dmo_1953

intron [Dmoj\GI22947-in]; exon [dmoj_GLEANR_8121:2]; CDS [Dmoj\GI22947-cds]; CDS [Dmoj\GI22947-cds]; exon [dmoj_GLEANR_8121:3]

Name	Class	Family	Strand
TART_DV	LINE	Jockey	-
(CTG)n	Simple_repeat	Simple_repeat	+

##################################################------------------------------------------------################################################## AACAGCCCAATGATCTGCTCAGCAGCATCATGCAGGCAGTTGGCATGCAGGTCCAGCAGCAGCAGCAGCAACAACAGCAACAGCATCAACCACAACAGCAACCACAGCAACAATATACAATTACTGTGGATAGTCATGTGCCGGCGCA ************************************************.....((.((....)).)).............................************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M046 female body
.......................................ATGGAATGCAGGTCCAGC...........................................................................................	18	2	7	0.14	1	1
..................................................................AGCAACAACAGCAACAGCAT..............................................................	20	0	8	0.13	1	1
..............................................................................................ACAGCAACCACAGCAACA....................................	18	0	10	0.10	1	1
............................................................AGCAGCAGCAACAACAGCA.....................................................................	19	0	20	0.05	1	1

TTGTCGGGTTACTAGACGAGTCGTCGTAGTACGTCCGTCAACCGTACGTCCAGGTCGTCGTCGTCGTCGTTGTTGTCGTTGTCGTAGTTGGTGTTGTCGTTGGTGTCGTTGTTATATGTTAATGACACCTATCAGTACACGGCCGCGT ************************************************.....((.((....)).)).............................************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M060 embryo	V056 head	M046 female body
......................................................................................................................TTACTCACACCTATCAGT............	18	2	6	1.50	9	8	0	1
............................................................................................................TTGTTCTATGTGAACGACACC...................	21	3	1	1.00	1	0	1	0
...................................................................................................TTGGTCTCTTTGTTATACGTT............................	21	3	20	0.05	1	0	1	0

Species	Coordinate	ID	Alignment
droMoj3	scaffold_6540:15374506-15374653 -	dmo_1953	AACAGCCCAATGA------TCTGCT--CAGCAGC---ATCATGCAGGCAG---------------TTGGCATG----CA---GGT-------------------------------------------------------CC---AGCAGCA---GCAG---------CAGCAACAACAGCA---------------------ACAGCATCAAC-CA------------------------CAACA------------------GCAACCACAGC-AACAATAT----------------------------------ACAATTA-------------------------------------------------CTGTGGATAGTCATGTGCCGGCGCA
droVir3	scaffold_12970:8194937-8195084 -		AGCAGCA--ACAGCAGCATACTC-----AGCAAC---AAA-------------CAC--------------------------------------------------AGCAGCAG---------------CAGCAGCAGCAAC---AACAACA---GCAG---------CAGCAACAACAGCA---------------------GCAGCAACAGCA-G------------------------CAGCA------------------ACAACAACAAC-AACAACA-----------------------------------GCAATTCGGCTG------CGT---CCAGTTA---------------TAG------------------------CGAGAGCA
droGri2	scaffold_14906:12617935-12618073 +		AACCAAA--TGAT-------CTGCT--TAGCAGC---ATTATGCAGGCTG---------------TGGGCAT-----------------------G---------------CA---------------------------GG---TGCAACA---ACAA---------CAACAACAACAGCC---------------------CCAACATCAGCA-T------------------------CAGCA------------------ACAACCACAGC----AATAC----------------------------------ACAATCA-------------------------------------------------CTGTGGATAGCCACGTGCAGACGCA
droWil2	scf2_1100000004902:726925-727068 +		CTCAGCA--TAATCTGCAACAGCAG--C---AGC---AGC---------------------------------------------------------------------GGCAGCAACAT---------CAGATGCA---GC------AGCA---GCAG---------CAGCAGCAACATCA------------------GCTA---CAGCAGC-AA------------------------CAAAA-----GC----------AGCAGCAGCAGC----ATCAT-----CA---------------------------GTTCCA------------------ACAGTCG-------------------------CAGTCGAGCAA------CTTGTGCC
dp5	XR_group5:526278-526412 -		ACCACCA--ATGAT---GG-CGCCG--CAGCAGC---AGC-----------------------------------AGCA-------------------------------------ACAG---------CA---------GC---AGCAACA---GCAG---------CAGCAACAGCAGCA---------------------GCAGCAGCAGAT-T------------------------CAACA-----GC----------AGCAGCAACAGC----AGCAGCAGAT--------------TC------AACAGCA---------------------ACA---GCAG---------------CAG------------------------CCGATGCT
droPer2	scaffold_6:2893619-2893754 -		AACAGCA--ACAACTACATCCAC-----AACAGC---AGC-----------------------------------GGCAGAA----------------------------------ACAA---------C----------------GCAGCA---GCAACAGCAACAGCAGCAGCAACAGCA---------------------ACAGCAGCAGC-AA------------------------CATCA------------------GCAACAGCAGC----A--------------------------------------ACATGT---ACT------GTT---TCAGCCG---------CAC---TTG------------------------C--ATGCA
droAna3	scaffold_13248:3481151-3481301 -		AACAGCA--GCAG------TCCCAG--C---AGCAGCAG---C----------AACAGCAGGCGGTGGTGCTT-----------------------------CACCAGCAGC------------------------------------AGCA---GCAG---------CAGCAACAACAACA---------------------GCAGCAGCAGC-AACAGAAGCACCAGCA------GCACCAGCA------------------C---------C----AACAGCA-----------------AC------A------GCAGGT---------------CCT---GCAC---------------CAG------------------------CAGGCTCA
droBip1	scf7180000395994:3856-4004 -		AACAACC--TGAT----GG-CACTGCACTACTAC---CTTAAGCATCCAGGGATGCAGCAGGTGCCCATCCC--------------------------------------------------------------------------ACAGCA---GCAG---------CAGCAACAACAACA------------------ACAA---CAGCAGC-AACAGCAC------------------CAGCA------------------ACACCATCAGC----A--------------------------------------GCAGTT---GCT------GGC---CCAGTCG------------------------------------------CAGACGCA
droKik1	scf7180000302695:234299-234444 +		ACAACCACATGAA------CCCCAA--C---ACCACCAA-G-----GT---------------------GCGT-----------------------------CGCCAGCAGCAGCAACA------------------------------GCA---GCAG---------CAGCACCAGCAGCA---------------------GCAGCAACAGCA-A------CAGCAGCA------GCAACAGCA------------------A---------C----AACAGCA--------------------------------ACAGCA---------------GCA---GAAC---------------AACAACAATGCTG--------------TCGCTCAA
droFic1	scf7180000453215:585325-585460 +		AGCAGCA--GCAACATCAGCATC-----AGCAGC---AAC------------------------------------------------------------------------------ATCAGCAGCAACAGCAGCA---ACACCACCAGCA---GCAG---------CAACAGCAACACCA-------------------------------------------------------------CCA-----GC----------AGCAGCAGCAGC----AACAA-----CCGCACCGACAGCA---------------TCAGTTC-------------------------------------------------CTGGAT-----------CCAGCGCA
droEle1	scf7180000491267:84524-84662 -		AACAGCA--TTGG------CCTC-----AGCAGCATTGG---C----------CGC-------------------------A----------------GCAGCATCAGCAGCAGCAACA------------------------------T------------------CAGCCGCAGCAGCATCAGCAGCAGCAACATCAGCCG---CAGCA-------------------------GCATCAGCA------------------G------CAGC----AACA--------------------TC------AGCCGCA---------------------GCA---GCAT---------------AAG------------------------CCGCAGCA
droRho1	scf7180000777093:11169-11304 +		AACATGCCAACCA--A----CTGG-----------------------------------------CCACCGC-GCA----------------------GCA---------A------------------CA------------------GTT---GCAACAGCAACAACAGCAACAACAGCA---------------------GCAGCAGCAGC-AA------------------------CAACA------------------GCAACAGCAGC-AACATCACAT-----------------AGTGATCACCCAGCA---------------------GCA---ACAG---------------GCA------------------------CCGCAGCA
droBia1	scf7180000302136:1402654-1402810 -		AGCAAGC--CCATCACCGGCTCC-----AGCAGG---AGCTCC----------AAGGTCAGGCGGCAGCCG-----------GGTCCATGGTCATGCAGCA---------G------------------CA------------------GCA---ACAA---------CAGCTGCCACAGCC---------------------ACAACAACAGCA-G------------------------CCGCAGCAGC-----------A-A------CAGC----A--------------------------------------ATCACT---GCCGCCTCA---TCC---GCAC---------------CTG------------------------CCACAGCA
droTak1	scf7180000415702:273817-273944 -		AACAACA--CCACTGATAG-CTC-----AGCTGC---CGCCGGCA-------------------------------------------------AC---------------CAG---------------------------------CAGCAGCAGCAG---------CAACACCAGCAGCA---------------------ACAGCAACATCA-G------------------------CAGCACCAGC-----------A-A------CAGC----AACA--------------------------------------GCT---GATGAACGG---GCT---GAGC---------------ATG------------------------TCGCCGCA
droEug1	scf7180000409181:5150-5286 -		ATGGCC-CAGGAA------TCGGAA--C---AGG---AAC-----------------------------------AGCAAGC----------------------------------CCAA---------CAGGCGCA---AC------AGCA---GCAG---------CAGCAGCAACAACA------------------ACAG---CAGCAGC-AG------------------------CAACA------------------G------CAGC----A--------------------------------------ACTGCC---ACA------GAT---CCAAATGCAGTTGCCACAGTCGGTG------------------------CCTAAGGT
dm3	chrX:11666806-11666936 -		ATGGCC-CAGGAA------TCGGAG--C---AGG---AGC-----------------------------------AGCAGGC----------------------------------ACA---------------------GG---CGCAGCA---GCAA---------CAGCAACAACAGCA---------------------GCAGCAGCAGCA-A------------------------CAGCA------------------GCAACAGCAGC-AGCATCAGCA--------------------------------ATTGCC---GCA------AAT---CCAGATG---------------CAG------------------------TTGCCACA
droSim2	x:10675772-10675910 +		AACTGGGCATGGG------TCTGAC--C---AACAGGAA---------------GC-------------------------T----------------GCAGCAGCAACAGCAGCAGCA---------------------------------------T---------CAGCAGCAACAGCAGCAACAACA---------GCAACAG---CA----------C------CAGCAGCAAGTCCAACA-----GC----------AGCAGCAGCAGG----TGCAG-----CC------------------------------------------------------TGTC---------------CAG------------------------CTGGCGCA
droSec2	scaffold_1:7906702-7906833 +		AACAGCA--ACTACTACA-----------ACAGT------------TC----ACGCTGCAGGCGGCGGCAGC-----------------------A---------------CA---------------------------GC---AACAGCA---GCAG---------CAGCAACAACAGCA---------------------CCAGCAACAACA-G------------------------CAGCA------------------GCAACAGCAAGCAACAAGTA----------------------------------GCAATTC-------------------------------------------------CTTGGG-----------CAAGACAT
droYak3	2L:12233794-12233935 -		AAGTGCC--CGTC------TCCCCA--C---AGCAACAG---C----------AAC-------------------------T----------------GCTGCAGCAGCAACAGCAACA------------------------------G------------------CAGCAGCAACAACA------------------GCAG---CAGCAGC-AACAGCTC------------------CTGCA-----GCAACAACAGCA-G---------C----AGCAGCAACT--------------CC------TGCAGCA---------------------GCA---GCAG---------------CTG------------------------CAACAGCA
droEre2	scaffold_4845:12504426-12504580 -		AACAATC--TAAT----GG-CGCTGCACTACTAC---CTGAAGCATCCCGGTATCCAGCAGATGCCCATCCC-----------------------------------ACAGCAGCAAC------------------------------ATCC---GCAG---------CAGCATCAGCATCA---------GCAACAACAGCAA---CACCA-------------------------------CCA------------------GCAGCATCAGC----A--------------------------------------ACAGTT---GTT------GGC---CCAGTCA------------------------------------------CAGACGCA

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droMoj3

AACAGCCCAATGA------TCTGCT--CAGCAGC---ATCATGCAGGCAG---------------TTGGCATG----CA---GGT-------------------------------------------------------CC---AGCAGCA---GCAG---------CAGCAACAACAGCA---------------------ACAGCATCAAC-CA------------------------CAACA------------------GCAACCACAGC-AACAATAT----------------------------------ACAATTA-------------------------------------------------CTGTGGATAGTCATGTGCCGGCGCA	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
.........................................................................................................................................................................AGCAACAACAGCA---------------------ACAGCAT.............................................................................................................................................................................................	20	8	0.13	1	1	0	0	0	0	0
...................................................................................................................................................................................................................................................ACA------------------GCAACCACAGC-AACA.......................................................................................................................	18	10	0.10	1	1	0	0	0	0	0
.......................................................................................................................................................A---GCAG---------CAGCAACAACAGCA---------------------....................................................................................................................................................................................................	19	20	0.05	1	1	0	0	0	0	0

droVir3

AGCAGCA--ACAGCAGCATACTC-----AGCAAC---AAA-------------CAC--------------------------------------------------AGCAGCAG---------------CAGCAGCAGCAAC---AACAACA---GCAG---------CAGCAACAACAGCA---------------------GCAGCAACAGCA-G------------------------CAGCA------------------ACAACAACAAC-AACAACA-----------------------------------GCAATTCGGCTG------CGT---CCAGTTA---------------TAG------------------------CGAGAGCA	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
..................................................................................................................................................................................................................................................................................C-AACAACA-----------------------------------GCAATTCGGCTG------CGT---CC.......................................................	25	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	3
.................................................................................................................................................................................................................................................................................................................................................GT---CCAGTTA---------------TAG------------------------CGAGAGCA	20	1	2.00	2	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................................................................................................................AACA-----------------------------------GCAATTCGGCTG------CGT---CCAGT....................................................	24	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	2
.............................................................................................................................................................................................................................................................................AACAAC-AACAACA-----------------------------------GCAATTCGGCTG------CG.............................................................	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	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
.................................................................................................................................................................................................................................................................................................................................ATTCGGCTG------CGT---CCAGTTA---------------T..................................	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	1	0	0
............................................................................................................................................................................................................................................................................CAACAAC-AACAACA-----------------------------------GCAATTCGGCT......................................................................	25	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	1	0
.................................................................................................................................................................................................................................................................................AC-AACAACA-----------------------------------GCAATTCGGC.......................................................................	19	1	1.00	1	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
...............GCATACTC-----AGCAAC---AAA-------------CAC--------------------------------------------------AGCAGCA..............................................................................................................................................................................................................................................................................................	27	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.................................................................................................................................................................................................................................................................................................................................................GT---CCAGTTA---------------TAG------------------------CGAGAGC.	19	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	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
........................................................................................................................................................................................................................................................................................ACA-----------------------------------GCAATTCGGCTG------CGT---CCAGTTA---------------...................................	25	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	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
.....................................................................................................................................................................................................................................................................................ACAACA-----------------------------------GCAATTCGGCTG------CGT---CCAGTT...................................................	27	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
................................................................................................................................................................................................................................................................................................................................................CGT---CCAGTTA---------------TAG------------------------CGAGAGC.	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	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
...........AGCAGCATACTC-----AGCAAC---A.........................................................................................................................................................................................................................................................................................................................................................................	19	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	1	0	0
................................................................................................................................................................................................................................................................................................................................AATTCGGCTG------CGT---CCAGTT...................................................	19	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
...............................AAC---AAA-------------CAC--------------------------------------------------AGCAGCAG---------------CAGCA.........................................................................................................................................................................................................................................................................	22	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
..............................CAAC---AAA-------------CAC--------------------------------------------------AGCAGCAG---------------CAGCA.........................................................................................................................................................................................................................................................................	23	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
......A--ACAGCAGCATACTC-----AGCAAC---..........................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	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
..................................................................................................................................................................................................................................................................................C-AACAACA-----------------------------------GCAATTCGGCTG------CGT---CCAGT....................................................	28	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
..........................................................................................................................................................................................................................................................................AACAACAAC-AACAACA-----------------------------------GCAATTCGGC.......................................................................	26	1	1.00	1	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
...........AGCAGCATACTC-----AGCAAC---..........................................................................................................................................................................................................................................................................................................................................................................	18	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
...AGCA--ACAGCAGCATACTC-----AGCAAC---A.........................................................................................................................................................................................................................................................................................................................................................................	25	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
......................C-----AGCAAC---AAA-------------CAC--------------------------------------------------AGCAGC...............................................................................................................................................................................................................................................................................................	19	3	0.33	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
.........................................................................................................................................................................AGCAACAACAGCA---------------------GCAGC...............................................................................................................................................................................................	18	20	0.15	3	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	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
...................................................................................................................................GCAGCAGCAAC---AACAACA---GCAG---------C......................................................................................................................................................................................................................................	23	20	0.10	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
...................................................................................................................................GCAGCAGCAAC---AACAACA---GCA.................................................................................................................................................................................................................................................	21	20	0.10	2	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
..................................................................................................................................................ACAACA---GCAG---------CAGCAACAACA............................................................................................................................................................................................................................	21	20	0.10	2	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
......................................AA-------------CAC--------------------------------------------------AGCAGCAG---------------CAGCAGCAG.....................................................................................................................................................................................................................................................................	22	11	0.09	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
......................................AA-------------CAC--------------------------------------------------AGCAGCAG---------------CAGCAGCAGC....................................................................................................................................................................................................................................................................	23	11	0.09	1	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
............................................................................................................................................................................................................CAGCAACAGCA-G------------------------CAGCA------------------ACA....................................................................................................................................	20	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
...............................................................................................................................................................................AACAGCA---------------------GCAGCAACAGCA-G------------------------CAGC..........................................................................................................................................................	24	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.............................................................................................................................................................AG---------CAGCAACAACAGCA---------------------GCAGC...............................................................................................................................................................................................	21	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.............................................................................................................................................C---AACAACA---GCAG---------CAGCAACAACAGCA---------------------GCA.................................................................................................................................................................................................	29	20	0.05	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
........................................................................................................................................................................................................................G------------------------CAGCA------------------ACAACAACAAC-AACAACA-----------------------------------GC...............................................................................	26	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
.................................................................................................................................................AACAACA---GCAG---------CAGCAACAACAGC..........................................................................................................................................................................................................................	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	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
..............................................................................................................................................................G---------CAGCAACAACAGCA---------------------GCAGC...............................................................................................................................................................................................	20	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
......................................................AC--------------------------------------------------AGCAGCAG---------------CAGCAGCAGCAAC---..............................................................................................................................................................................................................................................................	23	20	0.05	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................AGCA-G------------------------CAGCA------------------ACAACAACAA.............................................................................................................................	20	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
...............................................................................................................CAG---------------CAGCAGCAGCAAC---AACA..........................................................................................................................................................................................................................................................	20	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
...................................................................................................................................................................................................................AGCA-G------------------------CAGCA------------------ACAACAACAAC-...........................................................................................................................	21	20	0.05	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...............................................................................................................................................................................................................CAACAGCA-G------------------------CAGCA------------------ACAAC..................................................................................................................................	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	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
..........................................................................................................................................CAAC---AACAACA---GCAG---------CAGCAA.................................................................................................................................................................................................................................	21	20	0.05	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droGri2

AACCAAA--TGAT-------CTGCT--TAGCAGC---ATTATGCAGGCTG---------------TGGGCAT-----------------------G---------------CA---------------------------GG---TGCAACA---ACAA---------CAACAACAACAGCC---------------------CCAACATCAGCA-T------------------------CAGCA------------------ACAACCACAGC----AATAC----------------------------------ACAATCA-------------------------------------------------CTGTGGATAGCCACGTGCAGACGCA	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

droWil2

CTCAGCA--TAATCTGCAACAGCAG--C---AGC---AGC---------------------------------------------------------------------GGCAGCAACAT---------CAGATGCA---GC------AGCA---GCAG---------CAGCAGCAACATCA------------------GCTA---CAGCAGC-AA------------------------CAAAA-----GC----------AGCAGCAGCAGC----ATCAT-----CA---------------------------GTTCCA------------------ACAGTCG-------------------------CAGTCGAGCAA------CTTGTGCC	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
...................................................................................................................................................................................................................AGC-AA------------------------CAAAA-----GC----------AGCAGC..................................................................................................................................	18	6	0.33	2	0	1	0	1	0
...................................................................................................................................................................................................................AGC-AA------------------------CAAAA-----GC----------AGCAGCA.................................................................................................................................	19	5	0.20	1	0	0	0	1	0
.................................................................................................................................CAGATGCA---GC------AGCA---GCAG---------CA.....................................................................................................................................................................................................................................	20	8	0.13	1	0	0	0	1	0
.....................................................................................................................................................................................................................C-AA------------------------CAAAA-----GC----------AGCAGCAG................................................................................................................................	18	16	0.06	1	0	1	0	0	0
.............................................................................................................................................C------AGCA---GCAG---------CAGCAGCAACATC..........................................................................................................................................................................................................................	22	20	0.05	1	0	0	0	1	0
..................................................................................................................................................................................................................................................AAAA-----GC----------AGCAGCAGCAGC----A.......................................................................................................................	19	20	0.05	1	0	0	1	0	0

dp5

ACCACCA--ATGAT---GG-CGCCG--CAGCAGC---AGC-----------------------------------AGCA-------------------------------------ACAG---------CA---------GC---AGCAACA---GCAG---------CAGCAACAGCAGCA---------------------GCAGCAGCAGAT-T------------------------CAACA-----GC----------AGCAGCAACAGC----AGCAGCAGAT--------------TC------AACAGCA---------------------ACA---GCAG---------------CAG------------------------CCGATGCT	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
........................................................................................................................................................................................................................................................................................GCAGCAGAT--------------TC------AACAGCA---------------------............................................................	18	4	0.50	2	0	0	0	0	2	0	0	0	0	0
..................................................................................................................................................................................................................................................................................C----AGCAGCAGAT--------------TC------AACAGCA---------------------ACA---G.....................................................	24	2	0.50	1	0	1	0	0	0	0	0	0	0	0
..............................................................................................................................................................................................................GCAGCAGAT-T------------------------CAACA-----GC----------A.......................................................................................................................................	18	4	0.50	2	0	0	0	0	2	0	0	0	0	0
...........................................................................................................................................................GCAG---------CAGCAACAGCAGCA---------------------GCAGC...............................................................................................................................................................................................	23	20	0.10	2	0	2	0	0	0	0	0	0	0	0
.............................GCAGC---AGC-----------------------------------AGCA-------------------------------------ACAG---------CA---------GC---..............................................................................................................................................................................................................................................................	20	20	0.10	2	0	2	0	0	0	0	0	0	0	0
..............................CAGC---AGC-----------------------------------AGCA-------------------------------------ACAG---------CA---------GC---AG............................................................................................................................................................................................................................................................	21	20	0.10	2	0	2	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................................AACA-----GC----------AGCAGCAACAGC----AGCA....................................................................................................................	22	20	0.05	1	0	0	0	0	1	0	0	0	0	0
.................................................................................................................................................AGCAACA---GCAG---------CAGCAACAGCA............................................................................................................................................................................................................................	22	20	0.05	1	0	0	0	0	0	0	0	0	0	1
............................................................................................................................................GC---AGCAACA---GCAG---------CAGCAACAGCAGCA---------------------....................................................................................................................................................................................................	27	20	0.05	1	0	1	0	0	0	0	0	0	0	0
........................................................................................................................................................................CAGCAACAGCAGCA---------------------GCAGCAGC............................................................................................................................................................................................	22	20	0.05	1	0	0	0	0	0	0	0	0	1	0
......................................GC-----------------------------------AGCA-------------------------------------ACAG---------CA---------GC---AGCAACA---GCAG---------CA.....................................................................................................................................................................................................................................	27	20	0.05	1	0	1	0	0	0	0	0	0	0	0
..................................................................................................................................................GCAACA---GCAG---------CAGCAACAGCA............................................................................................................................................................................................................................	21	20	0.05	1	0	1	0	0	0	0	0	0	0	0
......................................GC-----------------------------------AGCA-------------------------------------ACAG---------CA---------GC---AGCAACA---GCA.................................................................................................................................................................................................................................................	24	20	0.05	1	0	0	0	0	0	0	0	0	0	1
....................................................................................................................................................AACA---GCAG---------CAGCAACAGCAGCA---------------------....................................................................................................................................................................................................	22	20	0.05	1	0	0	0	0	1	0	0	0	0	0
..............................................................................A-------------------------------------ACAG---------CA---------GC---AGCAACA---GCAG---------CA.....................................................................................................................................................................................................................................	22	20	0.05	1	0	0	0	0	1	0	0	0	0	0

droPer2

AACAGCA--ACAACTACATCCAC-----AACAGC---AGC-----------------------------------GGCAGAA----------------------------------ACAA---------C----------------GCAGCA---GCAACAGCAACAGCAGCAGCAACAGCA---------------------ACAGCAGCAGC-AA------------------------CATCA------------------GCAACAGCAGC----A--------------------------------------ACATGT---ACT------GTT---TCAGCCG---------CAC---TTG------------------------C--ATGCA	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
.....................................................................................................................CAA---------C----------------GCAGCA---GCAACAGCA...........................................................................................................................................................................................................................................	19	2	1.50	3	0	0	3	0	0	0
..................................................................................................................................................................................................................................................ATCA------------------GCAACAGCAGC----A--------------------------------------ACAT.............................................................................	20	1	1.00	1	0	0	1	0	0	0
.................................................................................................................................C----------------GCAGCA---GCAACAGCAACAGCA.....................................................................................................................................................................................................................................	22	5	0.20	1	0	1	0	0	0	0
............................................................................................................................................................CAACAGCAACAGCAGCAGC................................................................................................................................................................................................................................	19	20	0.05	1	0	0	1	0	0	0

droAna3

AACAGCA--GCAG------TCCCAG--C---AGCAGCAG---C----------AACAGCAGGCGGTGGTGCTT-----------------------------CACCAGCAGC------------------------------------AGCA---GCAG---------CAGCAACAACAACA---------------------GCAGCAGCAGC-AACAGAAGCACCAGCA------GCACCAGCA------------------C---------C----AACAGCA-----------------AC------A------GCAGGT---------------CCT---GCAC---------------CAG------------------------CAGGCTCA	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
................................................................................................................................................................................................................................ACCAGCA------GCACCAGCA------------------C---------C----AAC.....................................................................................................................	21	1	1.00	1	0	1	0	0	0	0
......................................G---C----------AACAGCAGGCGGTGGTGC........................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0
...................................GCAG---C----------AACAGCAGGCGGT.............................................................................................................................................................................................................................................................................................................................................	18	3	0.33	1	1	0	0	0	0	0
................................GCAGCAG---C----------AACAGCAGGCGG..............................................................................................................................................................................................................................................................................................................................................	20	3	0.33	1	1	0	0	0	0	0
..................................AGCAG---C----------AACAGCAGGCGG..............................................................................................................................................................................................................................................................................................................................................	18	4	0.25	1	0	0	0	1	0	0
.......................AG--C---AGCAGCAG---C----------AACAGCAGG.................................................................................................................................................................................................................................................................................................................................................	21	10	0.10	1	0	1	0	0	0	0
......................................................................................................CACCAGCAGC------------------------------------AGCA---GCAG---------CAGCAAC................................................................................................................................................................................................................................	25	14	0.07	1	0	1	0	0	0	0
........................................................................T-----------------------------CACCAGCAGC------------------------------------AGCA---GCAG---------CAGC...................................................................................................................................................................................................................................	23	15	0.07	1	0	1	0	0	0	0
...........................................................................................................................................................GCAG---------CAGCAACAACAACA---------------------GCAGCAGCAGC-........................................................................................................................................................................................	29	17	0.06	1	0	1	0	0	0	0
.......................................................................................................ACCAGCAGC------------------------------------AGCA---GCAG---------CAGCAAC................................................................................................................................................................................................................................	24	19	0.05	1	1	0	0	0	0	0
............................................................................................................................................................................AACAACAACA---------------------GCAGCAGCAGC-AAC.....................................................................................................................................................................................	24	20	0.05	1	0	1	0	0	0	0
..............................................................................................................................................................G---------CAGCAACAACAACA---------------------GCAGCAGC............................................................................................................................................................................................	23	20	0.05	1	0	1	0	0	0	0
......................................................................................................CACCAGCAGC------------------------------------AGCA---GCAG---------CAGC...................................................................................................................................................................................................................................	22	20	0.05	1	0	1	0	0	0	0
........................................................................T-----------------------------CACCAGCAGC------------------------------------AGCA---GCAG---------CA.....................................................................................................................................................................................................................................	21	20	0.05	1	0	0	0	0	1	0
..........................................................................................................................................................................GCAACAACAACA---------------------GCAGCAGCAGC-........................................................................................................................................................................................	23	20	0.05	1	0	1	0	0	0	0
.....................................................................................................................................................GCA---GCAG---------CAGCAACAACAACA---------------------GCA.................................................................................................................................................................................................	24	20	0.05	1	0	1	0	0	0	0
........................................................................................................................................................................CAGCAACAACAACA---------------------GCAGCAGC............................................................................................................................................................................................	22	20	0.05	1	1	0	0	0	0	0
...........................................................................................................................................................................CAACAACAACA---------------------GCAGCAGCAGC-AAC.....................................................................................................................................................................................	25	20	0.05	1	0	1	0	0	0	0
.......................................................................................................................................................A---GCAG---------CAGCAACAACAAC..........................................................................................................................................................................................................................	18	20	0.05	1	0	1	0	0	0	0
....................................................................................................................................................AGCA---GCAG---------CAGCAACAACAACA---------------------GC..................................................................................................................................................................................................	24	20	0.05	1	0	1	0	0	0	0
.....................................................................................................................................................................................A---------------------GCAGCAGCAGC-AACAGAA.................................................................................................................................................................................	19	20	0.05	1	0	1	0	0	0	0
......................................................................................................CACCAGCAGC------------------------------------AGCA---GCAG---------CAGCA..................................................................................................................................................................................................................................	23	20	0.05	1	1	0	0	0	0	0
..........................................................................................................................................................................GCAACAACAACA---------------------GCAGCAGCAGC-A.......................................................................................................................................................................................	24	20	0.05	1	0	0	0	0	0	1

droBip1

AACAACC--TGAT----GG-CACTGCACTACTAC---CTTAAGCATCCAGGGATGCAGCAGGTGCCCATCCC--------------------------------------------------------------------------ACAGCA---GCAG---------CAGCAACAACAACA------------------ACAA---CAGCAGC-AACAGCAC------------------CAGCA------------------ACACCATCAGC----A--------------------------------------GCAGTT---GCT------GGC---CCAGTCG------------------------------------------CAGACGCA	Size	Hit Count	Total Norm	Total
No Reads

droKik1

ACAACCACATGAA------CCCCAA--C---ACCACCAA-G-----GT---------------------GCGT-----------------------------CGCCAGCAGCAGCAACA------------------------------GCA---GCAG---------CAGCACCAGCAGCA---------------------GCAGCAACAGCA-A------CAGCAGCA------GCAACAGCA------------------A---------C----AACAGCA--------------------------------ACAGCA---------------GCA---GAAC---------------AACAACAATGCTG--------------TCGCTCAA	Size	Hit Count	Total Norm	Total
No Reads

droFic1

AGCAGCA--GCAACATCAGCATC-----AGCAGC---AAC------------------------------------------------------------------------------ATCAGCAGCAACAGCAGCA---ACACCACCAGCA---GCAG---------CAACAGCAACACCA-------------------------------------------------------------CCA-----GC----------AGCAGCAGCAGC----AACAA-----CCGCACCGACAGCA---------------TCAGTTC-------------------------------------------------CTGGAT-----------CCAGCGCA	Size	Hit Count	Total Norm	Total
No Reads

droEle1

AACAGCA--TTGG------CCTC-----AGCAGCATTGG---C----------CGC-------------------------A----------------GCAGCATCAGCAGCAGCAACA------------------------------T------------------CAGCCGCAGCAGCATCAGCAGCAGCAACATCAGCCG---CAGCA-------------------------GCATCAGCA------------------G------CAGC----AACA--------------------TC------AGCCGCA---------------------GCA---GCAT---------------AAG------------------------CCGCAGCA	Size	Hit Count	Total Norm	Total
No Reads

droRho1

AACATGCCAACCA--A----CTGG-----------------------------------------CCACCGC-GCA----------------------GCA---------A------------------CA------------------GTT---GCAACAGCAACAACAGCAACAACAGCA---------------------GCAGCAGCAGC-AA------------------------CAACA------------------GCAACAGCAGC-AACATCACAT-----------------AGTGATCACCCAGCA---------------------GCA---ACAG---------------GCA------------------------CCGCAGCA	Size	Hit Count	Total Norm	Total
No Reads

droBia1

AGCAAGC--CCATCACCGGCTCC-----AGCAGG---AGCTCC----------AAGGTCAGGCGGCAGCCG-----------GGTCCATGGTCATGCAGCA---------G------------------CA------------------GCA---ACAA---------CAGCTGCCACAGCC---------------------ACAACAACAGCA-G------------------------CCGCAGCAGC-----------A-A------CAGC----A--------------------------------------ATCACT---GCCGCCTCA---TCC---GCAC---------------CTG------------------------CCACAGCA	Size	Hit Count	Total Norm	Total
No Reads

droTak1

AACAACA--CCACTGATAG-CTC-----AGCTGC---CGCCGGCA-------------------------------------------------AC---------------CAG---------------------------------CAGCAGCAGCAG---------CAACACCAGCAGCA---------------------ACAGCAACATCA-G------------------------CAGCACCAGC-----------A-A------CAGC----AACA--------------------------------------GCT---GATGAACGG---GCT---GAGC---------------ATG------------------------TCGCCGCA	Size	Hit Count	Total Norm	Total
No Reads

droEug1

ATGGCC-CAGGAA------TCGGAA--C---AGG---AAC-----------------------------------AGCAAGC----------------------------------CCAA---------CAGGCGCA---AC------AGCA---GCAG---------CAGCAGCAACAACA------------------ACAG---CAGCAGC-AG------------------------CAACA------------------G------CAGC----A--------------------------------------ACTGCC---ACA------GAT---CCAAATGCAGTTGCCACAGTCGGTG------------------------CCTAAGGT	Size	Hit Count	Total Norm	Total
No Reads

dm3

ATGGCC-CAGGAA------TCGGAG--C---AGG---AGC-----------------------------------AGCAGGC----------------------------------ACA---------------------GG---CGCAGCA---GCAA---------CAGCAACAACAGCA---------------------GCAGCAGCAGCA-A------------------------CAGCA------------------GCAACAGCAGC-AGCATCAGCA--------------------------------ATTGCC---GCA------AAT---CCAGATG---------------CAG------------------------TTGCCACA	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
......................................................................................................................................................................................................................A-A------------------------CAGCA------------------GCAACAGCAGC-AGCATC.....................................................................................................................	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
.................................................................................................................................................CGCAGCA---GCAA---------CAGCAACAAC.............................................................................................................................................................................................................................	21	3	0.33	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
..............................................................................................................................................................A---------CAGCAACAACAGCA---------------------GCAGCAGCAGCA-A------------------------C.............................................................................................................................................................	29	4	0.25	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	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
...................................................................................................................................................................................................................................................GCA------------------GCAACAGCAGC-AGCATCAGCA--------------------------------.................................................................................	24	5	0.20	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
.................................................................................................................................................................................................................................................CAGCA------------------GCAACAGCAGC-AGCAT......................................................................................................................	21	13	0.15	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	1	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
.............................................................................................................................................................AA---------CAGCAACAACAGCA---------------------GCAGC...............................................................................................................................................................................................	21	20	0.15	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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.................................................................................................................................................................................CAGCA---------------------GCAGCAGCAGCA-A------------------------CAG...........................................................................................................................................................	21	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
................................................................................................................................................................................ACAGCA---------------------GCAGCAGCAGCA-A------------------------C.............................................................................................................................................................	20	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
................................................................................................................................................................................................................AGCAGCA-A------------------------CAGCA------------------GCAACAGC...............................................................................................................................	21	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
.............................................................................................................................................................................ACAACAGCA---------------------GCAGCAGCAGCA-A------------------------..............................................................................................................................................................	22	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	0	0	0	0	0	0	0	0	0	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---------CAGCAACAACAGCA---------------------GCAGCA..............................................................................................................................................................................................	21	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
............................................................................................................................................................CAA---------CAGCAACAACAGCA---------------------GCAGCA..............................................................................................................................................................................................	23	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
............................................................................................................................................................CAA---------CAGCAACAACAGCA---------------------GCA.................................................................................................................................................................................................	20	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
.............................................................................................................................................................................................................AGCAGCAGCA-A------------------------CAGCA------------------GCAACAG................................................................................................................................	23	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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

droSim2

AACTGGGCATGGG------TCTGAC--C---AACAGGAA---------------GC-------------------------T----------------GCAGCAGCAACAGCAGCAGCA---------------------------------------T---------CAGCAGCAACAGCAGCAACAACA---------GCAACAG---CA----------C------CAGCAGCAAGTCCAACA-----GC----------AGCAGCAGCAGG----TGCAG-----CC------------------------------------------------------TGTC---------------CAG------------------------CTGGCGCA	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
...TGGGCATGGG------TCTGAC--C---AACAGGAA---------------GC-------------------------..............................................................................................................................................................................................................................................................................................................................	27	1	2.00	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0
.................................................................................T----------------GCAGCAGCAACAGCAGCAGC.........................................................................................................................................................................................................................................................................................	21	20	1.45	29	0	0	0	0	0	29	0	0	0	0	0	0	0	0	0	0	0
....................................................................................................AGCAGCAACAGCAGCAGCA---------------------------------------T---------C......................................................................................................................................................................................................................................	21	19	1.05	20	0	0	0	0	0	20	0	0	0	0	0	0	0	0	0	0	0
...............................AACAGGAA---------------GC-------------------------T----------------GCAGCAGCA....................................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
AACTGGGCATGGG------TCTGAC--C---................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
AACTGGGCATGGG------TCTGAC--C---AACAGGA.........................................................................................................................................................................................................................................................................................................................................................................	27	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
.....................................................................................................................................................................................AGCAACAACA---------GCAACAG---CA----------C------..........................................................................................................................................................................	20	3	0.67	2	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0
..............................................................................................................................................................T---------CAGCAGCAACAGCA.........................................................................................................................................................................................................................	15	20	0.05	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
.............................................................................................................................................................................GCAACAGCAGCAACAACA---------.......................................................................................................................................................................................................	18	20	0.05	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0

droSec2

AACAGCA--ACTACTACA-----------ACAGT------------TC----ACGCTGCAGGCGGCGGCAGC-----------------------A---------------CA---------------------------GC---AACAGCA---GCAG---------CAGCAACAACAGCA---------------------CCAGCAACAACA-G------------------------CAGCA------------------GCAACAGCAAGCAACAAGTA----------------------------------GCAATTC-------------------------------------------------CTTGGG-----------CAAGACAT	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
................................................................................................................A---------------------------GC---AACAGCA---GCAG---------CAGCA..................................................................................................................................................................................................................................	19	20	0.15	3	0	0	0	3
....................................................................................................................................................AGCA---GCAG---------CAGCAACAACAGC..........................................................................................................................................................................................................................	21	20	0.05	1	0	0	1	0
.......................................................................................................................................................A---GCAG---------CAGCAACAACAGCA---------------------....................................................................................................................................................................................................	19	20	0.05	1	0	0	1	0
..................................................................................................................................................................................................................CAACA-G------------------------CAGCA------------------GCAACAGCA..............................................................................................................................	20	20	0.05	1	0	0	1	0
.................................................................................................................................................................................................................ACAACA-G------------------------CAGCA------------------GCAACAG................................................................................................................................	19	20	0.05	1	0	0	1	0

droYak3

AAGTGCC--CGTC------TCCCCA--C---AGCAACAG---C----------AAC-------------------------T----------------GCTGCAGCAGCAACAGCAACA------------------------------G------------------CAGCAGCAACAACA------------------GCAG---CAGCAGC-AACAGCTC------------------CTGCA-----GCAACAACAGCA-G---------C----AGCAGCAACT--------------CC------TGCAGCA---------------------GCA---GCAG---------------CTG------------------------CAACAGCA	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
..........................................................................................................................................................................................................................................................................................AGCAACT--------------CC------TGCAGCA---------------------GCA---GCAG---------------C..................................	24	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................................................GCA-G---------C----AGCAGCAACT--------------CC------TGCAGCA---------------------............................................................	24	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
.AGTGCC--CGTC------TCCCCA--C---AGCAACAG---C----------AAC-------------------------..............................................................................................................................................................................................................................................................................................................................	29	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
...................................ACAG---C----------AAC-------------------------T----------------GCTGCAGCAGCA.................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
.............................................................................................................................................................................................................................................................AACAACAGCA-G---------C----AGCAGCA.................................................................................................................	19	20	0.15	3	0	3	0	0	0	0	0	0	0	0	0
............................................................................................................................................................................AGCAACAACA------------------GCAG---CAGCAGC-AACAGC..................................................................................................................................................................................	27	17	0.06	1	0	0	1	0	0	0	0	0	0	0	0
........................................................................................................GCAGCAACAGCAACA------------------------------G------------------CAGCAGC................................................................................................................................................................................................................................	23	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
.....................................................................................................GCAGCAGCAACAGCAACA------------------------------G------------------CAGCAGCA...............................................................................................................................................................................................................................	27	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
............................................................................................................CAACAGCAACA------------------------------G------------------CAGCAGC................................................................................................................................................................................................................................	19	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
...................................................................................................................AACA------------------------------G------------------CAGCAGCAACAACA------------------GCAG---CA..............................................................................................................................................................................................	25	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0

droEre2

AACAATC--TAAT----GG-CGCTGCACTACTAC---CTGAAGCATCCCGGTATCCAGCAGATGCCCATCCC-----------------------------------ACAGCAGCAAC------------------------------ATCC---GCAG---------CAGCATCAGCATCA---------GCAACAACAGCAA---CACCA-------------------------------CCA------------------GCAGCATCAGC----A--------------------------------------ACAGTT---GTT------GGC---CCAGTCA------------------------------------------CAGACGCA	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
.......................................................................................................................................................................................................................................................................................................................................GTT------GGC---CCAGTCA------------------------------------------CAGACGC.	20	1	3.00	3	0	0	0	0	2	1	0
.............................ACTAC---CTGAAGCATCCCGGT...........................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	0	0	0	1	0	0
................................................................................................................AGCAAC------------------------------ATCC---GCAG---------CAGCATCAGCA............................................................................................................................................................................................................................	25	1	1.00	1	0	0	0	0	0	1	0
.......................................................................................................................................................................................................................................................................................A--------------------------------------ACAGTT---GTT------GGC---CCAGTC...................................................	19	1	1.00	1	0	0	0	0	1	0	0
.................................................................................................................................................................................................AACAACAGCAA---CACCA-------------------------------CCA------------------GC.....................................................................................................................................	21	1	1.00	1	0	1	0	0	0	0	0
.............................................................................................................................................................AG---------CAGCATCAGCATCA---------GCAACAACAGC.....................................................................................................................................................................................................	27	1	1.00	1	1	0	0	0	0	0	0
.................................................................................................................GCAAC------------------------------ATCC---GCAG---------CAGCATCAGCATC..........................................................................................................................................................................................................................	26	1	1.00	1	1	0	0	0	0	0	0
...........................................................................................................................................................................................................................................................................GCATCAGC----A--------------------------------------ACAGTT---GTT------GGC---CCAGTCA------------------------------------------C.......	29	1	1.00	1	0	1	0	0	0	0	0
...................................................................................................................AAC------------------------------ATCC---GCAG---------CAGCATCAGCA............................................................................................................................................................................................................................	22	1	1.00	1	1	0	0	0	0	0	0
...........................................................................................................................................................GCAG---------CAGCATCAGCATCA---------GC..............................................................................................................................................................................................................	20	20	0.05	1	1	0	0	0	0	0	0
...........................................................................................................................................................GCAG---------CAGCATCAGCATCA---------GCA.............................................................................................................................................................................................................	21	20	0.05	1	0	0	0	0	1	0	0

dmo_1953

scaffold_6540:15374556-15374603 -

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

-3.3	-2.5