dvi_6640

Name	Class	Family	Strand
(CAA)n	Simple_repeat	Simple_repeat	+

##################################################--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CAACCACTGACGGCACAGGAGCAGCAACCGTTGAGCAACCCGCTCACAGGGTTAGGGCATCAGCAACTATGGAGCAAAGCACTGAGGCGGCAGCAAAAACTCAATGTTCGACTGAAGTTGCAATGAAAGATGTGGAATCAGTCTCAATGAGGAATTCGAGCACAGCAATAACAACAACAACAACAACTTTAATTGCAAAACCAACAGAAAGATTAACAACACAAATAGTAGACAAGCCTGCAGCCCCCGAA ************************************************((((..((.(((((((((....((...((((.((((((....)).....)))).))))...))..))))))..)))....((((.......((((...))))........))))))..)))).............................************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M047 female body	M061 embryo	SRR060663 160_0-2h_embryos_total	SRR060666 160_males_carcasses_total	SRR060669 160x9_females_carcasses_total	SRR060686 Argx9_0-2h_embryos_total	SRR060672 9x160_females_carcasses_total
............................................................................................GCATAAACTCAATGTTCGACTGAA.......................................................................................................................................	24	1	1	1.00	1	0	1	0	0	0	0	0
....................................................................................................................GTTGCAATGAAAGATGTGGAATCAGT.............................................................................................................	26	0	1	1.00	1	1	0	0	0	0	0	0
........................................................................................................................CAATGAAAGATGGGGAATCAGT.............................................................................................................	22	1	1	1.00	1	0	0	1	0	0	0	0
..........................................................................................................TTTGACTGAAGCTCCAATGAA............................................................................................................................	21	3	7	0.29	2	0	0	0	1	1	0	0
.........................................................................................................................................................................................................................AACACAAACCGTTGACAAGCC.............	21	3	9	0.11	1	0	0	0	0	0	1	0
.............................................................................................................................GAAGATATGGAATCTGTCT...........................................................................................................	19	3	20	0.05	1	0	0	0	0	0	0	1

GTTGGTGACTGCCGTGTCCTCGTCGTTGGCAACTCGTTGGGCGAGTGTCCCAATCCCGTAGTCGTTGATACCTCGTTTCGTGACTCCGCCGTCGTTTTTGAGTTACAAGCTGACTTCAACGTTACTTTCTACACCTTAGTCAGAGTTACTCCTTAAGCTCGTGTCGTTATTGTTGTTGTTGTTGTTGAAATTAACGTTTTGGTTGTCTTTCTAATTGTTGTGTTTATCATCTGTTCGGACGTCGGGGGCTT ************************************************((((..((.(((((((((....((...((((.((((((....)).....)))).))))...))..))))))..)))....((((.......((((...))))........))))))..)))).............................************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	SRR060689 160x9_testes_total	V053 head	SRR060679 140x9_testes_total	SRR060678 9x140_testes_total	SRR060670 9_testes_total	SRR060681 Argx9_testes_total
................................................................................................................................CTACAGCCTAGTCAGAGTTA.......................................................................................................	20	2	1	1.00	1	1	0	0	0	0	0
..........................TGGCAACGCGGTGAGCGAGT.............................................................................................................................................................................................................	20	3	5	0.20	1	0	1	0	0	0	0
..................................CGTTTGGCTAGTGTCCC........................................................................................................................................................................................................	17	2	5	0.20	1	0	1	0	0	0	0
..................................................................................................................................ACACCTTAGACAGAGTTG.......................................................................................................	18	2	5	0.20	1	0	0	1	0	0	0
.......AATGCCGTGGCCTCGTCG..................................................................................................................................................................................................................................	18	2	10	0.10	1	0	0	0	1	0	0
...............................................................................................................................................................................TTGGTGTTGTTGAAATTA..........................................................	18	1	15	0.07	1	1	0	0	0	0	0
.............................................................................................................................................................................TGTTGTTGTTGTTGAAAT............................................................	18	0	20	0.05	1	0	0	0	0	1	0
.....................................................................................................................................................................GTTATTGTTGTTGTTGTTGTT.................................................................	21	0	20	0.05	1	0	0	0	0	0	1
.........................................................GTAGTAGTTGATACCTGGC...............................................................................................................................................................................	19	3	20	0.05	1	0	1	0	0	0	0

Species	Coordinate	ID	Alignment
droVir3	scaffold_12875:13272987-13273237 +	dvi_6640	----CAACCACTGACGGC---ACAGGAGCAG---CAACCGTTGAGCAACCCGCTCACAGGGTTAGG---G---------------CATCAGCAACTATGGAGCAAAGCACTGAGGCGGCA---GCAAAAAC------TCAATGTTCG-----------------ACTGAAGTTGCAATGAAAGATGTGGAATCAGTCTCAATGAGGAATTCGAGCA------------------CAGCAATAACAACAAC---AACAACAACTTTAATTGCAAAACCAACAGAAAGATTAACAAC---------------ACAAATAGTAGACAAGCCTGCA---------GCCCCCGAA
droMoj3	scaffold_6359:729375-729604 -		----CAACTGCTGCTCTC---GCAACAGCAG---CAGCA---G------------------CAACTGCTGCTCTCG------CAACAGCAACAACAACA---------AGAGAAGCAGCAGCAGCAACTGC------TGCTCTCGCA-----------------ACAGCAGCAGCAACAACAAGAGAAGCAGCAGCA------------GCAACTGCTGCTC------------TCGCAACAGCAGCAGC---AGCAACTGCTGCTCTCGCAACAGC---------------AACAGCAACAACAACAAGAGAAGCAGCAGCAGCAACTGCT---------GCTCTCGCA
droGri2	scaffold_15203:1310264-1310490 -		----CAACAACAGCAACA---ACAACAGCAA---CAACAACAG------------------CAACAACACCA---ACAATATCAACATCAACAACAACA---------GCACAAACAACAGCAACAAC-----------------------------------------AACTGCAACAACAAGAGCAGCAGCAAGAGCAACAACAACATCAACAACAACAG---------------CAACAACAACAGC---AACAACAACTGCAACAACAAGAGC---------------AACAGCAAGAGCAACAACAAGAGCAACAGCAAGAGCAACA---------ACAACAGCG
droWil2	scf2_1100000003625:682-908 +		----CAACAACAACAGCAGCAACAA---CAACAGCAG---CAG------------------CAACAACAGCATCAG------CAACAGCAACAGCAGCA---------ACGAATGCAACAGCAACAGC------AACA------GCAACAGCAACAGCAGCAAC-----------------AATTGCAGCAACAACA------------GCAACA------GCAGCAACAATGGCAGCAACAACAACAGC---AACAACAACTGCAGCAGCAACAAC---------------AACA---------------GCAGCAACAACAACAGCAGCAGCAACAACAGCAACAGGA
dp5	2:6797175-6797413 +		----CAACAGCAGAAGTTCCAGCAA---CAGGAACAG---CAG------------------CAATATATGCAACAG------CAACATATGCAACAGCA---------AAATATGCAGCAGCAACA---TCTGCAACA------GCAACATC-----------------TGCAGCAGCAACAGCAGAAGCAGCAGCA------------ACAGA------AGCAGCAGCAACAGCAGCAGCAACAGCAGCAGCAACAACAGAAGCAGCAGCAACAGCAGCAGCAGAAGCAGCCGC---------------AGCAGCAGCAGGTGCAGCAGCA---------ACATCAGCA
droAna3	scaffold_13117:4522578-4522804 -		----CAACAACAATCGAC---ATAAACGTTG---CAATCGGAG------------------CCAAAGTCGCA---GCAGCATCAGTAGCAACAGCAGCA---------GCATCAGCAGCA------------------------GCA-----------------ACAGCAGCAGCAGCGGCGGAAGCAGAAGCGGTAGCATCAACGCTACCAACAACAACAT---------------CAACAATAACAAC---AACAACAACAACAACAACAACAAC---------------AATAGCAACAGCCGAAATAGCAGCAGCTCGAAAAGCAGCA---------GCCACCGCA
droBip1	scf7180000395832:863333-863404 +		A-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAGCAACAACAACAAC---AACAACAACAACAACAGCGAGC------------------CCA---------------GCAGCAACATCAACAACAGCA---------ACAACAACA
droFic1	scf7180000453829:1092919-1093131 +		A-----TCATC-GATATC---GCGGGAGCAA---CAGCAGTTCAACAACAAGCCCTTCAACTTGGC---------------------------GCAGTT---------GATCAAGCAGCAGCAGCAGC------AACG------GCAGCAACTGCAGCAGCAGC-----------------AACTGCAGCAGCAACA------------ACAGC------AGCAGCAACAACAGCAGCAACAACAGCAGC---AGCAACAGCA---------------ACAGCAGCAACTACAACA---------------ACAACAGCAGCAACAGCAGCA---------GCAACAACA
droRho1	scf7180000760202:71814-71918 +		AATTCAACAACAGC---AGCAACAA---CAGCAGCAG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAACAACAACAGCAGCAGCAACAACAGCAGCAGCAACAACAGCA---------------GCAGCAACAACAACAGCAGCA---------GCAACAACA
droTak1	scf7180000415281:47449-47536 -		A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCAACAACTGCAAC---AATAACAACAACAATTGCAGCAGCAGCAACAACAACAATCACA---------------GCGATGACAATGAAACCGGCA---------GCAACAACA

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droVir3

----CAACCACTGACGGC---ACAGGAGCAG---CAACCGTTGAGCAACCCGCTCACAGGGTTAGG---G---------------CATCAGCAACTATGGAGCAAAGCACTGAGGCGGCA---GCAAAAAC------TCAATGTTCG-----------------ACTGAAGTTGCAATGAAAGATGTGGAATCAGTCTCAATGAGGAATTCGAGCA------------------CAGCAATAACAACAAC---AACAACAACTTTAATTGCAAAACCAACAGAAAGATTAACAAC---------------ACAAATAGTAGACAAGCCTGCA---------GCCCCCGAA	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
..........................................................................................................................................................................GTTGCAATGAAAGATGTGGAATCAGT..........................................................................................................................................................	26	1	1.00	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

droMoj3

----CAACTGCTGCTCTC---GCAACAGCAG---CAGCA---G------------------CAACTGCTGCTCTCG------CAACAGCAACAACAACA---------AGAGAAGCAGCAGCAGCAACTGC------TGCTCTCGCA-----------------ACAGCAGCAGCAACAACAAGAGAAGCAGCAGCA------------GCAACTGCTGCTC------------TCGCAACAGCAGCAGC---AGCAACTGCTGCTCTCGCAACAGC---------------AACAGCAACAACAACAAGAGAAGCAGCAGCAGCAACTGCT---------GCTCTCGCA	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
..............................................................................................................................................TCGCA-----------------ACAGCAGCAGCAAC............................................................................................................................................................................	19	6	0.17	1	0	0	0	0	1	0
..................................................................................................................................................A-----------------ACAGCAGCAGCAACAAC.........................................................................................................................................................................	18	20	0.10	2	0	0	0	0	2	0

droGri2

----CAACAACAGCAACA---ACAACAGCAA---CAACAACAG------------------CAACAACACCA---ACAATATCAACATCAACAACAACA---------GCACAAACAACAGCAACAAC-----------------------------------------AACTGCAACAACAAGAGCAGCAGCAAGAGCAACAACAACATCAACAACAACAG---------------CAACAACAACAGC---AACAACAACTGCAACAACAAGAGC---------------AACAGCAAGAGCAACAACAAGAGCAACAGCAAGAGCAACA---------ACAACAGCG	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

droWil2

----CAACAACAACAGCAGCAACAA---CAACAGCAG---CAG------------------CAACAACAGCATCAG------CAACAGCAACAGCAGCA---------ACGAATGCAACAGCAACAGC------AACA------GCAACAGCAACAGCAGCAAC-----------------AATTGCAGCAACAACA------------GCAACA------GCAGCAACAATGGCAGCAACAACAACAGC---AACAACAACTGCAGCAGCAACAAC---------------AACA---------------GCAGCAACAACAACAGCAGCAGCAACAACAGCAACAGGA	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
..................................................................................................................................................................................................................................AACAATGGCAGCAACAACAACAG.....................................................................................................	23	20	0.70	14	0	14	0	0	0
.........................................................................................................................................................................................................................................................................AGCAGCAACAAC---------------AACA---------------GCA....................................	19	20	0.20	4	0	0	0	4	0
..............................................................................................................................................................................................................................................AACAACAACAGC---AACAACAACTG......................................................................................	23	20	0.20	4	0	4	0	0	0
..........................................................................................................................AACAGC------AACA------GCAACAGCAACA..................................................................................................................................................................................................	22	20	0.20	4	0	1	0	0	3
.........ACAACAGCAGCAACAA---CA................................................................................................................................................................................................................................................................................................................................	18	20	0.15	3	0	0	0	3	0
..............................................................................................................................................................................................................................................................................CAACAAC---------------AACA---------------GCAGCAACA..............................	20	20	0.15	3	0	0	0	3	0
..............................................................................................................................................................................................................................................................................CAACAAC---------------AACA---------------GCAGCAAC...............................	19	20	0.15	3	0	0	0	3	0
..................................................................................................................................................................................................................................AACAATGGCAGCAACAACAACAGC---.................................................................................................	24	20	0.15	3	0	2	0	1	0
...................................................................................................................................................................................................................................................................................AC---------------AACA---------------GCAGCAACAACA...........................	18	20	0.15	3	0	0	0	3	0
....CAACAACAACAGCAGCAAC.......................................................................................................................................................................................................................................................................................................................................	19	20	0.15	3	0	0	0	3	0
....................................................................................................................AACAGCAACAGC------AACA------GCAACA........................................................................................................................................................................................................	22	20	0.15	3	0	0	0	3	0
....CAACAACAACAGCAGCAACA......................................................................................................................................................................................................................................................................................................................................	20	20	0.15	3	0	0	0	3	0
.................................................................................................................................................................AAC-----------------AATTGCAGCAACAACA------------GCA..........................................................................................................................................	22	20	0.15	3	0	1	0	2	0
.....................................................................................................................ACAGCAACAGC------AACA------GCAACA........................................................................................................................................................................................................	21	20	0.15	3	0	0	0	3	0
...........................................................................................................................................................................................AGCAACAACA------------GCAACA------GCAGC............................................................................................................................	21	20	0.15	3	0	2	0	1	0
.................................................................................................CA---------ACGAATGCAACAGCAACAGC------AAC.....................................................................................................................................................................................................................	25	8	0.13	1	0	1	0	0	0
........................................................................TCAG------CAACAGCAACAGCAGCA---------ACGAA.............................................................................................................................................................................................................................................	26	9	0.11	1	0	0	0	1	0
...........................................................................................................................................................................................................................................................................................................................CAACAACAACAGCAGCAGCAAC.............	22	20	0.10	2	0	0	0	2	0
...........................................................................................................................................................................................................................................AGCAACAACAACAGC---AACAACAACTG......................................................................................	26	20	0.10	2	0	2	0	0	0
...................CAACAA---CAACAGCAG---CAG------------------CAAC.............................................................................................................................................................................................................................................................................................	22	20	0.10	2	0	0	0	2	0
.................................................................................................................................................................................................AACA------------GCAACA------GCAGCAACAATGG....................................................................................................................	23	20	0.10	2	0	2	0	0	0
...........................................................................................................................................................................................................................................................................................................................CAACAACAACAGCAGCAGCAACA............	23	20	0.10	2	0	0	0	1	1
..............................................................................................................................................................................................AACAACA------------GCAACA------GCAGCAAC.........................................................................................................................	21	20	0.10	2	0	0	0	2	0
.................................................................................................................................................................................................AACA------------GCAACA------GCAGCAACAATGGC...................................................................................................................	24	20	0.10	2	0	2	0	0	0
..........................................................................AG------CAACAGCAACAGCAGCA---------ACG...............................................................................................................................................................................................................................................	22	11	0.09	1	0	0	0	1	0
................................................................CAACAGCATCAG------CAACAGCAACAGCAG.............................................................................................................................................................................................................................................................	27	12	0.08	1	0	0	0	1	0
............................CAACAGCAG---CAG------------------CAACAACAGCATCAG------............................................................................................................................................................................................................................................................................	27	12	0.08	1	0	0	0	1	0
.............................................................CAACAACAGCATCAG------CAACAGCAACAG................................................................................................................................................................................................................................................................	27	12	0.08	1	0	1	0	0	0
.............................................................CAACAACAGCATCAG------CAACAGC.....................................................................................................................................................................................................................................................................	22	14	0.07	1	0	0	0	1	0
......................................................................................................................................................................................................................................................................TGCAGCAGCAACAAC---------------AACA---------------GCAGCAACA..............................	28	14	0.07	1	0	0	0	1	0
................................................................................................................................................................................................................................................................AACAACTGCAGCAGCAACAAC---------------AACA---------------.......................................	25	15	0.07	1	0	1	0	0	0
.........................................................................................................................................A------GCAACAGCAACAGCAGCAAC-----------------AATT.....................................................................................................................................................................	25	16	0.06	1	0	0	0	1	0
................................................................CAACAGCATCAG------CAACAGC.....................................................................................................................................................................................................................................................................	19	17	0.06	1	0	0	0	1	0
....................................................................AGCATCAG------CAACAGCAACAGCAG.............................................................................................................................................................................................................................................................	23	17	0.06	1	0	1	0	0	0
.......................................................................ATCAG------CAACAGCAACAGCAGCA---------AC................................................................................................................................................................................................................................................	24	19	0.05	1	0	1	0	0	0
..............AGCAGCAACAA---CAACAGCAG---CAG------------------CAA..............................................................................................................................................................................................................................................................................................	26	20	0.05	1	0	1	0	0	0
...............................................................................................................................................................................................ACAACA------------GCAACA------GCAGCAACA........................................................................................................................	21	20	0.05	1	0	0	0	0	1
........................................................................................................................................................................................................................................GGCAGCAACAACAACAGC---AACAA............................................................................................	23	20	0.05	1	0	1	0	0	0
....................................................................................................................................................................................................................................................AACAGC---AACAACAACTGCAGCAGC...............................................................................	24	20	0.05	1	0	1	0	0	0
..................................................................................................................................................................................................................................................................................................................................AACAGCAGCAGCAACAACAGCA......	22	20	0.05	1	0	1	0	0	0
................................................................................................................................................................CAAC-----------------AATTGCAGCAACAACA------------GCAA.........................................................................................................................................	24	20	0.05	1	0	0	0	1	0
.....................................................................................................................................................................................................................................................................................................................................AGCAGCAGCAACAACAGCAACA...	22	20	0.05	1	0	0	0	1	0
..............................................................................................................................................................................................................................................................................................................................CAACAACAGCAGCAGCAACAACAG........	24	20	0.05	1	0	1	0	0	0
.................................................................................................................................................................................................................................CAACAATGGCAGCAACAACAACAG.....................................................................................................	24	20	0.05	1	0	0	0	1	0
.................AGCAACAA---CAACAGCAG---CAG------------------CAACA............................................................................................................................................................................................................................................................................................	25	20	0.05	1	0	0	0	1	0
.................................................................................................................................................................................................................................................AACAACAGC---AACAACAACTGCAG...................................................................................	23	20	0.05	1	0	1	0	0	0
.........................................................................................................................................................................................GCAGCAACAACA------------GCAACA------GCAGCA...........................................................................................................................	24	20	0.05	1	0	0	0	1	0
.......................................................................................................................................................................................TTGCAGCAACAACA------------GCAACA------GCAGC............................................................................................................................	25	20	0.05	1	0	1	0	0	0
......................CAA---CAACAGCAG---CAG------------------CAACAACAG........................................................................................................................................................................................................................................................................................	24	20	0.05	1	0	1	0	0	0
...................................................................................................................................................................................................................................ACAATGGCAGCAACAACAACAGC---A................................................................................................	24	20	0.05	1	0	1	0	0	0
.......................................................................................................................................................................................TTGCAGCAACAACA------------GCAACA------GCAG.............................................................................................................................	24	20	0.05	1	0	0	0	1	0
.......................................................................................................................................................................................................................................................................................................A---------------GCAGCAACAACAACAGCAGCAGCAA..............	26	20	0.05	1	0	1	0	0	0
..................................................................................................................................................................................................................................................................................AAC---------------AACA---------------GCAGCAACAACAAC.........................	21	20	0.05	1	0	0	0	1	0
............ACAGCAGCAACAA---CAACAGCAG---......................................................................................................................................................................................................................................................................................................................	22	20	0.05	1	0	1	0	0	0
..............................................................................................................................................................................................AACAACA------------GCAACA------GCAGCAACAATGGC...................................................................................................................	27	20	0.05	1	0	1	0	0	0
................................................................................................................................................................................................................................................................................................................................ACAACAGCAGCAGCAACAACA.........	21	20	0.05	1	0	1	0	0	0
........................................................................................................................................................................................TGCAGCAACAACA------------GCAACA------GCAGC............................................................................................................................	24	20	0.05	1	0	1	0	0	0
.......................................................................................................................................................................................................................................................AGC---AACAACAACTGCAGCAGCAACA...........................................................................	25	20	0.05	1	0	0	0	1	0
.....................................................................................................................................................................................................................................AATGGCAGCAACAACAACAGC---AACA.............................................................................................	25	20	0.05	1	0	1	0	0	0
...........................................................................................................................................................................................................................................AGCAACAACAACAGC---AACAACAACTGCAG...................................................................................	29	20	0.05	1	0	1	0	0	0
.................................................................................................................................................................AAC-----------------AATTGCAGCAACAACA------------GCAA.........................................................................................................................................	23	20	0.05	1	0	1	0	0	0
........................A---CAACAGCAG---CAG------------------CAACAACA.........................................................................................................................................................................................................................................................................................	21	20	0.05	1	0	1	0	0	0
........AACAACAGCAGCAACAA---CAAC..............................................................................................................................................................................................................................................................................................................................	21	20	0.05	1	0	0	0	1	0
....................AACAA---CAACAGCAG---CAG------------------CAA..............................................................................................................................................................................................................................................................................................	20	20	0.05	1	0	0	1	0	0
...............GCAGCAACAA---CAACAGCAG---CAG------------------CA...............................................................................................................................................................................................................................................................................................	24	20	0.05	1	0	0	0	1	0
......................................................................................................................................AACA------GCAACAGCAACAGCAGC.............................................................................................................................................................................................	21	20	0.05	1	0	1	0	0	0
......................................................................................................................................................................................................................A------GCAGCAACAATGGCAGCAACAACA.........................................................................................................	25	20	0.05	1	0	1	0	0	0
..............................................................................................................................................................................................................................................AACAACAACAGC---AACAACAACTGCAGC..................................................................................	27	20	0.05	1	0	1	0	0	0
.......................................................................................................................................................................................................................................................AGC---AACAACAACTGCAGCAGCAA.............................................................................	23	20	0.05	1	0	1	0	0	0
....................................................................................................................................................................................................................................................................................................AACA---------------GCAGCAACAACAACAGCA.....................	22	20	0.05	1	0	0	0	0	1
.........................................................................................................................................................................................................................................................................................................................AGCAACAACAACAGCAGCAGCAACA............	25	20	0.05	1	0	0	0	1	0
.......................................................................................................................................................................................................................................TGGCAGCAACAACAACAGC---AACAA............................................................................................	24	20	0.05	1	0	0	0	1	0
...............................................................................................................................................................................................................................................................................AACAAC---------------AACA---------------GCAGCAACAACAACAG.......................	26	20	0.05	1	0	0	0	1	0
.....AACAACAACAGCAGCAACAA---..................................................................................................................................................................................................................................................................................................................................	20	20	0.05	1	0	0	0	1	0
..........................................................................................................................................................................................................................................................................................................................GCAACAACAACAGCAGCAGCA...............	21	20	0.05	1	0	1	0	0	0
...................................................................................................................................................................................................................................ACAATGGCAGCAACAACAACAG.....................................................................................................	22	20	0.05	1	0	1	0	0	0
.....................................................................................................................................................................................................................................................ACAGC---AACAACAACTGCAGCA.................................................................................	21	20	0.05	1	0	1	0	0	0
....................................................................................................................................................................................................A------------GCAACA------GCAGCAACAATGG....................................................................................................................	20	20	0.05	1	0	1	0	0	0
.......................................................................................................................................ACA------GCAACAGCAACAGCAGCA............................................................................................................................................................................................	21	20	0.05	1	0	1	0	0	0
....................................................................................................................................................................................................................................................AACAGC---AACAACAACTGCAGCAGCAAC............................................................................	27	20	0.05	1	0	1	0	0	0
............................................................................................................................................................................................................................................................................AGCAACAAC---------------AACA---------------GCAGCAACAA.............................	23	20	0.05	1	0	0	0	1	0
................................................................................................................................................................................................CAACA------------GCAACA------GCAGCAACAATGGC...................................................................................................................	25	20	0.05	1	0	1	0	0	0
....CAACAACAACAGCAGCAACAA---CAACA.............................................................................................................................................................................................................................................................................................................................	26	20	0.05	1	0	0	0	1	0
...................................................................................................................CAACAGCAACAGC------AACA------GCAAC.........................................................................................................................................................................................................	22	20	0.05	1	0	0	0	0	1
............................................................................................................................................................................................................................................................................................................................AACAACAACAGCAGCAGCAA..............	20	20	0.05	1	0	0	1	0	0
..................................................................................................................................................................................................................................AACAATGGCAGCAACAACAACAGC---A................................................................................................	25	20	0.05	1	0	0	0	1	0
.......................................................................................................................................................................................................................................................................................................................GCAGCAACAACAACAGCAGCAGCA...............	24	20	0.05	1	0	0	0	1	0
...............................................................................................................................................................................................ACAACA------------GCAACA------GCAGCAACAATGG....................................................................................................................	25	20	0.05	1	0	1	0	0	0
..................GCAACAA---CAACAGCAG---CAG------------------CAACA............................................................................................................................................................................................................................................................................................	24	20	0.05	1	0	0	0	1	0
.................................................................................................................................................................................................................................................................................CAAC---------------AACA---------------GCAGCAACAACAACA........................	23	20	0.05	1	0	0	0	0	1
...........................................................................................................................................................................................AGCAACAACA------------GCAACA------GCAGCA...........................................................................................................................	22	20	0.05	1	0	1	0	0	0
.......................................................................................................................................................................................................................................................................GCAGCAGCAACAAC---------------AACA---------------GC.....................................	20	20	0.05	1	0	0	0	1	0
.....AACAACAACAGCAGCAACAA---CAACAG............................................................................................................................................................................................................................................................................................................................	26	20	0.05	1	0	0	0	1	0
..................GCAACAA---CAACAGCAG---CAG------------------CA...............................................................................................................................................................................................................................................................................................	21	20	0.05	1	0	1	0	0	0
..........................................................................................................................................................................................................................................................................................................................GCAACAACAACAGCAGCAGCAACA............	24	20	0.05	1	0	0	0	1	0
..............................................................................................................................................................................................................................................................................CAACAAC---------------AACA---------------GCAGCAACAACAACA........................	26	20	0.05	1	0	0	0	1	0
...............................................................................................................................................................................................................................................................................AACAAC---------------AACA---------------GCAGCAACAA.............................	20	20	0.05	1	0	0	0	1	0
.......................................................................ATCAG------CAACAGCAACAGCAGC............................................................................................................................................................................................................................................................	21	20	0.05	1	0	1	0	0	0
.................................................................................................................TGCAACAGCAACAGC------AACA------GC............................................................................................................................................................................................................	21	20	0.05	1	0	1	0	0	0
.....................................................................................................................................................................................AATTGCAGCAACAACA------------GCAACA------GC...............................................................................................................................	24	20	0.05	1	0	1	0	0	0
................................................................................................................................................................................................................................................CAACAACAGC---AACAACAACTGCAGC..................................................................................	25	20	0.05	1	0	1	0	0	0
.....................................................................................................................................................................................................................................................................................................ACA---------------GCAGCAACAACAACAGCAG....................	22	20	0.05	1	0	1	0	0	0
.........................................................................................................................................................................................GCAGCAACAACA------------GCAACA------GCAG.............................................................................................................................	22	20	0.05	1	0	1	0	0	0
.....................................................................................................................................................................................................................................AATGGCAGCAACAACAACAGC---A................................................................................................	22	20	0.05	1	0	1	0	0	0
...................CAACAA---CAACAGCAG---CAG------------------CAACA............................................................................................................................................................................................................................................................................................	23	20	0.05	1	0	0	0	1	0
...........AACAGCAGCAACAA---CAACAGCA..........................................................................................................................................................................................................................................................................................................................	22	20	0.05	1	0	0	0	0	1
.......................................................................................................................................................................................................................................TGGCAGCAACAACAACAGC---AACAACAAC........................................................................................	28	20	0.05	1	0	1	0	0	0
.............................................................................................................................................................................................................................................................AACAACAACTGCAGCAGCAACA...........................................................................	22	20	0.05	1	0	1	0	0	0
.................................................................................................................................................................................................................................................AACAACAGC---AACAACAACTGCAGCA.................................................................................	25	20	0.05	1	0	0	0	1	0
........................................................................................................................................................................................................................................GGCAGCAACAACAACAGC---AAC..............................................................................................	21	20	0.05	1	0	1	0	0	0
.................................................................................................................................................................AAC-----------------AATTGCAGCAACAACA------------GC...........................................................................................................................................	21	20	0.05	1	0	1	0	0	0
.....................................................................................................................................................AGCAACAGCAGCAAC-----------------AATTG....................................................................................................................................................................	20	20	0.05	1	0	1	0	0	0
...................................................................................................................................................................................................................................................CAACAGC---AACAACAACTGCAG...................................................................................	21	20	0.05	1	0	1	0	0	0
.................................................................................................................................................................................................................................CAACAATGGCAGCAACAACAACAGC---.................................................................................................	25	20	0.05	1	0	1	0	0	0
.............................AACAGCAG---CAG------------------CAACAACAGCA......................................................................................................................................................................................................................................................................................	22	20	0.05	1	0	1	0	0	0
.......CAACAACAGCAGCAACAA---CAACA.............................................................................................................................................................................................................................................................................................................................	23	20	0.05	1	0	0	0	0	1

dp5

----CAACAGCAGAAGTTCCAGCAA---CAGGAACAG---CAG------------------CAATATATGCAACAG------CAACATATGCAACAGCA---------AAATATGCAGCAGCAACA---TCTGCAACA------GCAACATC-----------------TGCAGCAGCAACAGCAGAAGCAGCAGCA------------ACAGA------AGCAGCAGCAACAGCAGCAGCAACAGCAGCAGCAACAACAGAAGCAGCAGCAACAGCAGCAGCAGAAGCAGCCGC---------------AGCAGCAGCAGGTGCAGCAGCA---------ACATCAGCA	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
..................................................................................................................................................................................................................................................................................AGCAGCAGCAGAAGCAGCCGC---------------AG......................................	23	1	1.00	1	0	0	1	0	0	0	0	0	0	0
....................AGCAA---CAGGAACAG---CAG------------------CA...............................................................................................................................................................................................................................................................................................	19	5	0.20	1	0	1	0	0	0	0	0	0	0	0
............................................................................................................................................................................................................................................................CAACAACAGAAGCAGCAGC...............................................................................	19	7	0.14	1	0	0	1	0	0	0	0	0	0	0
..........................................................................................................................................................................GCAGCAGCAACAGCAGAAG.................................................................................................................................................................	19	17	0.06	1	0	1	0	0	0	0	0	0	0	0
...........................................................................................................................................................................................................................................................................CAGCAACAGCAGCAGCAG.................................................................	18	20	0.05	1	0	1	0	0	0	0	0	0	0	0
...............................................................................................................................................................................................................................AGCAGCAACAGCAGCAGCAACAGC.......................................................................................................	24	20	0.05	1	0	0	1	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................AGCAACAGCAGCAGCAACAGCAGCAGC.................................................................................................	27	20	0.05	1	0	0	0	0	0	0	0	0	0	1
................................................................................................................................................................................................................................GCAGCAACAGCAGCAGCAACAGC.......................................................................................................	23	20	0.05	1	0	0	1	0	0	0	0	0	0	0
.................................................................................................................................................................................................................................CAGCAACAGCAGCAGCAACAGCAGCA...................................................................................................	26	20	0.05	1	0	0	0	1	0	0	0	0	0	0
..................................................................................................................................................................................................................................AGCAACAGCAGCAGCAACAGCAGC....................................................................................................	24	20	0.05	1	0	0	0	0	0	0	0	0	0	1
......................................................................................................................................................................................................................................ACAGCAGCAGCAACAGCAGC....................................................................................................	20	20	0.05	1	0	1	0	0	0	0	0	0	0	0
................................................................................................................................................................................................................................GCAGCAACAGCAGCAGCAACA.........................................................................................................	21	20	0.05	1	0	0	0	0	1	0	0	0	0	0
.....................................................................................................................................................................................................................................AACAGCAGCAGCAACAGCAGCA...................................................................................................	22	20	0.05	1	0	1	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................................................................................................GCAGCAGCAACAGCAGCAGCA..................................................................	21	20	0.05	1	0	0	0	0	0	1	0	0	0	0
...................................................................................................................................................................................................................................GCAACAGCAGCAGCAACAGCAGCAGC.................................................................................................	26	20	0.05	1	0	0	0	0	0	0	0	0	0	1
................................................................................................................................................................................................................................GCAGCAACAGCAGCAGCAACAGCAGCA...................................................................................................	27	20	0.05	1	0	1	0	0	0	0	0	0	0	0
............................................................................................................................................................................................................................................GCAGCAACAGCAGCAGCAACA.............................................................................................	21	20	0.05	1	0	0	0	0	1	0	0	0	0	0
.............................................................................................................................................................................................................................GCAGCAGCAACAGCAGCAGCA............................................................................................................	21	20	0.05	1	0	0	0	0	0	1	0	0	0	0

droAna3

----CAACAACAATCGAC---ATAAACGTTG---CAATCGGAG------------------CCAAAGTCGCA---GCAGCATCAGTAGCAACAGCAGCA---------GCATCAGCAGCA------------------------GCA-----------------ACAGCAGCAGCAGCGGCGGAAGCAGAAGCGGTAGCATCAACGCTACCAACAACAACAT---------------CAACAATAACAAC---AACAACAACAACAACAACAACAAC---------------AATAGCAACAGCCGAAATAGCAGCAGCTCGAAAAGCAGCA---------GCCACCGCA	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
...................................................................................AGTAGCAACAGCAGCA---------GCATCA............................................................................................................................................................................................................................................	22	1	1.00	1	0	0	0	0	0	1
.......................................................................................GCAACAGCAGCA---------GCATCAGCAGCA------------------------GCA-----------------AC........................................................................................................................................................................................	29	2	0.50	1	0	1	0	0	0	0
........................................................................................CAACAGCAGCA---------GCATCAGCAGC.......................................................................................................................................................................................................................................	22	9	0.22	2	0	0	0	0	0	2
................................................................................................GCA---------GCATCAGCAGCA------------------------GCA-----------------A.........................................................................................................................................................................................	19	13	0.15	2	2	0	0	0	0	0
........................................................................................................................................................................................................................................................AC---AACAACAACAACAACAACAACA...........................................................................	24	20	0.10	2	0	2	0	0	0	0
........................................................................................CAACAGCAGCA---------GCATCAGCA.........................................................................................................................................................................................................................................	20	20	0.10	2	0	0	0	0	1	1
..........................................................................................ACAGCAGCA---------GCATCAGCAGC.......................................................................................................................................................................................................................................	20	11	0.09	1	0	0	0	0	0	1
..............................................................................................................ATCAGCAGCA------------------------GCA-----------------ACAGCAGC..................................................................................................................................................................................	21	13	0.08	1	0	1	0	0	0	0
......................................................................................................................................................................................................................................................................AACAACAACAACAAC---------------AATAGCA...................................................	22	14	0.07	1	1	0	0	0	0	0
......................................................................................AGCAACAGCAGCA---------GCATCA............................................................................................................................................................................................................................................	19	17	0.06	1	0	0	0	0	0	1
..................................................................................................................................................................................................................................................................CAACAACAACAACAACAAC---------------AATA......................................................	23	20	0.05	1	0	1	0	0	0	0
..................................................................................................................GCAGCA------------------------GCA-----------------ACAGCAGCAGCA..............................................................................................................................................................................	21	20	0.05	1	0	0	0	0	0	1
...................................................................................................................................................................................................................................................TAACAAC---AACAACAACAAC.....................................................................................	19	20	0.05	1	0	1	0	0	0	0
.......................................................................................GCAACAGCAGCA---------GCATCA............................................................................................................................................................................................................................................	18	20	0.05	1	0	0	0	0	0	1
.................................................................................................................................................................................................................................................AATAACAAC---AACAACAACAACA....................................................................................	22	20	0.05	1	0	1	0	0	0	0

droBip1

A-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAGCAACAACAACAAC---AACAACAACAACAACAGCGAGC------------------CCA---------------GCAGCAACATCAACAACAGCA---------ACAACAACA	Size	Hit Count	Total Norm	Total
No Reads

droFic1

A-----TCATC-GATATC---GCGGGAGCAA---CAGCAGTTCAACAACAAGCCCTTCAACTTGGC---------------------------GCAGTT---------GATCAAGCAGCAGCAGCAGC------AACG------GCAGCAACTGCAGCAGCAGC-----------------AACTGCAGCAGCAACA------------ACAGC------AGCAGCAACAACAGCAGCAACAACAGCAGC---AGCAACAGCA---------------ACAGCAGCAACTACAACA---------------ACAACAGCAGCAACAGCAGCA---------GCAACAACA	Size	Hit Count	Total Norm	Total
No Reads

droRho1

AATTCAACAACAGC---AGCAACAA---CAGCAGCAG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAACAACAACAGCAGCAGCAACAACAGCAGCAGCAACAACAGCA---------------GCAGCAACAACAACAGCAGCA---------GCAACAACA	Size	Hit Count	Total Norm	Total
No Reads

droTak1

A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCAACAACTGCAAC---AATAACAACAACAATTGCAGCAGCAGCAACAACAACAATCACA---------------GCGATGACAATGAAACCGGCA---------GCAACAACA	Size	Hit Count	Total Norm	Total
No Reads

dvi_6640

scaffold_12875:13273037-13273187 +

Candidate

Unknown

Predicted structure

Flybase annnotation

Repeatable elements

Sense Strand Reads

Anti-sense strand reads

Re-alignment of all predicted orthologs

Re-alignment of all predicted orthologs with sRNA reads

-22.9	-22.9	-22.8