dpe_128

GAAAACATCGAATCGCTCCTGCACACCCATTAACGATCTCCCCCGGAGAACTTGGCGCACTTGGGCAGGAGGTCCATCTCATACCTCCTGCCCAAGTGCGCCAAGTACTCTGGTTCAGGTCAGGCCAGAATTCTCTTTACACTGAGGGATTTACACAAT *********************************((((...((((((.((((((((((((((((((((((((.........)))))))))))))))))))))))).))))))...))))...**********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V050 head	V057 head	V042 embryo	V111 male body	M042 female body
.......................................................................................CTGCCCAAGTGCGCCAAGTAC...................................................	21	0	1	11.00	11	5	5	1	0	0
.......................................................................................CTGCCCAAGTGCGCCAAGTA....................................................	20	0	1	5.00	5	3	0	0	2	0
................................................AACTTGGCGCACTTGGGCA............................................................................................	19	0	1	4.00	4	2	2	0	0	0
..................................................CTTGGCGCACTTGGGCAGGA.........................................................................................	20	0	2	2.50	5	4	0	0	0	1
................................................AACTTGGCGCACTTGGGCAG...........................................................................................	20	0	1	2.00	2	0	2	0	0	0
................................................AACTTGGCGCACTTGGGCAGGA.........................................................................................	22	0	1	2.00	2	0	0	2	0	0
..................................................CTTGGCGCACTTGGGCAGG..........................................................................................	19	0	2	2.00	4	2	2	0	0	0
................................................AACTTGGCGCACTTGGGCAGG..........................................................................................	21	0	1	1.00	1	0	1	0	0	0
.......................................................................................CTGCCCAAGTGCGCCAAGTACT..................................................	22	0	1	1.00	1	1	0	0	0	0
................................................AACGTGGCGCACTTGGGCAGT..........................................................................................	21	2	1	1.00	1	0	1	0	0	0
.......................................................................................CTGCACAAGTGGGCCAAGTACT..................................................	22	2	1	1.00	1	0	0	1	0	0
.......................................................................................CTGCCCAAGTGCGCCAAGTAT...................................................	21	1	1	1.00	1	1	0	0	0	0
................................................AACTTGGCGCACATGGGCA............................................................................................	19	1	1	1.00	1	1	0	0	0	0
.......................................................................................CTGCCCAAGTGCGCCACGTA....................................................	20	1	1	1.00	1	1	0	0	0	0
.......................................................................................CTGCCCAAGTGCGCCAAGT.....................................................	19	0	2	0.50	1	0	1	0	0	0
.................................................ACTTGGCGTACTTGGGCAGGAG........................................................................................	22	1	2	0.50	1	0	1	0	0	0
..................................................CTTGGCGCGCTTGGGCAGGA.........................................................................................	20	1	2	0.50	1	0	1	0	0	0
....................................................TGGCGCACTTGGGCAGGA.........................................................................................	18	0	2	0.50	1	1	0	0	0	0
...................................................TTGGCGCACTTGGGCAGG..........................................................................................	18	0	2	0.50	1	0	1	0	0	0
..................................................CTTGGCGCACTTGAGCAGGA.........................................................................................	20	1	2	0.50	1	1	0	0	0	0
...................................................TTGGCTCACTTGGGCAGGA.........................................................................................	19	1	2	0.50	1	0	0	0	0	1
.................................................ACTTGGCGCACTTGGGCAGG..........................................................................................	20	0	2	0.50	1	0	0	0	0	1
..................................................CGGGGCGCACTTGGGCAGGT.........................................................................................	20	3	14	0.07	1	0	1	0	0	0
..............................................AGAGCTTGACGCACTTGG...............................................................................................	18	2	20	0.05	1	0	0	0	0	1
........................................CCCCGGCTAACTTCGCGC.....................................................................................................	18	3	20	0.05	1	0	1	0	0	0

GAAAACATCGAATCGCTCCTGCACACCCATTAACGATCTCCCCCGGAGAACTTGGCGCACTTGGGCAGGAGGTCCATCTCATACCTCCTGCCCAAGTGCGCCAAGTACTCTGGTTCAGGTCAGGCCAGAATTCTCTTTACACTGAGGGATTTACACAAT
***********************************((((...((((((.((((((((((((((((((((((((.........)))))))))))))))))))))))).))))))...))))...************************************

Read size

# Mismatch

Hit Count

Total Norm

Total

V050
head

V057
head

V042
embryo

V111
male body

M042
female body

.......................................................................................CTGCCCAAGTGCGCCAAGTAC...................................................

11.00

.......................................................................................CTGCCCAAGTGCGCCAAGTA....................................................

5.00

................................................AACTTGGCGCACTTGGGCA............................................................................................

4.00

..................................................CTTGGCGCACTTGGGCAGGA.........................................................................................

2.50

................................................AACTTGGCGCACTTGGGCAG...........................................................................................

2.00

................................................AACTTGGCGCACTTGGGCAGGA.........................................................................................

2.00

..................................................CTTGGCGCACTTGGGCAGG..........................................................................................

2.00

................................................AACTTGGCGCACTTGGGCAGG..........................................................................................

1.00

.......................................................................................CTGCCCAAGTGCGCCAAGTACT..................................................

1.00

................................................AACGTGGCGCACTTGGGCAGT..........................................................................................

1.00

.......................................................................................CTGCACAAGTGGGCCAAGTACT..................................................

1.00

.......................................................................................CTGCCCAAGTGCGCCAAGTAT...................................................

1.00

................................................AACTTGGCGCACATGGGCA............................................................................................

1.00

.......................................................................................CTGCCCAAGTGCGCCACGTA....................................................

1.00

.......................................................................................CTGCCCAAGTGCGCCAAGT.....................................................

0.50

.................................................ACTTGGCGTACTTGGGCAGGAG........................................................................................

0.50

..................................................CTTGGCGCGCTTGGGCAGGA.........................................................................................

0.50

....................................................TGGCGCACTTGGGCAGGA.........................................................................................

0.50

...................................................TTGGCGCACTTGGGCAGG..........................................................................................

0.50

..................................................CTTGGCGCACTTGAGCAGGA.........................................................................................

0.50

...................................................TTGGCTCACTTGGGCAGGA.........................................................................................

0.50

.................................................ACTTGGCGCACTTGGGCAGG..........................................................................................

0.50

..................................................CGGGGCGCACTTGGGCAGGT.........................................................................................

0.07

..............................................AGAGCTTGACGCACTTGG...............................................................................................

0.05

........................................CCCCGGCTAACTTCGCGC.....................................................................................................

0.05

CTTTTGTAGCTTAGCGAGGACGTGTGGGTAATTGCTAGAGGGGGCCTCTTGAACCGCGTGAACCCGTCCTCCAGGTAGAGTATGGAGGACGGGTTCACGCGGTTCATGAGACCAAGTCCAGTCCGGTCTTAAGAGAAATGTGACTCCCTAAATGTGTTA **********************************((((...((((((.((((((((((((((((((((((((.........)))))))))))))))))))))))).))))))...))))...*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V050 head	V057 head	M042 female body
.....................................................................................AGGACGGGTTCACGCGGTTC......................................................	20	0	2	2.50	5	4	0	1
......................................................................................GGACGGGTTCACGCGGTTC......................................................	19	0	2	2.00	4	2	2	0
.................................................TGAACCGCGTGAACCCGTC...........................................................................................	19	0	2	0.50	1	0	1	0
.....................................................................................AGGACGGGTTCACTCGGTT.......................................................	19	1	2	0.50	1	0	0	1
.....................................................................................AGGACGGGTTCGCGCGGTTC......................................................	20	1	2	0.50	1	0	1	0
......................................................................................GGACGGGTTCACGCGGTT.......................................................	18	0	2	0.50	1	0	1	0
......................................................................................GGACGGGTTCACGCGGTTCA.....................................................	20	0	2	0.50	1	0	0	1
....................................................................................GAGGACGGGTTCATGCGGTTCA.....................................................	22	1	2	0.50	1	0	1	0
.....................................................................................AGGACGGGTTCACGCGGT........................................................	18	0	2	0.50	1	1	0	0
.....................................................................................AGGACGAGTTCACGCGGTTC......................................................	20	1	2	0.50	1	1	0	0
.....................................................................................TGGACGGGTTCACGCGGGGC......................................................	20	3	14	0.07	1	0	1	0

CTTTTGTAGCTTAGCGAGGACGTGTGGGTAATTGCTAGAGGGGGCCTCTTGAACCGCGTGAACCCGTCCTCCAGGTAGAGTATGGAGGACGGGTTCACGCGGTTCATGAGACCAAGTCCAGTCCGGTCTTAAGAGAAATGTGACTCCCTAAATGTGTTA
************************************((((...((((((.((((((((((((((((((((((((.........)))))))))))))))))))))))).))))))...))))...***********************************

Read size

# Mismatch

Hit Count

Total Norm

Total

V050
head

V057
head

M042
female body

.....................................................................................AGGACGGGTTCACGCGGTTC......................................................

2.50

......................................................................................GGACGGGTTCACGCGGTTC......................................................

2.00

.................................................TGAACCGCGTGAACCCGTC...........................................................................................

0.50

.....................................................................................AGGACGGGTTCACTCGGTT.......................................................

0.50

.....................................................................................AGGACGGGTTCGCGCGGTTC......................................................

0.50

......................................................................................GGACGGGTTCACGCGGTT.......................................................

0.50

......................................................................................GGACGGGTTCACGCGGTTCA.....................................................

0.50

....................................................................................GAGGACGGGTTCATGCGGTTCA.....................................................

0.50

.....................................................................................AGGACGGGTTCACGCGGT........................................................

0.50

.....................................................................................AGGACGAGTTCACGCGGTTC......................................................

0.50

.....................................................................................TGGACGGGTTCACGCGGGGC......................................................

0.07

Re-alignment of all predicted orthologs

Species	Coordinate	ID	Alignment
droPer2	scaffold_26:100979-101137 +	dpe_128	GA-AAACATCGAATCGCTCCTGCACACCCATTAACGATCTCCCCCGGAGAACTTGGCGCACTTGGGCAGGAGGTCCATCTCATACCTCCTGCCCAAGTGCGCCAAGTACTCTGGTTCAGGTCAGGCCAGAATTCTCTTTACACTGAGGGATTTACACAAT
dp5	XL_group1a:494885-494952 +		GA-AAACATCGAATCGCTCCTGCACACCCATTAACGATCTCCCCCGGAGAACTTGGCGCACTTGCGAAG-------------------------------------------------------------------------------------------
droAna3	scaffold_12929:1713906-1713914 -		AA-AGACATC------------------------------------------------------------------------------------------------------------------------------------------------------
droBip1	scf7180000396543:179203-179254 -		AA-GAACACAGAAGAG-----------------ACATCCACCCCAGGGGAATACGATGATCTGGAGCAAG------------------------------------------------------------------------------------------
droEle1	scf7180000491011:1091596-1091605 +		AG-AGACATCG-----------------------------------------------------------------------------------------------------------------------------------------------------
droRho1	scf7180000779506:879254-879263 +		AA-AGACATCG-----------------------------------------------------------------------------------------------------------------------------------------------------
droBia1	scf7180000301760:1057028-1057037 +		AA-AGACATCG-----------------------------------------------------------------------------------------------------------------------------------------------------
droTak1	scf7180000415179:44316-44327 +		GAAAGACATCGA----------------------------------------------------------------------------------------------------------------------------------------------------
droEug1	scf7180000409277:421554-421563 +		AG-AGACATCG-----------------------------------------------------------------------------------------------------------------------------------------------------

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droPer2

GA-AAACATCGAATCGCTCCTGCACACCCATTAACGATCTCCCCCGGAGAACTTGGCGCACTTGGGCAGGAGGTCCATCTCATACCTCCTGCCCAAGTGCGCCAAGTACTCTGGTTCAGGTCAGGCCAGAATTCTCTTTACACTGAGGGATTTACACAAT	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
........................................................................................CTGCCCAAGTGCGCCAAGTAC...................................................	21	1	11.00	11	0	0	1	5	5	0
........................................................................................CTGCCCAAGTGCGCCAAGTA....................................................	20	1	5.00	5	0	0	0	3	0	2
.................................................AACTTGGCGCACTTGGGCA............................................................................................	19	1	4.00	4	0	0	0	2	2	0
...................................................CTTGGCGCACTTGGGCAGGA.........................................................................................	20	2	2.50	5	0	1	0	4	0	0
.................................................AACTTGGCGCACTTGGGCAG...........................................................................................	20	1	2.00	2	0	0	0	0	2	0
.................................................AACTTGGCGCACTTGGGCAGGA.........................................................................................	22	1	2.00	2	0	0	2	0	0	0
...................................................CTTGGCGCACTTGGGCAGG..........................................................................................	19	2	2.00	4	0	0	0	2	2	0
.................................................AACTTGGCGCACTTGGGCAGG..........................................................................................	21	1	1.00	1	0	0	0	0	1	0
........................................................................................CTGCCCAAGTGCGCCAAGTACT..................................................	22	1	1.00	1	0	0	0	1	0	0
........................................................................................CTGCCCAAGTGCGCCAAGTAT...................................................	21	1	1.00	1	0	0	0	1	0	0
........................................................................................CTGCCCAAGTGCGCCAAGT.....................................................	19	2	0.50	1	0	0	0	0	1	0
.....................................................TGGCGCACTTGGGCAGGA.........................................................................................	18	2	0.50	1	0	0	0	1	0	0
....................................................TTGGCGCACTTGGGCAGG..........................................................................................	18	2	0.50	1	0	0	0	0	1	0
..................................................ACTTGGCGCACTTGGGCAGG..........................................................................................	20	2	0.50	1	0	1	0	0	0	0

dp5

GA-AAACATCGAATCGCTCCTGCACACCCATTAACGATCTCCCCCGGAGAACTTGGCGCACTTGCGAAG-------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

Total

M022
Male-body

M040
Female-body

M059
Embryo

M062
Head

V043
Embryo

V051
Head

V112
Male-body

SRR902010
Ovary

SRR902011
Testis

SRR902012
CNS imaginal disc

No Reads

droAna3

AA-AGACATC------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
No Reads

droBip1

AA-GAACACAGAAGAG-----------------ACATCCACCCCAGGGGAATACGATGATCTGGAGCAAG------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droEle1

AG-AGACATCG-----------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droRho1

AA-AGACATCG-----------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droBia1

AA-AGACATCG-----------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droTak1

GAAAGACATCGA----------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droEug1

AG-AGACATCG-----------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

dpe_128

scaffold_26:101029-101087 +

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