dpe_126

CAAGTGATCGAAGACAGTTTAATAAAGAAAATATTCAATTTGCATTTCAATTTAGAAACACAAATCATGTGTGGTATGCTTTAACTCATACATAACTTGTGTCTCTTAGATCAAATGTGAGTACTCAACGAATTCCCAATTGAGAAGTCCCAGTTTTAATTT *********************************..((((((((((..(((((((.((((((...(((((((((........)).)))))))...)))))).)).))))).))))))))))....**********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V111 male body	M042 female body	V050 head
........................................................................................TACATAACTTGTGTCTCTTAGAT...................................................	23	0	3	5.33	16	12	3	1
........................................................................................TACATAACTTGTGTCTCTTAG.....................................................	21	0	3	5.00	15	10	4	1
..................................................TTTAGAAACACAAATCATGTGT..........................................................................................	22	0	4	2.50	10	9	1	0
..................................................TTTAGAAACACAAATCATGTGTGT........................................................................................	24	1	4	1.25	5	5	0	0
........................................................................................TACATAACTTGTGTCTCTTAGAA...................................................	23	1	3	1.00	3	3	0	0
........................................................................................TACATAACTTGTGTCTCTTAGA....................................................	22	0	3	0.67	2	1	1	0
........................................................................................TACATAACTTGTGTCTCTTAGATCCT................................................	26	2	3	0.67	2	2	0	0
........................................................................................TACATAACTTGTGTCTCTTC......................................................	20	1	3	0.67	2	1	1	0
........................................................................................TACATAACTTGTGTCTCTTAGATT..................................................	24	1	3	0.67	2	2	0	0
..................................................TTTAGAAACACAAATCATGT............................................................................................	20	0	4	0.50	2	2	0	0
........................................................................................TACATAACTTGTGTCTCTTAGT....................................................	22	1	3	0.33	1	1	0	0
........................................................................................TACATAACTTGTGTCTCTTAA.....................................................	21	1	3	0.33	1	1	0	0
........................................................................................TACATAACTTGTGTCTCTTAGAAA..................................................	24	2	3	0.33	1	0	1	0
........................................................................................TACATAACTTGTGTCTCTTAGATCA.................................................	25	0	3	0.33	1	1	0	0
........................................................................................TACATAACTTGTGTCTCTTAGATC..................................................	24	0	3	0.33	1	1	0	0
..................................................TTTAGAAACACAAATCATGC............................................................................................	20	1	4	0.25	1	1	0	0
...................................................CTAGAAACACAAATCATGTGTGG........................................................................................	23	1	4	0.25	1	0	1	0
...................................................TTAGAAACACAAATCATGTGT..........................................................................................	21	0	4	0.25	1	1	0	0
....................................................TAGAAACACAAATCATGTGTGG........................................................................................	22	0	4	0.25	1	0	1	0
....................................................TAGAAACACAAATCATGTGTGGT.......................................................................................	23	0	4	0.25	1	1	0	0

GTTCACTAGCTTCTGTCAAATTATTTCTTTTATAAGTTAAACGTAAAGTTAAATCTTTGTGTTTAGTACACACCATACGAAATTGAGTATGTATTGAACACAGAGAATCTAGTTTACACTCATGAGTTGCTTAAGGGTTAACTCTTCAGGGTCAAAATTAAA **********************************..((((((((((..(((((((.((((((...(((((((((........)).)))))))...)))))).)).))))).))))))))))....*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V111 male body
...................................................................................................................................TAAGGGTTAACTCTTCAGGGT..........	21	0	7	0.14	1	1

Species	Coordinate	ID	Type	Alignment
droPer2	scaffold_7193:871-1032 +	dpe_126	candidate-rescued	CAAGTGATCGAAGACAGTTTAATAAAGAAAATATTCAATTTGCATTTCAATTTAGAAACACAAATCATGTGTGGTATGCTTTAACTCATACATAACTTGTGTCTCTTAGATCAAATGTGAGTACTCAACGAATTCCCAATTGAGAAGTCCCAGTTTTAATTT
dp5	4_group4:3552997-3553158 +	dps-mir-2566a-2	Known_mirbase	CAAGTGATCGAAGACAGTTTAATAAAAAAAATATTCAATTTGCATTTCAATTTAGAAACACAAATCATGTGTGGTATGTTTTAACTCATACATAACTTGTGTCTCTTAGATCAAATGTGAGTACACGACGAATTCCCAATTGAGAAGTCCCAGATTTAAGTT

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droPer2

CAAGTGATCGAAGACAGTTTAATAAAGAAAATATTCAATTTGCATTTCAATTTAGAAACACAAATCATGTGTGGTATGCTTTAACTCATACATAACTTGTGTCTCTTAGATCAAATGTGAGTACTCAACGAATTCCCAATTGAGAAGTCCCAGTTTTAATTT	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
........................................................................................TACATAACTTGTGTCTCTTAGAT...................................................	23	3	5.33	16	0	3	0	1	0	12
........................................................................................TACATAACTTGTGTCTCTTAG.....................................................	21	3	5.00	15	0	4	0	1	0	10
..................................................TTTAGAAACACAAATCATGTGT..........................................................................................	22	4	2.50	10	0	1	0	0	0	9
..................................................TTTAGAAACACAAATCATGTGTGT........................................................................................	24	4	1.25	5	0	0	0	0	0	5
........................................................................................TACATAACTTGTGTCTCTTAGAA...................................................	23	3	1.00	3	0	0	0	0	0	3
........................................................................................TACATAACTTGTGTCTCTTAGA....................................................	22	3	0.67	2	0	1	0	0	0	1
........................................................................................TACATAACTTGTGTCTCTTAGATCCT................................................	26	3	0.67	2	0	0	0	0	0	2
........................................................................................TACATAACTTGTGTCTCTTC......................................................	20	3	0.67	2	0	1	0	0	0	1
........................................................................................TACATAACTTGTGTCTCTTAGATT..................................................	24	3	0.67	2	0	0	0	0	0	2
..................................................TTTAGAAACACAAATCATGT............................................................................................	20	4	0.50	2	0	0	0	0	0	2
........................................................................................TACATAACTTGTGTCTCTTAGT....................................................	22	3	0.33	1	0	0	0	0	0	1
........................................................................................TACATAACTTGTGTCTCTTAA.....................................................	21	3	0.33	1	0	0	0	0	0	1
........................................................................................TACATAACTTGTGTCTCTTAGAAA..................................................	24	3	0.33	1	0	1	0	0	0	0
........................................................................................TACATAACTTGTGTCTCTTAGATCA.................................................	25	3	0.33	1	0	0	0	0	0	1
........................................................................................TACATAACTTGTGTCTCTTAGATC..................................................	24	3	0.33	1	0	0	0	0	0	1
..................................................TTTAGAAACACAAATCATGC............................................................................................	20	4	0.25	1	0	0	0	0	0	1
...................................................TTAGAAACACAAATCATGTGT..........................................................................................	21	4	0.25	1	0	0	0	0	0	1
....................................................TAGAAACACAAATCATGTGTGG........................................................................................	22	4	0.25	1	0	1	0	0	0	0
....................................................TAGAAACACAAATCATGTGTGGT.......................................................................................	23	4	0.25	1	0	0	0	0	0	1

dp5

CAAGTGATCGAAGACAGTTTAATAAAAAAAATATTCAATTTGCATTTCAATTTAGAAACACAAATCATGTGTGGTATGTTTTAACTCATACATAACTTGTGTCTCTTAGATCAAATGTGAGTACACGACGAATTCCCAATTGAGAAGTCCCAGATTTAAGTT	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
........................................................................................TACATAACTTGTGTCTCTTAGA....................................................	22	2	369.50	739	0	26	0	0	0	0	4	0	707	2
........................................................................................TACATAACTTGTGTCTCTTAG.....................................................	21	2	277.00	554	0	21	0	0	0	5	16	4	508	0
........................................................................................TACATAACTTGTGTCTCTTAGAT...................................................	23	2	99.50	199	1	15	2	2	6	3	19	2	149	0
........................................................................................TACATAACTTGTGTCTCTTAGAA...................................................	23	2	75.50	151	0	1	0	0	0	1	3	0	146	0
....................................................TAGAAACACAAATCATGTGTGG........................................................................................	22	1	37.00	37	0	4	0	0	1	0	1	0	31	0
........................................................................................TACATAACTTGTGTCTCTTAGATC..................................................	24	2	32.00	64	1	1	0	0	0	0	0	0	62	0
..................................................TTTAGAAACACAAATCATGTGTG.........................................................................................	23	1	20.00	20	0	0	0	0	0	0	0	0	20	0
..................................................TTTAGAAACACAAATCATGTGT..........................................................................................	22	1	18.00	18	0	0	0	0	0	1	7	0	10	0
........................................................................................TACATAACTTGTGTCTCTTA......................................................	20	2	17.00	34	0	2	0	1	0	0	0	0	31	0
........................................................................................TACATAACTTGTGTCTCTTAGATCC.................................................	25	2	17.00	34	0	2	0	1	0	0	1	0	30	0
........................................................................................TACATAACTTGTGTCTCTTAGAAA..................................................	24	2	16.00	32	0	2	0	0	0	0	0	0	30	0
........................................................................................TACATAACTTGTGTCTCTTAGATT..................................................	24	2	14.50	29	0	3	0	0	0	1	1	0	24	0
........................................................................................TACATAACTTGTGTCTCTTAGATCCC................................................	26	2	9.00	18	1	0	0	0	0	0	1	0	16	0
........................................................................................TACATAACTTGTGTCTCTTAGATA..................................................	24	2	8.50	17	0	2	0	1	0	0	0	0	14	0
..................................................TTTAGAAACACAAATCATGTGTGGTA......................................................................................	26	1	6.00	6	0	0	0	0	0	0	0	0	6	0
..................................................TTTAGAAACACAAATCATGTG...........................................................................................	21	1	6.00	6	0	1	0	0	0	0	0	0	5	0
........................................................................................TACATAACTTGTGTCTCTTAA.....................................................	21	2	4.50	9	0	0	0	0	0	1	0	0	8	0
........................................................................................TACATAACTTGTGTCTCTTAGATTT.................................................	25	2	4.00	8	0	1	0	0	0	0	0	0	7	0
..................................................TTTAGAAACACAAATCATGTGTGT........................................................................................	24	1	4.00	4	0	1	0	0	0	0	0	0	3	0
.......................................................................................ATACATAACTTGTGTCTCTTAGA....................................................	23	2	3.50	7	0	0	0	0	0	0	0	0	7	0
........................................................................................TACATAACTTGTGTCTCTTT......................................................	20	2	3.00	6	0	0	0	0	0	0	0	0	6	0
..................................................TTTAGAAACACAAATCATGTGTGGT.......................................................................................	25	1	3.00	3	0	1	0	0	0	0	1	0	1	0
..................................................TTTAGAAACACAAATCATGTGTGG........................................................................................	24	1	3.00	3	0	1	0	0	0	0	0	0	2	0
........................................................................................TACATAACTTGTGTCTCTTAGT....................................................	22	2	2.50	5	0	0	0	0	0	0	1	0	4	0
..................................................TTTAGAAACACAAATCATGTGTA.........................................................................................	23	1	2.00	2	0	0	0	0	0	0	0	0	2	0
...................................................TTAGAAACACAAATCATGTGTG.........................................................................................	22	1	2.00	2	0	0	0	0	0	0	0	0	2	0
........................................................................................TACATAACTTGTGTCTCTTAGATCA.................................................	25	2	2.00	4	0	0	0	0	0	0	0	0	4	0
....................................................TAGAAACACAAATCATGTGT..........................................................................................	20	1	2.00	2	0	0	0	0	0	0	2	0	0	0
............................................................................TGTTTTAACTCATACATAACTTGTGTC...........................................................	27	1	2.00	2	0	0	0	0	0	0	0	0	2	0
........................................................................................TACATAACTTGTGTCTCTTAGATCT.................................................	25	2	1.50	3	0	0	0	0	0	0	0	0	3	0
........................................................................................TACATAACTTGTGTCTCTTAGTCT..................................................	24	2	1.50	3	0	0	0	0	0	0	0	0	3	0
........................................................................................TACATAACTTGTGTCTCTTAGATTCC................................................	26	2	1.50	3	0	1	0	0	0	0	0	0	2	0
.........................................................................................ACATAACTTGTGTCTCTTAGA....................................................	21	2	1.50	3	0	0	0	0	0	0	0	0	3	0
........................................................................................TACATAACTTGTGTCTCTTAGATCCCC...............................................	27	2	1.00	2	0	0	0	0	0	0	0	0	2	0
.................................................................................TAACTCATACATAACTTGTGTCTCT........................................................	25	2	1.00	2	0	0	0	0	0	0	0	0	2	0
..................................................TTTAGAAACACAAATCATGT............................................................................................	20	1	1.00	1	0	1	0	0	0	0	0	0	0	0
..................................................TTTAGAAACACAAATCATGTGTGA........................................................................................	24	1	1.00	1	0	0	0	0	0	0	0	0	1	0
....................................................TAGAAACACAAATCATGTGTGGTA......................................................................................	24	1	1.00	1	0	0	0	0	0	0	0	0	1	0
....................................................TAGAAACACAAATCATGTGTG.........................................................................................	21	1	1.00	1	0	0	0	0	0	0	1	0	0	0
.................................................................................TAACTCATACATAACTTGTGTCTCTTAGA....................................................	29	2	1.00	2	0	0	0	0	0	0	0	0	2	0
..................................................TTTAGAAACACAAATCATG.............................................................................................	19	1	1.00	1	0	0	0	0	0	0	0	0	1	0
........................................................................................TACATAACTTGTGTCTCTTG......................................................	20	2	1.00	2	0	0	0	0	0	0	0	0	2	0
........................................................................................TACATAACTTGTGTCTCTTAGATCAA................................................	26	2	1.00	2	0	0	0	0	0	0	0	0	2	0
.........................................................................................ACATAACTTGTGTCTCTTAG.....................................................	20	2	1.00	2	0	2	0	0	0	0	0	0	0	0
....................................................TAGAAACACAAATCATGTGTGT........................................................................................	22	1	1.00	1	0	0	0	0	0	0	1	0	0	0
.........................................................................................ACATAACTTGTGTCTCTTAGAT...................................................	22	2	1.00	2	0	2	0	0	0	0	0	0	0	0
.................................................................................TAACTCATACATAACTTGTGTCT..........................................................	23	2	0.50	1	0	0	0	0	0	0	1	0	0	0
...........................................................................................ATAACTTGTGTCTCTTAGA....................................................	19	2	0.50	1	0	1	0	0	0	0	0	0	0	0
...............................................................................TTTAACTCATACATAACTTGTGTCTC.........................................................	26	2	0.50	1	0	0	0	0	0	0	0	0	1	0
........................................................................................TACATAACTTGTGTCTCTTAGATCG.................................................	25	2	0.50	1	0	1	0	0	0	0	0	0	0	0
........................................................................................TACATAACTTGTGTCTCTTAGAC...................................................	23	2	0.50	1	0	0	0	1	0	0	0	0	0	0
........................................................................................TACATAACTTGTGTCTCTTAGATAT.................................................	25	2	0.50	1	0	0	0	0	0	0	0	0	1	0
.........................................................................................ACATAACTTGTGTCTCTTAGATA..................................................	23	2	0.50	1	0	1	0	0	0	0	0	0	0	0
.......................................................................................ATACATAACTTGTGTCTCTTAG.....................................................	22	2	0.50	1	0	0	0	0	0	0	0	0	1	0
........................................................................................TACATAACTTGTGTCTCTTAGATCCCT...............................................	27	2	0.50	1	0	0	0	0	0	0	1	0	0	0
........................................................................................TACATAACTTGTGTCTCTTAGATG..................................................	24	2	0.50	1	0	0	0	0	0	1	0	0	0	0
.................................................................................TAACTCATACATAACTTGTGTCTCTTA......................................................	27	2	0.50	1	0	0	0	0	0	0	0	0	1	0
........................................................................................TACATAACTTGTGTCTCTTAGG....................................................	22	2	0.50	1	0	0	0	0	0	0	0	0	1	0
........................................................................................TACATAACTTGTGTCTCTTAGATCCT................................................	26	2	0.50	1	0	0	0	0	0	0	0	0	1	0
......................................................................................CATACATAACTTGTGTCTCTTAGAT...................................................	25	2	0.50	1	0	0	0	0	0	0	0	0	1	0
...............................................................................TTTAACTCATACATAACTTGTGTCTCT........................................................	27	2	0.50	1	0	0	0	0	0	0	0	0	1	0
.................................................................................................TGTGTCTCTTAGATCT.................................................	16	6	0.17	1	0	0	0	0	0	0	0	0	1	0

dpe_126

scaffold_7193:921-982 +

Known Ortholog

Testes-restricted

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

-22.9	-22.6