dan_285

CACTGAAATACAGGACTTTCAGTTGCAGGTTGTAGGTTGCAACTAAAACCTACACACACACACGGTTATATGCAACTGAAATGTGGTGGTAGTGGGTGGTGGGTGGTGGGTGGTGTTGCAACAGCATCAGAAGCACCAACTCCTTTTCAACAAACAATGCG *********************************((((((((....((((((.(((.(((.((.((((.(((.((((.....)))).))))))).))))).)))))))))...))))))))....*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V106 head	V105 male body	M044 female body	V055 head	V039 embryo	M058 embryo
..................................................................................GTGGTGGTAGTGGGTGGTGGG..........................................................	21	0	1	22.00	22	22	0	0	0	0	0
...........................................................................................GTGGGTGGTGGGTGGTGGG...................................................	19	0	20	17.20	344	341	0	0	3	0	0
...........................................................................................GTGGGTGGTGGGTGGTGGGT..................................................	20	0	20	11.35	227	226	1	0	0	0	0
............................................................................................TGGGTGGTGGGTGGTGGGT..................................................	19	0	20	8.95	179	176	3	0	0	0	0
..................................................................................GTGGTGGTAGTGGGTGGTGG...........................................................	20	0	1	5.00	5	5	0	0	0	0	0
..............................................................................................GGTGGTGGGTGGTGGGTG.................................................	18	0	20	3.55	71	70	0	0	1	0	0
.................................................................................TGTGGTGGTAGTGGGTGGTGGG..........................................................	22	0	1	3.00	3	3	0	0	0	0	0
............................................................................................TGGGTGGTGGGTGGTGGGTG.................................................	20	0	20	1.45	29	29	0	0	0	0	0
..................................................................................GTGGTGGAAGTGGGTGGTGGGT.........................................................	22	1	1	1.00	1	1	0	0	0	0	0
.................................................................................TGTGGTGGTAGTGGGTGGTGGGAA........................................................	24	2	1	1.00	1	1	0	0	0	0	0
..................................................................................GTGGTGGTAGTGGGTGGTGGGT.........................................................	22	0	1	1.00	1	1	0	0	0	0	0
.....................................................................................GTGGTAGTGGGTGGTGGGTG........................................................	20	0	3	1.00	3	1	2	0	0	0	0
.................................................................................TGTGGTGGAAGTGGGTGGTGGG..........................................................	22	1	1	1.00	1	1	0	0	0	0	0
..................................................................................................GTGGGTGGTGGGTGGTGTTG...........................................	20	0	3	0.67	2	2	0	0	0	0	0
...............................................................................AATGTGGCCGTAGTGCGTGGT.............................................................	21	3	4	0.50	2	1	0	1	0	0	0
...............................................................................AATGTGGCCGTAGTGCGTGG..............................................................	20	3	9	0.44	4	1	0	2	0	0	1
...........................................................................................GTGGGTGGTGGGTGGTGGGTG.................................................	21	0	20	0.35	7	7	0	0	0	0	0
...............................................................................AATGTGGCCGTAGTGAGTGGT.............................................................	21	3	3	0.33	1	1	0	0	0	0	0
..................................................................................GTGGCGGTAGTGGGTGGTGGG..........................................................	21	1	3	0.33	1	1	0	0	0	0	0
..............................................................................................GGTGGTGGGTGGTGGGTGGTGTT............................................	23	0	3	0.33	1	1	0	0	0	0	0
......................................................................................TGGTAGTGGGTGGTGGGTGGTG.....................................................	22	0	3	0.33	1	0	1	0	0	0	0
..............................................................................................GGTGGTGGGTGGTGGGTGGTGTA............................................	23	1	7	0.29	2	2	0	0	0	0	0
......................................................................................TGGTAGTGGGTGGTGGGTG........................................................	19	0	4	0.25	1	1	0	0	0	0	0
.................................................................................................GGTGGGTGGTGGGTGGTGTT............................................	20	0	4	0.25	1	1	0	0	0	0	0
..................................................................................................GTGGGTGTAGGGTGGTGTTG...........................................	20	2	5	0.20	1	1	0	0	0	0	0
..................................................................................................GTGGGTGGTGGGGGGTGTTG...........................................	20	1	5	0.20	1	1	0	0	0	0	0
..............................................................................CAATGTGGTCGTAGTGCGTGG..............................................................	21	3	6	0.17	1	0	0	1	0	0	0
...........................................................................................GTGGGTGGTGGGTGGTGG....................................................	18	0	20	0.15	3	0	3	0	0	0	0
...............................................................................................GTGGTGGGTGGTGGGTGGT...............................................	19	0	20	0.15	3	3	0	0	0	0	0
.........................CGGATTGTAGGCTGCAACTA....................................................................................................................	20	3	7	0.14	1	0	0	1	0	0	0
..................................................................................................GTGGGTGGTGGGTGGTGT.............................................	18	0	7	0.14	1	1	0	0	0	0	0
.............................................................................................GGGTGGTGGGTGGTGGGTGGTG..............................................	22	0	9	0.11	1	1	0	0	0	0	0
...............................................................................................GTGGTGGGTGGTGGGTGG................................................	18	0	20	0.10	2	2	0	0	0	0	0
............................................................................................TCGGTGGTGGGTGGTGGGT..................................................	19	1	20	0.10	2	2	0	0	0	0	0
.............................................................................................GGGTGGTGGGTGGTGGGTG.................................................	19	0	20	0.10	2	2	0	0	0	0	0
............................................AAAACCTACACACGCACAG..................................................................................................	19	2	15	0.07	1	0	0	0	0	1	0
................TTTTGGTTGCAGGTTGTAG..............................................................................................................................	19	2	16	0.06	1	0	0	0	0	1	0
.................................................................................................AGTGGGTGTAGGGTGGTGTTG...........................................	21	3	17	0.06	1	1	0	0	0	0	0
.............................................................................................GGGTGGTGGGTGGTGGGTGGT...............................................	21	0	18	0.06	1	1	0	0	0	0	0
...........................................................................................GTGGGTGTTGGGTGGTGGGT..................................................	20	1	20	0.05	1	1	0	0	0	0	0
...........................................................................................GTGGGTGGTCGGTGGTGGGT..................................................	20	1	20	0.05	1	1	0	0	0	0	0
............................................................................................TGGGTGTTGGGTGGTGGGT..................................................	19	1	20	0.05	1	1	0	0	0	0	0
..........................................................................................AGTGGGTGGTGGGTGGTGG....................................................	19	0	20	0.05	1	1	0	0	0	0	0
.................................................................................TGTGGTGGTAGTGGGTTTTGT...........................................................	21	3	20	0.05	1	0	0	0	1	0	0
.............................................................................................GGGTGGTGGGTGGTGGGTC.................................................	19	1	20	0.05	1	1	0	0	0	0	0
............................................................................................TGGGTGGTGCGTGGTGGGT..................................................	19	1	20	0.05	1	1	0	0	0	0	0
....................................................................................GATCGTAGTGGGTGGTGG...........................................................	18	2	20	0.05	1	0	0	1	0	0	0
...........................................................................................GTGGGTGGTGGGTGGTGAGT..................................................	20	1	20	0.05	1	1	0	0	0	0	0
........................................................................................................GGTGGGTGGTGTTGCAGT.......................................	18	2	20	0.05	1	0	0	0	1	0	0
.................................................................................TGGGGTGGTAGTGGGTGGG.............................................................	19	2	20	0.05	1	1	0	0	0	0	0
...........................................................................................GTGGGTGGTGGTTGGTGGGT..................................................	20	1	20	0.05	1	1	0	0	0	0	0
...........................................................................................GTGGGTGGTGGGTGGTGGGTGG................................................	22	0	20	0.05	1	1	0	0	0	0	0
............................................................................................TGGGTGGTGGGTGGTGGG...................................................	18	0	20	0.05	1	0	0	1	0	0	0

CACTGAAATACAGGACTTTCAGTTGCAGGTTGTAGGTTGCAACTAAAACCTACACACACACACGGTTATATGCAACTGAAATGTGGTGGTAGTGGGTGGTGGGTGGTGGGTGGTGTTGCAACAGCATCAGAAGCACCAACTCCTTTTCAACAAACAATGCG
***********************************((((((((....((((((.(((.(((.((.((((.(((.((((.....)))).))))))).))))).)))))))))...))))))))....***********************************

Read size

# Mismatch

Hit Count

Total Norm

Total

V106
head

V105
male body

M044
female body

V055
head

V039
embryo

M058
embryo

..................................................................................GTGGTGGTAGTGGGTGGTGGG..........................................................

22.00

...........................................................................................GTGGGTGGTGGGTGGTGGG...................................................

17.20

344

341

...........................................................................................GTGGGTGGTGGGTGGTGGGT..................................................

11.35

227

226

............................................................................................TGGGTGGTGGGTGGTGGGT..................................................

8.95

179

176

..................................................................................GTGGTGGTAGTGGGTGGTGG...........................................................

5.00

..............................................................................................GGTGGTGGGTGGTGGGTG.................................................

3.55

.................................................................................TGTGGTGGTAGTGGGTGGTGGG..........................................................

3.00

............................................................................................TGGGTGGTGGGTGGTGGGTG.................................................

1.45

..................................................................................GTGGTGGAAGTGGGTGGTGGGT.........................................................

1.00

.................................................................................TGTGGTGGTAGTGGGTGGTGGGAA........................................................

1.00

..................................................................................GTGGTGGTAGTGGGTGGTGGGT.........................................................

1.00

.....................................................................................GTGGTAGTGGGTGGTGGGTG........................................................

1.00

.................................................................................TGTGGTGGAAGTGGGTGGTGGG..........................................................

1.00

..................................................................................................GTGGGTGGTGGGTGGTGTTG...........................................

0.67

...............................................................................AATGTGGCCGTAGTGCGTGGT.............................................................

0.50

...............................................................................AATGTGGCCGTAGTGCGTGG..............................................................

0.44

...........................................................................................GTGGGTGGTGGGTGGTGGGTG.................................................

0.35

...............................................................................AATGTGGCCGTAGTGAGTGGT.............................................................

0.33

..................................................................................GTGGCGGTAGTGGGTGGTGGG..........................................................

0.33

..............................................................................................GGTGGTGGGTGGTGGGTGGTGTT............................................

0.33

......................................................................................TGGTAGTGGGTGGTGGGTGGTG.....................................................

0.33

..............................................................................................GGTGGTGGGTGGTGGGTGGTGTA............................................

0.29

......................................................................................TGGTAGTGGGTGGTGGGTG........................................................

0.25

.................................................................................................GGTGGGTGGTGGGTGGTGTT............................................

0.25

..................................................................................................GTGGGTGTAGGGTGGTGTTG...........................................

0.20

..................................................................................................GTGGGTGGTGGGGGGTGTTG...........................................

0.20

..............................................................................CAATGTGGTCGTAGTGCGTGG..............................................................

0.17

...........................................................................................GTGGGTGGTGGGTGGTGG....................................................

0.15

...............................................................................................GTGGTGGGTGGTGGGTGGT...............................................

0.15

.........................CGGATTGTAGGCTGCAACTA....................................................................................................................

0.14

..................................................................................................GTGGGTGGTGGGTGGTGT.............................................

0.14

.............................................................................................GGGTGGTGGGTGGTGGGTGGTG..............................................

0.11

...............................................................................................GTGGTGGGTGGTGGGTGG................................................

0.10

............................................................................................TCGGTGGTGGGTGGTGGGT..................................................

0.10

.............................................................................................GGGTGGTGGGTGGTGGGTG.................................................

0.10

............................................AAAACCTACACACGCACAG..................................................................................................

0.07

................TTTTGGTTGCAGGTTGTAG..............................................................................................................................

0.06

.................................................................................................AGTGGGTGTAGGGTGGTGTTG...........................................

0.06

.............................................................................................GGGTGGTGGGTGGTGGGTGGT...............................................

0.06

...........................................................................................GTGGGTGTTGGGTGGTGGGT..................................................

0.05

...........................................................................................GTGGGTGGTCGGTGGTGGGT..................................................

0.05

............................................................................................TGGGTGTTGGGTGGTGGGT..................................................

0.05

..........................................................................................AGTGGGTGGTGGGTGGTGG....................................................

0.05

.................................................................................TGTGGTGGTAGTGGGTTTTGT...........................................................

0.05

.............................................................................................GGGTGGTGGGTGGTGGGTC.................................................

0.05

............................................................................................TGGGTGGTGCGTGGTGGGT..................................................

0.05

....................................................................................GATCGTAGTGGGTGGTGG...........................................................

0.05

...........................................................................................GTGGGTGGTGGGTGGTGAGT..................................................

0.05

........................................................................................................GGTGGGTGGTGTTGCAGT.......................................

0.05

.................................................................................TGGGGTGGTAGTGGGTGGG.............................................................

0.05

...........................................................................................GTGGGTGGTGGTTGGTGGGT..................................................

0.05

...........................................................................................GTGGGTGGTGGGTGGTGGGTGG................................................

0.05

............................................................................................TGGGTGGTGGGTGGTGGG...................................................

0.05

GTGACTTTATGTCCTGAAAGTCAACGTCCAACATCCAACGTTGATTTTGGATGTGTGTGTGTGCCAATATACGTTGACTTTACACCACCATCACCCACCACCCACCACCCACCACAACGTTGTCGTAGTCTTCGTGGTTGAGGAAAAGTTGTTTGTTACGC *********************************((((((((....((((((.(((.(((.((.((((.(((.((((.....)))).))))))).))))).)))))))))...))))))))....*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M044 female body	M058 embryo	V039 embryo	V055 head
.........................................................................................................................GTCCCAGTCTTCGTGGATGAG...................	21	3	2	0.50	1	1	0	0	0
......................................................................................................CACCACCCACCTCAAGGTTG.......................................	20	2	5	0.20	1	0	1	0	0
.TCACTCTATGTACTGAAAGT............................................................................................................................................	20	3	10	0.10	1	0	1	0	0
.........................................................................................................................................CTGAGGAAGAGTTGTTGGTTA...	21	3	12	0.08	1	1	0	0	0
.................................................................................................CTACCCACCACCCAGCACATC...........................................	21	3	15	0.07	1	0	0	1	0
................................................................................................ACCACCCACCTCCAACCACTAC...........................................	22	3	15	0.07	1	0	1	0	0
...............................................................................................CACCACCCAACACCCGCTACA.............................................	21	3	20	0.05	1	0	1	0	0
..........................................................GTGTGCCAATAAACGAAGA....................................................................................	19	3	20	0.05	1	0	0	0	1

GTGACTTTATGTCCTGAAAGTCAACGTCCAACATCCAACGTTGATTTTGGATGTGTGTGTGTGCCAATATACGTTGACTTTACACCACCATCACCCACCACCCACCACCCACCACAACGTTGTCGTAGTCTTCGTGGTTGAGGAAAAGTTGTTTGTTACGC
***********************************((((((((....((((((.(((.(((.((.((((.(((.((((.....)))).))))))).))))).)))))))))...))))))))....***********************************

Read size

# Mismatch

Hit Count

Total Norm

Total

M044
female body

M058
embryo

V039
embryo

V055
head

.........................................................................................................................GTCCCAGTCTTCGTGGATGAG...................

0.50

......................................................................................................CACCACCCACCTCAAGGTTG.......................................

0.20

.TCACTCTATGTACTGAAAGT............................................................................................................................................

0.10

.........................................................................................................................................CTGAGGAAGAGTTGTTGGTTA...

0.08

.................................................................................................CTACCCACCACCCAGCACATC...........................................

0.07

................................................................................................ACCACCCACCTCCAACCACTAC...........................................

0.07

...............................................................................................CACCACCCAACACCCGCTACA.............................................

0.05

..........................................................GTGTGCCAATAAACGAAGA....................................................................................

0.05

Species	Coordinate	ID	Alignment
droAna3	scaffold_12929:3163640-3163800 +	dan_285	CACTGAAATACAGGACTTTC------AGTTGCAGGTTGTAGGTTGCAACTAAAACCTACACACACA-----------CACGGTTATATGC-AACTGAAATGTGGTGGTAGTGGGTG-GTGGG-----------------TGGTGGGTGGTGTTGCAACAGCATCAGAAGCACCAACTCCTTTTCAACAAACAATGCG
droBip1	scf7180000395987:16665-16752 +		CAAC---ATCCAGA-----C------AGTTGCA--G------TTGCAACTAAAA------------------TCCACCACGACTATATGC-AACTGAAACGTGG--------------------------------------------------------------------CAACTCCTCTTCCACAAACAATGCA
droFic1	scf7180000453775:101763-101882 -		CACCCACATTTTCCA------TTTCCACCTCCA--TT------TTCGCCCGC------------------ATCCTACTACGCCCAC--AC-AAGTGCGTCGCAG---TTTTCCCCCTCT-----------------TGCTGTTCT---------------------GATGAAAAGCTCCT-TTTCACAAACAATGTG
droBia1	scf7180000301703:111092-111222 -		CACTTCCACT-------TCCATTTCCACGTCCA--TT------TCC-CC--C---ATCCACCCGCTCGCGATCC---CACGCCCCC--ACGGACTGCGTCACAG---TTTTGCCTC-CTGGC-----------------TGGCCTCC-----------------GGGCTGACGAACTCCT--TTCACAAACAACGTG
droEug1	scf7180000409548:362683-362705 +		A-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTCCT-TTCAACAAACAATGTG
dm3	chrX:4586622-4586625 +		CATT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droSim2	x:4277417-4277438 +		A-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTCCT--TTCACAAGCAATGTG
droSec2	scaffold_4:2143322-2143444 -		TGTTTTCACAGCCCA------TTTTCAC------------------G-----------------CTCCGCATCC---AACGCCCAT--GC-AACTGCGTTGCAG---TTTTCCTTC-CTCTCTGTATTTTTTTTTTGGTTGTCCG---------------------CGTGAAGAACACCT--TTTACAAGCAATGTG

Species

Coordinate

Alignment

droAna3

scaffold_12929:3163640-3163800 +

dan_285

CACTGAAATACAGGACTTTC------AGTTGCAGGTTGTAGGTTGCAACTAAAACCTACACACACA-----------CACGGTTATATGC-AACTGAAATGTGGTGGTAGTGGGTG-GTGGG-----------------TGGTGGGTGGTGTTGCAACAGCATCAGAAGCACCAACTCCTTTTCAACAAACAATGCG

droBip1

scf7180000395987:16665-16752 +

CAAC---ATCCAGA-----C------AGTTGCA--G------TTGCAACTAAAA------------------TCCACCACGACTATATGC-AACTGAAACGTGG--------------------------------------------------------------------CAACTCCTCTTCCACAAACAATGCA

droFic1

scf7180000453775:101763-101882 -

CACCCACATTTTCCA------TTTCCACCTCCA--TT------TTCGCCCGC------------------ATCCTACTACGCCCAC--AC-AAGTGCGTCGCAG---TTTTCCCCCTCT-----------------TGCTGTTCT---------------------GATGAAAAGCTCCT-TTTCACAAACAATGTG

droBia1

scf7180000301703:111092-111222 -

CACTTCCACT-------TCCATTTCCACGTCCA--TT------TCC-CC--C---ATCCACCCGCTCGCGATCC---CACGCCCCC--ACGGACTGCGTCACAG---TTTTGCCTC-CTGGC-----------------TGGCCTCC-----------------GGGCTGACGAACTCCT--TTCACAAACAACGTG

droEug1

scf7180000409548:362683-362705 +

A-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTCCT-TTCAACAAACAATGTG

dm3

chrX:4586622-4586625 +

CATT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

droSim2

x:4277417-4277438 +

A-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTCCT--TTCACAAGCAATGTG

droSec2

scaffold_4:2143322-2143444 -

TGTTTTCACAGCCCA------TTTTCAC------------------G-----------------CTCCGCATCC---AACGCCCAT--GC-AACTGCGTTGCAG---TTTTCCTTC-CTCTCTGTATTTTTTTTTTGGTTGTCCG---------------------CGTGAAGAACACCT--TTTACAAGCAATGTG

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droAna3

CACTGAAATACAGGACTTTC------AGTTGCAGGTTGTAGGTTGCAACTAAAACCTACACACACA-----------CACGGTTATATGC-AACTGAAATGTGGTGGTAGTGGGTG-GTGGG-----------------TGGTGGGTGGTGTTGCAACAGCATCAGAAGCACCAACTCCTTTTCAACAAACAATGCG	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
....................................................................................................GTGGTGGTAGTGGGTG-GTGGG-----------------..........................................................	21	1	22.00	22	0	0	0	0	0	22
.............................................................................................................GTGGGTG-GTGGG-----------------TGGTGGG...................................................	19	20	17.20	344	0	0	0	3	0	341
.............................................................................................................GTGGGTG-GTGGG-----------------TGGTGGGT..................................................	20	20	11.35	227	0	0	0	0	1	226
..............................................................................................................TGGGTG-GTGGG-----------------TGGTGGGT..................................................	19	20	8.95	179	0	0	0	0	3	176
....................................................................................................GTGGTGGTAGTGGGTG-GTGG............................................................................	20	1	5.00	5	0	0	0	0	0	5
................................................................................................................GGTG-GTGGG-----------------TGGTGGGTG.................................................	18	20	3.55	71	0	0	0	1	0	70
...................................................................................................TGTGGTGGTAGTGGGTG-GTGGG-----------------..........................................................	22	1	3.00	3	0	0	0	0	0	3
..............................................................................................................TGGGTG-GTGGG-----------------TGGTGGGTG.................................................	20	20	1.45	29	0	0	0	0	0	29
...................................................................................................TGTGGTGGTAGTGGGTG-GTGGG-----------------AA........................................................	24	1	1.00	1	0	0	0	0	0	1
....................................................................................................GTGGTGGTAGTGGGTG-GTGGG-----------------T.........................................................	22	1	1.00	1	0	0	0	0	0	1
.......................................................................................................GTGGTAGTGGGTG-GTGGG-----------------TG........................................................	20	3	1.00	3	0	0	0	0	2	1
.....................................................................................................................GTGGG-----------------TGGTGGGTGGTGTTG...........................................	20	3	0.67	2	0	0	0	0	0	2
.............................................................................................................GTGGGTG-GTGGG-----------------TGGTGGGTG.................................................	21	20	0.35	7	0	0	0	0	0	7
................................................................................................................GGTG-GTGGG-----------------TGGTGGGTGGTGTT............................................	23	3	0.33	1	0	0	0	0	0	1
........................................................................................................TGGTAGTGGGTG-GTGGG-----------------TGGTG.....................................................	22	3	0.33	1	0	0	0	0	1	0
................................................................................................................GGTG-GTGGG-----------------TGGTGGGTGGTGTA............................................	23	7	0.29	2	0	0	0	0	0	2
........................................................................................................TGGTAGTGGGTG-GTGGG-----------------TG........................................................	19	4	0.25	1	0	0	0	0	0	1
...................................................................................................................G-GTGGG-----------------TGGTGGGTGGTGTT............................................	20	4	0.25	1	0	0	0	0	0	1
.............................................................................................................GTGGGTG-GTGGG-----------------TGGTGG....................................................	18	20	0.15	3	0	0	0	0	3	0
.................................................................................................................GTG-GTGGG-----------------TGGTGGGTGGT...............................................	19	20	0.15	3	0	0	0	0	0	3
.....................................................................................................................GTGGG-----------------TGGTGGGTGGTGT.............................................	18	7	0.14	1	0	0	0	0	0	1
...............................................................................................................GGGTG-GTGGG-----------------TGGTGGGTGGTG..............................................	22	9	0.11	1	0	0	0	0	0	1
.................................................................................................................GTG-GTGGG-----------------TGGTGGGTGG................................................	18	20	0.10	2	0	0	0	0	0	2
...............................................................................................................GGGTG-GTGGG-----------------TGGTGGGTG.................................................	19	20	0.10	2	0	0	0	0	0	2
...............................................................................................................GGGTG-GTGGG-----------------TGGTGGGTGGT...............................................	21	18	0.06	1	0	0	0	0	0	1
............................................................................................................AGTGGGTG-GTGGG-----------------TGGTGG....................................................	19	20	0.05	1	0	0	0	0	0	1
...............................................................................................................GGGTG-GTGGG-----------------TGGTGGGTC.................................................	19	20	0.05	1	0	0	0	0	0	1
............................................................................................................................................GGTGGGTGGTGTTGCAGT.......................................	18	20	0.05	1	0	0	0	1	0	0
.............................................................................................................GTGGGTG-GTGGG-----------------TGGTGGGTGG................................................	22	20	0.05	1	0	0	0	0	0	1
..............................................................................................................TGGGTG-GTGGG-----------------TGGTGGG...................................................	18	20	0.05	1	1	0	0	0	0	0

droBip1

CAAC---ATCCAGA-----C------AGTTGCA--G------TTGCAACTAAAA------------------TCCACCACGACTATATGC-AACTGAAACGTGG--------------------------------------------------------------------CAACTCCTCTTCCACAAACAATGCA	Size	Hit Count	Total Norm	Total
No Reads

droFic1

CACCCACATTTTCCA------TTTCCACCTCCA--TT------TTCGCCCGC------------------ATCCTACTACGCCCAC--AC-AAGTGCGTCGCAG---TTTTCCCCCTCT-----------------TGCTGTTCT---------------------GATGAAAAGCTCCT-TTTCACAAACAATGTG	Size	Hit Count	Total Norm	Total
No Reads

droBia1

CACTTCCACT-------TCCATTTCCACGTCCA--TT------TCC-CC--C---ATCCACCCGCTCGCGATCC---CACGCCCCC--ACGGACTGCGTCACAG---TTTTGCCTC-CTGGC-----------------TGGCCTCC-----------------GGGCTGACGAACTCCT--TTCACAAACAACGTG	Size	Hit Count	Total Norm	Total
No Reads

droEug1

A-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTCCT-TTCAACAAACAATGTG	Size	Hit Count	Total Norm	Total
No Reads

dm3

CATT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

Total

GSM154618
Ovary

GSM154620
Ovary

GSM154621
Ovary

GSM154622
Ovary

GSM180328
Head

GSM180329
Mixed-body

GSM180330
Embryo

GSM180331
Embryo

GSM180332
Embryo

GSM180333
Embryo

GSM180334
Larvae

GSM180335
Disc

GSM180336
Pupae

GSM180337
S2

GSM231091
Ovary

GSM239041
Head

GSM239050
Head

GSM239051
S2

GSM239052
S2

GSM246084
Head

GSM266765
S2

GSM280082
Ovary

GSM280083
Ovary

GSM280084
Ovary

GSM280085
Testis

GSM280086
Ovary

GSM280087
S2-NP

GSM280088
S2-NP

GSM312995
Head

GSM313160
Head

GSM313161
Head

GSM313162
Head

GSM313163
Head

GSM313164
Head

GSM313165
Head

GSM343287
Embryo

GSM379050
Ovary

GSM379051
Ovary

GSM379052
Ovary

GSM379053
Ovary

GSM379054
Ovary

GSM379055
Ovary

GSM379056
Ovary

GSM379057
Ovary

GSM379058
Ovary

GSM379059
Ovary

GSM379060
Ovary

GSM379061
Ovary

GSM379062
Ovary

GSM379063
Ovary

GSM379064
Ovary

GSM379065
Ovary

GSM379066
Ovary

GSM379067
Ovary

GSM424739
S2

GSM424740
S2

GSM424741
S2

GSM467729
Female-body

GSM467730
Female-body

GSM467731
Female-body

M002
CS

M003
Male-body

M004
Male-body

M005
ML-DmD32

M006
ML-DmD32

M029
OSC

M030
OSC

M031
OSC

M032
S2-R+

M033
S2-R+

M034
S2-R+

M035
S2-R+

M036
S2-R+

M037
S2-R+

M038
S2-R+

M039
S2-R+

M048
S2-R+

OSS2
OSS

OSS6
OSS

OSS7
OSS

OSS8
OSS

S1
Head

S10
Embryo

S11
Embryo

S12
Embryo

S13
Embryo

S14
Embryo

S15
S2-GMR

S16
Kc

S17
Larvae

S18
Larvae

S19
Pupae

S2
Head

S20
Pupae

S21
Disc

S22
Head

S23
Female-body

S24
Male-body

S25
Larvae

S26
Larvae

S27
Pupae

S28
Pupae

S29
Head

S3
Male-body

S30
S2-GMR

S31
S2

S32
S2

S33
Kc

S34
Kc

S35
Kc

S4
Female-body

S5
Disc

S6
Embryo

S7
Embryo

S8
S2

S9
Embryo

SRR001337
Head

SRR001338
Head

SRR001339
Head

SRR001340
Head

SRR001341
Head

SRR001342
Head

SRR001343
Head

SRR001344
Head

SRR001345
Head

SRR001346
Head

SRR001347
Head

SRR001348
Head

SRR001349
Head

SRR001664
Head

SRR010951
Ovary

SRR010952
Ovary

SRR010953
Ovary

SRR010954
Ovary

SRR010955
Ovary

SRR010956
Ovary

SRR010957
Ovary

SRR010958
Ovary

SRR010959
Ovary

SRR010960
Ovary

SRR014268
Embryo

SRR014269
Embryo

SRR014270
Embryo

SRR014271
Embryo

SRR014272
Embryo

SRR014273
Ovary

SRR014274
Ovary

SRR014275
Ovary

SRR014276
Ovary

SRR014277
Ovary

SRR014278
Ovary

SRR014279
Ovary

SRR014280
Ovary

SRR014281
Ovary

SRR014282
Ovary

SRR023197
S2

SRR023399
S2

SRR023400
S2

SRR023402
S2

SRR023407
S2

SRR029028
S2

SRR029029
S2

SRR029030
S2

SRR029031
S2

SRR029032
S2

SRR029033
S2

SRR029608
Head

SRR029633
Head

SRR030145
gb3

SRR031692
Head

SRR031693
Head

SRR031694
Head

SRR031696
Head

SRR031697
Head

SRR031698
Head

SRR031699
Head

SRR031700
Head

SRR031701
Head

SRR031702
Head

SRR031703
Head

SRR031704
Head

SRR032092
S2

SRR032093
S2

SRR032094
S2

SRR032095
S2-NP

SRR032096
S2-NP

SRR032152
Head

SRR060643
Testis

SRR060644
Ovary

SRR060645
Testis

SRR060646
Ovary

SRR060647
Ovary

SRR060648
Ovary

SRR060649
Ovary

SRR060650
Testis

SRR060651
Ovary

SRR060652
Testis

SRR060653
Ovary

SRR065151
Ovary

SRR065152
Ovary

SRR065153
Ovary

SRR065154
Ovary

SRR065155
Ovary

SRR065800
Ovary

SRR065801
Ovary

SRR065802
Ovary

SRR065803
Ovary

SRR065804
Ovary

SRR065805
Ovary

SRR065806
Ovary

SRR065807
Ovary

SRR097865
S2-NP

SRR097866
S2-NP

SRR097867
S2-NP

SRR298536
Ovary

SRR298537
Ovary

SRR298711
Ovary

SRR298712
Ovary

SRR317110
Ovary

SRR317111
Ovary

SRR317112
Ovary

SRR317113
Ovary

SRR317114
Ovary

SRR317115
Ovary

SRR317116
Ovary

SRR317117
Ovary

SRR341115
S2

SRR341116
S2

SRR341117
S2

SRR341118
S2

SRR351332
Mixed-body

SRR351333
Mixed-body

T004
OSC

T005
CME-L1

V001
Embryo

V002
Embryo

V003
S2

V006
Female-body

V007
Head

V008
S2

V009
CME-L1

V010
ML-DmD20-C5

V011
Sg4

V012
Male-body

V013
Head

V014
DTT

V015
DreRFHV

V018
Kc167

V019
GM2

V020
S2-R+

V021
ML-DmD21

V022
ML-DmD32

V023
Head

V024
Kc167

V025
S2-R+

V026
1182-2H

V027
ML-DmD21

V028
CME-W1-Cl.8+

V029
ML-DmD9

V030
ML-DmD8

V031
GM2

V032
S1

V033
CME-W1-Cl.8+

V034
ML-DmD16-C3

V035
ML-DmD32

V036
ML-DmD20-C5

V037
S2

V038
S2

V063
Ovary

V0632
Ovary

V064
Ovary

V0642
Ovary

V065
Ovary

V0652
Ovary

V066
Ovary

V0662
Ovary

V067
S2-NP

V073
mbn2

V074
S3

V075
ML-DmBG1-C1

V076
ML-DmBG3-C2

V077
Head

V078
Head

V079
Head

V080
Head

V081
Embryo

V082
Embryo

V083
Male-body

V084
Female-body

V085
CME-W2

V086
Female-body

V088
Ovary

V0882
Ovary

V089
Ovary

V0892
Ovary

V090
Male-body

V091
fGS/OSS

V092
Male-body

V093
Male-body

V094
S2-R+

V095
S2-R+

V096
Ovary

V097
Ovary

V098
Ovary

V125
ML-DmD9

V126
CME-L1

V127
G2

V128
S3

V129
ML-DmBG1-C1

V130
ML-DmBG3-C2

V131
ML-DmD16-C3

V132
ML-DmD32

V133
Sg4

V134
ML-DmD8

V135
CME-W2

V136
Male-body

V137
Head

V138
Male-body

V139
Female-body

V140
Female-body

V141
Female-body

V142
Female-body

V144
OSC

V145
S2

V146
S1

V147
1182-2H

V148
mbn2

GSM1528798
follicle cells

No Reads

droSim2

A-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTCCT--TTCACAAGCAATGTG

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

No Reads

droSec2

TGTTTTCACAGCCCA------TTTTCAC------------------G-----------------CTCCGCATCC---AACGCCCAT--GC-AACTGCGTTGCAG---TTTTCCTTC-CTCTCTGTATTTTTTTTTTGGTTGTCCG---------------------CGTGAAGAACACCT--TTTACAAGCAATGTG	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
No Reads

dan_285

scaffold_12929:3163690-3163750 +

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

-33.7	-32.9	-32.9