATTTCG---ATGCAGGCTA---TGAAGTGCGCGATTAAAAGCGCACA-----
droTak1	scf7180000415378:244673-244815 +		GCACGGCTCAAAAAACAAATCTCCGGCGCCAC--TTGGGGCGCCCAT--------------------CTCCGCGCAGT----CCAAGTGTCCGG-ACTCC-A------G--------GACCGGAT--GCACAGTGAAACT--GGCGGGACAACAAATGAAAATTTCGGTTGTGCAGGTTG------------CG-------TTGCGCA-----
droEle1	scf7180000491249:2129911-2130069 +		GCACGGCTCAAAAAACAAATTTTCGGCGCCCC-AAT--GGCGCCC-TCTTCTC--------------CTCCG-ACAGT----CCATGTGCCTGGTAATCC--------C--------GTCCAGCT--GCACAGTGGGACT-----GGGACGACAAATGAAAATTTCG---GTGCAGGCTA---TAAAGTGCGGGAAT--TTCCGCACTTTTTG
droRho1	scf7180000777063:101092-101237 +		GCACGGCTCAAAAAACAAATCTCCTGCGCCGA--AT--GGCGCCC-T--------------------CTCTG-TCAGT----CCATGTGCCCGGCAATCC--------G--------GGCCGGAT--GCACATTGGGACT-----GGGACAACAAATGAAAATTTCG---ATGCAGGCTA---TAAAGTGCGGGGTT---TCCGCACA-----
droFic1	scf7180000454105:1471583-1471729 -		GCACGGCTCAAAAAACAAATCTCCGGCGCCGT--TC--GGCGCCCCT--------------------TTCCG-GCAGT----CCATGTGCCCGG-AGTTC--------C--------GTCCTGACTGGCACAGCGGGACT-----GGGACAACAAATGAAAATTTCG---GAGCAGGCGT----AAAGTTCGCGCTT---TTCGCGCA-----
droKik1	scf7180000302577:1340103-1340249 -		GCACGTCTCAAAAAACAAATCTCCGGCTTTGC--AT--CT------------------TTGCTCCGCCCTTG-CCAGT----TTCTGTGC-------TCC-TGGATGTC--------TCCAGGAT--GCACAG----ACT------GGACAACAAATGAAAATTTCG---ATGCAGGTTTGATTG-ATCCCTCGATCA--ATCGCTCT-----
droAna3	scaffold_13337:8958762-8958919 +		GCACGACTCAA--AACAAATCTCCACCGCCTCCGCC--GGCGGCC-TTTGTTCCATTTGTGCTCCACC--TGC-------------GTG-------CTCCTTGGATGTCGGAGGCATCCCCGGAG--GCACAGCGTGATGTCAGCTGGACAACAAATTAAAATTTCAG--GTGCAGGTGC-----------TCGGT--------GGCA-----
droBip1	scf7180000395984:8994-9135 +		GCACGACTCAA--AACAAATCTCCACCGCCACCGCC--GGCGGCC-TGTGTTCCAT-----------GTCGGC-------------GTG-------CTCCTTGGATGTCG-AG---TCCCCGGAG--GCACAGCGCGATC---GCTGGACAACAAATTAAAATTTCGG--GTGCAGGTGC-----------ACGGT--------GGCA-----

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droSim3

GCACGACTCAAAAAACAATTCTCCGGCGCCAC--AT--GGCGCCC-T--------------------CTCCG-GCAGT----CCATGTGCCCGG-GCTCC--------G--------GTCCGGAT--GCACAGTGGGACT-----GGGACAACAAATGAA-ATTTGG---GTGCAGTTCG---TG-AGCGCGCTTTC---TTCGCGCT-----	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
......................................................................................................................TCCGGAT--GCACAGTGGGACT-----G...................................................................	21	1	6.00	6	0	3	3	0	0	0	0	0	0	0	0	0
............................................................................................................................T--GCACAGTGGGACT-----GGGACA..............................................................	20	1	1.00	1	0	0	0	0	0	0	0	1	0	0	0	0
......................................................................CG-GCAGT----CCATGTGCCCGG-GC....................................................................................................................	21	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0	0
....................................................................................................................................................................TGG---GTGCAGTTCG---TG-AGCGCG.....................	21	1	1.00	1	0	0	0	0	0	0	0	1	0	0	0	0
........................................................................................................................CGGAT--GCACAGTGGGACT-----G...................................................................	19	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0
............................................................................................................................................................TGAA-ATTTGG---GTGCAGTTCG---TG-AGCGCGC....................	29	1	1.00	1	0	0	0	0	0	0	0	1	0	0	0	0
..............................................................................................................................................................AA-ATTTGG---GTGCAGTTCG---TG-A..........................	21	1	1.00	1	0	0	0	0	0	0	0	1	0	0	0	0
.....................................................................................................................GTCCGGAT--GCACAGTGGGACT-----....................................................................	21	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0	0
...........................................................................................................................................T-----GGGACAACAAATGAA-ATTTG...............................................	21	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0	0

droSec2

GCACGACTCAAAAAACAATTCTCCGGCGCCAC--AT--GGCGCCC-T--------------------CTCCA-GCAGT----GCATGTGCCCGG-GCTCC--------G--------GTCCGGAT--GCACAGTGGGACT-----GGGACAACAAATGAAAATTTGG---GTGCAGTTCG---TG-AGTGCGCTTTC---TTCGCGCT-----	Size	Hit Count	Total Norm	Total	V113 Male-body	V114 Embryo	V115 Head	M054 Female-body
.................................................................................................TCC--------G--------GTCCGGAT--GCACAGTGG.............................................................................	21	1	1.00	1	0	0	0	1
.....................................................................................................................................................................GG---GTGCAGTTCG---TG-AGTGCGC....................	21	1	1.00	1	1	0	0	0

droEre2

GCACGGCTCAAAAAACAAATCTCCGGCGCCAC--AT--GGCGCCC-T--------------------CTCCG-GCAGTCCGTCCGTGTGCCCGG-GCTCC--------G--------GGCCGGAT--GCACAGTGGGACT-----GGGACAACAAATGAAAACTTTG---GTGCAGGTCG---TG-AGCGCGTGTTT---TTCGCGCT-----	Size	Hit Count	Total Norm	Total	V040 Embryo	V060 Head	V107 Male-body	V108 Head	M055 Female-body	M057 Embryo
......................................................................................................................GCCGGAT--GCACAGTGGGACT-----GG..................................................................	22	1	1.00	1	0	0	0	0	1	0
..........................................................................................................................GAT--GCACAGTGGGACT-----GGGA................................................................	20	1	1.00	1	0	0	1	0	0	0

droYak3

GCACGGCTCAAAAAACAAATCTCCGGCGCCAC--AT--GGCGCCC-T--------------------CTCCG-GCAGTCCGTCCATGTGCCCGG-ACTCC--------G--------GGCCGGAT--GCACAGTGGGACT-----GGGACAACAAATGAAAATTTTG---GTGCAGGTCG---TG-AGCGCGCGTTT---TTCGCGCT-----	Size	Hit Count	Total Norm	Total	V046 Embryo	V052 Head	V120 Male-body	V058 Head	M026 Head	M043 Female-body	M056 Embryo
......................................................................................................................GCCGGAT--GCACAGTGGGACT-----G...................................................................	21	1	1.00	1	0	0	0	0	0	1	0

droEug1

GCATGGCTCTAAAAACAAATCTTCCGCGCCAC--TT--AGCGCCC-T--------------------TTCTG-GCAGT----CCATGTGC-CGG-GCTCT--------G--------GGCCGGAT--GCACATTGGAACT-----GGGACAACAAATGAAAATTTCG---ATGCAGGTTG---TAAAATACGCGATT---TACACGCA-----	Size	Hit Count	Total Norm	Total
No Reads

droBia1

GCACGGCTCAAAAAACAAATCTCCGGGGCCTA--GT--GGCGCCCAT--------------------CTCCG-GCAGT----CCATGTGCCCGG-TCACC--------G--------GGCCGGAT--GCACAATGGGACT-----GGGACAACAAATGAAAATTTCG---ATGCAGGCTA---TGAAGTGCGCGATTAAAAGCGCACA-----	Size	Hit Count	Total Norm	Total
No Reads

droTak1

GCACGGCTCAAAAAACAAATCTCCGGCGCCAC--TTGGGGCGCCCAT--------------------CTCCGCGCAGT----CCAAGTGTCCGG-ACTCC-A------G--------GACCGGAT--GCACAGTGAAACT--GGCGGGACAACAAATGAAAATTTCGGTTGTGCAGGTTG------------CG-------TTGCGCA-----	Size	Hit Count	Total Norm	Total
No Reads

droEle1

GCACGGCTCAAAAAACAAATTTTCGGCGCCCC-AAT--GGCGCCC-TCTTCTC--------------CTCCG-ACAGT----CCATGTGCCTGGTAATCC--------C--------GTCCAGCT--GCACAGTGGGACT-----GGGACGACAAATGAAAATTTCG---GTGCAGGCTA---TAAAGTGCGGGAAT--TTCCGCACTTTTTG	Size	Hit Count	Total Norm	Total
No Reads

droRho1

GCACGGCTCAAAAAACAAATCTCCTGCGCCGA--AT--GGCGCCC-T--------------------CTCTG-TCAGT----CCATGTGCCCGGCAATCC--------G--------GGCCGGAT--GCACATTGGGACT-----GGGACAACAAATGAAAATTTCG---ATGCAGGCTA---TAAAGTGCGGGGTT---TCCGCACA-----	Size	Hit Count	Total Norm	Total
No Reads

droFic1

GCACGGCTCAAAAAACAAATCTCCGGCGCCGT--TC--GGCGCCCCT--------------------TTCCG-GCAGT----CCATGTGCCCGG-AGTTC--------C--------GTCCTGACTGGCACAGCGGGACT-----GGGACAACAAATGAAAATTTCG---GAGCAGGCGT----AAAGTTCGCGCTT---TTCGCGCA-----	Size	Hit Count	Total Norm	Total
No Reads

droKik1

GCACGTCTCAAAAAACAAATCTCCGGCTTTGC--AT--CT------------------TTGCTCCGCCCTTG-CCAGT----TTCTGTGC-------TCC-TGGATGTC--------TCCAGGAT--GCACAG----ACT------GGACAACAAATGAAAATTTCG---ATGCAGGTTTGATTG-ATCCCTCGATCA--ATCGCTCT-----	Size	Hit Count	Total Norm	Total
No Reads

droAna3

GCACGACTCAA--AACAAATCTCCACCGCCTCCGCC--GGCGGCC-TTTGTTCCATTTGTGCTCCACC--TGC-------------GTG-------CTCCTTGGATGTCGGAGGCATCCCCGGAG--GCACAGCGTGATGTCAGCTGGACAACAAATTAAAATTTCAG--GTGCAGGTGC-----------TCGGT--------GGCA-----	Size	Hit Count	Total Norm	Total	V105 Male-body	V106 Head	V055 Head	V039 Embryo	M044 Female-body	M058 Embryo
..................ATCTCCACCGCCTCCGCC--GGC............................................................................................................................................................................	21	1	2.00	2	0	0	0	0	2	0
................................................................CACC--TGC-------------GTG-------CTCCTTGGATG..........................................................................................................	21	1	1.00	1	0	0	0	0	1	0
...................................................................................................................ATCCCCGGAG--GCACAGCGTGA...........................................................................	21	1	1.00	1	0	1	0	0	0	0
....................................................................................................................................................................TCAG--GTGCAGGTGC-----------TCGGT--------GG.......	21	1	1.00	1	1	0	0	0	0	0
.......................................................................GC-------------GTG-------CTCCTTGGATGTCGGA.....................................................................................................	21	1	1.00	1	0	0	0	0	1	0
.............................................................................................................................................................TAAAATTTCAG--GTGCAGGTGC-----------......................	21	1	1.00	1	0	0	0	0	1	0
................................CGCC--GGCGGCC-TTTGTTCCAT.............................................................................................................................................................	21	1	1.00	1	0	0	0	0	1	0
...................................................TCCATTTGTGCTCCACC--TGC-------------G..............................................................................................................................	21	1	1.00	1	0	0	0	0	1	0
..................................................................................................................CATCCCCGGAG--GCACAGCGTG............................................................................	21	1	1.00	1	0	0	0	0	1	0
..............................................................................................................GAGGCATCCCCGGAG--GCACAG................................................................................	21	1	1.00	1	0	0	0	0	1	0
....................................................................................................................................................................TCAG--GTGCAGGTGC-----------TCGGT--------.........	19	1	1.00	1	0	0	0	0	1	0
........................................................................................................ATGTCGGAGGCATCCCCGGAG--G.....................................................................................	22	1	1.00	1	0	0	0	0	1	0
...............................................................................................................................GCACAGCGTGATGTCAGCTGG.................................................................	21	1	1.00	1	0	1	0	0	0	0
..................................................................................................................................................................TTTCAG--GTGCAGGTGC-----------TCGG..................	20	1	1.00	1	0	0	0	0	1	0

droBip1

GCACGACTCAA--AACAAATCTCCACCGCCACCGCC--GGCGGCC-TGTGTTCCAT-----------GTCGGC-------------GTG-------CTCCTTGGATGTCG-AG---TCCCCGGAG--GCACAGCGCGATC---GCTGGACAACAAATTAAAATTTCGG--GTGCAGGTGC-----------ACGGT--------GGCA-----	Size	Hit Count	Total Norm	Total
No Reads

dsi_156

3L:2686084-2686126 -

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

-29.0	-28.5