dmo_1209

intron [Dmoj\GI21030-in]; CDS [Dmoj\GI21030-cds]; exon [dmoj_GLEANR_5839:6]; exon [dmoj_GLEANR_5839:5]; CDS [Dmoj\GI21030-cds]

Name	Class	Family	Strand
TART_DV	LINE	Jockey	+

##################################################------------------------------------------------################################################## CGCCCAGCGCCTATCCCAGTGCCAGCGGCAGTAGCAATAGCAATAGCAACATGAGCAACATGAGCAACAATAGCAACAGCAACAGCAACAGTAGCAACAACACGCACGGTTTCGTTAATGGTTCCTCCAAGGATGCGGCCAGTGCCAG ************************************************....((.((.((.((.......((....))....))..)))).))...************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M046 female body	V041 embryo	V056 head
.............................................................................AGCAACAGCAACAGTAGCAACAACACGC...........................................	28	0	1	1.00	1	1	0	0
........................................................................................................CACGGTTTCGTTAATGGTTCCT......................	22	0	1	1.00	1	1	0	0
.....AGCGCCTATCCCAGTGCCAGCGGCA......................................................................................................................	25	0	1	1.00	1	1	0	0
............................................................................................................................CTACAAGGATGCGGCCCGTTC...	21	3	1	1.00	1	0	1	0
............ATCCCAGTGCCAGCGGCAGTAGCA................................................................................................................	24	0	1	1.00	1	1	0	0
.................AGTGCCAGCGGCAGTAGCAATAG............................................................................................................	23	0	1	1.00	1	1	0	0
........................................................................................................CGAGGTATCGTTAATGGTTCCT......................	22	3	1	1.00	1	0	0	1
................................................................CAACAATAGCAACAGCAACAGCAACAGT........................................................	28	0	2	0.50	1	1	0	0
..............................................................AGCAACAATAGCAACAGCAAC.................................................................	21	0	11	0.09	1	1	0	0

GCGGGTCGCGGATAGGGTCACGGTCGCCGTCATCGTTATCGTTATCGTTGTACTCGTTGTACTCGTTGTTATCGTTGTCGTTGTCGTTGTCATCGTTGTTGTGCGTGCCAAAGCAATTACCAAGGAGGTTCCTACGCCGGTCACGGTC ************************************************....((.((.((.((.......((....))....))..)))).))...************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V110 male body	V049 head
..............GAGTCAGGGTCGCCGTCATA..................................................................................................................	20	3	18	0.06	1	1	0
.....CCGCGGATGGGGTCGCGGTC...........................................................................................................................	20	3	20	0.05	1	0	1

Species	Coordinate	ID	Alignment
droMoj3	scaffold_6496:20111681-20111828 +	dmo_1209	CGCC-------CAGCGCCTA--TCCCAGTGCC----------AGCGGCAGTAGC--------AA------------------TAGCAATAGC-----------AA---CA------TGAGCAAC------A---TGAGCAACAA---TAGCAA---------CAGCAA---CAGCAAC---AGTAGCA------ACA-----ACACG----------CACGGTTTCG----------------------------------------TT--AATGGTTCC---TCC------AAGGATGCGGCCAG--TGCCAG
droVir3	scaffold_12875:12850013-12850142 +		CGCC-------CAGCGCC--TACC----------------CCAGCGGCTATCC--------------CAGC---------GCCAGCGGCAGC--------AGCAA---CA---------------------------------A---CAGCAA---------TAGCAA---CAGCAAC---AGCAGCA------GCA-----ACACG----------CACGGTTTCA----------------------------------------TT--AATGGTTCC---TCC------AAGGAGGCGGGCAG--CGCCAG
droGri2	scaffold_15245:7518669-7518818 -		CACC-------A-------------------------------ACAA------CAGCAGCAG-----------C------AGCAACAACATCA-----------A---CATGCCCAGCGGTACC---AGCA---GCAGCAACAATAGCAACAA---------CAGCAA---CAGCAGC---ATCACCA------ACA-----ACACG----------CACGGTTTCC----------------------------------------TC--AACGGTTCC---TCTTCCGCCAAAGATGTGGGAAA--TGGCAT
droWil2	scf2_1100000004776:18409-18550 -		CAGC-------AG-CA---A--CT----------------GCAACAA-----------------------CAGCAGCAGCAACAGCAACAACA--------ACAA---CA------TCAGCAGC------A---ACAGCAACAA---CAGCAA---------CAACAG---CAGCAAC---AGCAACA------ACA-----ACACG----------AGATAGAACA----------------------------------------TC--AAGAGTGCC-----C------ATGGGTGTGGCCAA--GACCGG
dp5	XR_group6:8985019-8985171 +		CGGC-------GAGCCGC--TGCT------CCAGACGCCGCCCGCCA----TGC--------AA------CAGCAGCAGCAACAGCAGCAGCAGC-----AACAA------------------------------------CAA---CAGCAG---------CAGCAA---CAGCAAC---AACAGCA------GCA-----GCAAA----------TGCCGCTCCT----------------------------------------TTGCAGCAGTCCCACATCG------ATGGCAGCGGCCAC--TTCCGT
droPer2	scaffold_76:249920-250065 +		GC----------AGCAACAA--CA----------------GCAGCAA------C--------AA---------C------AGCAGCAACAACA--GCAGCAACAA---CA------GCAGCAAC------A---ACAGCAGCAG---CAGCAA---------CAGCAA---CAGCAAC---AACAACA------ACA-----ACAAC----------AACAACAACA----------------------------------------GC--AGCAGCAGC---AGC------A-GGCGGCGGCCAATTGCCAGG
droAna3	scaffold_12916:13544384-13544522 +		AAC--------AG-CA---A--CC----------------CCAGCAA-----------------------CAGCAGCAGCAACAACAAACGCA--------ACAG---CAACA---TC---AAC------A------GCAGCAA---CAGCAA------------------CAGCAAC---AGCAGCAACAATCACATCCCAGCACC--GTGT-------------------T-----------------GGCCAG------------C--AATGGACCC---AGT------------AGCGCCGG--TGCCAG
droBip1	scf7180000391693:58064-58208 +		CCGC-------TGCCGCT---------CCATC----CTCGCCAGCAA------CAGGT-----------------GCAGCAACAGCAACAGCA--------GCAA---CAACA---GC---AGC------A---GCAGCAGCAA------CAA------------CAG---CAGCAGC---AGTTGCA------GCA-----GCAAT-------------------------C---------------------AATCGCCGGTTCGAT--TGTGGG--------C------GTGGACCCAGCCAG--TGACA-
droKik1	scf7180000302274:154350-154479 -		TGGC-------AGGACCC--AATC----------------CCGGCCAGAACAGT--------AAT---------------AATAACAATAAT-----------AATAACAGCG---GG---AGC---------------AACAA---CAACAG---------CGGCAA---CAGTAAC---AATAATA------ACA-----ACAAC-------------------------G-----------------TGTC-------G---TC--------GGTGC-------------AACATGTGGCCAA--TGCCGT
droFic1	scf7180000453829:134635-134788 +		AGCG-------CAGCACCAC--CAGCAGCACC----------AGCAGCAGCAGC--------AACAGCAAC------------------AGC-----------AA---CA------GCAGCAGT------A---GCAGCAGCAA---CAGCAA---------CAGCAA---AAGCAAC---AGCAACA------GCA-----ACAGAAACAGCAGCA----------GCAGCA-----------------C-------ACCG---CA--------GCACC---ACC-------AGCACACCACCAC--CACCAG
droEle1	scf7180000491087:122768-122899 +		CGCC-------CACACCC--TGCC----------------CCACCAGCAGCAGC--------AA---------C------AGCAGCAACAGC-----------AACAGCAGCA---GC---AGC------A------GCAGCAA------CAA---------CAGCAG---CAGCAAC---AGCAACA------GCT-----GCAC------------------------------------------------GGCGATCCC--------------GAC---GAC------GAGGAGGTGGAGAA--TGCCCG
droRho1	scf7180000779986:285334-285481 +		CCGC-------CGTCGCT-------------T----AGCATTAGCAA------TAG-----------CAACAGC------AACAGCAATAGCA-----------ATAACA------TCAATAGCATCAACA---ACAGCAATAA------------------CATCAA---CAACAAC---AATAGCA------GCA-----GC----------------------------A-----------------CGACGGCAACTGTTGCA--------GTTGC---AGC------AGCAACACCAACAG--TAGCAG
droBia1	scf7180000301760:365991-366129 +		CCGCCATCGCTAG--------------GCGCT----------AACAGCATTAGC--------AATAGCAACAGC------AATA---ACATCA--------GCAA---CAGCA---AC---AGC------A---------ATAG---CATCAA---------CAACAA---CATCAAC---AGTAGCA------GCA-----GC----------------------------A-----------------CGACGGCAAACGTTGCA--------GTTGC---G--------------G-CTGCAA--CACCAG
droTak1	scf7180000415078:354651-354797 +		AGCG-------CATT--C-----AGCAGCACC----------AGCAGCAGCAGC--------AATTGCAGCAGC------AACA--------------------------------TC---AGC------A---GCAGCAGCAA---CAGCAACACTCGCCGCAGCAGCAGCAG---CAACATCAGA-----------------CGGCACAGC-------------------A-----------------GGCCAG------------C--AGTTGCCTC---TAC------GATGAAG-CGGCGG--TGGCAG
droEug1	scf7180000409711:3473047-3473180 +		TGCC-------AACCAAC--TGGC----CAC-----------TGC-GCAACAAC--------AATTGCAAC------------AGCAACAGCA--------GCAG---CAGCA---GC---AGC------A---ACAGCAACAA------CAG---------CAGCAGCAGCAGCAAC---AGCAGCA------ACA-----TC----------------------------A-----------------C----------ATTGT--------GATCAC---C------------CAGCAGCAAC--AGACAA
dm3	chrX:11290332-11290481 +		CGCT-------TGGCGCTAA--CAGCAGCATT----AGCATTAGCAA------TAG-----------CAATAGC------AATAGCAACAGCA--------AT------------------------------------AATAT---CAACAACATTAATAGCATCAACAACAA---CAACAGTAGCA---GCAGCA-----GC----------------------------A-----------------CGACGGCAACTGT--------------TGC---AGC------AGCAACACCAACAG--CAGCAT
droSim2	x:10716748-10716900 +		CGCT-------TGGCGCTAA--CAGCAGCATT----AGCATTAGCAA------TAG-----------CAATAGC------AATAGCAACAGCA--------AT------------------------------------AATAT---CAACAACATTAATAGCATCAACAACAA---CAACAGTAGCA------GCA-----GCA----------------------GCAGCA-----------------CGACGGCAACTGT--------------TGC---AGC------AGCAACACCAACAG--CAGCAG
droSec2	scaffold_23:110879-111024 +		CAC--------AG-CACG------------------CCTCCCAGCAG------CAGCAGCAG-----------C------AGCAACAACAGCA--------GCAG---CAGCA---AC---ACC------A------GCAGCAG---CAGCAA------------CAG---CAGCAGC---ATCCCCA---GCAGCA-----GC----------------------------G-----------------CGGCCTCAAGCGCTCCGGC--AGCGACTGC---TAC------GAGG--ATCACCAC--CGCTCG
droYak3	3R:20117441-20117597 -		CGCC-------G--CAGGG--------TCACC----T---CCAGCAGCAG---CAGCAGCAG-----------C------AGCAGCAACATCA--------GCAG---CAGCA---TC---AGC------AGTTGCAGCAGCAACATCAGCAA---------CAGCAA---CAGCAGC---AGCAGCA------AC------------------------------------CGAATGCGAACAGCTCCTCGGCGGCATC-------------------------C------AGTGGAGCGGGAAG--CAGCAG
droEre2	scaffold_4690:2320688-2320841 +		GCAC-------AA-CATCT-ATGC----------------CCAGCAGCAGCAAC--------AAC---------------AGCAGCAGCAAC-----------AGCATCATCAGCAGCAGCAGC---------------AGCAA---CATCATCACTTC---CACCAC---CAGCAAC---AACAGCA------GCA-----GCAAC----------CACAGTCGCA----------------------------------------TC--ATTCGCACC---ATC------ATGGCCATGGTCAT--GACAAT

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droMoj3

CGCC-------CAGCGCCTA--TCCCAGTGCC----------AGCGGCAGTAGC--------AA------------------TAGCAATAGC-----------AA---CA------TGAGCAAC------A---TGAGCAACAA---TAGCAA---------CAGCAA---CAGCAAC---AGTAGCA------ACA-----ACACG----------CACGGTTTCG----------------------------------------TT--AATGGTTCC---TCC------AAGGATGCGGCCAG--TGCCAG	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
...................................................................................................................................................................AGCAA---CAGCAAC---AGTAGCA------ACA-----ACACG----------C................................................................................................	28	1	1.00	1	1	0	0	0	0	0
.........................................................................................................................................................................................................................CACGGTTTCG----------------------------------------TT--AATGGTTCC---T..............................	22	1	1.00	1	1	0	0	0	0	0
............AGCGCCTA--TCCCAGTGCC----------AGCGGCA.........................................................................................................................................................................................................................................................................	25	1	1.00	1	1	0	0	0	0	0
...................A--TCCCAGTGCC----------AGCGGCAGTAGC--------A...........................................................................................................................................................................................................................................................	24	1	1.00	1	1	0	0	0	0	0
..........................AGTGCC----------AGCGGCAGTAGC--------AA------------------TAG.....................................................................................................................................................................................................................................	23	1	1.00	1	1	0	0	0	0	0
..........................................................................................................................................CAACAA---TAGCAA---------CAGCAA---CAGCAAC---AGT..................................................................................................................................	28	2	0.50	1	1	0	0	0	0	0
........................................................................................................................................AGCAACAA---TAGCAA---------CAGCAA---C..............................................................................................................................................	21	11	0.09	1	1	0	0	0	0	0

droVir3

CGCC-------CAGCGCC--TACC----------------CCAGCGGCTATCC--------------CAGC---------GCCAGCGGCAGC--------AGCAA---CA---------------------------------A---CAGCAA---------TAGCAA---CAGCAAC---AGCAGCA------GCA-----ACACG----------CACGGTTTCA----------------------------------------TT--AATGGTTCC---TCC------AAGGAGGCGGGCAG--CGCCAG	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
...........................................................................................................................................................................................................................................................................TT--AATGGTTCC---TCC------AAGGAGGCGGGC..........	26	1	2.00	2	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	0	0	0	0	0	0	0	0	0
..............CGCC--TACC----------------CCAGCGGCTAT.......................................................................................................................................................................................................................................................................	19	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
..................................................................................................................................................................................................................................................................................GGTTCC---TCC------AAGGAGGCGGGCAG--C.....	24	1	1.00	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
.......................................................................................................................................................................................CAGCA------GCA-----ACACG----------CACGGTTT.........................................................................................	21	1	1.00	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	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
...............................................................................................................................................................................................................................................................................AATGGTTCC---TCC------AAGGAGGCGGGC..........	24	1	1.00	1	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
....................................................................................................................................................................................................A-----ACACG----------CACGGTTTCA----------------------------------------TT--AATGGT.....................................	24	1	1.00	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	0	0	0	0	0	0	0	0	0	0	0	0
................................................................................GCCAGCGGCAGC--------AGCAA---CA---------------------------------A---C......................................................................................................................................................................	21	2	0.50	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
................................................................................................................................................................................AC---AGCAGCA------GCA-----ACACG----------CA...............................................................................................	19	4	0.25	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
...................................................................................................................................................................AGCAA---CAGCAAC---AGCAGCA------........................................................................................................................	19	20	0.15	3	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	1	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
.......................................................................................................AA---CA---------------------------------A---CAGCAA---------TAGCAA---CAGCAAC---A....................................................................................................................................	25	8	0.13	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
............................................................................................................................................................................AGCAAC---AGCAGCA------GCA-----ACA.............................................................................................................	19	20	0.10	2	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
..................................................................................................................................................................TAGCAA---CAGCAAC---AGCAGCA------G.......................................................................................................................	21	10	0.10	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
......................................................................................................CAA---CA---------------------------------A---CAGCAA---------TAGCAA---...............................................................................................................................................	18	18	0.06	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
......................................................................................................................................................................AA---CAGCAAC---AGCAGCA------GC......................................................................................................................	18	20	0.05	1	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
....................................................................................................................................................................GCAA---CAGCAAC---AGCAGCA------G.......................................................................................................................	19	20	0.05	1	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
......................................................................................................................................................................AA---CAGCAAC---AGCAGCA------GCA-----ACA.............................................................................................................	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	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
...................................................................................................................................................................AGCAA---CAGCAAC---AGCAGCA------GCA-----................................................................................................................	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	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
....................................................................................................................................................................GCAA---CAGCAAC---AGCAGCA------GCA-----ACA.............................................................................................................	24	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
....................................................................................................................................................................GCAA---CAGCAAC---AGCAGCA------GCA-----................................................................................................................	21	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

droGri2

CACC-------A-------------------------------ACAA------CAGCAGCAG-----------C------AGCAACAACATCA-----------A---CATGCCCAGCGGTACC---AGCA---GCAGCAACAATAGCAACAA---------CAGCAA---CAGCAGC---ATCACCA------ACA-----ACACG----------CACGGTTTCC----------------------------------------TC--AACGGTTCC---TCTTCCGCCAAAGATGTGGGAAA--TGGCAT	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
..............................................A------CAGCAGCAG-----------C------AGCAACAACA................................................................................................................................................................................................................................	21	20	0.25	5	5	0
...................................................................................................................................................CAACAA---------CAGCAA---CAGCAGC---.....................................................................................................................................	19	20	0.05	1	1	0
...........................................ACAA------CAGCAGCAG-----------C------AGCAACA...................................................................................................................................................................................................................................	21	20	0.05	1	0	1
.......................................................................................................................................................AA---------CAGCAA---CAGCAGC---ATCA.................................................................................................................................	19	20	0.05	1	1	0

droWil2

CAGC-------AG-CA---A--CT----------------GCAACAA-----------------------CAGCAGCAGCAACAGCAACAACA--------ACAA---CA------TCAGCAGC------A---ACAGCAACAA---CAGCAA---------CAACAG---CAGCAAC---AGCAACA------ACA-----ACACG----------AGATAGAACA----------------------------------------TC--AAGAGTGCC-----C------ATGGGTGTGGCCAA--GACCGG	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
............................................................................................................................................................................................................................TAGAACA----------------------------------------TC--AAGAGTGCC-----C------ATGGGTG...............	26	5	1.00	5	0	1	0	4	0
.............................................................................................................................................................................................................................AGAACA----------------------------------------TC--AAGAGTGCC-----C------ATGGG.................	23	5	0.40	2	0	2	0	0	0
.............................................................................................................................................................................................................CG----------AGATAGAACA----------------------------------------TC--AAGAGTGCC-----C------......................	24	6	0.33	2	0	2	0	0	0
.............................................................................................................................................................................................................CG----------AGATAGAACA----------------------------------------TC--AAGAGTGCC-----C------A.....................	25	6	0.33	2	0	2	0	0	0
...........................................................................................................................................................................................................................................................................TC--AAGAGTGCC-----C------ATGGGTGTGGCCA.........	25	5	0.20	1	0	0	0	1	0
.................................................................................................................................................................................................................................CA----------------------------------------TC--AAGAGTGCC-----C------ATGGGTG...............	21	5	0.20	1	0	0	0	1	0
............................................................................................................................................................................................................................TAGAACA----------------------------------------TC--AAGAGTGCC-----C------ATGGGT................	25	5	0.20	1	0	0	0	1	0
.............................................................................................................................................................................................................................AGAACA----------------------------------------TC--AAGAGTGCC-----C------ATGGGTGTGGC...........	29	5	0.20	1	0	0	1	0	0
............................................................................................................................................................................................................................TAGAACA----------------------------------------TC--AAGAGTGCC-----C------ATGGGTGT..............	27	5	0.20	1	0	1	0	0	0
.............................................................................................................................................................................................................................AGAACA----------------------------------------TC--AAGAGTGCC-----C------ATGGGT................	24	5	0.20	1	0	1	0	0	0
.............................................................................................................................................................................................................................AGAACA----------------------------------------TC--AAGAGTGCC-----C------ATGG..................	22	6	0.17	1	0	1	0	0	0
.........................................................................................................................................................................................................................AGATAGAACA----------------------------------------TC--AAGAGTGCC-----C------ATG...................	25	6	0.17	1	0	0	0	1	0
..........................................................................................................................................................................................................................GATAGAACA----------------------------------------TC--AAGAGTGCC-----C------ATG...................	24	6	0.17	1	0	1	0	0	0
.............................................................................................................................................................................................................................AGAACA----------------------------------------TC--AAGAGTGCC-----C------......................	18	6	0.17	1	0	1	0	0	0
..............................................................................................................................................................................................................G----------AGATAGAACA----------------------------------------TC--AAGAGTGCC-----C------A.....................	24	6	0.17	1	0	1	0	0	0
.................................................................................................................................................................................C---AGCAACA------ACA-----ACACG----------AGAT.............................................................................................	20	15	0.13	2	0	2	0	0	0
...............................................................................................................................................................................................................................................................................AAGAGTGCC-----C------ATGGGTGTGGC...........	21	9	0.11	1	0	0	0	0	1
............................................................................................................................................................................................................................................................................C--AAGAGTGCC-----C------ATGGGTGTGGCCAA--T.....	26	9	0.11	1	0	0	0	1	0
......................................................................................................................AGCAGC------A---ACAGCAACAA---CAGCAA---------........................................................................................................................................................	23	20	0.10	2	0	2	0	0	0
............................................................................................A--------ACAA---CA------TCAGCAGC------A---ACA.................................................................................................................................................................................	19	20	0.10	2	0	0	0	2	0
............................................................................................................................................ACAA---CAGCAA---------CAACAG---CAGCAA.........................................................................................................................................	22	12	0.08	1	0	0	0	1	0
......................................................................................................................................................................AG---CAGCAAC---AGCAACA------ACA-----ACACG----------AGA..............................................................................................	27	14	0.07	1	0	0	0	1	0
...................................................................................................................................................................AACAG---CAGCAAC---AGCAACA------ACA-----ACAC............................................................................................................	26	14	0.07	1	0	1	0	0	0
................................................................................................................................................................................AC---AGCAACA------ACA-----ACACG----------AGAT.............................................................................................	21	15	0.07	1	0	1	0	0	0
.......................................................................................................AA---CA------TCAGCAGC------A---ACAGCAACAA---.......................................................................................................................................................................	23	17	0.06	1	0	1	0	0	0
....................................................................................................................................................................................................................................................................................TGCC-----C------ATGGGTGTGGCCAA--GACCGG	25	17	0.06	1	0	1	0	0	0
......................................................................................................................................................................................................................................................................................CC-----C------ATGGGTGTGGCCAA--GACCGG	23	17	0.06	1	0	1	0	0	0
..........................................................................................ACA--------ACAA---CA------TCAGCAGC------A---ACAGC...............................................................................................................................................................................	23	18	0.06	1	0	0	1	0	0
......................................................................................AACAACA--------ACAA---CA------TCAGCAGC------A---AC..................................................................................................................................................................................	24	19	0.05	1	0	0	0	1	0
......................................................................................AACAACA--------ACAA---CA------TCAGCAGC------A---ACA.................................................................................................................................................................................	25	19	0.05	1	0	1	0	0	0
..........................................................................................................................................CAACAA---CAGCAA---------CAACAG---CAGCA..........................................................................................................................................	23	20	0.05	1	0	0	0	0	1
............................................CAA-----------------------CAGCAGCAGCAACAGC....................................................................................................................................................................................................................................	19	20	0.05	1	0	0	0	0	1
.....................................................................................CAACAACA--------ACAA---CA------TCAGCAGC------........................................................................................................................................................................................	22	20	0.05	1	0	1	0	0	0
.............................................AA-----------------------CAGCAGCAGCAACAGC....................................................................................................................................................................................................................................	18	20	0.05	1	0	0	0	1	0
..........................................AACAA-----------------------CAGCAGCAGCAACAGC....................................................................................................................................................................................................................................	21	20	0.05	1	0	1	0	0	0
...............................................................................CAACAGCAACAACA--------ACAA---CA------TCAGC.................................................................................................................................................................................................	25	20	0.05	1	0	1	0	0	0
........................................................................................CAACA--------ACAA---CA------TCAGCAGC------A---AC..................................................................................................................................................................................	22	20	0.05	1	0	0	0	1	0
...........................................................................................CA--------ACAA---CA------TCAGCAGC------A---AC..................................................................................................................................................................................	19	20	0.05	1	0	0	0	1	0
....................................................................................................................................................AGCAA---------CAACAG---CAGCAAC---AGCAAC...............................................................................................................................	24	20	0.05	1	0	0	0	1	0

dp5

CGGC-------GAGCCGC--TGCT------CCAGACGCCGCCCGCCA----TGC--------AA------CAGCAGCAGCAACAGCAGCAGCAGC-----AACAA------------------------------------CAA---CAGCAG---------CAGCAA---CAGCAAC---AACAGCA------GCA-----GCAAA----------TGCCGCTCCT----------------------------------------TTGCAGCAGTCCCACATCG------ATGGCAGCGGCCAC--TTCCGT	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
..............................................................AA------CAGCAGCAGCAACAGCA...................................................................................................................................................................................................................................	19	20	0.25	5	0	0	0	0	5	0	0	0	0	0
.............................................................................................GC-----AACAA------------------------------------CAA---CAGCAG---------CAGC....................................................................................................................................................	20	20	0.10	2	0	2	0	0	0	0	0	0	0	0
.......................................................................................................AA------------------------------------CAA---CAGCAG---------CAGCAA---CAGC...........................................................................................................................................	21	20	0.10	2	0	2	0	0	0	0	0	0	0	0
.....................................................C--------AA------CAGCAGCAGCAACAGC....................................................................................................................................................................................................................................	19	20	0.10	2	0	0	1	0	0	0	0	0	1	0
..............................................................................................C-----AACAA------------------------------------CAA---CAGCAG---------CAGCAA---CA.............................................................................................................................................	23	20	0.10	2	0	1	0	0	1	0	0	0	0	0
.....................................................................................................ACAA------------------------------------CAA---CAGCAG---------CAGCAA---C..............................................................................................................................................	20	20	0.10	2	0	0	1	0	1	0	0	0	0	0
........................................................................................................................................................G---------CAGCAA---CAGCAAC---AACAGCA------GCA-----................................................................................................................	24	20	0.05	1	0	0	0	0	1	0	0	0	0	0
.......................................................................................................................................................................A---CAGCAAC---AACAGCA------GCA-----GCA.............................................................................................................	21	20	0.05	1	0	1	0	0	0	0	0	0	0	0
.....................................................................................................................................................GCAG---------CAGCAA---CAGCAAC---AACAGC...............................................................................................................................	23	20	0.05	1	0	0	0	0	1	0	0	0	0	0
.....................................................................................................................................................................CAA---CAGCAAC---AACAGCA------GCA-----................................................................................................................	20	20	0.05	1	0	0	0	0	1	0	0	0	0	0
.......................................................................................GCAGCAGC-----AACAA------------------------------------CAA---CAGC...................................................................................................................................................................	20	20	0.05	1	0	1	0	0	0	0	0	0	0	0
.....................................................................................CAGCAGCAGC-----AACAA------------------------------------CAA---CA.....................................................................................................................................................................	20	20	0.05	1	0	0	0	0	0	0	1	0	0	0
...................................................................................................................................................................AGCAA---CAGCAAC---AACAGCA------GC......................................................................................................................	21	20	0.05	1	0	1	0	0	0	0	0	0	0	0
..........................................................................................GCAGC-----AACAA------------------------------------CAA---CAGCAG---------CAGC....................................................................................................................................................	23	20	0.05	1	0	0	1	0	0	0	0	0	0	0
.............................................................................................................................................CAA---CAGCAG---------CAGCAA---CAGCAAC---.....................................................................................................................................	22	20	0.05	1	0	1	0	0	0	0	0	0	0	0
......................................................................................................CAA------------------------------------CAA---CAGCAG---------CAGCAA---CAG............................................................................................................................................	21	20	0.05	1	0	1	0	0	0	0	0	0	0	0
....................................................................................................AACAA------------------------------------CAA---CAGCAG---------CAGCA...................................................................................................................................................	19	20	0.05	1	0	1	0	0	0	0	0	0	0	0
...............................................................A------CAGCAGCAGCAACAGCAGC.................................................................................................................................................................................................................................	20	20	0.05	1	0	0	0	1	0	0	0	0	0	0
...................................................................................AGCAGCAGCAGC-----AACAA------------------------------------CAA---CAGCAG---------C.......................................................................................................................................................	27	20	0.05	1	0	1	0	0	0	0	0	0	0	0
.........................................................................................AGCAGC-----AACAA------------------------------------CAA---CAGCA..................................................................................................................................................................	19	20	0.05	1	0	1	0	0	0	0	0	0	0	0
....................................................................................................................................................................GCAA---CAGCAAC---AACAGCA------GCA-----GC..............................................................................................................	23	20	0.05	1	0	0	0	0	0	0	1	0	0	0
..............................................................................................C-----AACAA------------------------------------CAA---CAGCAG---------CAG.....................................................................................................................................................	18	20	0.05	1	0	1	0	0	0	0	0	0	0	0
....................................................GC--------AA------CAGCAGCAGCAACAGCAGCAGC..............................................................................................................................................................................................................................	26	20	0.05	1	0	0	0	0	0	0	0	0	0	1
............................................................................................................................................................................AGCAAC---AACAGCA------GCA-----GCAA............................................................................................................	20	20	0.05	1	0	0	0	0	1	0	0	0	0	0
........................................................................................CAGCAGC-----AACAA------------------------------------CAA---CAGCAG---------........................................................................................................................................................	21	20	0.05	1	0	1	0	0	0	0	0	0	0	0
......................................................................CAGCAGCAGCAACAGCAGC.................................................................................................................................................................................................................................	19	20	0.05	1	0	1	0	0	0	0	0	0	0	0

droPer2

GC----------AGCAACAA--CA----------------GCAGCAA------C--------AA---------C------AGCAGCAACAACA--GCAGCAACAA---CA------GCAGCAAC------A---ACAGCAGCAG---CAGCAA---------CAGCAA---CAGCAAC---AACAACA------ACA-----ACAAC----------AACAACAACA----------------------------------------GC--AGCAGCAGC---AGC------A-GGCGGCGGCCAATTGCCAGG	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
...............................................................................................................................................................................................................................................................................AGCAGCAGC---AGC------A-GGCGGCGG............	21	7	0.14	1	0	1	0	0	0	0
...............................................................................................................................................................................................................................AACA----------------------------------------GC--AGCAGCAGC---AGC------A-GGC.................	22	15	0.07	1	0	1	0	0	0	0
...........................................................................................................................................................................................................................................................................GC--AGCAGCAGC---AGC------A-GGCGGCGC............	23	16	0.06	1	1	0	0	0	0	0
......................................................................................................................................................................................ACAACA------ACA-----ACAAC----------AACAACAACA----------------------------------------GC--AG.........................................	28	20	0.05	1	0	1	0	0	0	0
....................................................................................................................................................................................................A-----ACAAC----------AACAACAACA----------------------------------------GC--AGCA.......................................	22	20	0.05	1	0	0	1	0	0	0
........................................................................................................................CAAC------A---ACAGCAGCAG---CAGCAA---------........................................................................................................................................................	21	20	0.05	1	0	0	1	0	0	0
...........................................................................................................................................................................................................CAAC----------AACAACAACA----------------------------------------GC--AGC........................................	19	20	0.05	1	0	0	1	0	0	0
.......................................................................................................................GCAAC------A---ACAGCAGCAG---CAGCA..................................................................................................................................................................	21	20	0.05	1	0	0	1	0	0	0
.......................................................................................................................................................................................CAACA------ACA-----ACAAC----------AACAACAA.........................................................................................	21	20	0.05	1	0	0	1	0	0	0
.......................................................................................................................GCAAC------A---ACAGCAGCAG---CAGC...................................................................................................................................................................	20	20	0.05	1	0	0	1	0	0	0
............................................................................................................................................................................................................AAC----------AACAACAACA----------------------------------------GC--AGCAGCAGC---...............................	24	20	0.05	1	0	0	1	0	0	0
..............................................................................................................................................................................CAAC---AACAACA------ACA-----ACAAC----------AACAACAAC........................................................................................	28	20	0.05	1	0	1	0	0	0	0
...................................................................................................................................................................................................CA-----ACAAC----------AACAACAACA----------------------------------------GC--...........................................	19	20	0.05	1	0	1	0	0	0	0
.......................................................................................................................GCAAC------A---ACAGCAGCAG---CAGCAA---------CA......................................................................................................................................................	24	20	0.05	1	0	0	1	0	0	0
...................A--CA----------------GCAGCAA------C--------AA---------C------AGCAGC....................................................................................................................................................................................................................................	20	20	0.05	1	0	0	1	0	0	0
...............................................................................................................................................................................................................................AACA----------------------------------------GC--AGCAGCAGC---AGC------A-....................	19	20	0.05	1	0	1	0	0	0	0
......................................................................................................................................................................................ACAACA------ACA-----ACAAC----------AACAACAACA----------------------------------------GC--...........................................	26	20	0.05	1	0	1	0	0	0	0
.............................................................................................................................................................................................................................ACAACA----------------------------------------GC--AGCAGCAGC---AGC------A-....................	21	20	0.05	1	0	0	1	0	0	0
...........................................................................................................................................................................................................................CAACAACA----------------------------------------GC--AGCAGCAGC---A..............................	20	20	0.05	1	0	0	1	0	0	0

droAna3

AAC--------AG-CA---A--CC----------------CCAGCAA-----------------------CAGCAGCAGCAACAACAAACGCA--------ACAG---CAACA---TC---AAC------A------GCAGCAA---CAGCAA------------------CAGCAAC---AGCAGCAACAATCACATCCCAGCACC--GTGT-------------------T-----------------GGCCAG------------C--AATGGACCC---AGT------------AGCGCCGG--TGCCAG	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
...................A--CC----------------CCAGCAA-----------------------CAGCAGCAGCA.........................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	1
................................................................................................................................................................................................TCACATCCCAGCACC--GTGT-------------------T-----------------GGCCAG------------C--A..........................................	28	1	1.00	1	0	1	0	0	0	0
.............................................................................................................AACA---TC---AAC------A------GCAGCAA---CAGCA..................................................................................................................................................................	22	3	0.33	1	0	0	0	0	0	1
.............................................................................................................AACA---TC---AAC------A------GCAGCAA---C......................................................................................................................................................................	18	10	0.20	2	0	0	0	0	0	2
..........................................................................................................................................CAGCAA---CAGCAA------------------CAGCAAC---AGCAGCA..............................................................................................................................	26	20	0.05	1	0	1	0	0	0	0
..........................................................................................................................AC------A------GCAGCAA---CAGCAA------------------CAGC...........................................................................................................................................	20	20	0.05	1	0	1	0	0	0	0
.......................................................................................................................................................AA------------------CAGCAAC---AGCAGCAACA...........................................................................................................................	19	20	0.05	1	0	1	0	0	0	0
..............................................................................................................................................AA---CAGCAA------------------CAGCAAC---AGCAGCA..............................................................................................................................	22	20	0.05	1	0	1	0	0	0	0
...............................................................................................................................................A---CAGCAA------------------CAGCAAC---AGCAGC...............................................................................................................................	20	20	0.05	1	0	1	0	0	0	0
.............................................................................................................................................CAA---CAGCAA------------------CAGCAAC---AGCAGC...............................................................................................................................	22	20	0.05	1	0	1	0	0	0	0
.............................................AA-----------------------CAGCAGCAGCAACAACA...................................................................................................................................................................................................................................	19	20	0.05	1	1	0	0	0	0	0
.........................................CAGCAA-----------------------CAGCAGCAGCAACA......................................................................................................................................................................................................................................	20	20	0.05	1	0	0	0	0	0	1

droBip1

CCGC-------TGCCGCT---------CCATC----CTCGCCAGCAA------CAGGT-----------------GCAGCAACAGCAACAGCA--------GCAA---CAACA---GC---AGC------A---GCAGCAGCAA------CAA------------CAG---CAGCAGC---AGTTGCA------GCA-----GCAAT-------------------------C---------------------AATCGCCGGTTCGAT--TGTGGG--------C------GTGGACCCAGCCAG--TGACA-	Size	Hit Count	Total Norm	Total
No Reads

droKik1

TGGC-------AGGACCC--AATC----------------CCGGCCAGAACAGT--------AAT---------------AATAACAATAAT-----------AATAACAGCG---GG---AGC---------------AACAA---CAACAG---------CGGCAA---CAGTAAC---AATAATA------ACA-----ACAAC-------------------------G-----------------TGTC-------G---TC--------GGTGC-------------AACATGTGGCCAA--TGCCGT	Size	Hit Count	Total Norm	Total
No Reads

droFic1

AGCG-------CAGCACCAC--CAGCAGCACC----------AGCAGCAGCAGC--------AACAGCAAC------------------AGC-----------AA---CA------GCAGCAGT------A---GCAGCAGCAA---CAGCAA---------CAGCAA---AAGCAAC---AGCAACA------GCA-----ACAGAAACAGCAGCA----------GCAGCA-----------------C-------ACCG---CA--------GCACC---ACC-------AGCACACCACCAC--CACCAG	Size	Hit Count	Total Norm	Total
No Reads

droEle1

CGCC-------CACACCC--TGCC----------------CCACCAGCAGCAGC--------AA---------C------AGCAGCAACAGC-----------AACAGCAGCA---GC---AGC------A------GCAGCAA------CAA---------CAGCAG---CAGCAAC---AGCAACA------GCT-----GCAC------------------------------------------------GGCGATCCC--------------GAC---GAC------GAGGAGGTGGAGAA--TGCCCG	Size	Hit Count	Total Norm	Total
No Reads

droRho1

CCGC-------CGTCGCT-------------T----AGCATTAGCAA------TAG-----------CAACAGC------AACAGCAATAGCA-----------ATAACA------TCAATAGCATCAACA---ACAGCAATAA------------------CATCAA---CAACAAC---AATAGCA------GCA-----GC----------------------------A-----------------CGACGGCAACTGTTGCA--------GTTGC---AGC------AGCAACACCAACAG--TAGCAG	Size	Hit Count	Total Norm	Total
No Reads

droBia1

CCGCCATCGCTAG--------------GCGCT----------AACAGCATTAGC--------AATAGCAACAGC------AATA---ACATCA--------GCAA---CAGCA---AC---AGC------A---------ATAG---CATCAA---------CAACAA---CATCAAC---AGTAGCA------GCA-----GC----------------------------A-----------------CGACGGCAAACGTTGCA--------GTTGC---G--------------G-CTGCAA--CACCAG	Size	Hit Count	Total Norm	Total
No Reads

droTak1

AGCG-------CATT--C-----AGCAGCACC----------AGCAGCAGCAGC--------AATTGCAGCAGC------AACA--------------------------------TC---AGC------A---GCAGCAGCAA---CAGCAACACTCGCCGCAGCAGCAGCAG---CAACATCAGA-----------------CGGCACAGC-------------------A-----------------GGCCAG------------C--AGTTGCCTC---TAC------GATGAAG-CGGCGG--TGGCAG	Size	Hit Count	Total Norm	Total
No Reads

droEug1

TGCC-------AACCAAC--TGGC----CAC-----------TGC-GCAACAAC--------AATTGCAAC------------AGCAACAGCA--------GCAG---CAGCA---GC---AGC------A---ACAGCAACAA------CAG---------CAGCAGCAGCAGCAAC---AGCAGCA------ACA-----TC----------------------------A-----------------C----------ATTGT--------GATCAC---C------------CAGCAGCAAC--AGACAA	Size	Hit Count	Total Norm	Total
No Reads

dm3

CGCT-------TGGCGCTAA--CAGCAGCATT----AGCATTAGCAA------TAG-----------CAATAGC------AATAGCAACAGCA--------AT------------------------------------AATAT---CAACAACATTAATAGCATCAACAACAA---CAACAGTAGCA---GCAGCA-----GC----------------------------A-----------------CGACGGCAACTGT--------------TGC---AGC------AGCAACACCAACAG--CAGCAT	Size	Hit Count	Total Norm	Total	GSM154618 Ovary	GSM154620 Ovary	GSM154621 Ovary	GSM154622 Ovary	GSM180328 Head	GSM180329 Mixed-body	GSM180330 Embryo	GSM180331 Embryo	GSM180332 Embryo	GSM180333 Embryo	GSM180334 Larvae	GSM180335 Disc	GSM180336 Pupae	GSM180337 S2	GSM231091 Ovary	GSM239041 Head	GSM239050 Head	GSM239051 S2	GSM239052 S2	GSM246084 Head	GSM266765 S2	GSM280082 Ovary	GSM280083 Ovary	GSM280084 Ovary	GSM280085 Testis	GSM280086 Ovary	GSM280087 S2-NP	GSM280088 S2-NP	GSM312995 Head	GSM313160 Head	GSM313161 Head	GSM313162 Head	GSM313163 Head	GSM313164 Head	GSM313165 Head	GSM343287 Embryo	GSM379050 Ovary	GSM379051 Ovary	GSM379052 Ovary	GSM379053 Ovary	GSM379054 Ovary	GSM379055 Ovary	GSM379056 Ovary	GSM379057 Ovary	GSM379058 Ovary	GSM379059 Ovary	GSM379060 Ovary	GSM379061 Ovary	GSM379062 Ovary	GSM379063 Ovary	GSM379064 Ovary	GSM379065 Ovary	GSM379066 Ovary	GSM379067 Ovary	GSM424739 S2	GSM424740 S2	GSM424741 S2	GSM467729 Female-body	GSM467730 Female-body	GSM467731 Female-body	M002 CS	M003 Male-body	M004 Male-body	M005 ML-DmD32	M006 ML-DmD32	M029 OSC	M030 OSC	M031 OSC	M032 S2-R+	M033 S2-R+	M034 S2-R+	M035 S2-R+	M036 S2-R+	M037 S2-R+	M038 S2-R+	M039 S2-R+	M048 S2-R+	OSS2 OSS	OSS6 OSS	OSS7 OSS	OSS8 OSS	S1 Head	S10 Embryo	S11 Embryo	S12 Embryo	S13 Embryo	S14 Embryo	S15 S2-GMR	S16 Kc	S17 Larvae	S18 Larvae	S19 Pupae	S2 Head	S20 Pupae	S21 Disc	S22 Head	S23 Female-body	S24 Male-body	S25 Larvae	S26 Larvae	S27 Pupae	S28 Pupae	S29 Head	S3 Male-body	S30 S2-GMR	S31 S2	S32 S2	S33 Kc	S34 Kc	S35 Kc	S4 Female-body	S5 Disc	S6 Embryo	S7 Embryo	S8 S2	S9 Embryo	SRR001337 Head	SRR001338 Head	SRR001339 Head	SRR001340 Head	SRR001341 Head	SRR001342 Head	SRR001343 Head	SRR001344 Head	SRR001345 Head	SRR001346 Head	SRR001347 Head	SRR001348 Head	SRR001349 Head	SRR001664 Head	SRR010951 Ovary	SRR010952 Ovary	SRR010953 Ovary	SRR010954 Ovary	SRR010955 Ovary	SRR010956 Ovary	SRR010957 Ovary	SRR010958 Ovary	SRR010959 Ovary	SRR010960 Ovary	SRR014268 Embryo	SRR014269 Embryo	SRR014270 Embryo	SRR014271 Embryo	SRR014272 Embryo	SRR014273 Ovary	SRR014274 Ovary	SRR014275 Ovary	SRR014276 Ovary	SRR014277 Ovary	SRR014278 Ovary	SRR014279 Ovary	SRR014280 Ovary	SRR014281 Ovary	SRR014282 Ovary	SRR023197 S2	SRR023399 S2	SRR023400 S2	SRR023402 S2	SRR023407 S2	SRR029028 S2	SRR029029 S2	SRR029030 S2	SRR029031 S2	SRR029032 S2	SRR029033 S2	SRR029608 Head	SRR029633 Head	SRR030145 gb3	SRR031692 Head	SRR031693 Head	SRR031694 Head	SRR031696 Head	SRR031697 Head	SRR031698 Head	SRR031699 Head	SRR031700 Head	SRR031701 Head	SRR031702 Head	SRR031703 Head	SRR031704 Head	SRR032092 S2	SRR032093 S2	SRR032094 S2	SRR032095 S2-NP	SRR032096 S2-NP	SRR032152 Head	SRR060643 Testis	SRR060644 Ovary	SRR060645 Testis	SRR060646 Ovary	SRR060647 Ovary	SRR060648 Ovary	SRR060649 Ovary	SRR060650 Testis	SRR060651 Ovary	SRR060652 Testis	SRR060653 Ovary	SRR065151 Ovary	SRR065152 Ovary	SRR065153 Ovary	SRR065154 Ovary	SRR065155 Ovary	SRR065800 Ovary	SRR065801 Ovary	SRR065802 Ovary	SRR065803 Ovary	SRR065804 Ovary	SRR065805 Ovary	SRR065806 Ovary	SRR065807 Ovary	SRR097865 S2-NP	SRR097866 S2-NP	SRR097867 S2-NP	SRR298536 Ovary	SRR298537 Ovary	SRR298711 Ovary	SRR298712 Ovary	SRR317110 Ovary	SRR317111 Ovary	SRR317112 Ovary	SRR317113 Ovary	SRR317114 Ovary	SRR317115 Ovary	SRR317116 Ovary	SRR317117 Ovary	SRR341115 S2	SRR341116 S2	SRR341117 S2	SRR341118 S2	SRR351332 Mixed-body	SRR351333 Mixed-body	T004 OSC	T005 CME-L1	V001 Embryo	V002 Embryo	V003 S2	V006 Female-body	V007 Head	V008 S2	V009 CME-L1	V010 ML-DmD20-C5	V011 Sg4	V012 Male-body	V013 Head	V014 DTT	V015 DreRFHV	V018 Kc167	V019 GM2	V020 S2-R+	V021 ML-DmD21	V022 ML-DmD32	V023 Head	V024 Kc167	V025 S2-R+	V026 1182-2H	V027 ML-DmD21	V028 CME-W1-Cl.8+	V029 ML-DmD9	V030 ML-DmD8	V031 GM2	V032 S1	V033 CME-W1-Cl.8+	V034 ML-DmD16-C3	V035 ML-DmD32	V036 ML-DmD20-C5	V037 S2	V038 S2	V063 Ovary	V0632 Ovary	V064 Ovary	V0642 Ovary	V065 Ovary	V0652 Ovary	V066 Ovary	V0662 Ovary	V067 S2-NP	V073 mbn2	V074 S3	V075 ML-DmBG1-C1	V076 ML-DmBG3-C2	V077 Head	V078 Head	V079 Head	V080 Head	V081 Embryo	V082 Embryo	V083 Male-body	V084 Female-body	V085 CME-W2	V086 Female-body	V088 Ovary	V0882 Ovary	V089 Ovary	V0892 Ovary	V090 Male-body	V091 fGS/OSS	V092 Male-body	V093 Male-body	V094 S2-R+	V095 S2-R+	V096 Ovary	V097 Ovary	V098 Ovary	V125 ML-DmD9	V126 CME-L1	V127 G2	V128 S3	V129 ML-DmBG1-C1	V130 ML-DmBG3-C2	V131 ML-DmD16-C3	V132 ML-DmD32	V133 Sg4	V134 ML-DmD8	V135 CME-W2	V136 Male-body	V137 Head	V138 Male-body	V139 Female-body	V140 Female-body	V141 Female-body	V142 Female-body	V144 OSC	V145 S2	V146 S1	V147 1182-2H	V148 mbn2	GSM1528798 follicle cells
...............................T----AGCATTAGCAA------TAG-----------CAATAGC------..........................................................................................................................................................................................................................................	22	1	4.00	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................A-----GC----------------------------A-----------------CGACGGCAACTGT--------------TG...................................	19	1	3.00	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
.........................................................................................................................................................CATTAATAGCATCAACAACAA---CA.......................................................................................................................................	23	1	2.00	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
........................................................................................................................................................ACATTAATAGCATCAACAACAA---CA.......................................................................................................................................	24	1	1.00	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	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................................................................................................................................ATAT---CAACAACATTAATAGCATCAACA................................................................................................................................................	27	1	1.00	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................................................................................................................................................TAATAGCATCAACAACAA---CAACAGTAGC...............................................................................................................................	28	1	1.00	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................................................................................................................................................................................................................................................ACGGCAACTGT--------------TGC---AGC------AGC...................	20	1	1.00	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
....................................................................AATAGC------AATAGCAACAGCA--------AT------------------------------------AATAT---C......................................................................................................................................................................	27	1	1.00	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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....................................................................................................................................................................................................................................................................................................AGCAACACCAACAG--CAGC..	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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............................................................................................................................................................................................................................................................................................GC------AGCAACACCAACAG--CAGC..	20	15	0.07	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	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...........................................................................................................................................................................................................................................................................................AGC------AGCAACACCAACAG--CAG...	20	16	0.06	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................................................................................................................C---AGC------AGCAACACCAACAG--C.....	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	0	0	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droSim2

CGCT-------TGGCGCTAA--CAGCAGCATT----AGCATTAGCAA------TAG-----------CAATAGC------AATAGCAACAGCA--------AT------------------------------------AATAT---CAACAACATTAATAGCATCAACAACAA---CAACAGTAGCA------GCA-----GCA----------------------GCAGCA-----------------CGACGGCAACTGT--------------TGC---AGC------AGCAACACCAACAG--CAGCAG	Size	Hit Count	Total Norm	Total	M023 Head	M024 Male-body	M025 Embryo	M053 Female-body	O001 Testis	O002 Head	SRR553485 Ovary	SRR553486 Ovary	SRR553487 Ovary	SRR553488 Ovary	SRR618934 Ovary	V044 Embryo	SRR902008 Ovary	SRR902009 Testis	SRR1275487 Male larvae	SRR1275485 Male prepupae	SRR1275483 Male prepupae
...........................................................................................................................................................................................................CA----------------------GCAGCA-----------------CGACGGCAACTGT--------------.....................................	21	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................GCA------GCA-----GCA----------------------GCAGCA-----------------................................................................	15	20	0.10	2	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0

droSec2

CAC--------AG-CACG------------------CCTCCCAGCAG------CAGCAGCAG-----------C------AGCAACAACAGCA--------GCAG---CAGCA---AC---ACC------A------GCAGCAG---CAGCAA------------CAG---CAGCAGC---ATCCCCA---GCAGCA-----GC----------------------------G-----------------CGGCCTCAAGCGCTCCGGC--AGCGACTGC---TAC------GAGG--ATCACCAC--CGCTCG	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
................................................................................................................................................................................................................................................................................GCGACTGC---TAC------GAGG--ATG.............	18	3	0.33	1	0	0	1	0
................................................................................................................A---AC---ACC------A------GCAGCAG---CAGCAA------------CAG---C..............................................................................................................................................	24	5	0.20	1	0	0	1	0
.........................................................................C------AGCAACAACAGCA--------GCAG---CAG...........................................................................................................................................................................................................	21	20	0.20	4	0	0	4	0
.....................................................................................................GCAG---CAGCA---AC---ACC------A------GCAGCAG---CAGCA..................................................................................................................................................................	27	7	0.14	1	0	0	1	0
............................................................................................A--------GCAG---CAGCA---AC---ACC------A------GCAGCA...........................................................................................................................................................................	22	11	0.09	1	0	0	1	0
................................................................................AGCAACAACAGCA--------GCAG---CAG...........................................................................................................................................................................................................	20	20	0.05	1	0	1	0	0
...........................................................CAG-----------C------AGCAACAACAGCA--------G....................................................................................................................................................................................................................	18	20	0.05	1	0	0	1	0
.................................................................................GCAACAACAGCA--------GCAG---CAGC..........................................................................................................................................................................................................	20	20	0.05	1	0	0	0	1
.........................................................................................AGCA--------GCAG---CAGCA---AC---ACC------A------.................................................................................................................................................................................	19	20	0.05	1	0	0	1	0
.............................................................................................................AGCA---AC---ACC------A------GCAGCAG---CA.....................................................................................................................................................................	19	20	0.05	1	0	0	1	0
.............................................................................................................AGCA---AC---ACC------A------GCAGCAG---C......................................................................................................................................................................	18	20	0.05	1	0	0	1	0
............................................................................................................................................GCAG---CAGCAA------------CAG---CAGCAGC---A....................................................................................................................................	21	20	0.05	1	0	0	1	0
..............................................G------CAGCAGCAG-----------C------AGCAACAACAGC..............................................................................................................................................................................................................................	23	20	0.05	1	0	0	1	0

droYak3

CGCC-------G--CAGGG--------TCACC----T---CCAGCAGCAG---CAGCAGCAG-----------C------AGCAGCAACATCA--------GCAG---CAGCA---TC---AGC------AGTTGCAGCAGCAACATCAGCAA---------CAGCAA---CAGCAGC---AGCAGCA------AC------------------------------------CGAATGCGAACAGCTCCTCGGCGGCATC-------------------------C------AGTGGAGCGGGAAG--CAGCAG	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
..........................................................GCAG-----------C------AGCAGCAACATCA--------GCAG---CA............................................................................................................................................................................................................	24	20	0.05	1	0	0	0	1	0	0	0	0	0	0	0
.................................................................................GCAGCAACATCA--------GCAG---CAGC..........................................................................................................................................................................................................	20	20	0.05	1	0	0	0	0	0	0	1	0	0	0	0
..............................................GCAG---CAGCAGCAG-----------C------AGCAGCAAC.................................................................................................................................................................................................................................	23	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0

droEre2

GCAC-------AA-CATCT-ATGC----------------CCAGCAGCAGCAAC--------AAC---------------AGCAGCAGCAAC-----------AGCATCATCAGCAGCAGCAGC---------------AGCAA---CATCATCACTTC---CACCAC---CAGCAAC---AACAGCA------GCA-----GCAAC----------CACAGTCGCA----------------------------------------TC--ATTCGCACC---ATC------ATGGCCATGGTCAT--GACAAT	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
..............................................................AAC---------------AGCAGCAGCAAC-----------AGC................................................................................................................................................................................................................	18	20	0.15	3	0	0	0	0	0	3	0
....................................................AC--------AAC---------------AGCAGCAGCAAC-----------AGC................................................................................................................................................................................................................	20	20	0.05	1	1	0	0	0	0	0	0
...........................................................................................................TCATCAGCAGCAGCAGC---------------AGC............................................................................................................................................................................	20	20	0.05	1	0	0	0	0	0	1	0
..............................................GCAGCAAC--------AAC---------------AGCAGCAGC.................................................................................................................................................................................................................................	20	20	0.05	1	0	1	0	0	0	0	0
.................................................GCAAC--------AAC---------------AGCAGCAGCAAC-----------A..................................................................................................................................................................................................................	21	20	0.05	1	0	0	0	0	1	0	0
.....................................................C--------AAC---------------AGCAGCAGCAAC-----------AG.................................................................................................................................................................................................................	18	20	0.05	1	0	0	0	0	0	1	0
...................................................AAC--------AAC---------------AGCAGCAGCAAC-----------AG.................................................................................................................................................................................................................	20	20	0.05	1	0	0	0	1	0	0	0

dmo_1209

scaffold_6496:20111731-20111778 +

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

-1.6	-1.5	-1.2