dmo_1527

exon [dmoj_GLEANR_1188:7]; CDS [Dmoj\GI11813-cds]; CDS [Dmoj\GI11813-cds]; exon [dmoj_GLEANR_1188:6]; intron [Dmoj\GI11813-in]

Name	Class	Family	Strand
(CTG)n	Simple_repeat	Simple_repeat	+

##################################################------------------------------------------------------------################################################## TCGTTGTGCAGCAACTGCAGCAACAAGGAGAATTCGCTCAATAGCTCGCAGCAGTTTTATCACAACAGCAGCGGCAGCAACAACAGCAACAGCAGCAGCAGCGGCAGCAGCAGCAGCAACAGCTCCTTCAATACATCCTGTGAGCTGAACAACAGCTTGT ************************************************.................((.((.((.((.......((....))....)).)).)).))..************************************************	Read size	Hit Count	Total Norm	Total	M046 female body
..................................................................................ACAGCAACAGCAGCAGCAGCG.........................................................	21	20	0.10	2	2
...................................................................................................AGCGGCAGCAGCAGCAGCAACAG......................................	23	14	0.07	1	1
................................................................................CAACAGCAACAGCAGCAGCAGCGG........................................................	24	19	0.05	1	1
...........................................................................AGCAACAACAGCAACAGCAGCAG..............................................................	23	20	0.05	1	1

AGCAACACGTCGTTGACGTCGTTGTTCCTCTTAAGCGAGTTATCGAGCGTCGTCAAAATAGTGTTGTCGTCGCCGTCGTTGTTGTCGTTGTCGTCGTCGTCGCCGTCGTCGTCGTCGTTGTCGAGGAAGTTATGTAGGACACTCGACTTGTTGTCGAACA ************************************************.................((.((.((.((.......((....))....)).)).)).))..************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M060 embryo	V110 male body
.......................................................................................................CGTCGGCGTCGTCGTTGTCGAGG..................................	23	1	7	0.14	1	1	0
.......................................................................GCCGTCGTTGTTGTCGTTG......................................................................	19	0	10	0.10	1	0	1

Species	Coordinate	ID	Alignment
droMoj3	scaffold_6500:12520011-12520170 -	dmo_1527	TCGTTGTG-------------------------------CAGCAA---------------------------------------CTGCAGCAACAAGGAGAATTCGC-TCAATAGCTC-----GCAGCAGTTTTATCA-CA-------------------------ACAGCAG---------------CGGCAGCAACAACAGCAACAGCAGCAG---CAGCGGCAGCAGCAGCAG---CAA---CAGCTCCTTCAATAC-------------AT------CCTGT------GAG-------------CTGAACAA------------------CAGCTTGT
droVir3	scaffold_12928:2241091-2241249 -		G--------------------------------------CAGCAG---------------------------------------CTGCAGCACCATCAGCA----GCATCTGCAGCAACAACAGCA------GCAGCTTCA-------------------------TCAGCAG---------------CTTCAGCAGCATCAGCAACAGCAGCAT---CAGCAACAACAGCAGCAG---CAA---CAGCAG------CAA----------------------------------CAGCA------A-CAGCAGCAACATCAGCTGCCACAGCCGCCACCAGT
droGri2	scaffold_15112:5104715-5104849 -		G--------------------------------------CAGCAT---------------------------------------CGGCAGCAGCAGCAGCA----TCAGCAGCAGCAGCAGCAGCG------TCAACATCA-------------------------GCAGCAG---------------CAGCAGCAGCAGCTA---------------AAACAACAGCAGCAGCAA---AAA---CAGCAGCAGCAGCAG----------------------------------TCAAA------A-CAACAGCAG------------------CAACAGCT
droWil2	scf2_1100000004511:5972459-5972617 +		TGCT-GTA-------------------------------CAACAACAACAGCATGGACAACATT------TGGTTGCTGCCGCG--GCAGCAGC-TGC----------------CCATCATCA---------------ACA-------------------------ACAACAG------------------CAGCAGGTACAGGTGCAACAGCAG---CAGCAACAGCATCAACAG---CAA---CAGCACCAGCAGCAAC-------------------------ATC------A---------T-CATCATCAA------------------CAGCAAGT
dp5	XR_group6:12702138-12702287 +		G--------------------------------------CAGCAA---------------------------------------CAGCAGCAGCAACAGCA----GCAGCAGCATCAGCAACATCA------GCAGCAAAA-------------------------GCATCAG---------------CAACAGCAGCAGCAGCAGCAGCATAAGCAGCAG---CAACAGCATCAGCAACAA---CAACAGCTGCAGCAA----------------------------------CAAAA------A-CATCAGCAA------------------CAGCAGCT
droPer2	scaffold_30:535208-535348 -		G--------------------------------------CAGCAA---------------------------------------CAGCAGCACCAGCAGTC----GGAGCTGCACCATCACCTGCA------GCA-------------------------------GCAGCAG---------------CAGCACCACCAGCAGCAACAGCACCAG---CAGCAGCAGCAGCACCAG---CAA---CAACAGCTGGAGGAT----------------------------------GCCCT------T-GAGGAGCAG------------------CAGCTGGC
droAna3	scaffold_12929:976911-977059 +		---------------------------------------CAGCAG---------------------------------------CAGCAGCAACAGCAACA----GTTGCAACAACAGCTG------------CAACAGCA-------------------------ACAGCAG---------------CAACTGCAACAACAGCAACTCCAGCAG---CAGCAGCAGCAGCAGCAG---CAA---CAACAGCAACAGCAA-------------ATGGTGGTGCC--ACCAG-----------------CTCCACCA------------------CAACCTGC
droBip1	scf7180000395567:7267-7412 -		G--------------------------------------CAGCAA---------------------------------------CAACAGCAGCAACATCA----GCTGCAACAGCACCAGCAACA------GTT---ACA-------------------------ACACCAG---------------CAGCAGCAGCAACAGCAACAGCACCTGCACCAG---CAACAGCTTCAG---CCGCACCAGCAGCAAATGCAA----------------------------------CACCA------C-CAGCAGCAA------------------CAACA-GC
droKik1	scf7180000302392:150320-150462 +		TTTTGCAG----------TTGG-------ATTA------TAGCAA---------------------------------------CAAGGATAATAATAATA-------GCAACAGCAGTAG------------TACCGGCA-------------------------ACAACAG---------------CAGCAGCAACAACAACAACAATAATAA---TAACAACAGCAGCAGCAA---CAA---CAACATCAATCGTGA----------------------------------G-------------CGAAACAA------------------CA----GC
droFic1	scf7180000453277:208326-208483 -		GTT--GCACAGCCTGCAGACGCAAACCAAATTGCTCAAGCAGCAA---------------------------------------CAGGAGCAGCAATTGCT----ATTGCAACAACAGCAG----------------------------------------------------------------------CAGCAGCAACAGCTGCACCAACAG---CAGCAGCAACAGCAGCAG---CAT---CATCACCAGCATCATC-------------------------ACCAGCATCATC-------------AACAA------------------CA----GC
droEle1	scf7180000491255:2474594-2474731 -		G--------------------------------------CAACAA---------------------------------------CAGCAGCAGCAACAACA-------ACAACAGCAGCAG------------CAACAACA-------------------------ACAACAG---------------CAGCAGCAACAACAACAGCAGCAGCAA---CAACAACAGCAGCAGCAA---CAA---CAGCAGCAACAACAA----------------------------------GTCTT------G-GCTCAGCAA------------------CAACCTCA
droRho1	scf7180000779976:80176-80329 +		TCCTCCTT-------------------------------CAGCAG---------------------------------------------CAGCAGCAGCA----ACAGCAACTCCAGCAGCAACA------ATTGCAGCA-------------------------GCAACAA---------------TTGCAGCAACAGCAACTTCAGCAGCAGCAACAGCAACTCCAGCAGCAG---CAA---CAGCTG------CA-------------------------------------CCT------C-CAACAGCTGCAGCAGCAATC------GCAGATGGT
droBia1	scf7180000302402:6519733-6519888 +		CCATCCAG-------------------------------CAGCAG---------------------------------------------CTGCAGCAGCA----TCTGCAACAGCACCAGCAAAT------GCAGCAGCA-------------------------ACACCAG---------------CAGCAGCAGCAACAGCAACACCAGCAG---ATGCAACAGCAGCAGCAG---CAG---CATCACCAGCAGCAAC-------------------------ATC------ACCG------C-CATCTGGAG-AAGC------------GCAACTCGG
droTak1	scf7180000415191:76977-77132 +		G--------------------------------------CTGCAA---------------------------------------CAACAACAACAATGGCA----GTGGCAGTGGCAATAGCTGCA------GCAACGGCA-------------------------GCAACAG---------------CAGCAGCAACAACGGCAGCAACAGTAT---GAGCAACGGAGGCGGCAG---CAA---CAGCAGCAACGGCAAC-------------------------ATC------AATG------CCCTGCTG-GGCGGAA------------TCGGCTTGA
droEug1	scf7180000409538:99984-100125 -		CTGAGGAG-------------------------------CAGCAG---------------------------------------------CAGCAGCAACA----ACAACAACAGCAGCAG------------CAGCAACA-------------------------GCATCAG---------------CAGCAGCATCAGCAGCAACATCAGCAA---CAGCAGCAGCAGCAACAA---CAG---CAGCAGCAGCAGCAAC-------------------------ATC------ATC----------AGCAACAG------------------CAACATAT
dm3	chrX:9649038-9649194 +		G--------------------------------------CAGCAA---------------------------------------CAGCAGCAACAGCAGCA----GCAGCAGCATCAACAGCAGCA------ACAGCAGCA-------------------------ACATCAA---------------CAGCAGCAGCAGCAACATCAGCAGCAGCAGCAG---CAACACCACCAG---------CAACAGCAGCAGCAT----------------------------------CATCACCAGCAATTTG-GCCAGCAGCAGCATCC-----------CCAT
droSim2	x:1004160-1004312 -		TTAT-TGC----CAGCAGCCGG-------ACTG---------------------------CATTCCTCAGGAGTTCCTTCTCC-----AGCAGCAGCAGCA----------ACAACAGCTGCAGCA------GCAACAACA-------------------------ACAGCAG---------------CAACTGCAGCAGCAGCTTCAGCAGC------AACAGCTGCAACTCCAA---CAA---CAGCAGCAACAG-----------------------------------------------------------------------------CAGATGGT
droSec2	scaffold_20:184232-184387 +		TG-------------------------------------CAGCAG---------------------------------------CCGCAGCAGCTGCCGCG----GTGGC--CAGCAACAC---------------------------GTTGCAGCA---------GCATCAG---------------CAGCACCACCAACAGCAGCAGCAACAA---CAGCAGCAGCAGCAACAA---CAG---CAGCAGCAGCAGCAACATTCACCGCAGCAG------CATTT------AAT-------------CAGAGCGA-------------------TACCTGT
droYak3	3L:8358746-8358893 -		G--------------------------------------CAGCAA---------------------------------------CAGCAGCAGCAGCAACA----ACAGCAACAGCAGCAGCAGCA------GCAACAGCA-------------------------ACAGCAG---------------CAGCAGCAACAACAGCAACAGCAGCAA---CAGCAGCAACAGCAGCAA---CAA---CAACAGCAGCAACAGC-------------------------AG------CAGTT------A-CAGCTGCAG------------------CAAC--AA
droEre2	scaffold_4784:3526911-3527069 +		CGTC-TTG-------------------------------CAGCAG---------------------------------------CAGCAGCAGCACTCTCA----------GCATCAGCAGCAA---------CATCA-CGGCCATCCGTTGCATCCGCATCATACACACCAGCAACAGCAACAACAGCAGCAGCAGCAGCAGC---------------AG---C------CGCCG---------CAACACCACCAGCAGC-------------------------AGC------A-------------GCAGCAA---------CA------GCAGCACGC

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droMoj3

TCGTTGTG-------------------------------CAGCAA---------------------------------------CTGCAGCAACAAGGAGAATTCGC-TCAATAGCTC-----GCAGCAGTTTTATCA-CA-------------------------ACAGCAG---------------CGGCAGCAACAACAGCAACAGCAGCAG---CAGCGGCAGCAGCAGCAG---CAA---CAGCTCCTTCAATAC-------------AT------CCTGT------GAG-------------CTGAACAA------------------CAGCTTGT	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
.......................................................................................................................................................................................................ACAGCAACAGCAGCAG---CAGCG.......................................................................................................................	21	20	0.10	2	2	0	0	0	0	0
...........................................................................................................................................................................................................................AGCGGCAGCAGCAGCAG---CAA---CAG..............................................................................................	23	14	0.07	1	1	0	0	0	0	0
.....................................................................................................................................................................................................CAACAGCAACAGCAGCAG---CAGCGG......................................................................................................................	24	19	0.05	1	1	0	0	0	0	0
................................................................................................................................................................................................AGCAACAACAGCAACAGCAGCAG---............................................................................................................................	23	20	0.05	1	1	0	0	0	0	0

droVir3

G--------------------------------------CAGCAG---------------------------------------CTGCAGCACCATCAGCA----GCATCTGCAGCAACAACAGCA------GCAGCTTCA-------------------------TCAGCAG---------------CTTCAGCAGCATCAGCAACAGCAGCAT---CAGCAACAACAGCAGCAG---CAA---CAGCAG------CAA----------------------------------CAGCA------A-CAGCAGCAACATCAGCTGCCACAGCCGCCACCAGT	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
.............................................................................................................................................................................................................ACAGCAGCAT---CAGCAACAAC..................................................................................................................	20	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
.....................................................................................TGCAGCACCATCAGCA----GCATCTGCAGC..................................................................................................................................................................................................................................	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
.......................................................................................................................................................................CAGCAG---------------CTTCAGCAGCATCAGCAAC.......................................................................................................................................	25	1	1.00	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
...........................................................................................ACCATCAGCA----GCATCTGCAGCAACAACA...........................................................................................................................................................................................................................	28	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
..................................................................................................................GCAACAACAGCA------GCAGCTTCA-------------------------TC..............................................................................................................................................................................	23	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
......................................................................................................................................AGCTTCA-------------------------TCAGCAG---------------CTTCAGCAGCATCAG...........................................................................................................................................	29	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
..................................................................................................................................................................................................................................................................................................................................CTGCCACAGCCGCCACCAGT	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	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
........................................................................................................................................CTTCA-------------------------TCAGCAG---------------CTTCAGCAGCATCAGC..........................................................................................................................................	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
......................................................................................GCAGCACCATCAGCA----GCATCT.......................................................................................................................................................................................................................................	21	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
......................................................................................................................................AGCTTCA-------------------------TCAGCAG---------------CTTCAGCAGC................................................................................................................................................	24	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
.....................................................................................................................................CAGCTTCA-------------------------TCAGCAG---------------CTTCAGCA..................................................................................................................................................	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
...................................................................................................................................................................................................AGCATCAGCAACAGCAGCAT---C...........................................................................................................................	21	2	0.50	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
................................................................................................................................................................................................................GCAGCAT---CAGCAACAACAGC...............................................................................................................	20	5	0.40	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
.................................................................................................................................................................................................GCAGCATCAGCAACAGCAGCAT---............................................................................................................................	22	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	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
...............................................................................................................................................................................................................AGCAGCAT---CAGCAACAACAGCA..............................................................................................................	22	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	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
.....................................................................................................................................................................................................................AT---CAGCAACAACAGCAGCAG---C......................................................................................................	21	6	0.17	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
..........................................................................................................................................................................................................GCAACAGCAGCAT---CAGCAACA....................................................................................................................	21	6	0.17	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
........................................................................................................................................................................................................CAGCAACAGCAGCAT---CAGCAACA....................................................................................................................	23	6	0.17	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
.........................................................................................................................................................................................................AGCAACAGCAGCAT---CAGCAAC.....................................................................................................................	21	6	0.17	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
....................................................................................................................................................................................................................CAT---CAGCAACAACAGCAGCAG---.......................................................................................................	21	6	0.17	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
...............................................................................................................................................................................................................AGCAGCAT---CAGCAACAACA.................................................................................................................	19	13	0.08	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
.........................................................................................................................................................................................................................................CAG---CAA---CAGCAG------CAA----------------------------------CAGCA------A-CAGCAGCA...........................	29	15	0.07	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1
.......................................................................................................................................................................................................................................AGCAG---CAA---CAGCAG------CAA----------------------------------CAGCA------A-CAGCA..............................	28	18	0.06	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
................................................................................................................................................................................................................................................AA---CAGCAG------CAA----------------------------------CAGCA------A-CAGCA..............................	22	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.................................................................................................................................................................................................................................................A---CAGCAG------CAA----------------------------------CAGCA------A-CAGCA..............................	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	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
.....................................................................................................................................................................................................................................................CAGCAG------CAA----------------------------------CAGCA------A-CAGCAGCA...........................	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	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
................................................................................................................................................................................................................................................AA---CAGCAG------CAA----------------------------------CAGCA------A-CAGC...............................	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
.................................................................................................................................................................................................................CAGCAT---CAGCAACAACAGCT..............................................................................................................	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	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
..........................................................................................................................................................................................................................................AG---CAA---CAGCAG------CAA----------------------------------CAGCA------.....................................	19	20	0.05	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.................................................................................................................................................................................................................................................A---CAGCAG------CAA----------------------------------CAGCA------A-CAGC...............................	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	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
..................................................................................................................................................................................................CAGCATCAGCAACAGCAGCA................................................................................................................................	20	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................................................................AG------CAA----------------------------------CAGCA------A-CAGCAGCAAC.........................	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	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

droGri2

G--------------------------------------CAGCAT---------------------------------------CGGCAGCAGCAGCAGCA----TCAGCAGCAGCAGCAGCAGCG------TCAACATCA-------------------------GCAGCAG---------------CAGCAGCAGCAGCTA---------------AAACAACAGCAGCAGCAA---AAA---CAGCAGCAGCAGCAG----------------------------------TCAAA------A-CAACAGCAG------------------CAACAGCT	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

droWil2

TGCT-GTA-------------------------------CAACAACAACAGCATGGACAACATT------TGGTTGCTGCCGCG--GCAGCAGC-TGC----------------CCATCATCA---------------ACA-------------------------ACAACAG------------------CAGCAGGTACAGGTGCAACAGCAG---CAGCAACAGCATCAACAG---CAA---CAGCACCAGCAGCAAC-------------------------ATC------A---------T-CATCATCAA------------------CAGCAAGT	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
.........................................................................................................................CA---------------ACA-------------------------ACAACAG------------------CAGCAGG................................................................................................................................................	19	20	0.10	2	0	0	0	2	0
................................................................................................................................................................................................................................CAGCATCAACAG---CAA---CAGC.............................................................................................	19	10	0.10	1	0	0	0	1	0
...............................................................................................................................................................................................................AACAGCAG---CAGCAACAGCA.................................................................................................................	19	20	0.10	2	0	0	0	2	0
...............................................................................................................................................................................................................AACAGCAG---CAGCAACAGCAT................................................................................................................	20	13	0.08	1	0	0	0	1	0
......................................................................................................................CATCA---------------ACA-------------------------ACAACAG------------------CAGCAG.................................................................................................................................................	21	14	0.07	1	0	0	0	0	1
............................................................................................................................................................................................................TGCAACAGCAG---CAGCAACAGCA.................................................................................................................	22	15	0.07	1	0	0	0	1	0
......................................................................................................................CATCA---------------ACA-------------------------ACAACAG------------------CAGC...................................................................................................................................................	19	20	0.05	1	0	1	0	0	0
......................................................................................................................CATCA---------------ACA-------------------------ACAACAG------------------CAGCA..................................................................................................................................................	20	20	0.05	1	0	0	0	1	0
..............................................................................................................................................................................................................CAACAGCAG---CAGCAACAGCA.................................................................................................................	20	20	0.05	1	0	0	0	0	1

dp5

G--------------------------------------CAGCAA---------------------------------------CAGCAGCAGCAACAGCA----GCAGCAGCATCAGCAACATCA------GCAGCAAAA-------------------------GCATCAG---------------CAACAGCAGCAGCAGCAGCAGCATAAGCAGCAG---CAACAGCATCAGCAACAA---CAACAGCTGCAGCAA----------------------------------CAAAA------A-CATCAGCAA------------------CAGCAGCT	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
............................................................................................................................................................................................................................................CAACAA---CAACAGCTGCAGCA...................................................................................	20	3	0.33	1	0	1	0	0	0	0	0	0	0	0
......................................................................................................................................................................................................................................CATCAGCAACAA---CAACAGC..........................................................................................	19	6	0.17	1	0	0	1	0	0	0	0	0	0	0
.............................................................................................CAACAGCA----GCAGCAGCATCAGCA..............................................................................................................................................................................................................................	23	12	0.08	1	0	1	0	0	0	0	0	0	0	0
G--------------------------------------CAGCAA---------------------------------------CAGCAGCAGCAACAGC..................................................................................................................................................................................................................................................	23	20	0.05	1	0	0	1	0	0	0	0	0	0	0
............................................................................................................................................A-------------------------GCATCAG---------------CAACAGCAGCAGT.............................................................................................................................................	21	20	0.05	1	0	0	0	0	1	0	0	0	0	0
.......................................CAGCAA---------------------------------------CAGCAGCAGCAACAGCA----GCA..........................................................................................................................................................................................................................................	26	20	0.05	1	0	0	0	1	0	0	0	0	0	0
............................................................................................................................................................................................CAACAGCAGCAGCAGCAGCA......................................................................................................................................	20	20	0.05	1	0	0	0	0	1	0	0	0	0	0
............................................................................................................................................................................G---------------CAACAGCAGCAGCAGCAGCA......................................................................................................................................	21	20	0.05	1	0	0	0	0	1	0	0	0	0	0
........................................AGCAA---------------------------------------CAGCAGCAGCAACAGCA----GC...........................................................................................................................................................................................................................................	24	20	0.05	1	0	0	0	0	0	0	0	0	0	1
...........................................AA---------------------------------------CAGCAGCAGCAACAGCA----GCA..........................................................................................................................................................................................................................................	22	20	0.05	1	0	1	0	0	0	0	0	0	0	0
.........................................................................................GCAGCAACAGCA----GCAGCAGCA....................................................................................................................................................................................................................................	21	20	0.05	1	0	0	0	0	1	0	0	0	0	0
.............................................................................................CAACAGCA----GCAGCAGCATCA.................................................................................................................................................................................................................................	20	20	0.05	1	0	0	0	0	0	0	1	0	0	0
.............................................................................................................................................................................................AACAGCAGCAGCAGCAGCAGCA...................................................................................................................................	22	20	0.05	1	0	0	0	0	1	0	0	0	0	0
.........................................................................................................................................................................TCAG---------------CAACAGCAGCAGCAGCAGC.......................................................................................................................................	23	20	0.05	1	0	0	0	0	1	0	0	0	0	0
.............................................................................................................................................................................................AACAGCAGCAGCAGCAGCAG.....................................................................................................................................	20	20	0.05	1	0	0	0	0	1	0	0	0	0	0
................................................................................................CAGCA----GCAGCAGCATCAGCA..............................................................................................................................................................................................................................	20	20	0.05	1	0	1	0	0	0	0	0	0	0	0
........................................AGCAA---------------------------------------CAGCAGCAGCAACAGCA----GCAGC........................................................................................................................................................................................................................................	27	20	0.05	1	0	0	0	0	0	0	0	0	0	1

droPer2

G--------------------------------------CAGCAA---------------------------------------CAGCAGCACCAGCAGTC----GGAGCTGCACCATCACCTGCA------GCA-------------------------------GCAGCAG---------------CAGCACCACCAGCAGCAACAGCACCAG---CAGCAGCAGCAGCACCAG---CAA---CAACAGCTGGAGGAT----------------------------------GCCCT------T-GAGGAGCAG------------------CAGCTGGC	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
.............................................................................................CAGCAGTC----GGAGCTGCACCATCACCT...........................................................................................................................................................................................................................	26	1	2.00	2	2	0	0	0	0	0
........................................................................................AGCACCAGCAGTC----GGAGCTG......................................................................................................................................................................................................................................	20	1	1.00	1	1	0	0	0	0	0

droAna3

---------------------------------------CAGCAG---------------------------------------CAGCAGCAACAGCAACA----GTTGCAACAACAGCTG------------CAACAGCA-------------------------ACAGCAG---------------CAACTGCAACAACAGCAACTCCAGCAG---CAGCAGCAGCAGCAGCAG---CAA---CAACAGCAACAGCAA-------------ATGGTGGTGCC--ACCAG-----------------CTCCACCA------------------CAACCTGC	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
..........................................CAG---------------------------------------CAGCAGCAACAGCAACA----GTTGCAACA....................................................................................................................................................................................................................................	29	1	1.00	1	0	0	0	0	0	1
.............................................................................................................................................................................................................................................................ACAGCAA-------------ATGGTGGTGCC--ACC.....................................................	21	1	1.00	1	0	1	0	0	0	0
............................................................................................................................................................................G---------------CAACTGCAACAACAGCAACTCCAGC.................................................................................................................................	26	1	1.00	1	0	1	0	0	0	0
..........................................................................................................................................................................................................................................AG---CAA---CAACAGCAACAGCAA-------------ATGGT................................................................	25	1	1.00	1	0	1	0	0	0	0
...................................................................................................................................................................................................AACAACAGCAACTCCAGCAG---CAGC........................................................................................................................	24	1	1.00	1	0	1	0	0	0	0
............................................G---------------------------------------CAGCAGCAACAGCAACA----GTTGCAACAAC..................................................................................................................................................................................................................................	29	1	1.00	1	0	1	0	0	0	0
............................................................................................................GCAACAACAGCTG------------CAACAGC..........................................................................................................................................................................................................	20	2	0.50	1	0	1	0	0	0	0
...............................................................................................GCAACA----GTTGCAACAACAGC...............................................................................................................................................................................................................................	20	2	0.50	1	0	1	0	0	0	0
..........................................................................................................................................................................................................GCAACTCCAGCAG---CAGCA.......................................................................................................................	18	10	0.20	2	2	0	0	0	0	0
.........................................................................................................................................................................................................AGCAACTCCAGCAG---CAGCA.......................................................................................................................	19	7	0.14	1	1	0	0	0	0	0
.........................................................................................................................................AGCA-------------------------ACAGCAG---------------CAACTGCA..................................................................................................................................................	19	7	0.14	1	0	0	0	1	0	0
............................................................................................................................................................................................................AACTCCAGCAG---CAGCAGCAGCA.................................................................................................................	22	7	0.14	1	0	0	0	0	0	1
............................................................................................................................................................................................................AACTCCAGCAG---CAGCAGCA....................................................................................................................	19	10	0.10	1	0	0	0	1	0	0
.................................................................................................................................................................................................................................AGCAGCAGCAG---CAA---CAACAGCA.........................................................................................	22	20	0.10	2	0	2	0	0	0	0
........................................AGCAG---------------------------------------CAGCAGCAACAGCAACA----.............................................................................................................................................................................................................................................	22	20	0.10	2	0	2	0	0	0	0
..............................................................................................................................................................................................................CTCCAGCAG---CAGCAGCAGCAGCAG.............................................................................................................	24	10	0.10	1	1	0	0	0	0	0
.............................................................................................................................................................................................................ACTCCAGCAG---CAGCAGCAGC..................................................................................................................	20	11	0.09	1	0	0	0	0	0	1
.....................................................................................................................................CAACAGCA-------------------------ACAGCAG---------------CAACT.....................................................................................................................................................	20	14	0.07	1	1	0	0	0	0	0
..............................................................................................................................................................................................................CTCCAGCAG---CAGCAGCAGCAGCA..............................................................................................................	23	14	0.07	1	0	1	0	0	0	0
................................................................................................................................................................................................................................CAGCAGCAGCAG---CAA---CAACAGCAACAG.....................................................................................	27	17	0.06	1	1	0	0	0	0	0
.................................................................................................................................................................................................................................AGCAGCAGCAG---CAA---CAACAGCAACA......................................................................................	25	20	0.05	1	0	0	0	0	0	1
.......................................................................................................................................................................................................................................AGCAG---CAA---CAACAGCAACAGCA...................................................................................	22	20	0.05	1	0	1	0	0	0	0
.....................................................................................................................................................................................................................................GCAGCAG---CAA---CAACAGCAAC.......................................................................................	20	20	0.05	1	1	0	0	0	0	0
.............................................................................................................................................................................................................................CAGCAGCAGCAGCAG---CAA---CAACAGC..........................................................................................	25	20	0.05	1	0	1	0	0	0	0
.................................................................................................................................................................................................................................AGCAGCAGCAG---CAA---CAACAGCAAC.......................................................................................	24	20	0.05	1	0	1	0	0	0	0
...................................................................................................................................................................................................................GCAG---CAGCAGCAGCAGCAGCA...........................................................................................................	21	20	0.05	1	0	1	0	0	0	0
.......................................................................................................................................................................................................................................AGCAG---CAA---CAACAGCAACAGC....................................................................................	21	20	0.05	1	0	1	0	0	0	0
..............................................................................................................................................................................................................................AGCAGCAGCAGCAG---CAA---CAA..............................................................................................	20	20	0.05	1	0	0	0	0	0	1
....................................................................................................................................................................................................................CAG---CAGCAGCAGCAGCAGCAG---CAA---C................................................................................................	25	20	0.05	1	0	1	0	0	0	0
.......................................CAGCAG---------------------------------------CAGCAGCAACAGCAAC..................................................................................................................................................................................................................................................	22	20	0.05	1	0	1	0	0	0	0
........................................................................................................................................................................................................................................GCAG---CAA---CAACAGCAACAGC....................................................................................	20	20	0.05	1	0	1	0	0	0	0
....................................................................................................................................................................................................................................AGCAGCAG---CAA---CAACAGCAACAGC....................................................................................	24	20	0.05	1	0	1	0	0	0	0
.....................................................................................................................................CAACAGCA-------------------------ACAGCAG---------------CAAC......................................................................................................................................................	19	20	0.05	1	0	1	0	0	0	0
.....................................................................................................................................................................................................................AG---CAGCAGCAGCAGCAGCAG---CAA---C................................................................................................	24	20	0.05	1	0	1	0	0	0	0

droBip1

G--------------------------------------CAGCAA---------------------------------------CAACAGCAGCAACATCA----GCTGCAACAGCACCAGCAACA------GTT---ACA-------------------------ACACCAG---------------CAGCAGCAGCAACAGCAACAGCACCTGCACCAG---CAACAGCTTCAG---CCGCACCAGCAGCAAATGCAA----------------------------------CACCA------C-CAGCAGCAA------------------CAACA-GC	Size	Hit Count	Total Norm	Total
No Reads

droKik1

TTTTGCAG----------TTGG-------ATTA------TAGCAA---------------------------------------CAAGGATAATAATAATA-------GCAACAGCAGTAG------------TACCGGCA-------------------------ACAACAG---------------CAGCAGCAACAACAACAACAATAATAA---TAACAACAGCAGCAGCAA---CAA---CAACATCAATCGTGA----------------------------------G-------------CGAAACAA------------------CA----GC	Size	Hit Count	Total Norm	Total
No Reads

droFic1

GTT--GCACAGCCTGCAGACGCAAACCAAATTGCTCAAGCAGCAA---------------------------------------CAGGAGCAGCAATTGCT----ATTGCAACAACAGCAG----------------------------------------------------------------------CAGCAGCAACAGCTGCACCAACAG---CAGCAGCAACAGCAGCAG---CAT---CATCACCAGCATCATC-------------------------ACCAGCATCATC-------------AACAA------------------CA----GC	Size	Hit Count	Total Norm	Total
No Reads

droEle1

G--------------------------------------CAACAA---------------------------------------CAGCAGCAGCAACAACA-------ACAACAGCAGCAG------------CAACAACA-------------------------ACAACAG---------------CAGCAGCAACAACAACAGCAGCAGCAA---CAACAACAGCAGCAGCAA---CAA---CAGCAGCAACAACAA----------------------------------GTCTT------G-GCTCAGCAA------------------CAACCTCA	Size	Hit Count	Total Norm	Total
No Reads

droRho1

TCCTCCTT-------------------------------CAGCAG---------------------------------------------CAGCAGCAGCA----ACAGCAACTCCAGCAGCAACA------ATTGCAGCA-------------------------GCAACAA---------------TTGCAGCAACAGCAACTTCAGCAGCAGCAACAGCAACTCCAGCAGCAG---CAA---CAGCTG------CA-------------------------------------CCT------C-CAACAGCTGCAGCAGCAATC------GCAGATGGT	Size	Hit Count	Total Norm	Total
No Reads

droBia1

CCATCCAG-------------------------------CAGCAG---------------------------------------------CTGCAGCAGCA----TCTGCAACAGCACCAGCAAAT------GCAGCAGCA-------------------------ACACCAG---------------CAGCAGCAGCAACAGCAACACCAGCAG---ATGCAACAGCAGCAGCAG---CAG---CATCACCAGCAGCAAC-------------------------ATC------ACCG------C-CATCTGGAG-AAGC------------GCAACTCGG	Size	Hit Count	Total Norm	Total
No Reads

droTak1

G--------------------------------------CTGCAA---------------------------------------CAACAACAACAATGGCA----GTGGCAGTGGCAATAGCTGCA------GCAACGGCA-------------------------GCAACAG---------------CAGCAGCAACAACGGCAGCAACAGTAT---GAGCAACGGAGGCGGCAG---CAA---CAGCAGCAACGGCAAC-------------------------ATC------AATG------CCCTGCTG-GGCGGAA------------TCGGCTTGA	Size	Hit Count	Total Norm	Total
No Reads

droEug1

CTGAGGAG-------------------------------CAGCAG---------------------------------------------CAGCAGCAACA----ACAACAACAGCAGCAG------------CAGCAACA-------------------------GCATCAG---------------CAGCAGCATCAGCAGCAACATCAGCAA---CAGCAGCAGCAGCAACAA---CAG---CAGCAGCAGCAGCAAC-------------------------ATC------ATC----------AGCAACAG------------------CAACATAT	Size	Hit Count	Total Norm	Total
No Reads

dm3

G--------------------------------------CAGCAA---------------------------------------CAGCAGCAACAGCAGCA----GCAGCAGCATCAACAGCAGCA------ACAGCAGCA-------------------------ACATCAA---------------CAGCAGCAGCAGCAACATCAGCAGCAGCAGCAG---CAACACCACCAG---------CAACAGCAGCAGCAT----------------------------------CATCACCAGCAATTTG-GCCAGCAGCAGCATCC-----------CCAT	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
....................................................................................................................................................................................................................................................................................................................TG-GCCAGCAGCAGCATCC-----------CCAT	22	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	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
.............................................................................................................CAGCATCAACAGCAGCA------ACAGC.............................................................................................................................................................................................................	22	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
..........................................CAA---------------------------------------CAGCAGCAACAGCAGCA----G............................................................................................................................................................................................................................................	21	20	0.70	14	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................................................AGCAGCAG---CAACACCACCAG---------C................................................................................................	21	9	0.67	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
.....................................................................................................................................................................................................CAGCAACATCAGCAGCAGCAGCAG---CA....................................................................................................................	26	15	0.53	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	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
......................................................................................................................................................................................................................................................AACAGCAGCAGCAT----------------------------------CATCACC.........................................	21	2	0.50	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
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.....................................................................................AGCAGCAACAGCAGCA----GCAGCA.......................................................................................................................................................................................................................................	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
..........................................................................................CAACAGCAGCA----GCAGCAGCATC..................................................................................................................................................................................................................................	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.........................................GCAA---------------------------------------CAGCAGCAACAGCAGCA----GC...........................................................................................................................................................................................................................................	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
...................................................................................................................................................................................................AGCAGCAACATCAGCAGCAGCAGC...........................................................................................................................	24	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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

TTAT-TGC----CAGCAGCCGG-------ACTG---------------------------CATTCCTCAGGAGTTCCTTCTCC-----AGCAGCAGCAGCA----------ACAACAGCTGCAGCA------GCAACAACA-------------------------ACAGCAG---------------CAACTGCAGCAGCAGCTTCAGCAGC------AACAGCTGCAACTCCAA---CAA---CAGCAGCAACAG-----------------------------------------------------------------------------CAGATGGT	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
.........................................................................................................................................................................................................................................CAA---CAA---CAGCAGCAACAG-----------------------------------------------------------------------------CA......	20	20	2.70	54	0	0	0	0	54	0	0	0	0	0	0	0	0	0	0	0	0
.............................................................................................................................A------GCAACAACA-------------------------ACAGCAG---------------CAAC......................................................................................................................................................	21	16	1.00	16	0	0	0	0	16	0	0	0	0	0	0	0	0	0	0	0	0
...........................................................................................................................................................................................................................AACAGCTGCAACTCC............................................................................................................	15	1	1.00	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
..AT-TGC----CAGCAGCCGG-------ACTG---------------------------C.........................................................................................................................................................................................................................................................................................	20	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...................................................................................................................CAGCTGCAGCA------GCAACAACA-------------------------A...............................................................................................................................................................................	21	3	1.00	3	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0
........................................................................................................................................CAACA-------------------------ACAGCAG---------------CAACTG....................................................................................................................................................	18	7	0.71	5	3	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droSec2

TG-------------------------------------CAGCAG---------------------------------------CCGCAGCAGCTGCCGCG----GTGGC--CAGCAACAC---------------------------GTTGCAGCA---------GCATCAG---------------CAGCACCACCAACAGCAGCAGCAACAA---CAGCAGCAGCAGCAACAA---CAG---CAGCAGCAGCAGCAACATTCACCGCAGCAG------CATTT------AAT-------------CAGAGCGA-------------------TACCTGT	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
.................................................................................................................................................................................................................................................................CAACATTCACCGCAGCAG------C............................................................	19	1	1.00	1	0	0	1	0
............................................................................................................................................................................................................................................................AGCAGCAACATTCACCGCAGCAG------.............................................................	23	1	1.00	1	1	0	0	0
..............................................................................................................................................................................................................................................................................AGCAG------CATTT------AAT-------------CAGAGCGA-------------------TA.....	23	1	1.00	1	0	1	0	0
..............................................................................................................................................................................................................CAGCAACAA---CAGCAGCAGCAG................................................................................................................	21	20	0.15	3	0	0	0	3
....................................................................................................................................................................................................................................AGCAACAA---CAG---CAGCAGCAG........................................................................................	20	20	0.10	2	0	1	1	0
.................................................................................................................................................................................................................CAACAA---CAGCAGCAGCAGC...............................................................................................................	19	20	0.10	2	0	0	2	0
..............................................................................................................................................................................................................CAGCAACAA---CAGCAGCAG...................................................................................................................	18	20	0.10	2	0	0	2	0
........................................................................................................................................................................................................................................ACAA---CAG---CAGCAGCAGCA......................................................................................	18	20	0.10	2	0	0	2	0
...................................................................................................................................................................................................................ACAA---CAGCAGCAGCAGCA..............................................................................................................	18	20	0.10	2	0	0	2	0
...................................................................................................................................................................................................................................CAGCAACAA---CAG---CAGCAG...........................................................................................	18	20	0.10	2	0	0	2	0
......................................................................................................................................................................................................................................CAACAA---CAG---CAGCAGCAGC.......................................................................................	19	20	0.10	2	0	0	2	0
..................................................................................................................................................................................................CACCAACAGCAGCAGCAACA................................................................................................................................	20	13	0.08	1	0	1	0	0
...........................................................................................................................................................................................................CAGCAGCAACAA---CAGCAGCA....................................................................................................................	20	20	0.05	1	0	0	1	0
.................................................................................................................................................................................................................................AGCAGCAACAA---CAG---CAGCA............................................................................................	19	20	0.05	1	0	0	1	0
............................................................................................................................................................................................................AGCAGCAACAA---CAGCAGCA....................................................................................................................	19	20	0.05	1	0	0	1	0
.....................................................................................................................................................................................................................................GCAACAA---CAG---CAGCAGCAGC.......................................................................................	20	20	0.05	1	0	0	0	1
...............................................................................................................................................................................................................AGCAACAA---CAGCAGCAGCAG................................................................................................................	20	20	0.05	1	0	0	1	0
...........................................................................................................................................................................................................................AGCAGCAGCAGCAACAA---CAG---C................................................................................................	21	20	0.05	1	0	0	1	0
..............................................................................................................................................................................................................................AGCAGCAGCAACAA---CAG---CA...............................................................................................	19	20	0.05	1	0	0	1	0
................................................................................................................................................................................................................GCAACAA---CAGCAGCAGCAGC...............................................................................................................	20	20	0.05	1	0	0	0	1

droYak3

G--------------------------------------CAGCAA---------------------------------------CAGCAGCAGCAGCAACA----ACAGCAACAGCAGCAGCAGCA------GCAACAGCA-------------------------ACAGCAG---------------CAGCAGCAACAACAGCAACAGCAGCAA---CAGCAGCAACAGCAGCAA---CAA---CAACAGCAGCAACAGC-------------------------AG------CAGTT------A-CAGCTGCAG------------------CAAC--AA	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
.........................................................................................................................................AGCA-------------------------ACAGCAG---------------CAGCAGCAACAACAGC..........................................................................................................................................	27	20	1.20	24	0	0	0	0	0	0	0	0	0	0	24
........................................AGCAA---------------------------------------CAGCAGCAGCAGCAACA----ACAGC........................................................................................................................................................................................................................................	27	20	1.20	24	0	0	0	0	0	0	0	0	0	0	24
......................................................................................................................................................................................................................................................AACAGCAGCAACAGC-------------------------AG------CAGTT------.....................................	22	3	0.33	1	0	0	0	0	0	0	1	0	0	0	0
.................................................................................................AACA----ACAGCAACAGCAGCAGCAGCA------GC................................................................................................................................................................................................................	27	4	0.25	1	0	0	1	0	0	0	0	0	0	0	0
..............................................................................................................................................................................................................................AGCAACAGCAGCAA---CAA---CAACAGCA.........................................................................................	25	12	0.08	1	0	1	0	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................................................CAA---CAA---CAACAGCAGCAACAGC-------------------------........................................................	22	18	0.06	1	0	0	1	0	0	0	0	0	0	0	0
..............................................................................................AGCAACA----ACAGCAACAGCAGC...............................................................................................................................................................................................................................	21	20	0.05	1	0	0	1	0	0	0	0	0	0	0	0
...............................................................................................................ACAGCAGCAGCAGCA------GCA...............................................................................................................................................................................................................	18	20	0.05	1	0	0	0	1	0	0	0	0	0	0	0
...........................................................................................................................................CA-------------------------ACAGCAG---------------CAGCAGCAACA...............................................................................................................................................	20	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
........................................................................................................................GCAGCA------GCAACAGCA-------------------------ACAGCAG---------------CAGCA.....................................................................................................................................................	27	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
.........................................GCAA---------------------------------------CAGCAGCAGCAGCAACA----A............................................................................................................................................................................................................................................	22	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................ACAACAGCAACAGCAGCA................................................................................................................................	18	20	0.05	1	0	0	0	1	0	0	0	0	0	0	0
................................................................................................................................................................................................AGCAACAACAGCAACAGCAGC.................................................................................................................................	21	20	0.05	1	0	0	1	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................ACAGCAGCAA---CAA---CAACAGC..........................................................................................	20	20	0.05	1	0	0	1	0	0	0	0	0	0	0	0
.....................................................................................................................GCAGCAGCA------GCAACAGCA-------------------------AC..............................................................................................................................................................................	20	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
............................................................................................................GCAACAGCAGCAGCAGCA------GCA...............................................................................................................................................................................................................	21	20	0.05	1	0	0	0	0	1	0	0	0	0	0	0
..................................................................................................ACA----ACAGCAACAGCAGCA..............................................................................................................................................................................................................................	18	20	0.05	1	0	0	0	1	0	0	0	0	0	0	0
.................................................................................................................................................................................................................CAGCAA---CAGCAGCAACAGCA..............................................................................................................	20	20	0.05	1	0	0	1	0	0	0	0	0	0	0	0
..............................................................................................................................................................................................................................AGCAACAGCAGCAA---CAA---CAA..............................................................................................	20	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
..........................................................................................................................AGCA------GCAACAGCA-------------------------ACAGCAG---------------C.........................................................................................................................................................	21	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
......................................................................................................................................................................................................AACAGCAACAGCAGCAA---CAG.........................................................................................................................	20	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................................................................................CAACAGCAGCAACAGC-------------------------AG------CA..............................................	20	20	0.05	1	0	0	0	1	0	0	0	0	0	0	0
.....................................................................................................................................................................................................................AA---CAGCAGCAACAGCAGC............................................................................................................	18	20	0.05	1	0	0	0	1	0	0	0	0	0	0	0

droEre2

CGTC-TTG-------------------------------CAGCAG---------------------------------------CAGCAGCAGCACTCTCA----------GCATCAGCAGCAA---------CATCA-CGGCCATCCGTTGCATCCGCATCATACACACCAGCAACAGCAACAACAGCAGCAGCAGCAGCAGC---------------AG---C------CGCCG---------CAACACCACCAGCAGC-------------------------AGC------A-------------GCAGCAA---------CA------GCAGCACGC	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
..........................................................................................................................AA---------CATCA-CGGCCATCCGTTGCATCCG........................................................................................................................................................................................	26	1	1.00	1	1	0	0	0	0	0	0
...........................................AG---------------------------------------CAGCAGCAGCACTCTCA----------GC.....................................................................................................................................................................................................................................	21	1	1.00	1	1	0	0	0	0	0	0
.................................................................................................CTCA----------GCATCAGCAGCAA---------CATCA-CGGC.......................................................................................................................................................................................................	26	1	1.00	1	0	0	0	0	0	1	0
........................................AGCAG---------------------------------------CAGCAGCAGCACTCTCA----------GCATC..................................................................................................................................................................................................................................	27	1	1.00	1	1	0	0	0	0	0	0
........................................................................................................................................CA-CGGCCATCCGTTGCATCCGCATC....................................................................................................................................................................................	25	1	1.00	1	1	0	0	0	0	0	0
.................................................................................................................ATCAGCAGCAA---------CATCA-CGGCC......................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	1	0
...........................................................................................................................A---------CATCA-CGGCCATCCGTTGC.............................................................................................................................................................................................	20	1	1.00	1	1	0	0	0	0	0	0
..........................................................................................................................................................................................................................................CG---------CAACACCACCAGCAGC-------------------------AGC------...............................................	21	2	0.50	1	1	0	0	0	0	0	0
.....TTG-------------------------------CAGCAG---------------------------------------CAGCAG............................................................................................................................................................................................................................................................	15	20	0.20	4	0	0	0	0	0	0	4
.......................................................................................................................................................................................AACAGCAGCAGCAGCAGCA............................................................................................................................................	19	20	0.15	3	0	0	0	0	0	3	0
............................................................................................................................................................................GCAACAGCAACAACAGCAGC......................................................................................................................................................	20	20	0.10	2	1	1	0	0	0	0	0
...................................................................................................................................................................................CAACAACAGCAGCAGCAGCA...............................................................................................................................................	20	20	0.10	2	0	0	0	0	0	2	0
...........................................................................................................................................................................................................................................................CACCAGCAGC-------------------------AGC------A-------------GCAGCAA---------CA------GCA......	26	13	0.08	1	1	0	0	0	0	0	0
...............................................................................................................................................................................................................................................................................................GC------A-------------GCAGCAA---------CA------GCAGCAC..	19	19	0.05	1	1	0	0	0	0	0	0
.................................................................................................................................................................................AGCAACAACAGCAGCAGCA..................................................................................................................................................	19	20	0.05	1	1	0	0	0	0	0	0
...............................................................................................................................................................................................................................................................AGCAGC-------------------------AGC------A-------------GCAGCAA---------CA------GCAGC....	24	20	0.05	1	0	1	0	0	0	0	0
..........................................................................................................................................................................................................................................................CCACCAGCAGC-------------------------AGC------A-------------GCAGCA...........................	21	20	0.05	1	0	0	0	0	0	1	0
..............................................................................................................................................................................AACAGCAACAACAGCAGCAGCA..................................................................................................................................................	22	20	0.05	1	0	0	0	0	0	1	0
..........................................................................................................................................................................................................................................................CCACCAGCAGC-------------------------AGC------A-------------GCAGC............................	20	20	0.05	1	0	0	0	1	0	0	0
...................................................................................................................................................................................................................................................................GC-------------------------AGC------A-------------GCAGCAA---------CA------GCA......	18	20	0.05	1	1	0	0	0	0	0	0
....................................................................................................................................................................................AACAACAGCAGCAGCAGCA...............................................................................................................................................	19	20	0.05	1	0	0	0	0	1	0	0
..............................................................................................................................................................................AACAGCAACAACAGCAGCAGC...................................................................................................................................................	21	20	0.05	1	0	0	1	0	0	0	0
.....................................................................................................................................................................................ACAACAGCAGCAGCAGCAGC.............................................................................................................................................	20	20	0.05	1	0	0	0	1	0	0	0
..............................................................................................................................................................................................................................................................................................AGC------A-------------GCAGCAA---------CA------GCAGCA...	19	20	0.05	1	0	0	0	1	0	0	0
....................................................................................................................................................................................AACAACAGCAGCAGCAGCAGCAG...........................................................................................................................................	23	20	0.05	1	0	1	0	0	0	0	0
...........................................................................................................................................................................AGCAACAGCAACAACAGCAG.......................................................................................................................................................	20	20	0.05	1	1	0	0	0	0	0	0
.................................................................................................................................................................................AGCAACAACAGCAGCAGCAGCAGCA............................................................................................................................................	25	20	0.05	1	0	0	0	0	0	1	0
..................................................................................................................................................................................GCAACAACAGCAGCAGCAGCA...............................................................................................................................................	21	20	0.05	1	0	0	0	0	1	0	0
........................................................................................................................................................................................................................................................CACCACCAGCAGC-------------------------AGC------A-------------GC...............................	19	20	0.05	1	1	0	0	0	0	0	0

dmo_1527

scaffold_6500:12520061-12520120 -

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