dsi_203

CCATCTTGGAATGGATGAGATTGGAAAAGATTGTGTAGAGGTGTTACATAAATTTCTTCAAACCGAAGGTCTTTGTTAATTTGATTAGAATTCTGTGCGAAGAAATTTTTATAGCATCTTAAGAGCCTGAATCTTTCGAGCCAATCAGTTAAAAGTCGAA *********************************..(((((((((...((((((((((..((.(((..(((..((((...)))).))).))).))..))))))))))...)))))))))....**********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	O001 Testis	SRR618934 Ovary	M024 male body	O002 Head	M023 head	SRR553488 Ovary
..................................................AATTTCTTCAAACCGAAGGTCT........................................................................................	22	0	1	73.00	73	60	5	6	1	0	1
.......................................................................................GAATTCTGTGCGAAGAAATTTT...................................................	22	0	1	28.00	28	16	11	1	0	0	0
........................................................................................AATTCTGTGCGAAGAAATTTT...................................................	21	0	1	25.00	25	3	22	0	0	0	0
.......................................................................................GAATTCTGTGCGAAGAAA.......................................................	18	0	1	15.00	15	14	0	0	1	0	0
..................................................AATTTCTTCAAACCGAAGGTC.........................................................................................	21	0	1	14.00	14	11	0	1	0	2	0
..................................................AATTTCTTCAAACCGAAG............................................................................................	18	0	1	14.00	14	14	0	0	0	0	0
..................................................AATTTCTTCAAACCGAAGG...........................................................................................	19	0	1	14.00	14	14	0	0	0	0	0
.......................................................................................GAATTCTGTGCGAAGAAAT......................................................	19	0	1	13.00	13	11	0	0	2	0	0
..................................................AATTTCTTCAAACCGAAGGT..........................................................................................	20	0	1	12.00	12	12	0	0	0	0	0
.......................................................................................GAATTCTGTGCGAAGAAATTT....................................................	21	0	1	6.00	6	6	0	0	0	0	0
.......................................................................................GAATTCTGTGCGAAGAAATT.....................................................	20	0	1	5.00	5	5	0	0	0	0	0
........................................................................................AATTCTGTGCGAAGAAAT......................................................	18	0	1	3.00	3	3	0	0	0	0	0
........................................................................................AATTCTGTGCGAAGAAATTTTTA.................................................	23	0	1	1.00	1	1	0	0	0	0	0
...........................................................................................TCTGTGCGAAGAAATTT....................................................	17	0	1	1.00	1	0	1	0	0	0	0
........................................................................................AATTCTGTGCGAAGAAATT.....................................................	19	0	1	1.00	1	1	0	0	0	0	0
.........................................................................TGTTAATTTGATTAGAAT.....................................................................	18	0	1	1.00	1	1	0	0	0	0	0
.........................................................................TGTTAATTTGATTAGAATTCTGTGC..............................................................	25	0	1	1.00	1	0	0	1	0	0	0
........................................................................................AACACTGTGCGAAGAATTTTTTA.................................................	23	3	2	0.50	1	0	0	0	0	0	0
.......................................................................................GAATTCTGTCCGAAGA.........................................................	16	1	4	0.25	1	0	0	0	0	0	0
........................................................TCCAAACCGAAGGTCT........................................................................................	16	1	5	0.20	1	0	1	0	0	0	0
..............ATGGGATTGGAAAAGA..................................................................................................................................	16	1	6	0.17	1	0	0	0	0	0	0
...........................................................AAACCGATGGGCTTTGT....................................................................................	17	2	17	0.12	2	0	2	0	0	0	0
...............TGAGATTGGAAAAGG..................................................................................................................................	15	1	18	0.06	1	0	1	0	0	0	0
....................CTGGATTAGATTGTGTAGA.........................................................................................................................	19	3	20	0.05	1	0	0	0	0	0	0
.....................................................................................................................CTTATGAGCCTGAATG...........................	16	2	20	0.05	1	0	0	0	0	0	1

TTCGACTTTTAACTGATTGGCTCGAAAGATTCAGGCTCTTAAGATGCTATAAAAATTTCTTCGCACAGAATTCTAATCAAATTAACAAAGACCTTCGGTTTGAAGAAATTTATGTAACACCTCTACACAATCTTTTCCAATCTCATCCATTCCAAGATGG **********************************....(((((((((...((((((((((..((.(((.(((.((((...))))..)))..))).))..))))))))))...)))))))))..*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total
.........................AAGATTCCGGTTCTTGAGATG..................................................................................................................	21	3	3	1.00	3
...........................GATTCAGGCGCTTAAGAG...................................................................................................................	18	2	3	0.33	1
..........................AGATTCCGGTTCTTGAGATG..................................................................................................................	20	3	4	0.25	1
...........................GATTCCGGTTCTTGAGATG..................................................................................................................	19	3	20	0.15	3
..........................AGATTCCGGTTCTTGAGAT...................................................................................................................	19	3	20	0.05	1

Species	Coordinate	ID	Alignment
droSim3	chrX_Mrandom_959:5640-5799 +	dsi_203	CCATCTTGGAATGGATGAGATTGGAAAAGATTGTG-----TAGAGGTGTTACATAAATTTCTTCAAACCGAAGGTCTTTGTTAATTTGATTAGAATTCTGTGCGAAGAAATTTTTATAGCATCTTA---AGAGCCTGAATCTTTCGAGCCAATCAGTT---AAAAGTCGAA
droSec2	scaffold_8:1718425-1718582 +	dse_116	CAA--ATGGAATGGATGAGATTGGAAAAGATTGTG-----TAGAGGTGTTACATAAATTTCTTCAAGCCGAAGGTCTTTGTTAATTTGATTAGAATTCTGTGCGAAGAAATTTTTATAGCATCTTA---AGAGCCTGAATCTTTCGAGCCAATCAGTT---GAGAGTCGAA
dm3	chrX:19436179-19436344 +		CAA--ATGGAATGGATAAGATTGGATAAGATTGTGTAAGATAGGGTTGTTATATAAATTTCTTCAAACCGAAAGTCTTTGTTAGTTTGATTAGAATTCTATGCGATGAAATTTGTATAGCATCCTT---TGAGTCTGAATCTTTCGAGTCAATCAGATGATGAAAGTCGAA
droEre2	scaffold_4690:9673150-9673307 +	der_57	CAC--AGAGTATGGATGAGGTTGGATGAGATTTTA-----CAGGGCTGTTACATAAATCTCTTCAAGCCGAAGGTCTATGTAAGTTTGGTTGGAATTCTGTGAGAAGAGATTTCTATAGCATCCTGAATACAGTCGGAATCTTCCAAGCTAATCAGTT---GAATGTC---
droYak3	X:11900761-11900923 -	dya_55	AAAGACAAAGATGGATGAGGTTGGATGAGATTGTA-----CAGGGGTGTTACATAAATTTCTTCAAGCCGAAAGTCTATGTAAATTTGGTTGGAATTCGGTGAGAAGAGATTTCTATAGCACTCTGAATAGAGCCTGAATCTTCCAAGCTAATCAGTT---GAAAGTCGAA

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droSim3

CCATCTTGGAATGGATGAGATTGGAAAAGATTGTG-----TAGAGGTGTTACATAAATTTCTTCAAACCGAAGGTCTTTGTTAATTTGATTAGAATTCTGTGCGAAGAAATTTTTATAGCATCTTA---AGAGCCTGAATCTTTCGAGCCAATCAGTT---AAAAGTCGAA	Size	Hit Count	Total Norm	Total	V044 Embryo	M023 Head	M024 Male-body	M025 Embryo	O001 Testis	O002 Head	M053 Female-body	SRR553485 Ovary	SRR553486 Ovary	SRR553487 Ovary	SRR553488 Ovary	SRR618934 Ovary
.......................................................AATTTCTTCAAACCGAAGGTCT..............................................................................................	22	1	73.00	73	0	0	6	0	60	1	0	0	0	0	1	5
............................................................................................GAATTCTGTGCGAAGAAATTTT.........................................................	22	1	28.00	28	0	0	1	0	16	0	0	0	0	0	0	11
.............................................................................................AATTCTGTGCGAAGAAATTTT.........................................................	21	1	25.00	25	0	0	0	0	3	0	0	0	0	0	0	22
............................................................................................GAATTCTGTGCGAAGAAA.............................................................	18	1	15.00	15	0	0	0	0	14	1	0	0	0	0	0	0
.......................................................AATTTCTTCAAACCGAAGGTC...............................................................................................	21	1	14.00	14	0	2	1	0	11	0	0	0	0	0	0	0
.......................................................AATTTCTTCAAACCGAAG..................................................................................................	18	1	14.00	14	0	0	0	0	14	0	0	0	0	0	0	0
.......................................................AATTTCTTCAAACCGAAGG.................................................................................................	19	1	14.00	14	0	0	0	0	14	0	0	0	0	0	0	0
............................................................................................GAATTCTGTGCGAAGAAAT............................................................	19	1	13.00	13	0	0	0	0	11	2	0	0	0	0	0	0
.......................................................AATTTCTTCAAACCGAAGGT................................................................................................	20	1	12.00	12	0	0	0	0	12	0	0	0	0	0	0	0
............................................................................................GAATTCTGTGCGAAGAAATTT..........................................................	21	1	6.00	6	0	0	0	0	6	0	0	0	0	0	0	0
............................................................................................GAATTCTGTGCGAAGAAATT...........................................................	20	1	5.00	5	0	0	0	0	5	0	0	0	0	0	0	0
.............................................................................................AATTCTGTGCGAAGAAAT............................................................	18	1	3.00	3	0	0	0	0	3	0	0	0	0	0	0	0
.............................................................................................AATTCTGTGCGAAGAAATTTTTA.......................................................	23	1	1.00	1	0	0	0	0	1	0	0	0	0	0	0	0
................................................................................................TCTGTGCGAAGAAATTT..........................................................	17	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	1
.............................................................................................AATTCTGTGCGAAGAAATT...........................................................	19	1	1.00	1	0	0	0	0	1	0	0	0	0	0	0	0
..............................................................................TGTTAATTTGATTAGAAT...........................................................................	18	1	1.00	1	0	0	0	0	1	0	0	0	0	0	0	0
..............................................................................TGTTAATTTGATTAGAATTCTGTGC....................................................................	25	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0

droSec2

CAA--ATGGAATGGATGAGATTGGAAAAGATTGTG-----TAGAGGTGTTACATAAATTTCTTCAAGCCGAAGGTCTTTGTTAATTTGATTAGAATTCTGTGCGAAGAAATTTTTATAGCATCTTA---AGAGCCTGAATCTTTCGAGCCAATCAGTT---GAGAGTCGAA	Size	Hit Count	Total Norm	Total	V113 Male-body	V114 Embryo	V115 Head	M054 Female-body
.............................................................................................AATTCTGTGCGAAGAAATTTT.........................................................	21	1	59.00	59	48	7	3	1
.......................................................AATTTCTTCAAGCCGAAGGTCT..............................................................................................	22	1	31.00	31	26	4	0	1
............................................................................................GAATTCTGTGCGAAGAAATTTT.........................................................	22	1	7.00	7	5	1	1	0
.......................................................AATTTCTTCAAGCCGAAGGTC...............................................................................................	21	1	1.00	1	1	0	0	0
........................................................ATTTCTTCAAGCCGAAGGTCT..............................................................................................	21	1	1.00	1	0	0	0	1

droEre2

CAC--AGAGTATGGATGAGGTTGGATGAGATTTTA-----CAGGGCTGTTACATAAATCTCTTCAAGCCGAAGGTCTATGTAAGTTTGGTTGGAATTCTGTGAGAAGAGATTTCTATAGCATCCTGAATACAGTCGGAATCTTCCAAGCTAATCAGTT---GAATGTC---	Size	Hit Count	Total Norm	Total	V040 Embryo	V060 Head	V107 Male-body	V108 Head	M055 Female-body	M057 Embryo
............................................................................................GAATTCTGTGAGAAGAGATTTC.........................................................	22	1	506.00	506	0	1	480	20	5	0
.............................................................................................AATTCTGTGAGAAGAGATTTCT........................................................	22	1	426.00	426	0	1	394	29	2	0
............................................................................................GAATTCTGTGAGAAGAGATTT..........................................................	21	1	65.00	65	0	0	62	3	0	0
.............................................................................................AATTCTGTGAGAAGAGATTTC.........................................................	21	1	11.00	11	0	0	11	0	0	0
............................................................................................GAATTCTGTGAGAAGAGATTTCT........................................................	23	1	6.00	6	0	0	6	0	0	0
............................................................................................GAATTCTGTGAGAAGAGATT...........................................................	20	1	5.00	5	0	1	4	0	0	0
..............................................................................................ATTCTGTGAGAAGAGATTTCT........................................................	21	1	5.00	5	0	0	4	0	1	0
......................................................AAATCTCTTCAAGCCGAAGGTC...............................................................................................	22	1	3.00	3	0	0	3	0	0	0
......................................................AAATCTCTTCAAGCCGAAGGTCT..............................................................................................	23	1	2.00	2	0	0	1	1	0	0
......................................................AAATCTCTTCAAGCCGAAGGT................................................................................................	21	1	2.00	2	0	0	1	1	0	0
............................GATTTTA-----CAGGGCTGTTACAT.....................................................................................................................	21	1	1.00	1	0	0	1	0	0	0
.......................................................AATCTCTTCAAGCCGAAGGTC...............................................................................................	21	1	1.00	1	0	0	1	0	0	0
.............................................................................ATGTAAGTTTGGTTGGAATTC.........................................................................	21	1	1.00	1	0	0	1	0	0	0
...........................................................................................GGAATTCTGTGAGAAGAGATTTC.........................................................	23	1	1.00	1	0	0	1	0	0	0
...............................TTTA-----CAGGGCTGTTACATA....................................................................................................................	19	1	1.00	1	0	0	1	0	0	0
.............................................................................................AATTCTGTGAGAAGAGATTT..........................................................	20	1	1.00	1	0	0	1	0	0	0
.......................................................AATCTCTTCAAGCCGAAGGTCTA.............................................................................................	23	1	1.00	1	0	0	1	0	0	0
..............................................................................................ATTCTGTGAGAAGAGATTT..........................................................	19	1	1.00	1	0	0	0	1	0	0
.......................................................AATCTCTTCAAGCCGAAGGTCT..............................................................................................	22	1	1.00	1	0	0	0	1	0	0

droYak3

AAAGACAAAGATGGATGAGGTTGGATGAGATTGTA-----CAGGGGTGTTACATAAATTTCTTCAAGCCGAAAGTCTATGTAAATTTGGTTGGAATTCGGTGAGAAGAGATTTCTATAGCACTCTGAATAGAGCCTGAATCTTCCAAGCTAATCAGTT---GAAAGTCGAA	Size	Hit Count	Total Norm	Total	V046 Embryo	V052 Head	V120 Male-body	V058 Head	M026 Head	M043 Female-body	M056 Embryo
............................................................................................GAATTCGGTGAGAAGAGATTTC.........................................................	22	1	71.00	71	0	1	57	1	7	3	2
............................................................................................GAATTCGGTGAGAAGAGATTT..........................................................	21	1	43.00	43	0	0	43	0	0	0	0
.............................................................................................AATTCGGTGAGAAGAGATTTCT........................................................	22	1	30.00	30	0	0	28	2	0	0	0
............................................................................................GAATTCGGTGAGAAGAGATTTCT........................................................	23	1	16.00	16	0	0	16	0	0	0	0
............................................................................................GAATTCGGTGAGAAGAGATT...........................................................	20	1	7.00	7	0	0	7	0	0	0	0
.............................................................................................AATTCGGTGAGAAGAGATTTC.........................................................	21	1	5.00	5	0	0	4	0	1	0	0
.............................................................................................AATTCGGTGAGAAGAGATTT..........................................................	20	1	3.00	3	0	0	3	0	0	0	0
...............................................................................................TTCGGTGAGAAGAGATTTCT........................................................	20	1	2.00	2	0	0	2	0	0	0	0
..............................................................................................ATTCGGTGAGAAGAGATTTCT........................................................	21	1	2.00	2	0	0	2	0	0	0	0
.............................................................................................AATTCGGTGAGAAGAGATT...........................................................	19	1	1.00	1	0	0	1	0	0	0	0
..............................................................................TGTAAATTTGGTTGGAATTCGGTGA....................................................................	25	1	1.00	1	0	0	1	0	0	0	0
..............................................................................................ATTCGGTGAGAAGAGATTTC.........................................................	20	1	1.00	1	0	0	1	0	0	0	0
......................................................AAATTTCTTCAAGCCGAAAGTCT..............................................................................................	23	1	1.00	1	0	0	1	0	0	0	0
.......................................................................................GGTTGGAATTCGGTGAGAAG................................................................	20	1	1.00	1	0	0	1	0	0	0	0

dsi_203

chrX_Mrandom_959:5690-5749 +

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

-22.2	-22.1	-21.9