dpe_143

CATGAACTGCCTCCTTTCTGGAGGACTTTTGTCGTTTGAAAGCGTCATATCCCCGCTCGGAGATATATCGCTTTAAATGTCTCCGCCGTTTAACAAACGACATATCTCCGCGCAGAGCTAGGACGTTTTCCGACGACATGTCGTCGGAGATATTGTCGCTGCCCCCAC *********************************..(((((((((........((.(((((((((.(((..(((((((.......)))))))....))).))))))))).))........)))))))))..**********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M042 female body	V111 male body	V057 head	V050 head	M021 embryo
..................................................CCCCGCTCGGAGATATATCGCT................................................................................................	22	0	1	19.00	19	12	5	2	0	0
.................................................................................................CGACATATCTCCGCGCAGAG...................................................	20	0	1	11.00	11	3	3	3	2	0
.................................................................................................CGACATATCTCCGCGCAGAGC..................................................	21	0	1	4.00	4	2	2	0	0	0
..................................................CCCCGCTCGGAGATATATCGC.................................................................................................	21	0	1	2.00	2	0	0	2	0	0
..................................................CCCCGCTCGGAGATATGTCGCT................................................................................................	22	1	1	1.00	1	0	1	0	0	0
......................................................................................................................................GACATGTCGTCGGAGATATTGT............	22	0	1	1.00	1	0	0	0	0	1
..................................................CCCCGCTCGGAGATATATCGCTC...............................................................................................	23	1	1	1.00	1	0	1	0	0	0
...................................................................................................ACATATCTCCGCGCAGAG...................................................	18	0	1	1.00	1	1	0	0	0	0
..................................................CCCCGCTCGGAGATATCTAGCT................................................................................................	22	2	1	1.00	1	0	0	1	0	0
...................................................CCCGCTCGGAGATATATCGCT................................................................................................	21	0	1	1.00	1	1	0	0	0	0
..................................................................ATCGCTTTAAATGTCTCCGCCGTTT.............................................................................	25	0	1	1.00	1	1	0	0	0	0
..................................................CCCCGCTCGGCGATATCTCGCT................................................................................................	22	2	1	1.00	1	0	0	1	0	0
.................................................................................................CGACATATCTCCTCGCAGAG...................................................	20	1	1	1.00	1	0	1	0	0	0
.................................................................................................CGACATATCTCCGCGCAGTT...................................................	20	2	4	0.25	1	0	1	0	0	0
.......TGCCTCGTTTCTGGACGTCT.............................................................................................................................................	20	3	5	0.20	1	0	0	1	0	0

GTACTTGACGGAGGAAAGACCTCCTGAAAACAGCAAACTTTCGCAGTATAGGGGCGAGCCTCTATATAGCGAAATTTACAGAGGCGGCAAATTGTTTGCTGTATAGAGGCGCGTCTCGATCCTGCAAAAGGCTGCTGTACAGCAGCCTCTATAACAGCGACGGGGGTG **********************************..(((((((((........((.(((((((((.(((..(((((((.......)))))))....))).))))))))).))........)))))))))..*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V111 male body
............................................................................................TGTTTGCTGTATAGAGGCG.........................................................	19	0	12	0.08	1	1

Species	Coordinate	ID	Type	Alignment
droPer2	scaffold_13:1836385-1836552 +	dpe_143	confident	CATGAACTG--------------CC--T-CCTTTC---TGGAGGACTTTT--GTCGT-TTGAAAGCGTCATATCCCC-----------GCTCG------------------------------------GAGATA--TATCGCTTT-------AAA----T-------GTCTCCGCCGTTTAACAAACGACATATCTCCGCGCAGAGCTAGGACGTTTTCCGACGACATGTCGTC----GGAG--------------ATATTGTCGC---TG--CCCCCAC
dp5	XL_group1a:7224881-7225066 +	dps_3821	candidate-rescued	CATGAACTGCCGGCGGAATTATGTCGCT-TCTTTC---TGGAGGACTTGT--GTCGT-TTGAAAGCGGCATATCCCC-----------GCTCG------------------------------------GAAATATATATCGCTTT-------AAA----T-------GTCTCCGCCATTTAACAACTGACATATCTCCGCGCAGAGCTATGACGCTTTCCGACGACATTTCGTC----GGAG--------------ATATTGTCGA---TG--CCCCCAC
droWil2	scf2_1100000004382:395502-395671 -			TG---------------------TC--G-TTTTTCTAACGGCGGAGATAT--GTCGT-TGTAAAACGGTG---ATCT-----------GCGCGAAGATATGTCGTTTCAAATCG---------------------------------------TCA----C-------ATCTCCGCCGTTAAAAAAACGACATATCTCCGCGCGAAATTATGTTGTTTCAGAACGACATATCTCCGCGCGGAGATATG---------------TCGT---TT--TTCTAAC
droVir3	scaffold_12822:4001968-4002116 +			TG-AAAC-G--------------TC--ATATCTCC---GCGCGGAGTTAT--GTCGT-TTTGAAACGTCATATCTCC-----------GCGCG------------------------------------GAGTTA--TGTCGTTTT-------G------------------------------AAACGTCATATCTCCCCGCGGAGCTATGTCGTTTTGAAACGTCATATCTCCA---GGAA--------------AAAGTTTCGA---TT--TTCGCAC
droKik1	scf7180000301535:16585-16745 -			CT---------------------------TTTTTC---CGGCGGAGCTAT--ATCGT-TTTAAAGCGACATAACTCC-----------GCGCGGAGATATTTCGTTATAAAACG---------------------------------------ACA----T-------AGCTCCGCCGGAAAAAAAGCGACATAAGTCCGCTCGAAAA-ATG-------------------TACCGGGCGGAGATATGTCGTCGGACTTA-TGTCGC---TA--TGCCGGA
droEle1	scf7180000487721:5933-6015 +			CG---------------------------------------------------------------------------------------CG---------------------CG---------------------------------------ACA----T-------ATCTCCGCCTTTTTACAAACGACATATCTCCGCGCGAAGATAAGACGTTTGCAGAA-----------GGGCGAAGATATG---------------TC---GT-----------
droRho1	scf7180000759646:427-558 -			TA-----------------------------------------------------------AAAACGACATATCTCC-----------GCGGGGAGATATGACGTTTAAAAACGACATATCTCCGCTCGAAAATA--TTTCGTTTT--------------------------------------AAACGACATATCTCCGCGCGGAGATATGTCGTTTGTAGAA-----------GGGCGGAG--------------TTA-TGTC---GCT----------
droBia1	scf7180000299101:14097-14263 +			TT----------------------------TTTTT---TGGCGGAGCTAT--ATCGTTTTTAAAACGTCATATCTCC-----------GCGCG------------------------------------GAGTTA--TGTCGCTTTTAAAACGACATATGT-------ATCTCCGCTGACCAAAAAGCGACATATTTCCGCGCGGAGATATGACGTTTCAAGACGACATATCTCCGCGCGGAG---------------TACCATCTCCGC----------C
droTak1	scf7180000411271:5074-5237 +			TT------------------------------------TGGCGGAGATAT--GACAT-TTAAAAACGACATATTTCCCCCGTTAATCAACGCGGAGATATGTCTTTTTTAAACG---------------------------------------TGA----T-------ATCTCCGCCCTTCTGCAAACGACATATCTCCGCGCGGAGATGTGACGTTTAAAAACCAAATATTTTCGCGCGGAGATATG---------------TC---GTT----------
droYak3	v2_chrUn_1994:6664-6816 +			TC---------------------------TCCTCC------CGAAGTTTTTTG-AGTTTTGAAAACGACATATCTCC-----------GCTAG------------------------------------GAGGTA--TGTCGTTTT-------AAT----TTCGGATGAGATATGTCGTTTTGAAAACGACATATCTCCGCTAGGAGG----AGGTTTAT-----------TAT-CGGCGGAGATGTG---------------TC---GTTTTTGGAGATA
droEre2	scaffold_4929:23995222-23995358 -			CT---------------------------TTTTTT---TGACGGAGCTTT--TTAGTTTTGTAAATGTCATATCTCC-----------AAGCG------------------------------------GAGTTA--TAACGTTTTCTTAACGACA----T-------TTCTCCGCCGAACCGAAAACGACATATCGCCGCGCGGAGCTAAGTTGCTTTGAAACGGCAT----------------------------------------------------

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droPer2

CATGAACTG--------------CC--T-CCTTTC---TGGAGGACTTTT--GTCGT-TTGAAAGCGTCATATCCCC-----------GCTCG------------------------------------GAGATA--TATCGCTTT-------AAA----T-------GTCTCCGCCGTTTAACAAACGACATATCTCCGCGCAGAGCTAGGACGTTTTCCGACGACATGTCGTC----GGAG--------------ATATTGTCGC---TG--CCCCCAC	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
.........................................................................CCCC-----------GCTCG------------------------------------GAGATA--TATCGCT.........................................................................................................................................	22	1	19.00	19	0	12	0	0	2	5
...........................................................................................................................................................................................CGACATATCTCCGCGCAGAG..........................................................................	20	1	11.00	11	0	3	0	2	3	3
...........................................................................................................................................................................................CGACATATCTCCGCGCAGAGC.........................................................................	21	1	4.00	4	0	2	0	0	0	2
.........................................................................CCCC-----------GCTCG------------------------------------GAGATA--TATCGC..........................................................................................................................................	21	1	2.00	2	0	0	0	0	2	0
................................................................................................................................................................................................................................GACATGTCGTC----GGAG--------------ATATTGT.................	22	1	1.00	1	1	0	0	0	0	0
.........................................................................CCCC-----------GCTCG------------------------------------GAGATA--TATCGCTC........................................................................................................................................	23	1	1.00	1	0	0	0	0	0	1
.............................................................................................................................................................................................ACATATCTCCGCGCAGAG..........................................................................	18	1	1.00	1	0	1	0	0	0	0
..........................................................................CCC-----------GCTCG------------------------------------GAGATA--TATCGCT.........................................................................................................................................	21	1	1.00	1	0	1	0	0	0	0
..........................................................................................................................................ATCGCTTT-------AAA----T-------GTCTCCGCCGTTT....................................................................................................	25	1	1.00	1	0	1	0	0	0	0
...........................................................................................................................................................................................CGACATATCTCCGCGCAGTT..........................................................................	20	4	0.25	1	0	0	0	0	0	1

dp5

CATGAACTGCCGGCGGAATTATGTCGCT-TCTTTC---TGGAGGACTTGT--GTCGT-TTGAAAGCGGCATATCCCC-----------GCTCG------------------------------------GAAATATATATCGCTTT-------AAA----T-------GTCTCCGCCATTTAACAACTGACATATCTCCGCGCAGAGCTATGACGCTTTCCGACGACATTTCGTC----GGAG--------------ATATTGTCGA---TG--CCCCCAC	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
..................................................................................................................................................................................................TCTCCGCGCAGAGCTATGACG..................................................................	21	1	27.00	27	0	23	0	0	1	1	2	0	0	0
..................................................................................................................................................................................................TCTCCGCGCAGAGCTATGACGC.................................................................	22	1	4.00	4	0	3	1	0	0	0	0	0	0	0
.................................................................................................................................................................................................................ATGACGCTTTCCGACGACATG...................................................	21	1	2.00	2	0	2	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................CTCCGCGCAGAGCTATGACG..................................................................	20	1	2.00	2	0	2	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................TCCGCGCAGAGCTATGACGCTT...............................................................	22	1	2.00	2	0	2	0	0	0	0	0	0	0	0
.............................................CTTGT--GTCGT-TTGAAAGCGGCA...................................................................................................................................................................................................................	22	1	1.00	1	0	0	0	0	0	0	0	0	1	0
....................................................................................................................................................................................................TCCGCGCAGAGCTATGACGCT................................................................	21	1	1.00	1	0	1	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................TCCGCGCAGAGCTATGACG..................................................................	19	1	1.00	1	0	0	0	0	0	1	0	0	0	0
.................................................................................................................................................................................................ATCTCCGCGCAGAGCTATGACG..................................................................	22	1	1.00	1	0	0	0	0	1	0	0	0	0	0
...........................................................................................................................................................A----T-------GTCTCCGCCATTTAACAACTGAC..........................................................................................	25	1	1.00	1	0	0	0	0	0	0	0	0	0	1
...................................................................GCATATCCCC-----------GCTCG------------------------------------GAAATAT.................................................................................................................................................	22	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................GCAGAGCTATGACGCTTTCCGA..........................................................	22	1	1.00	1	0	1	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................TGACGCTTTCCGACGACATG...................................................	20	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.................................................................CGGCATATCCCC-----------GCTCG------------------------------------GAA.....................................................................................................................................................	20	1	1.00	1	0	0	0	0	0	0	0	0	1	0
...................................................................................................................................................................................................CTCCGCGCAGAGCTATGACGCT................................................................	22	1	1.00	1	0	0	1	0	0	0	0	0	0	0
.......TGCCGGCGGAATTATGTCGCT-T...........................................................................................................................................................................................................................................................	22	8	0.13	1	0	1	0	0	0	0	0	0	0	0

droWil2

TG---------------------TC--G-TTTTTCTAACGGCGGAGATAT--GTCGT-TGTAAAACGGTG---ATCT-----------GCGCGAAGATATGTCGTTTCAAATCG---------------------------------------TCA----C-------ATCTCCGCCGTTAAAAAAACGACATATCTCCGCGCGAAATTATGTTGTTTCAGAACGACATATCTCCGCGCGGAGATATG---------------TCGT---TT--TTCTAAC	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
...................................................................................................................................................................................TAAAAAAACGACATATCTCCGCGCGAA...........................................................................	27	5	0.20	1	0	1	0	0	0
.........................................................................................................................................................................................................................................CCGCGCGGAGATATG---------------TCGT---TT--.......	21	20	0.05	1	0	0	0	0	1
.........................................................................................................................................................................................................................................CCGCGCGGAGATATG---------------TCGT---TT--TTC....	24	20	0.05	1	0	1	0	0	0
........................................................................................................................................................................................................................................TCCGCGCGGAGATATG---------------TCGT---T..........	21	20	0.05	1	1	0	0	0	0

droVir3

TG-AAAC-G--------------TC--ATATCTCC---GCGCGGAGTTAT--GTCGT-TTTGAAACGTCATATCTCC-----------GCGCG------------------------------------GAGTTA--TGTCGTTTT-------G------------------------------AAACGTCATATCTCCCCGCGGAGCTATGTCGTTTTGAAACGTCATATCTCCA---GGAA--------------AAAGTTTCGA---TT--TTCGCAC	Size	Hit Count	Total Norm	Total	M027 Male-body	M028 Head	M047 Female-body	M061 Embryo	SRR060654 Ovary	SRR060655 Testis	SRR060656 Ovary	SRR060657 Testis	SRR060658 Ovary	SRR060659 Testis	SRR060660 Ovary	SRR060661 Embryo	SRR060662 Embryo	SRR060663 Embryo	SRR060664 Male-body	SRR060665 Female-body	SRR060666 Male-body	SRR060667 Female-body	SRR060668 Male-body	SRR060669 Female-body	SRR060670 Testis	SRR060671 Male-body	SRR060672 Female-body	SRR060673 Ovary	SRR060674 Ovary	SRR060675 Ovary	SRR060676 Ovary	SRR060677 Ovary	SRR060678 Testis	SRR060679 Testis	SRR060680 Testis	SRR060681 Testis	SRR060682 Embryo	SRR060683 Testis	SRR060684 Embryo	SRR060685 Embryo	SRR060686 Embryo	SRR060687 Embryo	SRR060688 Ovary	SRR060689 Testis	SRR1106712 embryo_0-2h	SRR1106713 embryo_0-2h	SRR1106714 embryo_2-4h	SRR1106715 embryo_4-6h	SRR1106716 embryo_4-6h	SRR1106717 embryo_6-8h	SRR1106718 embryo_6-8h	SRR1106719 embryo_8-10h	SRR1106720 embryo_8-10h	SRR1106721 embryo_10-12h	SRR1106722 embryo_10-12h	SRR1106723 embryo_12-14h	SRR1106724 embryo_12-14h	SRR1106725 embryo_14-16h	SRR1106726 embryo_14-16h	SRR1106727 larvae	SRR1106728 larvae	SRR1106729 mixed whole adult body	SRR1106730 embryo_16-30h	V047 Embryo	V053 Head	V116 Male-body	GSM1528803 follicle cells	SRR2096013 Ovary_Strain_9_oxidized	SRR2096014 Ovary_Strain_160_oxidized	SRR2096026 embryo_0-2h from 14 day old Strain 9 mothers	SRR2096038 embryo_0-2h from 14 day old Strain 9 mothers	SRR2096050 embryo_0-2h from 14 day old Strain 160 mothers	SRR2096055 Ovary_Min_43	SRR2096056 Ovary_Min_46	SRR2096057 Ovary_Min_50	SRR2096058 Ovary_Min_98	SRR2096059 Ovary_Min_164	SRR2096060 Ovary_Min_193	SRR2096061 embryo_0-2h from 14 day old Strain 160 mothers	SRR2096072 embryo_0-2h from 15to16 day old dysgenic mothers	SRR2096079 embryo_0-2h from 15to16 day old dysgenic mothers	SRR2096080 embryo_0-2h from 15to16 day old nondysgenic mothers	SRR2096081 embryo_0-2h from 15to16 day old nondysgenic mothers
......................................................................TATCTCC-----------GCGCG------------------------------------GAGTTA--TGTCG...........................................................................................................................................	23	20	1.05	21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.......................TC--ATATCTCC---GCGCGGAGTTAT--.....................................................................................................................................................................................................................................	22	20	0.85	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
........................................................................................................................................................................................................................TTTGAAACGTCATATCTCCA---GG........................................	22	20	0.30	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.........................................CGGAGTTAT--GTCGT-TTTGAAACG......................................................................................................................................................................................................................	23	20	0.25	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0
.................................................................................................................................................................................................................................TCATATCTCCA---GGAA--------------AAAGTTTCGA---T..........	26	20	0.20	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..........................................................TTTGAAACGTCATATCTCC-----------GC...............................................................................................................................................................................................	21	20	0.15	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0
.............................................................................................................................................................................................TCATATCTCCCCGCGGAGCT........................................................................	20	20	0.15	3	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
................................................................................................................................................................................................TATCTCCCCGCGGAGCTATGTCG..................................................................	23	20	0.10	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.G-AAAC-G--------------TC--ATATCTCC---GCGCG..............................................................................................................................................................................................................................................	21	20	0.10	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
........................................................T-TTTGAAACGTCATATCTCC-----------GC...............................................................................................................................................................................................	22	20	0.10	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.............................................................................................................................................................................................TCATATCTCCCCGCGGAGCTATGTC...................................................................	25	20	0.10	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................................................................................................................................................................................................................AAACGTCATATCTCCA---GG........................................	18	20	0.10	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.................................................................CGTCATATCTCC-----------GCGCG------------------------------------GAGTT...................................................................................................................................................	22	20	0.10	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................CATATCTCCA---GGAA--------------AAAGTTTCGA---TT--.......	26	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................................................TGAAACGTCATATCTCC-----------GC...............................................................................................................................................................................................	19	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................................................TTTTGAAACGTCATATCTCC..............................................	20	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................................................................................................................................CGTTTT-------G------------------------------AAACGTCATATCTCC..................................................................................	22	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................................................................................................................................................................................................................AAACGTCATATCTCCA---GGAA--------------AAAGT...................	25	20	0.05	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.......................................CGCGGAGTTAT--GTCGT-TTTGAAACG......................................................................................................................................................................................................................	25	20	0.05	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.............................................................................................................................................................................................................AGCTATGTCGTTTTGAAACGT.......................................................	21	20	0.05	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................TCGTTTTGAAACGTCATATCTCC..............................................	23	20	0.05	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
................................................AT--GTCGT-TTTGAAACGTCA...................................................................................................................................................................................................................	19	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.....................................................TCGT-TTTGAAACGTCATATCTCC-----------GCGC.............................................................................................................................................................................................	27	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..............................................................................................................................................................................................................GCTATGTCGTTTTGAAACGTCA.....................................................	22	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..............................................................................................................................................................................................................GCTATGTCGTTTTGAAACGTC......................................................	21	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...................................................................................................................................GTTA--TGTCGTTTT-------G------------------------------AAACG............................................................................................	19	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
........................................................................TCTCC-----------GCGCG------------------------------------GAGTTA--TGTCG...........................................................................................................................................	21	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
................................................................................................................................................................................................TATCTCCCCGCGGAGCTATG.....................................................................	20	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
TG-AAAC-G--------------TC--ATATCTCC---GC.................................................................................................................................................................................................................................................	19	20	0.05	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...................................................................................................................................GTTA--TGTCGTTTT-------G------------------------------AAACGTC..........................................................................................	21	20	0.05	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...........................................................................................CG------------------------------------GAGTTA--TGTCGTTTT-------G------------------------------AAAC.............................................................................................	22	20	0.05	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
................................TCC---GCGCGGAGTTAT--GTCG.................................................................................................................................................................................................................................	19	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................CATATCTCCA---GGAA--------------AAAGTTTCGA---T..........	25	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.................................................................................................................................................................................................................................TCATATCTCCA---GGAA--------------AAAGTTTCGA---TC--.......	27	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.................................................................................................................................................................................................................................TCATATCTCCA---GGAA--------------AAAGTTTCGA---TA--G......	28	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
......C-G--------------TC--ATATCTCC---GCGCGGAGT..........................................................................................................................................................................................................................................	21	20	0.05	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...............................................................AACGTCATATCTCC-----------GCGCG------------------------------------GA......................................................................................................................................................	21	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................TATCTCC---GCGCGGAGTTAT--GTCG.................................................................................................................................................................................................................................	23	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
..........................................................................................................................................................................................................CGGAGCTATGTCGTTTTGA............................................................	19	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...................................................................TCATATCTCC-----------GCGCG------------------------------------GAGTTA--................................................................................................................................................	21	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
......................................................CGT-TTTGAAACGTCATATCTCC-----------.................................................................................................................................................................................................	22	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...AAAC-G--------------TC--ATATCTCC---GCGCGGA............................................................................................................................................................................................................................................	22	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.......................................CGCGGAGTTAT--GTCGT-TTTGA..........................................................................................................................................................................................................................	21	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
........................................................................................................................................................................................................................TTTGAAACGTCATATCTCCA---GGAA--------------A.......................	25	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................GCGGAGCTATGTCGTTTTGAAACGTC......................................................	26	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droKik1

CT---------------------------TTTTTC---CGGCGGAGCTAT--ATCGT-TTTAAAGCGACATAACTCC-----------GCGCGGAGATATTTCGTTATAAAACG---------------------------------------ACA----T-------AGCTCCGCCGGAAAAAAAGCGACATAAGTCCGCTCGAAAA-ATG-------------------TACCGGGCGGAGATATGTCGTCGGACTTA-TGTCGC---TA--TGCCGGA	Size	Hit Count	Total Norm	Total
No Reads

droEle1

CG---------------------------------------------------------------------------------------CG---------------------CG---------------------------------------ACA----T-------ATCTCCGCCTTTTTACAAACGACATATCTCCGCGCGAAGATAAGACGTTTGCAGAA-----------GGGCGAAGATATG---------------TC---GT-----------	Size	Hit Count	Total Norm	Total
No Reads

droRho1

TA-----------------------------------------------------------AAAACGACATATCTCC-----------GCGGGGAGATATGACGTTTAAAAACGACATATCTCCGCTCGAAAATA--TTTCGTTTT--------------------------------------AAACGACATATCTCCGCGCGGAGATATGTCGTTTGTAGAA-----------GGGCGGAG--------------TTA-TGTC---GCT----------	Size	Hit Count	Total Norm	Total
No Reads

droBia1

TT----------------------------TTTTT---TGGCGGAGCTAT--ATCGTTTTTAAAACGTCATATCTCC-----------GCGCG------------------------------------GAGTTA--TGTCGCTTTTAAAACGACATATGT-------ATCTCCGCTGACCAAAAAGCGACATATTTCCGCGCGGAGATATGACGTTTCAAGACGACATATCTCCGCGCGGAG---------------TACCATCTCCGC----------C	Size	Hit Count	Total Norm	Total
No Reads

droTak1

TT------------------------------------TGGCGGAGATAT--GACAT-TTAAAAACGACATATTTCCCCCGTTAATCAACGCGGAGATATGTCTTTTTTAAACG---------------------------------------TGA----T-------ATCTCCGCCCTTCTGCAAACGACATATCTCCGCGCGGAGATGTGACGTTTAAAAACCAAATATTTTCGCGCGGAGATATG---------------TC---GTT----------	Size	Hit Count	Total Norm	Total
No Reads

droYak3

TC---------------------------TCCTCC------CGAAGTTTTTTG-AGTTTTGAAAACGACATATCTCC-----------GCTAG------------------------------------GAGGTA--TGTCGTTTT-------AAT----TTCGGATGAGATATGTCGTTTTGAAAACGACATATCTCCGCTAGGAGG----AGGTTTAT-----------TAT-CGGCGGAGATGTG---------------TC---GTTTTTGGAGATA	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
.....................................................................................................................................TA--TGTCGTTTT-------AAT----TTCGGATGAGA..............................................................................................................	25	3	3.33	10	0	0	0	0	0	0	0	0	0	0	10
.........................................................................................................................................................................................................................TAT-----------TAT-CGGCGGAGATGTG---------------TC---.............	21	4	0.50	2	0	1	0	0	0	0	1	0	0	0	0
.................................................................................................................................GAGGTA--TGTCGTTTT-------AAT----TTCGGAT..................................................................................................................	25	3	0.33	1	0	1	0	0	0	0	0	0	0	0	0
...............................................................................................................................................................................TCGTTTTGAAAACGACATATCTCC..................................................................................	24	3	0.33	1	0	1	0	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................................................................TAT-CGGCGGAGATGTG---------------TC---GTTTT........	23	4	0.25	1	0	1	0	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................................TAT-----------TAT-CGGCGGAGATGTG---------------TC---GTTT.........	25	4	0.25	1	0	1	0	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................................TAT-----------TAT-CGGCGGAGATGTG---------------TC---G............	22	4	0.25	1	0	0	0	0	0	0	1	0	0	0	0

droEre2

CT---------------------------TTTTTT---TGACGGAGCTTT--TTAGTTTTGTAAATGTCATATCTCC-----------AAGCG------------------------------------GAGTTA--TAACGTTTTCTTAACGACA----T-------TTCTCCGCCGAACCGAAAACGACATATCGCCGCGCGGAGCTAAGTTGCTTTGAAACGGCAT----------------------------------------------------	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
No Reads

dpe_143

scaffold_13:1836435-1836502 +

confident

Canonical miRNA

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

-33.3	-32.5