dpe_258

GTGCAAGACCCTGGTACGGCCTCCACGATGGACTCAAGTTCTAAGTCGGTTTTCCACCTCGCCTGCCTGTAGGTTGTGTGCGTCCTTGTCTTTGGGGTGGAGCTTTTTGAGGCACAGGTAGACACTACCCATGCCCCACGCCATCTTCCCGAAT *********************************..(((.((((..(((..(((((((((((((....)))))...................))))))))))).)))).))).....**********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M042 female body	M021 embryo	V057 head
..................................................TTTCCACCTCGCCTGCCTGTAGG.................................................................................	23	0	10	3.90	39	39	0	0
..................................................TTTCCACCTCGCCTGCCTGTAGGTTG..............................................................................	26	0	4	3.50	14	13	1	0
..................................................TTTCCACCTCGCCTGCCTGTAGGT................................................................................	24	0	4	3.25	13	12	1	0
..................................................TTTCCACCTCGCCTGCCTGTAGGTT...............................................................................	25	0	4	2.25	9	2	7	0
..................................................TTTCCACCTCGCCTGCCTG.....................................................................................	19	0	20	1.45	29	8	21	0
........................................................................................................TTTTGAGGCACAGGTAGACACTAC..........................	24	0	3	1.33	4	0	4	0
..................................................TTTCCACCTCGCCTGCCTGTAG..................................................................................	22	0	10	1.30	13	4	9	0
........................................................................................................TTTTGAGGCACAGGTAGACACTACCCA.......................	27	0	3	1.00	3	3	0	0
.........................................................................................................TTTGAGGCACAGGTAGACACTA...........................	22	0	3	0.33	1	1	0	0
..................................................................................TCCTTGTCTTTGGGGTGGAGC...................................................	21	0	3	0.33	1	1	0	0
...................................................................................CCTTGTCTTTGGGGTGGAGCT..................................................	21	0	3	0.33	1	1	0	0
..................................................TTTCCACCGCGCCTGCCTGTATGTTG..............................................................................	26	2	4	0.25	1	1	0	0
............................................................................TGTGCGTCGTTGTCTTTGGGG.........................................................	21	1	4	0.25	1	1	0	0
...........................................................................GTGTGCGTCCTTGTCTTTGGGGTG.......................................................	24	0	4	0.25	1	1	0	0
.................................................ATTTCCACCTCGCCTGCCTGTAGGT................................................................................	25	1	4	0.25	1	1	0	0
...................................................TTCCACCTCGCCTGCCTGTAGG.................................................................................	22	0	10	0.20	2	2	0	0
..................................................TTTCCACCTCGCCTGCCTGT....................................................................................	20	0	10	0.20	2	2	0	0
....................................................TCCACCTCGCCTGCCTGTAGG.................................................................................	21	0	10	0.20	2	2	0	0
..................................................TTTCCACCTCGCCTGCCTGTA...................................................................................	21	0	10	0.10	1	1	0	0
.................................................GTTTCCACCTCGCCTGCCTGTAGG.................................................................................	24	1	10	0.10	1	1	0	0
..................................................TTTCCACCGCGCATGCCTGTAGG.................................................................................	23	2	10	0.10	1	1	0	0
...............................................................................GCGTCCTTGTCTTCGGGGT........................................................	19	1	14	0.07	1	1	0	0
.............................................................................................................................TACCCATGCCCCACACCATCTTCC.....	24	1	20	0.05	1	1	0	0
........................AAGAGGGTCTCAAGTTCTA...............................................................................................................	19	3	20	0.05	1	0	0	1
..............................................................................................................................ACCCATGCCCCACACCATCTTC......	22	1	20	0.05	1	1	0	0
.............................................................................................................................TACCCATGCCCCACGCCATCTTC......	23	0	20	0.05	1	1	0	0
.............................................................................................................................TACCCATGCCCCACGCCATCTTCC.....	24	0	20	0.05	1	1	0	0

CACGTTCTGGGACCATGCCGGAGGTGCTACCTGAGTTCAAGATTCAGCCAAAAGGTGGAGCGGACGGACATCCAACACACGCAGGAACAGAAACCCCACCTCGAAAAACTCCGTGTCCATCTGTGATGGGTACGGGGTGCGGTAGAAGGGCTTA **********************************..(((.((((..(((..(((((((((((((....)))))...................))))))))))).)))).))).....*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M042 female body	M021 embryo	V057 head	V111 male body
...........ACCACGCCGGAGGTGCTACCT..........................................................................................................................	21	1	1	1.00	1	1	0	0	0
...............................................................ACGGACATCCAACACACGCAGGAA...................................................................	24	0	4	0.50	2	2	0	0	0
................................................................CGGACATCCAACACACGCAGGAA...................................................................	23	0	4	0.50	2	2	0	0	0
.................................TGGTCAAGATTCAGCCAACA.....................................................................................................	20	3	5	0.40	2	0	2	0	0
.....................................................................................................CGAAAAACTCCGTGTCCATCTGTGAT...........................	26	0	3	0.33	1	1	0	0	0
..............................................................GACGGACATCCAACACACGCAGGAAC..................................................................	26	0	4	0.25	1	1	0	0	0
...............................................................ACGGACATCCAACACACGCAGGAAC..................................................................	25	0	4	0.25	1	1	0	0	0
.................................................................GGACATCCAACACACGCAGGAAC..................................................................	23	0	4	0.25	1	1	0	0	0
............................................................................................................................GATGGGTACGGGGTGCGGTAG.........	21	0	20	0.05	1	0	0	0	1
................................................................................................................GTGTCCATCAGTTATGGGC.......................	19	3	20	0.05	1	0	0	1	0

Species	Coordinate	ID	Alignment
droPer2	scaffold_309:3146-3299 +	dpe_258	GTGCAAGACCCTGGTACGGCCTCCACGATGGACTCAAGTTCTAAGTCGGTTTTCCACCTCGCCTGCCTGTAGGTTGTGTGCGTCCTTGTCTTTGGGGTGGAGCTTTTTGAGGCACAGGTAGACACTACCCATGCCCCACGCCATCTTCCCGAAT
dp5	Unknown_group_60:4661-4812 -		GCGCAAGACCCTGGT-CGGCCTCCACGATGGACTCAAGTTCTAAGTCG-TTTTCCACCTCGCCTGCCTGTAGGTTGTGTGCGTCCTTGTCTTTGGGGTGGCGCTTTTTGAGGCACAGGTAGACACTACCCATGCCCCACGCCATCTTCCCGAAT
droWil2	scf2_1100000004961:2381945-2381989 -		-------------------------------------------------------------------------------------------------------------AGATGTAGGTACACGCTCTCTTCTCCCCACGTCATCTTCCCGAAT
droVir3	scaffold_12963:5335582-5335653 -		GCAT----------------------------------------------------------------------------------TCTTTTCCCTGTGGCGTTTCTTAACATGCACCCGCACGGTGCTCATGCCCCAGGCCATCTTTCCATGT
droBip1	scf7180000393866:3236-3239 +		GTGC------------------------------------------------------------------------------------------------------------------------------------------------------
droKik1	scf7180000301969:921-1072 +		GCGTCATTTCCCGGT-CGGCATCCACGATGGTTTCCAGATCTAGGTCC-TTCTCCACCACATCTGCCTTCAGGGTGTGAGCATCCTTATCCCCGGGGTGGCGCTTTTTGAGGCGCAGGTATACGCTACCCATGCCCCACGCCATCTTCCCGTAT
droEle1	scf7180000490439:4807-4957 -		ACTTCAGGTCCTGGG-TAGCCTCCATCACACTGTCAAGGCCCAGGTCC-TTCTCCACCTCGCCTGCCTGCAGTGTTTGGTCGTCCTTGTCCCCGGGATGGCGTT-TTTGAGGTGCAGGTAGACGCTACCCATGCCCCACGCCATCTTCCCGTAC
droRho1	scf7180000757807:901-937 -		TTGAAAAGCCGTCCT---------------------------------------------------------------------------------------------------------------------CCGGCACACCAGGGGCCTCCAC
droBia1	scf7180000302246:9601-9738 -		GCGCACGGTCGTGGG-CTCCATCCACAATGGCTTCCAGTTTT--------T-------CTGCCTGCCTGCAGGGTGTGTGCGCCTTTGTCGTTGGGGTGGTACTTCTTGAGATGCAGGTAGACACTACTTATGCCCCACGCCATCTTCCCGACT
droTak1	scf7180000413313:18647-18798 +		GAGCAAGTTCCTGGG-CGGCATCCACGATGGTTTCCAGACCTAGGTCC-TTCTCCACCTCGCCTGCCTGCAGGATGTGTGCGCCTTTGTCGTCGGGGTGTTGCTTCTTGAGGCGCAGCTAGACACTACCCATGCCCCACGCCATCTTCCCGAAT
droYak3	3L:23572588-23572739 +		GCGAAAGTCCCTGGG-CGGCTTCCGCGATGGTTTCCAGACCTAGGTCC-TTCTCCACCTCGCCTGCCTTCAGGGTGTGAGCATCCTTATCCCCGGGATGGCGTTTGTTGAGGCCCAGGTACACGCTCCCCATGCCCCACGCCATCTTCCCGTAT

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droPer2

GTGCAAGACCCTGGTACGGCCTCCACGATGGACTCAAGTTCTAAGTCGGTTTTCCACCTCGCCTGCCTGTAGGTTGTGTGCGTCCTTGTCTTTGGGGTGGAGCTTTTTGAGGCACAGGTAGACACTACCCATGCCCCACGCCATCTTCCCGAAT	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
..................................................TTTCCACCTCGCCTGCCTGTAGG.................................................................................	23	10	3.90	39	0	39	0	0	0	0
..................................................TTTCCACCTCGCCTGCCTGTAGGTTG..............................................................................	26	4	3.50	14	1	13	0	0	0	0
..................................................TTTCCACCTCGCCTGCCTGTAGGT................................................................................	24	4	3.25	13	1	12	0	0	0	0
..................................................TTTCCACCTCGCCTGCCTGTAGGTT...............................................................................	25	4	2.25	9	7	2	0	0	0	0
..................................................TTTCCACCTCGCCTGCCTG.....................................................................................	19	20	1.45	29	21	8	0	0	0	0
........................................................................................................TTTTGAGGCACAGGTAGACACTAC..........................	24	3	1.33	4	4	0	0	0	0	0
..................................................TTTCCACCTCGCCTGCCTGTAG..................................................................................	22	10	1.30	13	9	4	0	0	0	0
........................................................................................................TTTTGAGGCACAGGTAGACACTACCCA.......................	27	3	1.00	3	0	3	0	0	0	0
.........................................................................................................TTTGAGGCACAGGTAGACACTA...........................	22	3	0.33	1	0	1	0	0	0	0
..................................................................................TCCTTGTCTTTGGGGTGGAGC...................................................	21	3	0.33	1	0	1	0	0	0	0
...................................................................................CCTTGTCTTTGGGGTGGAGCT..................................................	21	3	0.33	1	0	1	0	0	0	0
...........................................................................GTGTGCGTCCTTGTCTTTGGGGTG.......................................................	24	4	0.25	1	0	1	0	0	0	0
...................................................TTCCACCTCGCCTGCCTGTAGG.................................................................................	22	10	0.20	2	0	2	0	0	0	0
..................................................TTTCCACCTCGCCTGCCTGT....................................................................................	20	10	0.20	2	0	2	0	0	0	0
....................................................TCCACCTCGCCTGCCTGTAGG.................................................................................	21	10	0.20	2	0	2	0	0	0	0
..................................................TTTCCACCTCGCCTGCCTGTA...................................................................................	21	10	0.10	1	0	1	0	0	0	0
.............................................................................................................................TACCCATGCCCCACGCCATCTTC......	23	20	0.05	1	0	1	0	0	0	0
.............................................................................................................................TACCCATGCCCCACGCCATCTTCC.....	24	20	0.05	1	0	1	0	0	0	0

dp5

GCGCAAGACCCTGGT-CGGCCTCCACGATGGACTCAAGTTCTAAGTCG-TTTTCCACCTCGCCTGCCTGTAGGTTGTGTGCGTCCTTGTCTTTGGGGTGGCGCTTTTTGAGGCACAGGTAGACACTACCCATGCCCCACGCCATCTTCCCGAAT	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
...............................................................TGCCTGTAGGTTGTGTGCGTCCTTG..................................................................	25	2	2.50	5	0	5	0	0	0	0	0	0	0	0
............................TGGACTCAAGTTCTAAGTCG-TTTT.....................................................................................................	24	2	2.00	4	0	0	0	0	0	0	0	0	4	0
...............................................................TGCCTGTAGGTTGTGTGCG........................................................................	19	2	2.00	4	0	3	0	0	0	0	0	0	1	0
...............................................................TGCCTGTAGGTTGTGTGCGTCCTT...................................................................	24	2	1.00	2	0	0	0	0	0	0	2	0	0	0
..................................................................................TCCTTGTCTTTGGGGTGGCGCTTTT...............................................	25	2	1.00	2	0	2	0	0	0	0	0	0	0	0
..........................................................................TGTGTGCGTCCTTGTCTTTGGG..........................................................	22	2	1.00	2	0	0	0	0	0	0	0	0	2	0
...............................................................TGCCTGTAGGTTGTGTGCGT.......................................................................	20	2	1.00	2	0	1	0	0	1	0	0	0	0	0
......................................................CACCTCGCCTGCCTGTAGGTT...............................................................................	21	2	0.50	1	0	1	0	0	0	0	0	0	0	0
......................................TTCTAAGTCG-TTTTCCACCTCGC............................................................................................	23	2	0.50	1	0	0	0	0	0	0	1	0	0	0
...................................AAGTTCTAAGTCG-TTTTCCAC.................................................................................................	21	2	0.50	1	0	0	0	0	0	0	1	0	0	0
..........................................................................TGTGTGCGTCCTTGTCTTTGGGG.........................................................	23	2	0.50	1	0	1	0	0	0	0	0	0	0	0
...............................................................TGCCTGTAGGTTGTGTGCGTCC.....................................................................	22	2	0.50	1	0	0	0	0	0	0	1	0	0	0
..................................................................................................GGCGCTTTTTGAGGCACAGGTAGA................................	24	2	0.50	1	0	1	0	0	0	0	0	0	0	0
..................................................................................TCCTTGTCTTTGGGGTGGCGCTTT................................................	24	2	0.50	1	0	1	0	0	0	0	0	0	0	0
.........................................................................................................................ACACTACCCATGCCCCACGC.............	20	2	0.50	1	0	1	0	0	0	0	0	0	0	0
...............................................................TGCCTGTAGGTTGTGTGCGTCCTTGT.................................................................	26	2	0.50	1	0	1	0	0	0	0	0	0	0	0
............................................GTCG-TTTTCCACCTCGCCTGC........................................................................................	21	2	0.50	1	0	0	0	1	0	0	0	0	0	0
.......................................TCTAAGTCG-TTTTCCACCTCGCCTGC........................................................................................	26	2	0.50	1	0	1	0	0	0	0	0	0	0	0
......................................................................................................................TAGACACTACCCATGCCCCACGCC............	24	2	0.50	1	0	1	0	0	0	0	0	0	0	0
......................................................CACCTCGCCTGCCTGTAGGTTGTGTGC.........................................................................	27	2	0.50	1	0	1	0	0	0	0	0	0	0	0
.........................................TAAGTCG-TTTTCCACCTCGCCTGCCT......................................................................................	26	2	0.50	1	0	1	0	0	0	0	0	0	0	0
........................................................................................................................GACACTACCCATGCCCCACGCCATCT........	26	2	0.50	1	0	1	0	0	0	0	0	0	0	0
............................TGGACTCAAGTTCTAAGTCG-TTTTCCACC................................................................................................	29	2	0.50	1	0	1	0	0	0	0	0	0	0	0
...................................................................TGTAGGTTGTGTGCGTCCTTG..................................................................	21	2	0.50	1	0	1	0	0	0	0	0	0	0	0
.................................................TTTTCCACCTCGCCTGCCTGTAG..................................................................................	23	4	0.50	2	0	0	0	0	0	0	0	0	2	0
................................................................GCCTGTAGGTTGTGTGCGTCCTTG..................................................................	24	2	0.50	1	0	1	0	0	0	0	0	0	0	0
.........................................TAAGTCG-TTTTCCACCTCGCCTGCCTG.....................................................................................	27	2	0.50	1	0	1	0	0	0	0	0	0	0	0
..........................................................TCGCCTGCCTGTAGGTTGTGTG..........................................................................	22	2	0.50	1	0	0	0	0	0	0	1	0	0	0
...............................................................TGCCTGTAGGTTGTGTGCGTCCT....................................................................	23	2	0.50	1	0	1	0	0	0	0	0	0	0	0
...............................................................TGCCTGTAGGTTGTGTGCGTCCTTGTC................................................................	27	2	0.50	1	0	1	0	0	0	0	0	0	0	0
..........................................................................................................................CACTACCCATGCCCCACGCCATCTTCC.....	27	2	0.50	1	0	1	0	0	0	0	0	0	0	0
....................................................................GTAGGTTGTGTGCGTCCTTGTCTTT.............................................................	25	2	0.50	1	0	1	0	0	0	0	0	0	0	0
......................................TTCTAAGTCG-TTTTCCACCTCGCC...........................................................................................	24	2	0.50	1	0	1	0	0	0	0	0	0	0	0
........................................................................................................................GACACTACCCATGCCCCACGCC............	22	2	0.50	1	0	1	0	0	0	0	0	0	0	0
.............................GGACTCAAGTTCTAAGTCG-TT.......................................................................................................	21	2	0.50	1	0	1	0	0	0	0	0	0	0	0
...........................................................................................................TGAGGCACAGGTAGACACTACCC........................	23	2	0.50	1	0	1	0	0	0	0	0	0	0	0
................................................................GCCTGTAGGTTGTGTGCGTCCTTGTCC...............................................................	27	2	0.50	1	0	1	0	0	0	0	0	0	0	0
..........................................................TCGCCTGCCTGTAGGTTGTGTGCGT.......................................................................	25	2	0.50	1	0	1	0	0	0	0	0	0	0	0
.............................................................................................................................TACCCATGCCCCACGCCATCTTCC.....	24	16	0.25	4	0	4	0	0	0	0	0	0	0	0
.............................................................................................................................TACCCATGCCCCACGCCATCTTC......	23	16	0.19	3	0	2	1	0	0	0	0	0	0	0
.............................................................................................................................TACCCATGCCCCACGCCATCTT.......	22	16	0.19	3	0	3	0	0	0	0	0	0	0	0
.................................................TTTTCCACCTCGCCTGCCTG.....................................................................................	20	14	0.14	2	0	2	0	0	0	0	0	0	0	0
............................................................................................................................CTACCCATGCCCCACGCCAT..........	20	16	0.13	2	0	2	0	0	0	0	0	0	0	0
.............................................................................................................................TACCCATGCCCCACGCCATCTTCCCGA..	27	16	0.13	2	0	2	0	0	0	0	0	0	0	0
.............................................................................................................................TACCCATGCCCCACGCCATCTTCCC....	25	16	0.13	2	0	2	0	0	0	0	0	0	0	0
............................................................................................................................CTACCCATGCCCCACGCCATCTTCC.....	25	16	0.13	2	0	2	0	0	0	0	0	0	0	0
..............................................................................................................................ACCCATGCCCCACGCCATCTTCC.....	23	16	0.06	1	0	1	0	0	0	0	0	0	0	0
..............................................................................................................................ACCCATGCCCCACGCCATCTTCCCGA..	26	16	0.06	1	0	1	0	0	0	0	0	0	0	0
.............................................................................................................................TACCCATGCCCCACGCCATCT........	21	16	0.06	1	0	1	0	0	0	0	0	0	0	0
............................................................................................................................CTACCCATGCCCCACGCCA...........	19	16	0.06	1	0	1	0	0	0	0	0	0	0	0
..............................................................................................GGGTGGCGCTTTTTGAGGA.........................................	19	20	0.05	1	0	1	0	0	0	0	0	0	0	0

droWil2

-------------------------------------------------------------------------------------------------------------AGATGTAGGTACACGCTCTCTTCTCCCCACGTCATCTTCCCGAAT	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
No Reads

droVir3

GCAT----------------------------------------------------------------------------------TCTTTTCCCTGTGGCGTTTCTTAACATGCACCCGCACGGTGCTCATGCCCCAGGCCATCTTTCCATGT

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

No Reads

droBip1

GTGC------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droKik1

GCGTCATTTCCCGGT-CGGCATCCACGATGGTTTCCAGATCTAGGTCC-TTCTCCACCACATCTGCCTTCAGGGTGTGAGCATCCTTATCCCCGGGGTGGCGCTTTTTGAGGCGCAGGTATACGCTACCCATGCCCCACGCCATCTTCCCGTAT	Size	Hit Count	Total Norm	Total
No Reads

droEle1

ACTTCAGGTCCTGGG-TAGCCTCCATCACACTGTCAAGGCCCAGGTCC-TTCTCCACCTCGCCTGCCTGCAGTGTTTGGTCGTCCTTGTCCCCGGGATGGCGTT-TTTGAGGTGCAGGTAGACGCTACCCATGCCCCACGCCATCTTCCCGTAC	Size	Hit Count	Total Norm	Total
No Reads

droRho1

TTGAAAAGCCGTCCT---------------------------------------------------------------------------------------------------------------------CCGGCACACCAGGGGCCTCCAC	Size	Hit Count	Total Norm	Total
No Reads

droBia1

GCGCACGGTCGTGGG-CTCCATCCACAATGGCTTCCAGTTTT--------T-------CTGCCTGCCTGCAGGGTGTGTGCGCCTTTGTCGTTGGGGTGGTACTTCTTGAGATGCAGGTAGACACTACTTATGCCCCACGCCATCTTCCCGACT	Size	Hit Count	Total Norm	Total
No Reads

droTak1

GAGCAAGTTCCTGGG-CGGCATCCACGATGGTTTCCAGACCTAGGTCC-TTCTCCACCTCGCCTGCCTGCAGGATGTGTGCGCCTTTGTCGTCGGGGTGTTGCTTCTTGAGGCGCAGCTAGACACTACCCATGCCCCACGCCATCTTCCCGAAT	Size	Hit Count	Total Norm	Total
No Reads

droYak3

GCGAAAGTCCCTGGG-CGGCTTCCGCGATGGTTTCCAGACCTAGGTCC-TTCTCCACCTCGCCTGCCTTCAGGGTGTGAGCATCCTTATCCCCGGGATGGCGTTTGTTGAGGCCCAGGTACACGCTCCCCATGCCCCACGCCATCTTCCCGTAT	Size	Hit Count	Total Norm	Total	M026 Head	M043 Female-body	M056 Embryo	V046 Embryo	V052 Head	V058 Head	V120 Male-body	SRR1275488 Male larvae	SRR1275486 Male prepupae	SRR1275484 Male prepupae	GSM1528802 follicle cells
........................................................................................TCCCCGGGATGGCGTTTGTTGAGGC.........................................	25	1	13.00	13	0	0	0	0	0	0	0	0	0	0	13
..................................................................................TCCTTATCCCCGGGATGGCGTTTG................................................	24	1	5.00	5	0	5	0	0	0	0	0	0	0	0	0
........................................................................................................TGTTGAGGCCCAGGTACACGCTCCCCA.......................	27	1	4.00	4	0	4	0	0	0	0	0	0	0	0	0
............................TGGTTTCCAGACCTAGGTCC-TTCTCC...................................................................................................	26	7	3.57	25	0	18	0	0	0	0	0	0	0	0	7
...........................ATGGTTTCCAGACCTAGGTCC-TTCTCC...................................................................................................	27	7	1.57	11	0	10	1	0	0	0	0	0	0	0	0
.................................................TTCTCCACCTCGCCTGCCTTCAGGG................................................................................	25	13	1.54	20	0	0	1	0	0	0	0	0	0	0	19
............................TGGTTTCCAGACCTAGGTCC-TTCTC....................................................................................................	25	8	1.25	10	0	10	0	0	0	0	0	0	0	0	0
......................................................................................................................TACACGCTCCCCATGCCCCACGCCA...........	25	5	1.20	6	0	6	0	0	0	0	0	0	0	0	0
..................................................................................TCCTTATCCCCGGGATGGCGTTTGT...............................................	25	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
...................................................................................CCTTATCCCCGGGATGGCGTTTGT...............................................	24	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
...........................ATGGTTTCCAGACCTAGGTCC-TTCT.....................................................................................................	25	9	1.00	9	0	8	1	0	0	0	0	0	0	0	0
.....................................................................................TTATCCCCGGGATGGCGTTTGTTGAGG..........................................	27	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
......................................................................................................TTTGTTGAGGCCCAGGTACACGCTCC..........................	26	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
...................................................................................CCTTATCCCCGGGATGGCGTTTGTTG.............................................	26	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
...........................................................................................................TGAGGCCCAGGTACACGCTCCCCAT......................	25	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
..................................................................................TCCTTATCCCCGGGATGGCGTTTGTT..............................................	26	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
.................................................................................................TGGCGTTTGTTGAGGCCCAGGTA..................................	23	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
..................................................................................................................CAGGTACACGCTCCCCATGCCCCACG..............	26	4	1.00	4	0	4	0	0	0	0	0	0	0	0	0
............................TGGTTTCCAGACCTAGGTCC-TTCTCCA..................................................................................................	27	7	0.71	5	0	5	0	0	0	0	0	0	0	0	0
...........................ATGGTTTCCAGACCTAGGTCC-TTC......................................................................................................	24	9	0.67	6	0	5	1	0	0	0	0	0	0	0	0
..................................................................................................................CAGGTACACGCTCCCCATGCCCCACGCCA...........	29	3	0.67	2	0	2	0	0	0	0	0	0	0	0	0
...........................ATGGTTTCCAGACCTAGGTCC-TTCTC....................................................................................................	26	8	0.63	5	0	5	0	0	0	0	0	0	0	0	0
.............................GGTTTCCAGACCTAGGTCC-TTCTCCA..................................................................................................	26	7	0.57	4	0	4	0	0	0	0	0	0	0	0	0
..................................................................................................................CAGGTACACGCTCCCCATGCCCCACGCC............	28	4	0.50	2	0	2	0	0	0	0	0	0	0	0	0
......................................................................................................................TACACGCTCCCCATGCCCCACGCCATC.........	27	4	0.50	2	0	2	0	0	0	0	0	0	0	0	0
............................TGGTTTCCAGACCTAGGTCC-TTCT.....................................................................................................	24	9	0.44	4	0	4	0	0	0	0	0	0	0	0	0
...........................ATGGTTTCCAGACCTAGGTCC-TTCTCCA..................................................................................................	28	7	0.43	3	0	3	0	0	0	0	0	0	0	0	0
.............................................................................GAGCATCCTTATCCCCGGGATGGCGT...................................................	26	5	0.40	2	0	2	0	0	0	0	0	0	0	0	0
........................................................................................................................CACGCTCCCCATGCCCCACGCCATCTTCC.....	29	3	0.33	1	0	1	0	0	0	0	0	0	0	0	0
......................CCGCGATGGTTTCCAGACCTAGGTCC-.........................................................................................................	26	6	0.33	2	0	2	0	0	0	0	0	0	0	0	0
.....................TCCGCGATGGTTTCCAGACCTAGGTCC-.........................................................................................................	27	6	0.33	2	0	2	0	0	0	0	0	0	0	0	0
...................................................................................................................AGGTACACGCTCCCCATGCCCCACGCCA...........	28	3	0.33	1	0	1	0	0	0	0	0	0	0	0	0
............................TGGTTTCCAGACCTAGGTCC-TTCTCCAC.................................................................................................	28	7	0.29	2	0	2	0	0	0	0	0	0	0	0	0
..........................................................TCGCCTGCCTTCAGGGTGTGAGC.........................................................................	23	12	0.25	3	0	3	0	0	0	0	0	0	0	0	0
........................................................................................................................CACGCTCCCCATGCCCCACGCCATCTT.......	27	4	0.25	1	0	1	0	0	0	0	0	0	0	0	0
.........................................TAGGTCC-TTCTCCACCTCGCCTGCC.......................................................................................	25	12	0.25	3	0	2	1	0	0	0	0	0	0	0	0
....................................................TCCACCTCGCCTGCCTTCAGGGTGTG............................................................................	26	12	0.25	3	0	3	0	0	0	0	0	0	0	0	0
..................................................................................................................CAGGTACACGCTCCCCATGCCCCACGC.............	27	4	0.25	1	0	1	0	0	0	0	0	0	0	0	0
........................................................................................................................CACGCTCCCCATGCCCCACGCCATC.........	25	4	0.25	1	0	1	0	0	0	0	0	0	0	0	0
......................................................................................................................TACACGCTCCCCATGCCCCACGCCATCT........	28	4	0.25	1	0	1	0	0	0	0	0	0	0	0	0
............................TGGTTTCCAGACCTAGGTCC-TTC......................................................................................................	23	9	0.22	2	0	2	0	0	0	0	0	0	0	0	0
...........................ATGGTTTCCAGACCTAGGTCC-TT.......................................................................................................	23	9	0.22	2	0	2	0	0	0	0	0	0	0	0	0
.......................................................................................................................ACACGCTCCCCATGCCCCACGCCA...........	24	5	0.20	1	0	1	0	0	0	0	0	0	0	0	0
....................................................................................................................GGTACACGCTCCCCATGCCCCACGCC............	26	5	0.20	1	0	1	0	0	0	0	0	0	0	0	0
.............................................................................................................................TCCCCATGCCCCACGCCATCTTCCCG...	26	5	0.20	1	0	1	0	0	0	0	0	0	0	0	0
....................................................................................................................GGTACACGCTCCCCATGCCCCAC...............	23	5	0.20	1	0	1	0	0	0	0	0	0	0	0	0
.............................................................................................................................TCCCCATGCCCCACGCCATCTTCCCGTA.	28	5	0.20	1	0	1	0	0	0	0	0	0	0	0	0
............................................................................TGAGCATCCTTATCCCCGGGATGGCGTT..................................................	28	5	0.20	1	0	1	0	0	0	0	0	0	0	0	0
..........................................................................TGTGAGCATCCTTATCCCCGGGATGGCG....................................................	28	5	0.20	1	0	1	0	0	0	0	0	0	0	0	0
...............................................................................................................................CCCATGCCCCACGCCATCTTCCCGTA.	26	5	0.20	1	0	1	0	0	0	0	0	0	0	0	0
............................................................................TGAGCATCCTTATCCCCGGGATGGCG....................................................	26	5	0.20	1	0	1	0	0	0	0	0	0	0	0	0
.............................................................................GAGCATCCTTATCCCCGGGATGGC.....................................................	24	5	0.20	1	0	1	0	0	0	0	0	0	0	0	0
.....................................GACCTAGGTCC-TTCTCCACCTCGCCT..........................................................................................	26	11	0.18	2	0	2	0	0	0	0	0	0	0	0	0
..........................................................TCGCCTGCCTTCAGGGTGTGAGCA........................................................................	24	12	0.17	2	0	2	0	0	0	0	0	0	0	0	0
...............................................................TGCCTTCAGGGTGTGAGCATCCTTA..................................................................	25	12	0.17	2	0	2	0	0	0	0	0	0	0	0	0
........................................................................................................................CACGCTCCCCATGCCCCACG..............	20	6	0.17	1	0	1	0	0	0	0	0	0	0	0	0
.............................GGTTTCCAGACCTAGGTCC-TTCTCCACCT...............................................................................................	29	6	0.17	1	0	1	0	0	0	0	0	0	0	0	0
..........................................................................TGTGAGCATCCTTATCCCCGGGATG.......................................................	25	6	0.17	1	0	1	0	0	0	0	0	0	0	0	0
....................TTCCGCGATGGTTTCCAGACCTAGGTCC-.........................................................................................................	28	6	0.17	1	0	1	0	0	0	0	0	0	0	0	0
......................................................................................................................TACACGCTCCCCATGCCCCACGCC............	24	6	0.17	1	0	0	1	0	0	0	0	0	0	0	0
.....................TCCGCGATGGTTTCCAGACCTAGGTCC-T........................................................................................................	28	6	0.17	1	0	1	0	0	0	0	0	0	0	0	0
.................................................TTCTCCACCTCGCCTGCCTTCAGG.................................................................................	24	13	0.15	2	0	2	0	0	0	0	0	0	0	0	0
.............................GGTTTCCAGACCTAGGTCC-TTCTCCACC................................................................................................	28	7	0.14	1	0	1	0	0	0	0	0	0	0	0	0
.............................GGTTTCCAGACCTAGGTCC-TTCTCCAC.................................................................................................	27	7	0.14	1	0	1	0	0	0	0	0	0	0	0	0
..................GCTTCCGCGATGGTTTCCAGACCTAGG.............................................................................................................	27	7	0.14	1	0	1	0	0	0	0	0	0	0	0	0
............................TGGTTTCCAGACCTAGGTCC-TTCTCCACC................................................................................................	29	7	0.14	1	0	1	0	0	0	0	0	0	0	0	0
...........................ATGGTTTCCAGACCTAGGTCC-TTCTCCAC.................................................................................................	29	7	0.14	1	0	1	0	0	0	0	0	0	0	0	0
..................GCTTCCGCGATGGTTTCCAGACC.................................................................................................................	23	8	0.13	1	0	1	0	0	0	0	0	0	0	0	0
.................................TCCAGACCTAGGTCC-TTCTCCACCT...............................................................................................	25	8	0.13	1	0	1	0	0	0	0	0	0	0	0	0
....................................AGACCTAGGTCC-TTCTCCACCTCGCCT..........................................................................................	27	8	0.13	1	0	1	0	0	0	0	0	0	0	0	0
.................................TCCAGACCTAGGTCC-TTCTCCACCTC..............................................................................................	26	8	0.13	1	0	1	0	0	0	0	0	0	0	0	0
..................................................................................TCCTTATCCCCGGGATGGCGTTT.................................................	23	8	0.13	1	0	1	0	0	0	0	0	0	0	0	0
..................GCTTCCGCGATGGTTTCCAGAC..................................................................................................................	22	9	0.11	1	0	1	0	0	0	0	0	0	0	0	0
............................TGGTTTCCAGACCTAGGTCC-TTCA.....................................................................................................	24	9	0.11	1	0	1	0	0	0	0	0	0	0	0	0
...............................TTTCCAGACCTAGGTCC-TTCTCCACC................................................................................................	26	9	0.11	1	0	1	0	0	0	0	0	0	0	0	0
..................................CCAGACCTAGGTCC-TTCTCCACCTT..............................................................................................	25	9	0.11	1	0	1	0	0	0	0	0	0	0	0	0
....................TTCCGCGATGGTTTCCAGACCTAGG.............................................................................................................	25	9	0.11	1	0	1	0	0	0	0	0	0	0	0	0
............................TGGTTTCCAGACCTAGGTCC-TT.......................................................................................................	22	9	0.11	1	0	1	0	0	0	0	0	0	0	0	0
..................................................................................TCCTTATCCCCGGGATGGCG....................................................	20	9	0.11	1	0	1	0	0	0	0	0	0	0	0	0
.............................GGTTTCCAGACCTAGGTCC-TTCT.....................................................................................................	23	9	0.11	1	0	1	0	0	0	0	0	0	0	0	0
......................................................CACCTCGCCTGCCTTCAGGGTGTGAGCA........................................................................	28	9	0.11	1	0	0	0	0	0	0	1	0	0	0	0
....................................................................TCAGGGTGTGAGCATCCTTATCCC..............................................................	24	11	0.09	1	0	1	0	0	0	0	0	0	0	0	0
...............................................................TGCCTTCAGGGTGTGAGCATCCTTAAA................................................................	27	12	0.08	1	0	1	0	0	0	0	0	0	0	0	0
.........................................TAGGTCC-TTCTCCACCTCGCCC..........................................................................................	22	12	0.08	1	0	0	1	0	0	0	0	0	0	0	0
.........................................TAGGTCC-TTCTCCACCTCGCCTGCCT......................................................................................	26	12	0.08	1	0	1	0	0	0	0	0	0	0	0	0
..........................................................TCGCCTGCCTTCAGGGTGTGAGCATC......................................................................	26	12	0.08	1	0	0	1	0	0	0	0	0	0	0	0
..........................................................TCGCCTGCCTTCAGGGTGTGAGCATCC.....................................................................	27	12	0.08	1	0	0	1	0	0	0	0	0	0	0	0
...................................................CTCCACCTCGCCTGCCTTCAGGG................................................................................	23	13	0.08	1	0	1	0	0	0	0	0	0	0	0	0
.................................................TTCTCCACCTCGCCTGCCTTCAG..................................................................................	23	13	0.08	1	0	1	0	0	0	0	0	0	0	0	0
............................................GTCC-TTCTCCACCTCGCC...........................................................................................	18	13	0.08	1	0	1	0	0	0	0	0	0	0	0	0
.................................................TTCTCCACCTCGCCTGCCTTCAGGGTG..............................................................................	27	13	0.08	1	0	1	0	0	0	0	0	0	0	0	0
....................................................TCCACCTCGCCTGCCTTCAGGGTGT.............................................................................	25	13	0.08	1	0	1	0	0	0	0	0	0	0	0	0
..................................................TCTCCACCTCGCCTGCCTTCAGGGT...............................................................................	25	13	0.08	1	0	1	0	0	0	0	0	0	0	0	0
...............................................................TGCCTTCAGGGTGTGAGCATC......................................................................	21	16	0.06	1	0	0	1	0	0	0	0	0	0	0	0

dpe_258

scaffold_309:3196-3249 +

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

-17.1	-16.7	-16.6