dwi_79

TTTTTTTTTTTTAAGTCGTCTTGAAATTAATTAATTTGCTTTTTGAAATCGGCTGGAAATTGACGAAAATACAGTCTGAGTTGTAAATCTGTCAATTTGTCAATTTTTGATCGATTTTCAAAATTCATTTCCACCAAGAAGTAAAATTTTGACCATTTTCGCATAA *********************************.((..((((((((((((.((((((((((((((...((((..............))))...)))))))))))))).)))).))))))))..))...**********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M020 head	V118 embryo	M045 female body	V119 head	V117 male body
...........................................................................................TCAATTTGTCAATTTTTGATCGAT...................................................	24	0	3	35.00	105	39	33	10	23	0
...........................................................................................TCAATTTGTCAATTTTTGATCGA....................................................	23	0	3	24.00	72	24	22	13	13	0
...........................................................................................TCAATTTGTCAATTTTTGATCG.....................................................	22	0	3	17.33	52	13	3	30	6	0
...........................................................................................TCAATTTGTCAATTTTTGATCGT....................................................	23	1	3	8.67	26	26	0	0	0	0
..................................................GGCTGGAAATTGACGAAAATACA.............................................................................................	23	0	3	4.33	13	0	11	1	1	0
.............................................................................................AATTTGTCAATTTTTGATCGAT...................................................	22	0	3	3.67	11	6	0	2	3	0
...........................................................................................TCAATTTGTCAATTTTTGATC......................................................	21	0	3	3.33	10	0	0	5	5	0
...........................................................................................TCAATTTGTCAATTTTTGATCGG....................................................	23	1	3	1.67	5	5	0	0	0	0
.....................................................TGGAAATTGACGAAAATACAGT...........................................................................................	22	0	5	1.40	7	0	4	1	2	0
.........................................................................GTCTGAGTTGTAAATCTG...........................................................................	18	0	3	1.33	4	0	4	0	0	0
............................................................................................CAATTTGTCAATTTTTGATCGAT...................................................	23	0	3	1.33	4	2	0	2	0	0
.............................................................................................AATTTGTCAATTTTTGATCGA....................................................	21	0	3	0.67	2	1	1	0	0	0
...........................................................................................TCAATTTGTCAATTTTTGA........................................................	19	0	3	0.67	2	0	0	2	0	0
...........................................................................................TCAATTTGTCAATTTTTGATCGAC...................................................	24	1	3	0.67	2	2	0	0	0	0
.........................................................................................TGTCAATTTGTCAATTTTTGA........................................................	21	0	3	0.67	2	0	0	1	1	0
...........................................................................................TCAATTTTTCAATTTTTGATCGAT...................................................	24	1	3	0.67	2	2	0	0	0	0
...................................................GCTGGAAATTGACGAAAATACA.............................................................................................	22	0	3	0.67	2	0	2	0	0	0
....................................................................................................................TTCTACATTCATTACCACCA..............................	20	3	20	0.40	8	0	0	6	2	0
.........................................................................................TGTCAATTTGTCAATTTTTGATT......................................................	23	1	3	0.33	1	0	0	0	1	0
............................................................................................CAATTTGTCAATTTTTGATC......................................................	20	0	3	0.33	1	0	0	1	0	0
..........................................................................................GTCAATTTGTCAATTTTTG.........................................................	19	0	3	0.33	1	0	0	1	0	0
.........................................................................................TGTCAATTTGTCAATTTTTGAT.......................................................	22	0	3	0.33	1	0	0	1	0	0
...........................................................................................TCAATTTGTCAATTTTTGATCAAT...................................................	24	1	3	0.33	1	0	1	0	0	0
...........................................................................................TCAATTTCTCAATTTTTGATCGAT...................................................	24	1	3	0.33	1	1	0	0	0	0
..........................................................................................TTCAATTTGTCAATTTTTGATCG.....................................................	23	1	3	0.33	1	0	0	1	0	0
...........................................................................................TCAATTTGTCAATTTTTGATAG.....................................................	22	1	3	0.33	1	0	0	0	1	0
...............................................................................................TTTGTCAATTTTTGATCG.....................................................	18	0	3	0.33	1	0	0	1	0	0
...........................................................................................TCAATTTGTCAGTTTTTGATCGA....................................................	23	1	3	0.33	1	0	0	1	0	0
...........................................................................................TCAATTTGTCAATTTTTGATCGCT...................................................	24	1	3	0.33	1	1	0	0	0	0
............................................................................................CAATTTGTCAATTTTTGATCG.....................................................	21	0	3	0.33	1	0	0	1	0	0
...........................................................................................TTAATTTGTCAATTTTTGATCGAT...................................................	24	1	3	0.33	1	0	0	0	1	0
...........................................................................................TCAATTTGTCAATTTTTGAT.......................................................	20	0	3	0.33	1	0	0	0	1	0
...........................................................................................CCAATTTGTCAATTTTTGATCGAT...................................................	24	1	3	0.33	1	0	1	0	0	0
..................................................GGCTGGAAATTGACGAAAATAC..............................................................................................	22	0	3	0.33	1	0	1	0	0	0
................................................................................................TTGTCAATTTTTGATCGAT...................................................	19	0	3	0.33	1	0	0	1	0	0
...........................................................................................TCAATTTGTTAATTTTTGATCGAT...................................................	24	1	3	0.33	1	0	1	0	0	0
.....................................................TGGAAATTGACGAACATACAGT...........................................................................................	22	1	5	0.20	1	0	0	0	0	1
.....................................................TGGAAATTGAAGAAAATACAGT...........................................................................................	22	1	6	0.17	1	0	0	0	1	0

TTTTTTTTTTTTAAGTCGTCTTGAAATTAATTAATTTGCTTTTTGAAATCGGCTGGAAATTGACGAAAATACAGTCTGAGTTGTAAATCTGTCAATTTGTCAATTTTTGATCGATTTTCAAAATTCATTTCCACCAAGAAGTAAAATTTTGACCATTTTCGCATAA

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

Read size

# Mismatch

Hit Count

Total Norm

Total

M020

head

V118

embryo

M045

female body

V119

head

V117

male body

...........................................................................................TCAATTTGTCAATTTTTGATCGAT...................................................

35.00

105

...........................................................................................TCAATTTGTCAATTTTTGATCGA....................................................

24.00

...........................................................................................TCAATTTGTCAATTTTTGATCG.....................................................

17.33

...........................................................................................TCAATTTGTCAATTTTTGATCGT....................................................

8.67

..................................................GGCTGGAAATTGACGAAAATACA.............................................................................................

4.33

.............................................................................................AATTTGTCAATTTTTGATCGAT...................................................

3.67

...........................................................................................TCAATTTGTCAATTTTTGATC......................................................

3.33

...........................................................................................TCAATTTGTCAATTTTTGATCGG....................................................

1.67

.....................................................TGGAAATTGACGAAAATACAGT...........................................................................................

1.40

.........................................................................GTCTGAGTTGTAAATCTG...........................................................................

1.33

............................................................................................CAATTTGTCAATTTTTGATCGAT...................................................

1.33

.............................................................................................AATTTGTCAATTTTTGATCGA....................................................

0.67

...........................................................................................TCAATTTGTCAATTTTTGA........................................................

0.67

...........................................................................................TCAATTTGTCAATTTTTGATCGAC...................................................

0.67

.........................................................................................TGTCAATTTGTCAATTTTTGA........................................................

0.67

...........................................................................................TCAATTTTTCAATTTTTGATCGAT...................................................

0.67

...................................................GCTGGAAATTGACGAAAATACA.............................................................................................

0.67

....................................................................................................................TTCTACATTCATTACCACCA..............................

0.40

.........................................................................................TGTCAATTTGTCAATTTTTGATT......................................................

0.33

............................................................................................CAATTTGTCAATTTTTGATC......................................................

0.33

..........................................................................................GTCAATTTGTCAATTTTTG.........................................................

0.33

.........................................................................................TGTCAATTTGTCAATTTTTGAT.......................................................

0.33

...........................................................................................TCAATTTGTCAATTTTTGATCAAT...................................................

0.33

...........................................................................................TCAATTTCTCAATTTTTGATCGAT...................................................

0.33

..........................................................................................TTCAATTTGTCAATTTTTGATCG.....................................................

0.33

...........................................................................................TCAATTTGTCAATTTTTGATAG.....................................................

0.33

...............................................................................................TTTGTCAATTTTTGATCG.....................................................

0.33

...........................................................................................TCAATTTGTCAGTTTTTGATCGA....................................................

0.33

...........................................................................................TCAATTTGTCAATTTTTGATCGCT...................................................

0.33

............................................................................................CAATTTGTCAATTTTTGATCG.....................................................

0.33

...........................................................................................TTAATTTGTCAATTTTTGATCGAT...................................................

0.33

...........................................................................................TCAATTTGTCAATTTTTGAT.......................................................

0.33

...........................................................................................CCAATTTGTCAATTTTTGATCGAT...................................................

0.33

..................................................GGCTGGAAATTGACGAAAATAC..............................................................................................

0.33

................................................................................................TTGTCAATTTTTGATCGAT...................................................

0.33

...........................................................................................TCAATTTGTTAATTTTTGATCGAT...................................................

0.33

.....................................................TGGAAATTGACGAACATACAGT...........................................................................................

0.20

.....................................................TGGAAATTGAAGAAAATACAGT...........................................................................................

0.17

AAAAAAAAAAAATTCAGCAGAACTTTAATTAATTAAACGAAAAACTTTAGCCGACCTTTAACTGCTTTTATGTCAGACTCAACATTTAGACAGTTAAACAGTTAAAAACTAGCTAAAAGTTTTAAGTAAAGGTGGTTCTTCATTTTAAAACTGGTAAAAGCGTATT **********************************.((..((((((((((((.((((((((((((((...((((..............))))...)))))))))))))).)))).))))))))..))...*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V118 embryo
..AAAAAAAAAATTCAGCAGGAC...............................................................................................................................................	21	1	4	0.25	1	1
..AAAAAAAAAATTCAGCAG..................................................................................................................................................	18	0	4	0.25	1	1

AAAAAAAAAAAATTCAGCAGAACTTTAATTAATTAAACGAAAAACTTTAGCCGACCTTTAACTGCTTTTATGTCAGACTCAACATTTAGACAGTTAAACAGTTAAAAACTAGCTAAAAGTTTTAAGTAAAGGTGGTTCTTCATTTTAAAACTGGTAAAAGCGTATT

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

Read size

# Mismatch

Hit Count

Total Norm

Total

V118

embryo

..AAAAAAAAAATTCAGCAGGAC...............................................................................................................................................

0.25

..AAAAAAAAAATTCAGCAG..................................................................................................................................................

0.25

Species	Coordinate	ID	Type	Alignment
droWil2	scf2_1100000004909:4166585-4166750 +	dwi_79	confident	TTTTTTTTTTTTAAGTCGTCTTGAAATTAATTAATTTGCTTTTTGAAATCGGCTGGAAATTGACGAAAATACAGTCTGAGTTGTAAATCTGTCAATTTGTCAATTTTTGATCGATTTTCAAAATTCATTTCCACCAAGAAGTAAAATTTTGACCATTTTCGCATAA

Species

Coordinate

Type

Alignment

droWil2

scf2_1100000004909:4166585-4166750 +

dwi_79

confident

TTTTTTTTTTTTAAGTCGTCTTGAAATTAATTAATTTGCTTTTTGAAATCGGCTGGAAATTGACGAAAATACAGTCTGAGTTGTAAATCTGTCAATTTGTCAATTTTTGATCGATTTTCAAAATTCATTTCCACCAAGAAGTAAAATTTTGACCATTTTCGCATAA

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droWil2

TTTTTTTTTTTTAAGTCGTCTTGAAATTAATTAATTTGCTTTTTGAAATCGGCTGGAAATTGACGAAAATACAGTCTGAGTTGTAAATCTGTCAATTTGTCAATTTTTGATCGATTTTCAAAATTCATTTCCACCAAGAAGTAAAATTTTGACCATTTTCGCATAA	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
...........................................................................................TCAATTTGTCAATTTTTGATCGAT...................................................	24	3	35.00	105	39	10	0	33	23
...........................................................................................TCAATTTGTCAATTTTTGATCGA....................................................	23	3	24.00	72	24	13	0	22	13
...........................................................................................TCAATTTGTCAATTTTTGATCG.....................................................	22	3	17.33	52	13	30	0	3	6
...........................................................................................TCAATTTGTCAATTTTTGATCGT....................................................	23	3	8.67	26	26	0	0	0	0
..................................................GGCTGGAAATTGACGAAAATACA.............................................................................................	23	3	4.33	13	0	1	0	11	1
.............................................................................................AATTTGTCAATTTTTGATCGAT...................................................	22	3	3.67	11	6	2	0	0	3
...........................................................................................TCAATTTGTCAATTTTTGATC......................................................	21	3	3.33	10	0	5	0	0	5
...........................................................................................TCAATTTGTCAATTTTTGATCGG....................................................	23	3	1.67	5	5	0	0	0	0
.....................................................TGGAAATTGACGAAAATACAGT...........................................................................................	22	5	1.40	7	0	1	0	4	2
.........................................................................GTCTGAGTTGTAAATCTG...........................................................................	18	3	1.33	4	0	0	0	4	0
............................................................................................CAATTTGTCAATTTTTGATCGAT...................................................	23	3	1.33	4	2	2	0	0	0
.............................................................................................AATTTGTCAATTTTTGATCGA....................................................	21	3	0.67	2	1	0	0	1	0
...........................................................................................TCAATTTGTCAATTTTTGA........................................................	19	3	0.67	2	0	2	0	0	0
...........................................................................................TCAATTTGTCAATTTTTGATCGAC...................................................	24	3	0.67	2	2	0	0	0	0
.........................................................................................TGTCAATTTGTCAATTTTTGA........................................................	21	3	0.67	2	0	1	0	0	1
...................................................GCTGGAAATTGACGAAAATACA.............................................................................................	22	3	0.67	2	0	0	0	2	0
.........................................................................................TGTCAATTTGTCAATTTTTGATT......................................................	23	3	0.33	1	0	0	0	0	1
............................................................................................CAATTTGTCAATTTTTGATC......................................................	20	3	0.33	1	0	1	0	0	0
..........................................................................................GTCAATTTGTCAATTTTTG.........................................................	19	3	0.33	1	0	1	0	0	0
.........................................................................................TGTCAATTTGTCAATTTTTGAT.......................................................	22	3	0.33	1	0	1	0	0	0
...............................................................................................TTTGTCAATTTTTGATCG.....................................................	18	3	0.33	1	0	1	0	0	0
............................................................................................CAATTTGTCAATTTTTGATCG.....................................................	21	3	0.33	1	0	1	0	0	0
...........................................................................................TCAATTTGTCAATTTTTGAT.......................................................	20	3	0.33	1	0	0	0	0	1
..................................................GGCTGGAAATTGACGAAAATAC..............................................................................................	22	3	0.33	1	0	0	0	1	0
................................................................................................TTGTCAATTTTTGATCGAT...................................................	19	3	0.33	1	0	1	0	0	0

dwi_79

scf2_1100000004909:4166635-4166700 +

confident

Canonical miRNA

intergenic

Predicted structure

Flybase annnotation

Sense Strand Reads

Anti-sense strand reads

Re-alignment of all predicted orthologs

Re-alignment of all predicted orthologs with sRNA reads

-25.3	-25.3	-25.3