dwi_163

ATTTTCAATTGCCATGTCTATTGCCTTTCCTATAGCAATTAGCTCTGCGCTCAACGATGATCTCTTGGACCCTGTATAAAACTTTTTAGTGGTGTTTGAATTTTTGTGTGTAAGGGCACTGCCCTTAAGTCCTTTAAAACTGAGCCGTAATTTCGTATCCC *********************************......(((((((((...((((.(((.((....((((((............))).)))....))))).))))))))).))))........**********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V118 embryo	M045 female body	M020 head
......................................................................................TAGTGGTGTTTGAATTTTTGTGTG...................................................	24	0	5	3.00	15	12	3	0
......................................................................................TAGTGGTGTTTGAATTTTTGTGTGT..................................................	25	0	5	1.80	9	7	2	0
..................................................TCAACGATGATCTCTTGGACCCTGTA.....................................................................................	26	0	2	1.50	3	2	1	0
........................................................................................................TCTGGGTAAGGTCACTGCCC.....................................	20	3	1	1.00	1	1	0	0
.................................AGCAATTAGCTCTGCGCTCAACGA........................................................................................................	24	0	1	1.00	1	0	1	0
.......................................TAGCTCTGCGCTCAACGATGATCTCTT...............................................................................................	27	0	1	1.00	1	0	1	0
..............................TATAGCAATTAGCTCTGCGCTCAACGA........................................................................................................	27	0	1	1.00	1	0	1	0
................................................................................................TGAATTTTTGTGTGTAAGGGCACTGCC......................................	27	0	1	1.00	1	1	0	0
.............................................TGCGCTCAACGATGATCTCTTGGACC..........................................................................................	26	0	1	1.00	1	0	1	0
......................................................................................TAGTGGTGTTTGAATTTTTGTGTGTA.................................................	26	0	5	0.60	3	2	1	0
...................................................CAACGATGATCTCTTGGACCCTGTA.....................................................................................	25	0	4	0.50	2	0	2	0
......................................................................................TAGTGGTGTTTGAATTTTTGTGT....................................................	23	0	5	0.40	2	2	0	0
.....................................................................................TTAGTGGTGTTTGAATTTTTGTGTGT..................................................	26	0	5	0.40	2	2	0	0
......................................................................................TAGTGGTGTTTGAATTTTTGTGTGTAA................................................	27	0	5	0.40	2	2	0	0
......................................................................................TAGTGGTGTTTGAATTTTTGTGTGTTT................................................	27	2	5	0.40	2	1	1	0
.........................................................................................TGGTGTTTGAATTTTTGTGTGTA.................................................	23	0	6	0.33	2	2	0	0
...................................................CAACGATGATCTCTTGGACCCTGTATAA..................................................................................	28	0	4	0.25	1	0	1	0
.....................................................ACGATGATCTCTTGGACCCTGTATAAAA................................................................................	28	0	4	0.25	1	0	1	0
....................................................AACGATGATATCTTGGACCCTGTATAA..................................................................................	27	1	4	0.25	1	0	1	0
......................................................CGATGATCTCTTGGACCCTGTATAAA.................................................................................	26	0	4	0.25	1	0	1	0
....................................................AACGATGATCTCTTGGACCCTGTA.....................................................................................	24	0	4	0.25	1	0	0	1
.......................................................................................AGTGGTGTTTGAATTTTTGTGTGTA.................................................	25	0	5	0.20	1	0	1	0
.....................................................................................ATAGTGGTGTTTGAATTTTTGTGTGT..................................................	26	1	5	0.20	1	0	1	0
.....................................................................................TTAGTGGTGTTTGAATTTTTGTGTG...................................................	25	0	5	0.20	1	1	0	0
...................................................................................TTTTAGTGGTGTTTGAATTTTTGTGTG...................................................	27	0	5	0.20	1	1	0	0
.....................................................................................TTAGTGGTGTTTGAATTTTTGTG.....................................................	23	0	6	0.17	1	1	0	0
.........................................................................................TGGTGTTTGAATTTTTGTGTG...................................................	21	0	6	0.17	1	0	1	0
.........................................................................................TGGTGTTTGAATTTTTGTGT....................................................	20	0	6	0.17	1	1	0	0

TAAAAGTTAACGGTACAGATAACGGAAAGGATATCGTTAATCGAGACGCGAGTTGCTACTAGAGAACCTGGGACATATTTTGAAAAATCACCACAAACTTAAAAACACACATTCCCGTGACGGGAATTCAGGAAATTTTGACTCGGCATTAAAGCATAGGG **********************************......(((((((((...((((.(((.((....((((((............))).)))....))))).))))))))).))))........*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M045 female body	V118 embryo	V117 male body
...................................................GTTGCTACTAGAGAACCTGGGACA......................................................................................	24	0	4	0.25	1	0	0	1
....................................................TTGCTACTAGAGAACCTGGGACA......................................................................................	23	0	4	0.25	1	1	0	0
...................................................ATTGCTACTAGAGAACCTGGGACAT.....................................................................................	25	1	4	0.25	1	0	1	0
.........................................................................................................................................TGGACTTGGCATTAAAGCATT...	21	3	5	0.20	1	1	0	0
......................................................................................................AAAGACCCATTCCAGTGAC........................................	19	3	20	0.10	2	0	2	0

Re-alignment of all predicted orthologs

Species	Coordinate	ID	Alignment
droWil2	scf2_1100000004909:391701-391861 +	dwi_163	ATTT---TCA--ATTGCCATGTCTATTGCCTTTCCTATAGCAATTAGCTCTGCGCTCAACGATGATCTCTTGGACCCTGTATAAAACTTTTTAGTGGTGTTTGAATTTTTGTGTGTAAGGGCACTGCCCTTA-AGTCCTTTAAAACTGAGCCGT----------AATTTCG-TATCCC
droAna3	scaffold_7240:6805-6976 +		TTGT---TCA--ATTGCAAACTCAATGGCTTTCTCTAGGGCTGTAAGTTCTGCAGTGAGCGAGGATAATTTTTTGTTCATATAAAAACTCTTCGTTGTGTTGCTATTTATATGGTAAAAAGCACTCCCAGTGAAATTATCTTTAACAGAACCGTCGGTAAAAATAACGTCA-TAACTT
droBip1	scf7180000394210:13453-13624 +		TTTT---GAA--ATAGCAAAGTCGATGGCTTTCTCCAGGGCTGTTAGCTCGGCAGTAAGCGAGGAACGTTTAGTGTTAGCATAAAAACTTTTAATGGTATTAGAATTTGTATGTACAAGGGCACACCCTGTAAAATTTTCTTGAACTGAGCCGTCAGTAAAAAGGATTTCA-CTTCCC
droFic1	scf7180000452679:15570-15743 -		TGTT--AGAA--ATGCCAAAGTCAACGGCTTTTTCTAGGGCTGTGAGTTCAGCAGTCAGCGACGACAGTTTTTTGTCTGAGTAAAAACTTTGTACTGTATTAGATTTCATGTGGACGAAAGCACTACCTGTAAAATTCTCGGATACGGAACCATCTGTATAAATAATTTCAACGTTTT
droRho1	scf7180000778090:3541-3710 -		GTTT--TGCATGATGGCAAAATCTAATGCTTTTTCTATTGCAGTGAGTTCTGCAGTCAGCGATGACAGTTTTTTGTTTGTGAAGAAACTTTTTGTTGTGTTCGACTTTATGTGGACAAAGGCACTACCTGCGAAATTGTCCGCCACTGAGCCGTCTGTGTATATTATTTCC------A
droBia1	scf7180000302422:8296690-8296856 -		TTTT---GAA--ATACCGAAGTCAATGGCTTTTTCTAGGGCTGTGAGTTCAGCAGTCAGCGACGATAGTTTTTTGTCGGTGTAGAAACTTTTTATCGAATTGGAATTTAAGTGAACAAAGGCACTGCCTGTAAAATTTTCCGACACAGAACCATCCGTGAAGATGATTTCC------A
droTak1	scf7180000412336:19267-19439 -		TTTC--AGAA--TTAGCAAAGTCGATGGCTTTCTCCAGGGCTGTTAGCTCGGCAGTAAGCGAGGAACGTTTAGTATTAGCGTAAAAGCTTTTAATGGTGTTTGAATTTGAATGTACAAAAGCACACCCCATAAAATTTTCTTGAACTGAGCCGTCAGTATATAAAATCTGA-AAACCT
droEug1	scf7180000405435:2094-2268 +		ATTTTCAGAA--TTAGCAAAGTCGATGGCTTTCTCCAGGGCTGTAAGCTCGGCAGTAAGCGAGGAACGTTTAGTATTAGCGTAAAAACTTTTAATTGTATTTGAATTTGAGTGTACAAAAGCGCATCCCATAAAATTTTCTTGAACTGAGCCGTCAGTATATAAAATCTCA-AAACCC

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droWil2

ATTT---TCA--ATTGCCATGTCTATTGCCTTTCCTATAGCAATTAGCTCTGCGCTCAACGATGATCTCTTGGACCCTGTATAAAACTTTTTAGTGGTGTTTGAATTTTTGTGTGTAAGGGCACTGCCCTTA-AGTCCTTTAAAACTGAGCCGT----------AATTTCG-TATCCC	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
...........................................................................................TAGTGGTGTTTGAATTTTTGTGTG...............................................................	24	5	3.00	15	0	3	0	12	0
...........................................................................................TAGTGGTGTTTGAATTTTTGTGTGT..............................................................	25	5	1.80	9	0	2	0	7	0
.......................................................TCAACGATGATCTCTTGGACCCTGTA.................................................................................................	26	2	1.50	3	0	1	0	2	0
......................................AGCAATTAGCTCTGCGCTCAACGA....................................................................................................................	24	1	1.00	1	0	1	0	0	0
............................................TAGCTCTGCGCTCAACGATGATCTCTT...........................................................................................................	27	1	1.00	1	0	1	0	0	0
...................................TATAGCAATTAGCTCTGCGCTCAACGA....................................................................................................................	27	1	1.00	1	0	1	0	0	0
.....................................................................................................TGAATTTTTGTGTGTAAGGGCACTGCC..................................................	27	1	1.00	1	0	0	0	1	0
..................................................TGCGCTCAACGATGATCTCTTGGACC......................................................................................................	26	1	1.00	1	0	1	0	0	0
...........................................................................................TAGTGGTGTTTGAATTTTTGTGTGTA.............................................................	26	5	0.60	3	0	1	0	2	0
........................................................CAACGATGATCTCTTGGACCCTGTA.................................................................................................	25	4	0.50	2	0	2	0	0	0
...........................................................................................TAGTGGTGTTTGAATTTTTGTGT................................................................	23	5	0.40	2	0	0	0	2	0
..........................................................................................TTAGTGGTGTTTGAATTTTTGTGTGT..............................................................	26	5	0.40	2	0	0	0	2	0
...........................................................................................TAGTGGTGTTTGAATTTTTGTGTGTAA............................................................	27	5	0.40	2	0	0	0	2	0
...........................................................................................TAGTGGTGTTTGAATTTTTGTGTGTTT............................................................	27	5	0.40	2	0	1	0	1	0
..............................................................................................TGGTGTTTGAATTTTTGTGTGTA.............................................................	23	6	0.33	2	0	0	0	2	0
........................................................CAACGATGATCTCTTGGACCCTGTATAA..............................................................................................	28	4	0.25	1	0	1	0	0	0
..........................................................ACGATGATCTCTTGGACCCTGTATAAAA............................................................................................	28	4	0.25	1	0	1	0	0	0
...........................................................CGATGATCTCTTGGACCCTGTATAAA.............................................................................................	26	4	0.25	1	0	1	0	0	0
.........................................................AACGATGATCTCTTGGACCCTGTA.................................................................................................	24	4	0.25	1	1	0	0	0	0
............................................................................................AGTGGTGTTTGAATTTTTGTGTGTA.............................................................	25	5	0.20	1	0	1	0	0	0
..........................................................................................TTAGTGGTGTTTGAATTTTTGTGTG...............................................................	25	5	0.20	1	0	0	0	1	0
........................................................................................TTTTAGTGGTGTTTGAATTTTTGTGTG...............................................................	27	5	0.20	1	0	0	0	1	0
..........................................................................................TTAGTGGTGTTTGAATTTTTGTG.................................................................	23	6	0.17	1	0	0	0	1	0
..............................................................................................TGGTGTTTGAATTTTTGTGTG...............................................................	21	6	0.17	1	0	1	0	0	0
..............................................................................................TGGTGTTTGAATTTTTGTGT................................................................	20	6	0.17	1	0	0	0	1	0

droAna3

TTGT---TCA--ATTGCAAACTCAATGGCTTTCTCTAGGGCTGTAAGTTCTGCAGTGAGCGAGGATAATTTTTTGTTCATATAAAAACTCTTCGTTGTGTTGCTATTTATATGGTAAAAAGCACTCCCAGTGAAATTATCTTTAACAGAACCGTCGGTAAAAATAACGTCA-TAACTT	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
.........................................TGTAAGTTCTGCAGTGAGCGAGGA.................................................................................................................	24	5	0.20	1	0	0	0	0	1	0
.......................................GCTGTAAGTTCTGCAGTGAGCGAGG..................................................................................................................	25	5	0.20	1	1	0	0	0	0	0
..............TGCAAACTCAATGGCTTTCTCTAGGGC.........................................................................................................................................	27	6	0.17	1	0	0	0	0	1	0
.............TTGCAAACTCAATGGCTTTCTCTAGGGC.........................................................................................................................................	28	6	0.17	1	0	1	0	0	0	0
.TGT---TCA--ATTGCAAACTCAATGGCTTTCC................................................................................................................................................	28	7	0.14	1	0	1	0	0	0	0
TTGT---TCA--ATTGCAAACTCAATGGC.....................................................................................................................................................	24	8	0.13	1	0	1	0	0	0	0

droBip1

TTTT---GAA--ATAGCAAAGTCGATGGCTTTCTCCAGGGCTGTTAGCTCGGCAGTAAGCGAGGAACGTTTAGTGTTAGCATAAAAACTTTTAATGGTATTAGAATTTGTATGTACAAGGGCACACCCTGTAAAATTTTCTTGAACTGAGCCGTCAGTAAAAAGGATTTCA-CTTCCC	Size	Hit Count	Total Norm	Total
No Reads

droFic1

TGTT--AGAA--ATGCCAAAGTCAACGGCTTTTTCTAGGGCTGTGAGTTCAGCAGTCAGCGACGACAGTTTTTTGTCTGAGTAAAAACTTTGTACTGTATTAGATTTCATGTGGACGAAAGCACTACCTGTAAAATTCTCGGATACGGAACCATCTGTATAAATAATTTCAACGTTTT	Size	Hit Count	Total Norm	Total
No Reads

droRho1

GTTT--TGCATGATGGCAAAATCTAATGCTTTTTCTATTGCAGTGAGTTCTGCAGTCAGCGATGACAGTTTTTTGTTTGTGAAGAAACTTTTTGTTGTGTTCGACTTTATGTGGACAAAGGCACTACCTGCGAAATTGTCCGCCACTGAGCCGTCTGTGTATATTATTTCC------A	Size	Hit Count	Total Norm	Total
No Reads

droBia1

TTTT---GAA--ATACCGAAGTCAATGGCTTTTTCTAGGGCTGTGAGTTCAGCAGTCAGCGACGATAGTTTTTTGTCGGTGTAGAAACTTTTTATCGAATTGGAATTTAAGTGAACAAAGGCACTGCCTGTAAAATTTTCCGACACAGAACCATCCGTGAAGATGATTTCC------A	Size	Hit Count	Total Norm	Total
No Reads

droTak1

TTTC--AGAA--TTAGCAAAGTCGATGGCTTTCTCCAGGGCTGTTAGCTCGGCAGTAAGCGAGGAACGTTTAGTATTAGCGTAAAAGCTTTTAATGGTGTTTGAATTTGAATGTACAAAAGCACACCCCATAAAATTTTCTTGAACTGAGCCGTCAGTATATAAAATCTGA-AAACCT	Size	Hit Count	Total Norm	Total
No Reads

droEug1

ATTTTCAGAA--TTAGCAAAGTCGATGGCTTTCTCCAGGGCTGTAAGCTCGGCAGTAAGCGAGGAACGTTTAGTATTAGCGTAAAAACTTTTAATTGTATTTGAATTTGAGTGTACAAAAGCGCATCCCATAAAATTTTCTTGAACTGAGCCGTCAGTATATAAAATCTCA-AAACCC	Size	Hit Count	Total Norm	Total
No Reads

dwi_163

scf2_1100000004909:391751-391811 +

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

-16.6	-16.5	-16.3