dvi_403

TTTATAGGAACCTAGTGCATATGTGATCCAGCGATTTGGGTAATTCCACTCGCAGCTGTGGTTAATTTGTGGAAAACTTCCGATTTCCGCCAATTTACCACAGTTGCGGGTGGAATTGCCCAAGCTCAACATTTTCCCTGAGCAAGGCCTGCGAATGCTCG *********************************(((((((((((((((((((((((((((.((((.(((((((........))))))).)))).)))))))))))))))))))))))))))...*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M047 female body	V116 male body	SRR060683 160_testes_total	SRR2096014 Ovary_Strain_160_oxidized	M027 male body	SRR060689 160x9_testes_total	SRR060684 140x9_0-2h_embryos_total	SRR060672 9x160_females_carcasses_total	SRR060686 Argx9_0-2h_embryos_total	SRR1106714 embryo_2-4h	SRR2096056 Ovary_Min_46	V053 head	SRR060663 160_0-2h_embryos_total
.........................................................................................CCAATTTACCACAGTTGCGGGT..................................................	22	0	3	4.33	13	5	2	2	3	0	0	1	0	0	0	0	0	0
..................................................CGCAGCTGTGGTTAATTTGTGGA........................................................................................	23	0	1	4.00	4	0	2	1	0	0	1	0	0	0	0	0	0	0
........................................................................................GCCAATTTACCACAGTTGCGGG...................................................	22	0	2	3.00	6	6	0	0	0	0	0	0	0	0	0	0	0	0
.........................................................................................CCAATTTACCACAGTTGCGGG...................................................	21	0	3	2.00	6	4	0	0	2	0	0	0	0	0	0	0	0	0
........................................................................................GCCAATTTACCACAGTTGCGG....................................................	21	0	2	1.50	3	3	0	0	0	0	0	0	0	0	0	0	0	0
.......................................................................................CGCCAATTTACCACAGTTGCGG....................................................	22	0	2	1.50	3	3	0	0	0	0	0	0	0	0	0	0	0	0
..................................................CGCAGCTGTGGTTAATTTGCGG.........................................................................................	22	1	1	1.00	1	0	0	0	0	1	0	0	0	0	0	0	0	0
....................................................CAGCTGTGGTTAATTTGTGGA........................................................................................	21	0	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0	0	0
..................................................CGCAGCTGTGGTTAATTTGAAGA........................................................................................	23	2	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0	0	0
........................................................................................GCCAATTTACCACAGTTGCG.....................................................	20	0	3	0.33	1	1	0	0	0	0	0	0	0	0	0	0	0	0
.........................................................................................CCAATTTACCACAGTTGCGGGTT.................................................	23	1	3	0.33	1	1	0	0	0	0	0	0	0	0	0	0	0	0
....................................................................................................................TGCCCAGGCTCATCATTATCC........................	21	3	4	0.25	1	0	0	0	0	0	0	0	0	1	0	0	0	0
......................................AGTTATTCCAATCGCAGCTGT......................................................................................................	21	3	4	0.25	1	0	0	0	0	0	0	0	1	0	0	0	0	0
........................................................................................................................AGAGCTCAACATGTTCCCTG.....................	20	3	9	0.22	2	0	0	0	0	0	0	0	0	0	2	0	0	0
..............................................................................................................................................CAAGGCCTGCGAATTCGC.	18	2	7	0.14	1	0	0	0	0	0	0	0	0	0	0	1	0	0
.......................................................................................TGCCAATTTACCACAGTTGCG.....................................................	21	1	9	0.11	1	1	0	0	0	0	0	0	0	0	0	0	0	0
.....................................................................................................AGTTGCGGGTGGCATAGACC........................................	20	3	12	0.08	1	0	0	0	0	0	0	0	0	0	0	0	1	0
.....................................................ATCGGTGGTTAAGTTGTGGA........................................................................................	20	3	19	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	1

TTTATAGGAACCTAGTGCATATGTGATCCAGCGATTTGGGTAATTCCACTCGCAGCTGTGGTTAATTTGTGGAAAACTTCCGATTTCCGCCAATTTACCACAGTTGCGGGTGGAATTGCCCAAGCTCAACATTTTCCCTGAGCAAGGCCTGCGAATGCTCG

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

Read size

# Mismatch

Hit Count

Total Norm

Total

M047

female body

V116

male body

SRR060683

160_testes_total

SRR2096014

Ovary_Strain_160_oxidized

M027

male body

SRR060689

160x9_testes_total

SRR060684

140x9_0-2h_embryos_total

SRR060672

9x160_females_carcasses_total

SRR060686

Argx9_0-2h_embryos_total

SRR1106714

embryo_2-4h

SRR2096056

Ovary_Min_46

V053

head

SRR060663

160_0-2h_embryos_total

.........................................................................................CCAATTTACCACAGTTGCGGGT..................................................

4.33

..................................................CGCAGCTGTGGTTAATTTGTGGA........................................................................................

4.00

........................................................................................GCCAATTTACCACAGTTGCGGG...................................................

3.00

.........................................................................................CCAATTTACCACAGTTGCGGG...................................................

2.00

........................................................................................GCCAATTTACCACAGTTGCGG....................................................

1.50

.......................................................................................CGCCAATTTACCACAGTTGCGG....................................................

1.50

..................................................CGCAGCTGTGGTTAATTTGCGG.........................................................................................

1.00

....................................................CAGCTGTGGTTAATTTGTGGA........................................................................................

1.00

..................................................CGCAGCTGTGGTTAATTTGAAGA........................................................................................

1.00

........................................................................................GCCAATTTACCACAGTTGCG.....................................................

0.33

.........................................................................................CCAATTTACCACAGTTGCGGGTT.................................................

0.33

....................................................................................................................TGCCCAGGCTCATCATTATCC........................

0.25

......................................AGTTATTCCAATCGCAGCTGT......................................................................................................

0.25

........................................................................................................................AGAGCTCAACATGTTCCCTG.....................

0.22

..............................................................................................................................................CAAGGCCTGCGAATTCGC.

0.14

.......................................................................................TGCCAATTTACCACAGTTGCG.....................................................

0.11

.....................................................................................................AGTTGCGGGTGGCATAGACC........................................

0.08

.....................................................ATCGGTGGTTAAGTTGTGGA........................................................................................

0.05

AAATATCCTTGGATCACGTATACACTAGGTCGCTAAACCCATTAAGGTGAGCGTCGACACCAATTAAACACCTTTTGAAGGCTAAAGGCGGTTAAATGGTGTCAACGCCCACCTTAACGGGTTCGAGTTGTAAAAGGGACTCGTTCCGGACGCTTACGAGC *********************************(((((((((((((((((((((((((((.((((.(((((((........))))))).)))).)))))))))))))))))))))))))))...*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V053 head
.........................................................................TTCGAACGCTCAAGGCGGT.....................................................................	19	3	16	0.06	1	1

AAATATCCTTGGATCACGTATACACTAGGTCGCTAAACCCATTAAGGTGAGCGTCGACACCAATTAAACACCTTTTGAAGGCTAAAGGCGGTTAAATGGTGTCAACGCCCACCTTAACGGGTTCGAGTTGTAAAAGGGACTCGTTCCGGACGCTTACGAGC

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

Read size

# Mismatch

Hit Count

Total Norm

Total

V053

head

.........................................................................TTCGAACGCTCAAGGCGGT.....................................................................

0.06

Species	Coordinate	ID	Type	Alignment
droVir3	scaffold_12928:874860-875020 -	dvi_403	candidate	TTTATAGGAACCTAGTGCATATGTGATCCAGCGATTTGGGTAATTCCACTCGCAGCTGTGGTTAATTTGTGGAAAACTTCCGATTTCCGCCAATTTACCACAGTTGCGGGTGGAATTGCCCAAGCTCAACATTTTCCCTGAGCAAGGCCTGCGAATGCTCG

Species

Coordinate

Type

Alignment

droVir3

scaffold_12928:874860-875020 -

dvi_403

candidate

TTTATAGGAACCTAGTGCATATGTGATCCAGCGATTTGGGTAATTCCACTCGCAGCTGTGGTTAATTTGTGGAAAACTTCCGATTTCCGCCAATTTACCACAGTTGCGGGTGGAATTGCCCAAGCTCAACATTTTCCCTGAGCAAGGCCTGCGAATGCTCG

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droVir3

TTTATAGGAACCTAGTGCATATGTGATCCAGCGATTTGGGTAATTCCACTCGCAGCTGTGGTTAATTTGTGGAAAACTTCCGATTTCCGCCAATTTACCACAGTTGCGGGTGGAATTGCCCAAGCTCAACATTTTCCCTGAGCAAGGCCTGCGAATGCTCG	Size	Hit Count	Total Norm	Total	M027 Male-body	M028 Head	M047 Female-body	M061 Embryo	SRR060654 Ovary	SRR060655 Testis	SRR060656 Ovary	SRR060657 Testis	SRR060658 Ovary	SRR060659 Testis	SRR060660 Ovary	SRR060661 Embryo	SRR060662 Embryo	SRR060663 Embryo	SRR060664 Male-body	SRR060665 Female-body	SRR060666 Male-body	SRR060667 Female-body	SRR060668 Male-body	SRR060669 Female-body	SRR060670 Testis	SRR060671 Male-body	SRR060672 Female-body	SRR060673 Ovary	SRR060674 Ovary	SRR060675 Ovary	SRR060676 Ovary	SRR060677 Ovary	SRR060678 Testis	SRR060679 Testis	SRR060680 Testis	SRR060681 Testis	SRR060682 Embryo	SRR060683 Testis	SRR060684 Embryo	SRR060685 Embryo	SRR060686 Embryo	SRR060687 Embryo	SRR060688 Ovary	SRR060689 Testis	SRR1106712 embryo_0-2h	SRR1106713 embryo_0-2h	SRR1106714 embryo_2-4h	SRR1106715 embryo_4-6h	SRR1106716 embryo_4-6h	SRR1106717 embryo_6-8h	SRR1106718 embryo_6-8h	SRR1106719 embryo_8-10h	SRR1106720 embryo_8-10h	SRR1106721 embryo_10-12h	SRR1106722 embryo_10-12h	SRR1106723 embryo_12-14h	SRR1106724 embryo_12-14h	SRR1106725 embryo_14-16h	SRR1106726 embryo_14-16h	SRR1106727 larvae	SRR1106728 larvae	SRR1106729 mixed whole adult body	SRR1106730 embryo_16-30h	V047 Embryo	V053 Head	V116 Male-body	GSM1528803 follicle cells	SRR2096013 Ovary_Strain_9_oxidized	SRR2096014 Ovary_Strain_160_oxidized	SRR2096026 embryo_0-2h from 14 day old Strain 9 mothers	SRR2096038 embryo_0-2h from 14 day old Strain 9 mothers	SRR2096050 embryo_0-2h from 14 day old Strain 160 mothers	SRR2096055 Ovary_Min_43	SRR2096056 Ovary_Min_46	SRR2096057 Ovary_Min_50	SRR2096058 Ovary_Min_98	SRR2096059 Ovary_Min_164	SRR2096060 Ovary_Min_193	SRR2096061 embryo_0-2h from 14 day old Strain 160 mothers	SRR2096072 embryo_0-2h from 15to16 day old dysgenic mothers	SRR2096079 embryo_0-2h from 15to16 day old dysgenic mothers	SRR2096080 embryo_0-2h from 15to16 day old nondysgenic mothers	SRR2096081 embryo_0-2h from 15to16 day old nondysgenic mothers
.........................................................................................CCAATTTACCACAGTTGCGGGT..................................................	22	3	4.33	13	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..................................................CGCAGCTGTGGTTAATTTGTGGA........................................................................................	23	1	4.00	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
........................................................................................GCCAATTTACCACAGTTGCGGG...................................................	22	2	3.00	6	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.........................................................................................CCAATTTACCACAGTTGCGGG...................................................	21	3	2.00	6	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0
........................................................................................GCCAATTTACCACAGTTGCGG....................................................	21	2	1.50	3	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.......................................................................................CGCCAATTTACCACAGTTGCGG....................................................	22	2	1.50	3	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
....................................................CAGCTGTGGTTAATTTGTGGA........................................................................................	21	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
........................................................................................GCCAATTTACCACAGTTGCG.....................................................	20	3	0.33	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.........................................................................................CCAATTTACCACAGTTGCGGGTT.................................................	23	3	0.33	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

dvi_403

scaffold_12928:874910-874970 -

candidate

Canonical miRNA

antisense_to_intron

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

-60.3	-60.1