dmo_464

exon [dmoj_GLEANR_17027:8]; CDS [Dmoj\GI16306-cds]; CDS [Dmoj\GI16306-cds]; exon [dmoj_GLEANR_17027:7]; intron [Dmoj\GI16306-in]

Name	Class	Family	Strand
(CAG)n	Simple_repeat	Simple_repeat	+

##################################################------------------------------------------------------------------################################################## AGGATCTGCTCAATGCCAGCATCCAGCAGCAGCAGCAGCAGCAACAAGCTGTTGCAACGGAGTTGCTCATCTATGATCACGAACAGCAGCAGCAGCAGCAGCAGCAGGAGGAGGAGAAAAATAAGCCCAAGCAGCAGAAGCAACTGGACGAGGAGGAGTCGCTGCT *****************************************************************..................((.((.((....)).)).))..........*************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M060 embryo	V056 head	M046 female body	V110 male body	V041 embryo	V049 head
.......................................................................................................GCAGGAGGGGGAGAAAA..............................................	17	1	3	2.67	8	0	8	0	0	0	0
.......................................................................................................GCAGGAGGGGGAGAAAAACCA..........................................	21	3	3	2.00	6	4	1	0	0	1	0
.......................................................................................................GCAGGAGGGGGAGAAAACCA...........................................	20	3	20	1.60	32	6	14	1	2	2	7
.......................................................................................................GCAGGAGGGGGAGAAAAC.............................................	18	2	11	1.27	14	8	1	1	0	2	2
...................................................................CATCTATGATCACGAACAGC...............................................................................	20	0	1	1.00	1	0	0	1	0	0	0
........CGCAATGCCAGCATCCAGC...........................................................................................................................................	19	1	1	1.00	1	1	0	0	0	0	0
.......................................................................................................GCAGGAGGGGGAGAAAAA.............................................	18	1	3	1.00	3	1	0	0	0	2	0
..........................................AACAAGCTGTTGCAACGGAGTTG.....................................................................................................	23	0	1	1.00	1	0	0	0	1	0	0
....................................................................................................CCCGCAGGAGGGGGAGAAAA..............................................	20	3	4	0.75	3	1	0	2	0	0	0
....................................................................................................CCCGCAGGAGGGGGAGAAAAA.............................................	21	3	3	0.33	1	0	0	0	1	0	0
.......................................................................................................GCAGGAGGGGGAGAAAAACA...........................................	20	2	4	0.25	1	1	0	0	0	0	0
.............................................AGGGTGTTGCAGCGGAGTTGC....................................................................................................	21	3	4	0.25	1	0	0	0	0	0	1
....................................................................................................CCAGCTGGAGGAGGAGAAAAA.............................................	21	2	5	0.20	1	0	0	1	0	0	0
........................................................................................................CAGGAGGGGGAGAAAAAC............................................	18	2	6	0.17	1	1	0	0	0	0	0
.......................................................................................................GCAGGAGGGGGAGAAAAAAC...........................................	20	3	20	0.15	3	1	1	0	0	0	1
.......................................................................................................GCAGGAGGGGGAGACAAA.............................................	18	2	20	0.15	3	1	0	0	0	0	2
.....................................................................................................CCGCAGGAGGGGGAGAAA...............................................	18	2	7	0.14	1	0	0	0	1	0	0
.......................................................................................................GCAGGAGGGGGAGAAACAT............................................	19	2	8	0.13	1	0	0	0	0	1	0
..............................................................................ACGAACAGCAGCAGCAGCAGCA..................................................................	22	0	10	0.10	1	1	0	0	0	0	0
......................................................................................................CGCAGGAGGGGGAGAAAA..............................................	18	2	10	0.10	1	0	0	1	0	0	0
.......................................................................................................GCAGGAGGGGGAGAAAAAA............................................	19	2	12	0.08	1	0	0	0	0	0	1
.............................................................................................AGCAGCAGCAGCAGGAGGAGGA...................................................	22	0	20	0.05	1	1	0	0	0	0	0
........................................................................................................CAGGAGGGGGAGAAAACCA...........................................	19	3	20	0.05	1	0	1	0	0	0	0
.........................................................................................CAGCAGCAGCAGCAGCAGG..........................................................	19	0	20	0.05	1	0	0	1	0	0	0
.......................................................................................................GCAGGAGGGGGAGAAAAAACA..........................................	21	3	20	0.05	1	0	0	0	0	1	0
.......................................................................................................GCAGGAGTGGGAGAAAAA.............................................	18	2	20	0.05	1	0	0	0	0	1	0
.....................TCCAGCAGCAGCAGCAGCA..............................................................................................................................	19	0	20	0.05	1	0	0	0	0	0	1

TCCTAGACGAGTTACGGTCGTAGGTCGTCGTCGTCGTCGTCGTTGTTCGACAACGTTGCCTCAACGAGTAGATACTAGTGCTTGTCGTCGTCGTCGTCGTCGTCGTCCTCCTCCTCTTTTTATTCGGGTTCGTCGTCTTCGTTGACCTGCTCCTCCTCAGCGACGA *************************************************..................((.((.((....)).)).))..........*****************************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M046 female body
...........................................................................TAGTGCTTGCAGTCTTCGTCG......................................................................	21	3	8	0.13	1	1

Species	Coordinate	ID	Alignment
droMoj3	scaffold_6328:598757-598922 +	dmo_464	AGG-----ATCTGCTCAATGCCAGCATCC--------------AG---------C---A--------------------------GCAGC---------AGCA---GC------------------------A---------G---CAACAAGCTGTTGCAACGG-AGTTGCTCATCT--------ATGATC---A---CGAACAG----CAGCAG------------CAGCAG---------CAGCAGCAGGAGGAGGAGAAAA---------ATAAGCCCAAG------CAGCAGAA--GCAA-------------------------------------------------CTGGA---------CGAGGAGGAGTCGCTGCT
droVir3	scaffold_13042:3067287-3067428 -		AGG-----ATCTGCTAAATGCCAGCATCC--------------AG---------C---A--------------------------GCAGC---------AGCA---GC------------------------A---------G---CAACAGACC------ACAG-AGCTG-----------------TTGA---T---CTACGAG----CAACAG------------GAGCAG---------CTGCAGCAAGAGAAG------------------AAGCCCAAG------CAGCAGAA--GCAG-------------------------------------------------CTCGA---------CGAGGAGGAGTCGCTGTT
droGri2	scaffold_14828:10943-11108 -		AGC-----AGCAGCAG--------------CAGCAG------------------CAGCA---GCAGCAGCAGCAGCAGC--------------------------AGC------------------AGCAGCAGCAGCAGCAGCAG------------------------------------------CAGCAGCA---GCA---G----CAGCAGCAGCAGCAGCAGCAGCAG---------CAGCAGCAGCAGCAGCAGCAGC---------AGCAGCAGCAG------CAGCAGCA--GCAG-------------------------------------------------CAGCA---------GCAGCAGCAGCAGCAGCA
droWil2	scf2_1100000004577:3108108-3108270 -		AAC-----ATCAGCAC--------------TGCCAG------------------CAGCA---CCAGCAGCAGTAGCAGCAACAT--------------------------------------CAGCACTGCCAGCAGCACCAGCAG------------------------------------------CAGCACTG---CGA---G----TAGCAGCA---------GCAGCAC---------CAGCAGCAGTAGCAGCAACATC---------AGCACTGCCAG------CAGCACCA--GCAG-------------------------------------------------CAGCA---------CTGCGAGTAGCAGCAGCA
dp5	Unknown_group_66:9759-9918 +		AGC-----AGCAGCAC--------------CAACAT------------------CAGCA---GCCGC---AGCAGCAG-----------C---------AGC---AGCAG---------------CAG---CAGCAGCACCAACAT------------------------------------------CAGCAGCA---CCA---G----CAGCAGCAGCAGCA---GCAGCAG---------------CAGCAGCAGCAGCAGC---------AGCAGCAGCAGCAG---CAGCAGCA--GCAG-------------------------------------------------CAAGA---------GAACGGGCAGTGGCAGCA
droPer2	scaffold_3927:134-296 -		AGG-----AGGAGCAG--------------CAGCAG------------------CAGCA---CCAGCAGCAGC--------------AGCAGCCGCAGCAGC---AGC------------------------------AGCAGCAG------------------------------------------CAGCTCCA---GCA---T----CAGCAGCACCAGCAGCAGCAGCCG---------CAGCAGCAGCAGCAGCACCAGC---------ATCAGCAGCGC------CAGCAGCA--TCAG-------------------------------------------------CAGGA---------GAAGGGGCAGTGGCAGCA
droAna3	scaffold_13117:4508234-4508387 -		AGC-----AACTGTTG--------------CACGAATCGCAGCAG---CA---GC---A------------ACAGCAGC--------------------------AGC------------------------AGCA------GCAA----------TACCA-----------------T---------CCGCATCACCTGCATCCGCAC-AGTCTGCC---------GCACCAG---------------CAGCAGCAGCAGCAGC---------AACAGCAGCAA------CAACAGCA--GCAG-------------------------------------------------CAGCA---------ACTGGCCGAGCAGCAGCT
droBip1	scf7180000396569:751647-751818 +		AGC-----AACCGCAT--------------TCACTG------------------CATCA---GCAGCATGGACAGCAGCAACTC--------------------------------------CACGGCCATACACAGCACCAACAT------------------------------------------CATTCCCA---CCA---G----CAGCAGCAGCAACAGCAGCAGCAG---------CAACAACAGCAGCAGCAGCAAC---------ACCATCATCAG------CAGCAGCA--GCAA-------------------------------------------------CACGC---------TCAGCAGCAGCAGCAGCA
droKik1	scf7180000302809:425-574 +		CAG-----C-----A--------------CCAGC------------AGCA---GCAGCA---CC------AGCAGCAGC--------AGC---------------TCCAG---------------CAG---CAGCAGCACCAGCAG------------------------------------------CAGCACCA---CCA---G----CAGCAGCA------------GCAC---------CAGCAGCAGCAGCACCAGCAGC---------AGCAGCACCAG------CAGCAGCAGC-ACA-------------------------------------------------CAGCA---------GCAGCAGCAACAGCAGCA
droFic1	scf7180000453927:1367305-1367458 +		AAT-----CTCTGCCC--------------CGCGAGCAGCAGCAA---------CAGCA------------ACAGCAGC--------------------------AGCAA---------------CAG---CAG----------------------CAGCA-----------------ACAGCAA---CATC---A---GCAACAGCGA-CAGCAGCA---------GCAGCAG---------------CAGCAGCAACAGCAGC---------AACAGCAACAG------CAGCAGCA--GCAG-------------------------------------------------CAACA---------CGAGGAGGAGATGATGAT
droEle1	scf7180000491272:1355171-1355318 +		AGG-----ATCTGGTCAATGCCTCAATTC--------------AG---CAGGAACAGGA---A---------AAGAAGC-----CGCCGC---------AGCC---GC------------------------A---------G---CC------------------------------ACAGCCGCAGCCGC-------------------------------------AACCC---------AAGCTGCAGTTGGAGGTGGAGG---------AGGAGGAGCAG------AAGCAGCA--GCAG-------------------------------------------------GAGGA---------GGAGGAGGAGACGCTGCT
droRho1	scf7180000779985:42982-43120 +		CAA-----C-----A--------------ACAGC------------ACCA---GC---A------------ACAGCAG-----------C---------AGCAGCAACAA---------------C------A---------ACAA------------------------------------------CACA---C---CCAACAGTGCGCAGCAG------------CAGCAG---------CAGCAACATCAGCAGCAGCAAC---------ACCATCAGCAG------CAGCAGCA--GCAGCA---------------------------------TCACCAGC----AGCAA--------------------CGTGTTGTT
droBia1	scf7180000301506:2887178-2887343 +		AGG-----TCTTCATCATCACACGCAATC-AGGGAGC------AGCAGC---------------------AGCAGCAGC--------------------------AGCGGCGGCAG---------CTG---CA------GCAGGAG------------------------------------------GAGCC--G---GCAAC-G----GAGGAG------------CACCAGCAGCAGCAGC---TGCAGGAGGAGGAGGAGG---------AGATGGAGGAG------GAGCAGGA--GCCG-------------------------------------------------TTG-G---------CCAGCAGGCGTCCATGCA
droTak1	scf7180000415313:393808-393959 +		AGCAT----ATCGCCACAGGCCCTTGGC---------------CA---------CAGCA--------------------------GCAGC---------AGCA---GC------------------------A---------A---CAACA----------ACGGCAGCAA-----------------CTCG---C---CCAAGAG----------------------CACCAGCAGCAGCAGC---AGCAGCAGTAGTAGCAGC---------AGCAGCAGCAG------CAGCAGCA--GCGACC---------------------------------A-GCCGACACACAGC-----------------------AACATTCC
droEug1	scf7180000409462:2907155-2907311 -		AGC-----GTCTGCAG--------------CAGCAG------------------CAGGC---CATG---------CAGC-----AGCAGC---------AACA---GC------------------------A---------A---CAACA---------------------------ACAGCAG---CAGC---A---GCAA-------------------------------------------------------CAACAAC---------ACCATCAGCAG------CAGCAGCA--GCAGCAACCCAAAATGGGAGGTGTGCCCAACTTCAATAAGCAA----------CAGCA---------GCAACAGGTGCCGCAGCA
dm3	chrX:1895298-1895441 +		CAA-----C-----A--------------ACAGC------------AGCA---GC---A------------GC--------------------------AGCA---GC------AGCAACAGCAGGCCTCGCCGCATCTCTC---------------------------------------------------------GCT------T-AGCTCACC---------GCACCAGCAGCAGCAGC---AGCAGCAGGGACAGCACC---------AAA------ACCACCACCAGCAAC----AAG-------------------------------------------------GTGGG---------GGTGGCGGAGGAGCTGGT
droSim2	x:8499192-8499336 -		AGC-----AGCAGCTG--------------------------------------CAGTT---GC------AACAACA--------GCAGC---------AGCA---GC------------------------A---------G---CA------------------------------ACAGTTGCAGCTGCAACA---CCAACAG-------CATCA---------GCAGCAG---------CAGCAGCATCAACAGCAACATC---------AACAGCAGCAG------CAGCAGCA--GCAA-------------------------------------------------CAACA---------TCAGGCGCTGCAGCTGTC
droSec2	scaffold_2:3734107-3734264 -		CAG-----T-----A--------------CCAGC------------AACC---GC---AACAGC------AACAACAAC--------------------------AACAG---------------CAA---CAGCTACTGCAACAG------------------------------------------GAGCAGCA---CCA---G----CAACTGCAACAGCA------------------------------ACAGCAGCAGCATCAGCAGCTACTGCAGCAA------CAGCTGCC--ACAG------------------------------------------C----AGCGACGGCAAACGTACAAGGAATACTTGCAGCA
droYak3	X:19447757-19447926 -		GCT-TAGCGCCAGCAG--------------CAGCAG------------------CAGCA---GCAGCAACAGCAACAGC--------AG------------------------------------CAGCAGCAGCAGCAGCAGCAG------------------------------------------CAGCAGCA---ACA---G----CAGCAACAACAGCAGCAGCAGCAA---------CAGCAGCAGCAGCAGCAGCAGC---------AGCAGCAGCAG------CAGCAGCA--GCAG-------------------------------------------------CAGCA---------ACAGCAGCAGCAGCAGCA
droEre2	scaffold_4690:5954367-5954538 +		AGC-----TAATGCTG--------------CAGCAA------------------CAGCA---GCAGCAACAGCAGCAGCAACAA--------------------------------------CAGCAGCTGCAGCAGCAGCAACAA------------------------------------------CAGCAGCT---ACA---G----CAGCAGCAACAACAGCAGCTGCAG---------CAGCAGCAACAACAGCAGCTGC---------AGCAGCAACAA------CTGCAGCA--GCAA-------------------------------------------------CTGCA---------ACAACAGCAGCTGCAACT

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droMoj3

AGG-----ATCTGCTCAATGCCAGCATCC--------------AG---------C---A--------------------------GCAGC---------AGCA---GC------------------------A---------G---CAACAAGCTGTTGCAACGG-AGTTGCTCATCT--------ATGATC---A---CGAACAG----CAGCAG------------CAGCAG---------CAGCAGCAGGAGGAGGAGAAAA---------ATAAGCCCAAG------CAGCAGAA--GCAA-------------------------------------------------CTGGA---------CGAGGAGGAGTCGCTGCT	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
.............................................................................................................................................................................CATCT--------ATGATC---A---CGAACAG----C...............................................................................................................................................................................	20	1	1.00	1	1	0	0	0	0	0
...................................................................................................................................................AACAAGCTGTTGCAACGG-AGTTG.......................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	1
...................................................................................................................................................................................................A---CGAACAG----CAGCAG------------CAGCAG---------CA.............................................................................................................................................	22	10	0.10	1	0	0	0	0	1	0
.....................................................................................................................................................................................................................................AGCAG---------CAGCAGCAGGAGGAGGA..............................................................................................................................	22	20	0.05	1	0	0	0	0	1	0
.....................................................................................................................................................................................................................CAG------------CAGCAG---------CAGCAGCAGG.....................................................................................................................................	19	20	0.05	1	1	0	0	0	0	0
..........................TCC--------------AG---------C---A--------------------------GCAGC---------AGCA---GC------------------------A---------....................................................................................................................................................................................................................................................	19	20	0.05	1	0	0	1	0	0	0

droVir3

AGG-----ATCTGCTAAATGCCAGCATCC--------------AG---------C---A--------------------------GCAGC---------AGCA---GC------------------------A---------G---CAACAGACC------ACAG-AGCTG-----------------TTGA---T---CTACGAG----CAACAG------------GAGCAG---------CTGCAGCAAGAGAAG------------------AAGCCCAAG------CAGCAGAA--GCAG-------------------------------------------------CTCGA---------CGAGGAGGAGTCGCTGTT	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
..................................................................................................................................................CAACAGACC------ACAG-AGCTG-----------------T.....................................................................................................................................................................................................	19	1	2.00	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
.......................................................................................................................................................................................................................................................................................................AGAA--GCAG-------------------------------------------------CTCGA---------CGAGGAGGA.........	22	1	2.00	2	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..........................................................A--------------------------GCAGC---------AGCA---GC------------------------A---------G---CAACAGACC------AC...............................................................................................................................................................................................................................	25	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..............................................................................................................................................G---CAACAGACC------ACAG-AGCT........................................................................................................................................................................................................................	18	1	1.00	1	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
......................................................................................................................................................AGACC------ACAG-AGCTG-----------------TTGA---T---...........................................................................................................................................................................................	19	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
.............................................................................................................................................................................................TGA---T---CTACGAG----CAACAG------------GAGC..........................................................................................................................................................	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
.......................................................................................................................................................................................................CTACGAG----CAACAG------------GAGCAG---------CT.............................................................................................................................................	21	1	1.00	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
...............................................................................................................................................................................................A---T---CTACGAG----CAACAG------------GAGCAG---------CTG............................................................................................................................................	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
..............................................................................................................................................................................................................................................................GAAG------------------AAGCCCAAG------CAGCA..........................................................................................	18	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
...................................................................................................................................................................AG-AGCTG-----------------TTGA---T---CTACGAG----CAACA...........................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
............................................................................................................................................................................................................AG----CAACAG------------GAGCAG---------CTGCAGCA.......................................................................................................................................	22	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	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
........................CATCC--------------AG---------C---A--------------------------GCAGC---------AGCA---........................................................................................................................................................................................................................................................................................	18	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	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
.........................ATCC--------------AG---------C---A--------------------------GCAGC---------AGCA---GC------------------------..............................................................................................................................................................................................................................................................	19	18	0.06	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
.........................ATCC--------------AG---------C---A--------------------------GCAGC---------AGCA---GC------------------------A---------....................................................................................................................................................................................................................................................	20	18	0.06	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droGri2

AGC-----AGCAGCAG--------------CAGCAG------------------CAGCA---GCAGCAGCAGCAGCAGC--------------------------AGC------------------AGCAGCAGCAGCAGCAGCAG------------------------------------------CAGCAGCA---GCA---G----CAGCAGCAGCAGCAGCAGCAGCAG---------CAGCAGCAGCAGCAGCAGCAGC---------AGCAGCAGCAG------CAGCAGCA--GCAG-------------------------------------------------CAGCA---------GCAGCAGCAGCAGCAGCA	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

droWil2

AAC-----ATCAGCAC--------------TGCCAG------------------CAGCA---CCAGCAGCAGTAGCAGCAACAT--------------------------------------CAGCACTGCCAGCAGCACCAGCAG------------------------------------------CAGCACTG---CGA---G----TAGCAGCA---------GCAGCAC---------CAGCAGCAGTAGCAGCAACATC---------AGCACTGCCAG------CAGCACCA--GCAG-------------------------------------------------CAGCA---------CTGCGAGTAGCAGCAGCA	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
..........................................................................................................................................................................................................................................................AGTAGCAGCAACATC---------AGC.............................................................................................................	18	17	0.18	3	0	0	0	3	0
......................................................................AGTAGCAGCAACAT--------------------------------------CAGC....................................................................................................................................................................................................................................................................	18	17	0.18	3	0	0	0	3	0
.....................................................................CAGTAGCAGCAACAT--------------------------------------CAG.....................................................................................................................................................................................................................................................................	18	17	0.12	2	0	0	0	2	0
.........................................................................................................................................................................................................................................................CAGTAGCAGCAACATC---------AG..............................................................................................................	18	17	0.12	2	0	0	0	2	0
.....................................................................CAGTAGCAGCAACAT--------------------------------------CAGCA...................................................................................................................................................................................................................................................................	20	17	0.12	2	0	0	0	2	0
.........................................................................................................................................................................................................................................................CAGTAGCAGCAACATC---------AGCA............................................................................................................	20	17	0.12	2	0	0	0	2	0
....................................................................................................................................................................................................................................................................ACATC---------AGCACTGCCAG------CAGC...........................................................................................	20	9	0.11	1	0	1	0	0	0
...............................................................................AACAT--------------------------------------CAGCACTGCCAGCAG.........................................................................................................................................................................................................................................................	20	9	0.11	1	0	0	0	1	0
................................................................................ACAT--------------------------------------CAGCACTGCCAGCAGC........................................................................................................................................................................................................................................................	20	9	0.11	1	0	1	0	0	0
.AC-----ATCAGCAC--------------TGCCAG------------------CAGC........................................................................................................................................................................................................................................................................................................................................	20	9	0.11	1	0	1	0	0	0
..................................................................................................................................................................................................................................................................CAACATC---------AGCACTGCCAG------CAG............................................................................................	21	9	0.11	1	0	0	0	1	0
...................................................................................................................................................................................................................................................................AACATC---------AGCACTGCCAG------CAG............................................................................................	20	9	0.11	1	0	0	0	1	0
..............................................................................CAACAT--------------------------------------CAGCACTGCCAGCAG.........................................................................................................................................................................................................................................................	21	9	0.11	1	0	0	0	1	0
..........................................................................................................................................................................................................................................................AGTAGCAGCAACATC---------AGCACT..........................................................................................................	21	9	0.11	1	0	1	0	0	0
......................................................................AGTAGCAGCAACAT--------------------------------------CAGCACT.................................................................................................................................................................................................................................................................	21	9	0.11	1	0	1	0	0	0
AAC-----ATCAGCAC--------------TGCCAG------------------CAG.........................................................................................................................................................................................................................................................................................................................................	20	9	0.11	1	0	0	0	1	0
...............................................................CAGCAGCAGTAGCAGCAACAT--------------------------------------CAG.....................................................................................................................................................................................................................................................................	24	10	0.10	1	0	0	0	1	0
.................................................................................................................................................................................................................................................................GCAACATC---------AGCACTGCCAG------CA.............................................................................................	21	10	0.10	1	0	1	0	0	0
...................................................................................................................................................................................................................................................CAGCAGCAGTAGCAGCAACATC---------AG..............................................................................................................	24	10	0.10	1	0	0	0	1	0
.............................................................................GCAACAT--------------------------------------CAGCACTGCCAGCA..........................................................................................................................................................................................................................................................	21	10	0.10	1	0	1	0	0	0
..........................................................................................................................................................................................................................................................AGTAGCAGCAACATC---------AGCA............................................................................................................	19	17	0.06	1	0	0	0	1	0
......................................................................AGTAGCAGCAACAT--------------------------------------CAGCA...................................................................................................................................................................................................................................................................	19	17	0.06	1	0	0	0	1	0

dp5

AGC-----AGCAGCAC--------------CAACAT------------------CAGCA---GCCGC---AGCAGCAG-----------C---------AGC---AGCAG---------------CAG---CAGCAGCACCAACAT------------------------------------------CAGCAGCA---CCA---G----CAGCAGCAGCAGCA---GCAGCAG---------------CAGCAGCAGCAGCAGC---------AGCAGCAGCAGCAG---CAGCAGCA--GCAG-------------------------------------------------CAAGA---------GAACGGGCAGTGGCAGCA	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
..................................................................................................................................................................................................................................................................................................................................................................CAAGA---------GAACGGGCAGTGG.....	18	11	16.91	186	0	120	0	0	2	0	1	62	1	0
..................................................................................................................................................................................................................................................................................................................................................................CAAGA---------GAACGGGCAGTGGCAGC.	22	11	10.00	110	0	90	1	1	1	2	5	10	0	0
..................................................................................................................................................................................................................................................................................................................................................................CAAGA---------GAACGGGCAGTGGCAG..	21	11	8.82	97	0	87	1	0	0	1	2	6	0	0
...............................................................................................................................................................................................................................................................................................................AG-------------------------------------------------CAAGA---------GAACGGGCAGTGG.....	20	11	8.00	88	0	0	0	0	0	0	0	88	0	0
..................................................................................................................................................................................................................................................................................................................................................................CAAGA---------GAACGGGCAGTGGC....	19	11	7.09	78	0	67	2	0	4	0	2	3	0	0
..................................................................................................................................................................................................................................................................................................................................................................CAAGA---------GAACGGGCAGTGGCAGCA	23	11	5.27	58	0	53	0	0	0	0	3	2	0	0
...............................................................................................................................................................................................................................................................................................................AG-------------------------------------------------CAAGA---------GAACGGGCAGTGGCAG..	23	11	2.18	24	0	3	0	0	0	0	0	21	0	0
...................................................................................................................................................................................................................................................................................................................................................................AAGA---------GAACGGGCAGTGGCAGC.	21	11	1.45	16	0	16	0	0	0	0	0	0	0	0
...............................................................................................................................................................................................................................................................................................................AG-------------------------------------------------CAAGA---------GAACGGGCAGTGGC....	21	11	1.36	15	0	6	1	0	0	0	0	8	0	0
.................................................................................................................................................T------------------------------------------CAGCAGCA---CCA---G----CAGCAGCAG.......................................................................................................................................................................	22	10	1.30	13	0	6	0	0	0	0	0	7	0	0
..................................................................................................................................................................................................................................................................................................................................................................CAAGA---------GAACGGGCAGTGGCA...	20	11	1.27	14	0	14	0	0	0	0	0	0	0	0
................................................................................................................................................................................................................................................................................................................G-------------------------------------------------CAAGA---------GAACGGGCAGTGG.....	19	11	1.18	13	0	3	0	0	0	0	0	10	0	0
...............................................................................................................................................................................................................................................................................................................AG-------------------------------------------------CAAGA---------GAACGGGCAGTGGCA...	22	11	0.91	10	0	2	0	0	0	0	0	8	0	0
...................................................................................................................................................................................................................................................................................................................................................................AAGA---------GAACGGGCAGTGGC....	18	11	0.82	9	0	9	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................................................................................................................AAGA---------GAACGGGCAGTGGCAG..	20	11	0.73	8	0	7	1	0	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................................................................................................................AAGA---------GAACGGGCAGTGGCAGCA	22	11	0.64	7	0	7	0	0	0	0	0	0	0	0
..............................................................................................................................................................................................................................................................................................................CAG-------------------------------------------------CAAGA---------GAACGGGCAGTGG.....	21	11	0.55	6	0	4	0	0	0	0	0	2	0	0
..........................................................................................................................................ACCAACAT------------------------------------------CAGCAGCA---CCA---G----CA..............................................................................................................................................................................	22	2	0.50	1	0	1	0	0	0	0	0	0	0	0
...........................................................................................................................................CCAACAT------------------------------------------CAGCAGCA---CCA---G----CAGC............................................................................................................................................................................	23	2	0.50	1	0	1	0	0	0	0	0	0	0	0
..........................................................................................................................................ACCAACAT------------------------------------------CAGCAGCA---CCA---G----CAGCA...........................................................................................................................................................................	25	2	0.50	1	0	1	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................................................................................................................................................CAAGA---------GAACGGGCAGTGGCAGT.	22	11	0.45	5	0	3	2	0	0	0	0	0	0	0
...............................................................................................................................................................................................................................................................................................................AG-------------------------------------------------CAAGA---------GAACGGGCAGTGGCAGC.	24	11	0.45	5	0	1	0	0	0	0	0	4	0	0
....................................................................................................................................................................................................................................................................................................................................................................AGA---------GAACGGGCAGTGGCAGC.	20	11	0.36	4	0	4	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................................................................................................................AAGA---------GAACGGGCAGTGG.....	17	11	0.36	4	0	0	0	0	0	0	0	4	0	0
..............................................................................................................................................................................................................................................................................................................CAG-------------------------------------------------CAAGA---------GAACGGGCAGTG......	20	11	0.36	4	0	2	0	0	1	0	0	1	0	0
..................................................................................................................................................................................................................................................................................................................................................................CAAGA---------GAACGGGCAGTGGA....	19	11	0.36	4	0	3	0	0	1	0	0	0	0	0
.................................................................................................................................................T------------------------------------------CAGCAGCA---CCA---G----CAGCAGCAGC......................................................................................................................................................................	23	10	0.30	3	0	3	0	0	0	0	0	0	0	0
........................................................................................................................................................................................................................................................................................................GCA--GCAG-------------------------------------------------CAAGA---------GAACGGGCAGTGG.....	25	11	0.27	3	0	0	0	0	0	0	0	3	0	0
..................................................................................................................................................................................................................................................................................................................................................................CAAGA---------GAACGGGCAGTGGT....	19	11	0.27	3	0	3	0	0	0	0	0	0	0	0
..............AC--------------CAACAT------------------CAGCA---GCCGC---AGC.........................................................................................................................................................................................................................................................................................................................	21	15	0.27	4	0	1	0	1	2	0	0	0	0	0
..............AC--------------CAACAT------------------CAGCA---GCCGC---AGCAG.......................................................................................................................................................................................................................................................................................................................	23	15	0.27	4	0	4	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................................................CAGCAGCA--GCAG-------------------------------------------------CAAGA---------GAACGGG...........	24	13	0.23	3	0	0	0	0	0	0	0	3	0	0
...................................................................................................................................................................................................................................................................................................CAGCAGCA--GCAG-------------------------------------------------CAAGA---------GAACGG............	23	13	0.23	3	0	0	0	0	0	0	0	3	0	0
.................................................................................................................................................T------------------------------------------CAGCAGCA---CCA---G----CAGCAGCAGCAG....................................................................................................................................................................	25	9	0.22	2	0	1	0	0	0	0	0	1	0	0
.................................................................................................................................................T------------------------------------------CAGCAGCA---CCA---G----CAGCAGCAGCA.....................................................................................................................................................................	24	10	0.20	2	0	1	0	0	1	0	0	0	0	0
..................................................................................................................................................................................................................................................................................................................................................................CAAGA---------GAACGGGCAGTGGCAGA.	22	11	0.18	2	0	2	0	0	0	0	0	0	0	0
...............................................................................................................................................................................................................................................................................................................AG-------------------------------------------------CAAGA---------GAACGGGCAGTGGA....	21	11	0.18	2	0	0	0	0	0	0	0	2	0	0
.........................................................................................................................................................................................................................................................................................................CA--GCAG-------------------------------------------------CAAGA---------GAACGGGCAGTGG.....	24	11	0.18	2	0	1	0	0	0	0	0	1	0	0
..................................................................................................................................................................................................................................................................................................................................................................CAAGA---------GAACGGGCAGTGA.....	18	11	0.18	2	0	2	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................................................................................................................................................CAAGA---------GAACGGGCAGTGGCAA..	21	11	0.18	2	0	2	0	0	0	0	0	0	0	0
..............AC--------------CAACAT------------------CAGCA---GCCGC---AGCAGCAG-----------.........................................................................................................................................................................................................................................................................................................	26	11	0.18	2	0	2	0	0	0	0	0	0	0	0
................................................................................................................................................................................................................................................................................................................G-------------------------------------------------CAAGA---------GAACGGGCAGTGGC....	20	11	0.18	2	0	1	0	0	0	0	0	1	0	0
................................................................................................................................................................................................................................................................................................................G-------------------------------------------------CAAGA---------GAACGGGCAGTGGCA...	21	11	0.18	2	0	1	0	0	0	0	0	1	0	0
...............................AACAT------------------CAGCA---GCCGC---AGCAGCAG-----------.........................................................................................................................................................................................................................................................................................................	23	11	0.18	2	0	2	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................................................................................................................................................AGA---------GAACGGGCAGTGGCAGCA	21	11	0.18	2	0	2	0	0	0	0	0	0	0	0
................................................................................................................................................................................................................................................................................................................G-------------------------------------------------CAAGA---------GAACGGGCAGTGGCAGCA	24	11	0.18	2	0	0	0	0	0	0	0	2	0	0
..............................................................................................................................................................................................................................................................................................................CAG-------------------------------------------------CAAGA---------GAACGGGCAGTGGCAGC.	25	11	0.18	2	0	0	0	0	0	0	0	2	0	0
.................................................................................................................................................T------------------------------------------CAGCAGCA---CCA---G----CAGCAGCA........................................................................................................................................................................	21	12	0.17	2	0	2	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................................................................................................................................................CAAGA---------GAACGGGCAGTGT.....	18	12	0.17	2	0	1	0	0	1	0	0	0	0	0
..................................................................................................................................................................................................................................................................................................................................................................CAAGA---------GAACGGGCAGTGGCATAT	23	12	0.17	2	0	0	0	0	0	0	0	2	0	0
.......................................................................................................................................................................................................................................................................................................AGCA--GCAG-------------------------------------------------CAAGA---------GAACGGGC..........	21	13	0.15	2	0	2	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................................................................................................................CA--GCAG-------------------------------------------------CAAGA---------GAACGGGCA.........	20	13	0.15	2	0	1	0	0	0	0	0	1	0	0
..............AC--------------CAACAT------------------CAGCA---GCCGC---AG..........................................................................................................................................................................................................................................................................................................................	20	15	0.13	2	0	2	0	0	0	0	0	0	0	0
...............................................................................................................................................CAT------------------------------------------CAGCAGCA---CCA---G----CAGCAGC.........................................................................................................................................................................	22	8	0.13	1	0	1	0	0	0	0	0	0	0	0
................................................................................................................................................AT------------------------------------------CAGCAGCA---CCA---G----CAGCAGCAGC......................................................................................................................................................................	24	8	0.13	1	0	1	0	0	0	0	0	0	0	0
......................................................................................................................................................................................................................................................................AGC---------AGCAGCAGCAGCAG---CAGC...........................................................................................	21	20	0.10	2	0	2	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................................................................AGCAGCAGCAGCAG---CAGCAGC........................................................................................	21	20	0.10	2	0	2	0	0	0	0	0	0	0	0
........................................................................................................................................................................................................................................................................................AGCAGCAG---CAGCAGCA--GCAG-------------------------------------------------C...............................	21	20	0.10	2	0	2	0	0	0	0	0	0	0	0
...........................................................................................................................................................................................................................CAGCA---GCAGCAG---------------CAGCAG...................................................................................................................................	18	20	0.10	2	0	2	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................................................................................................................AGCAGCAGCAG---CAGCAGCA--GC...................................................................................	21	20	0.10	2	0	2	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................................................CAGCAGCAGCA---GCAGCAG---------------CAG......................................................................................................................................	21	20	0.10	2	0	2	0	0	0	0	0	0	0	0
................................................................................................................................................................................................................................................................AGCAGCAGC---------AGCAGCAGCAGC....................................................................................................	21	20	0.10	2	0	2	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................AGCAGC---------AGCAGCAGCAGCAG---C..............................................................................................	21	20	0.10	2	0	2	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................................................................................................................................................................................................GA---------GAACGGGCAGTGGCAGCA	20	11	0.09	1	0	1	0	0	0	0	0	0	0	0
...............................AACAT------------------CAGCA---GCCGC---AGCAGCAG-----------C---------AGC---.........................................................................................................................................................................................................................................................................................	27	11	0.09	1	0	1	0	0	0	0	0	0	0	0
...............................AACAT------------------CAGCA---GCCGC---AGCAGCAG-----------C---------AG.............................................................................................................................................................................................................................................................................................	26	11	0.09	1	0	1	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................................................................................................................AAGA---------GAACGGGCAGTGGCA...	19	11	0.09	1	0	1	0	0	0	0	0	0	0	0
..............................................................................................................................................................................................................................................................................................................CAG-------------------------------------------------CAAGA---------GAACGGGCAGTGGCAGCC	26	11	0.09	1	0	0	1	0	0	0	0	0	0	0
.....................................................................................................................................................................................................................................................................................................................................................................GA---------GAACGGGCAGTGGCAG..	18	11	0.09	1	0	1	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................................................................................................................................................AGA---------GAACGGGCAGTGGCA...	18	11	0.09	1	0	1	0	0	0	0	0	0	0	0
..............AC--------------CAACAT------------------CAGCA---GCCGC---AGCAGCAG-----------C---------...............................................................................................................................................................................................................................................................................................	27	11	0.09	1	0	1	0	0	0	0	0	0	0	0
...............................................................................................................................................................................................................................................................................................................AG-------------------------------------------------CAAGA---------GAACGGGCAGTGGCAGG.	24	11	0.09	1	0	0	0	0	0	0	0	1	0	0
................................................................................................................................................................................................................................................................................................................G-------------------------------------------------CAAGA---------GAACGGGCAGTGGCAG..	22	11	0.09	1	0	0	0	0	0	0	0	1	0	0
...................................................................................................................................................................................................................................................................................................................................................................AAGA---------GAACGGGCAGTGGCAGT.	21	11	0.09	1	0	1	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................................................................................................................CA--GCAG-------------------------------------------------CAAGA---------GAACGGGCAGT.......	22	11	0.09	1	0	1	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................................................................................................................................AGCA--GCAG-------------------------------------------------CAAGA---------GAACGGGCAGT.......	24	11	0.09	1	0	1	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................................................................................................................................................AGA---------GAACGGGCAGTGGCAG..	19	11	0.09	1	0	1	0	0	0	0	0	0	0	0
................................................................................................................................................................................................................................................................................................................G-------------------------------------------------CAAGA---------GAACGGGCAGTGGCAGC.	23	11	0.09	1	0	1	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................................................................................................................................................CAAGA---------GAACGGGCAGTGGCAGTT	23	11	0.09	1	0	1	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................................................................................................................................................AGA---------GAACGGGCAGTGGCAGT.	20	11	0.09	1	0	1	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................................................................................................................AAGA---------GAACGGGCAGTGGCAGCC	22	11	0.09	1	0	1	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................................................................................................................................................CAAGA---------GAACGGGCAGTGC.....	18	12	0.08	1	0	0	1	0	0	0	0	0	0	0
......................................................................................................................................................................................................................................................................................................CAGCA--GCAG-------------------------------------------------CAAGA---------GAACGGGCAG........	24	13	0.08	1	0	0	0	0	0	0	0	1	0	0
..............AC--------------CAACAT------------------CAGCA---GCCGC---AGCAGCA.....................................................................................................................................................................................................................................................................................................................	25	13	0.08	1	0	1	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................................................CAGCAGCA--GCAG-------------------------------------------------CAAGA---------GAACGGGCA.........	26	13	0.08	1	0	1	0	0	0	0	0	0	0	0
...............................AACAT------------------CAGCA---GCCGC---AGCAGCA.....................................................................................................................................................................................................................................................................................................................	22	13	0.08	1	0	1	0	0	0	0	0	0	0	0
...............C--------------CAACAT------------------CAGCA---GCCGC---AGCAGCA.....................................................................................................................................................................................................................................................................................................................	24	13	0.08	1	0	1	0	0	0	0	0	0	0	0
.............................................................................................................................................................................................................................................................................................CAG---CAGCAGCA--GCAG-------------------------------------------------CAAGA---------GAACGG............	26	13	0.08	1	0	0	0	0	0	0	0	1	0	0
......................................................................................................................................................................................................................................................................................................CAGCA--GCAG-------------------------------------------------CAAGA---------GAACGGG...........	21	13	0.08	1	0	0	0	0	0	0	0	0	1	0
..................................................................................................................................................................................................................................................................................................................................................................CAAGA---------GAACGGGCAGTGAA....	19	13	0.08	1	0	1	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................................................................................................................................AGCA--GCAG-------------------------------------------------CAAGA---------GAACG.............	18	13	0.08	1	0	1	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................................................................................................................................AGCA--GCAG-------------------------------------------------CAAGA---------GAACGGG...........	20	13	0.08	1	0	1	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................................................................................................................................AGCA--GCAG-------------------------------------------------CAAGA---------GAACGG............	19	13	0.08	1	0	0	0	0	0	0	0	1	0	0
.............................................................................................................................................................................................................................................................................................CAG---CAGCAGCA--GCAG-------------------------------------------------CAAGA---------GAAC..............	24	13	0.08	1	0	1	0	0	0	0	0	0	0	0
.................................................................................................................................................T------------------------------------------CAGCAGCA---CCA---G----CAGCAG..........................................................................................................................................................................	19	14	0.07	1	0	1	0	0	0	0	0	0	0	0
..............................CAACAT------------------CAGCA---GCCGC---AGCAG.......................................................................................................................................................................................................................................................................................................................	21	15	0.07	1	0	0	0	0	0	0	0	1	0	0
.............CAC--------------CAACAT------------------CAGCA---GCCGC---AGCA........................................................................................................................................................................................................................................................................................................................	23	15	0.07	1	0	1	0	0	0	0	0	0	0	0
..............AC--------------CAACAT------------------CAGCA---GCCGC---A...........................................................................................................................................................................................................................................................................................................................	19	15	0.07	1	0	1	0	0	0	0	0	0	0	0
..............AC--------------CAACAT------------------CAGCA---GCCGC---AGCA........................................................................................................................................................................................................................................................................................................................	22	15	0.07	1	0	1	0	0	0	0	0	0	0	0
...............................AACAT------------------CAGCA---GCCGC---AGCAG.......................................................................................................................................................................................................................................................................................................................	20	15	0.07	1	0	1	0	0	0	0	0	0	0	0
..................................AT------------------CAGCA---GCCGC---AGCAGCAG-----------.........................................................................................................................................................................................................................................................................................................	20	15	0.07	1	0	1	0	0	0	0	0	0	0	0
...............C--------------CAACAT------------------CAGCA---GCCGC---AGCA........................................................................................................................................................................................................................................................................................................................	21	15	0.07	1	0	1	0	0	0	0	0	0	0	0
.............CAC--------------CAACAT------------------CAGCA---GCCGC---AGCAG.......................................................................................................................................................................................................................................................................................................................	24	15	0.07	1	0	1	0	0	0	0	0	0	0	0
.............CAC--------------CAACAT------------------CAGCA---GCCGC---A...........................................................................................................................................................................................................................................................................................................................	20	15	0.07	1	0	1	0	0	0	0	0	0	0	0
...............C--------------CAACAT------------------CAGCA---GCCGC---AGCAGC......................................................................................................................................................................................................................................................................................................................	23	15	0.07	1	0	0	1	0	0	0	0	0	0	0
...............C--------------CAACAT------------------CAGCA---GCCGC---AGCAG.......................................................................................................................................................................................................................................................................................................................	22	15	0.07	1	0	1	0	0	0	0	0	0	0	0
...............................................................................................................................................CAT------------------------------------------CAGCAGCA---CCA---G----CAGC............................................................................................................................................................................	19	16	0.06	1	0	1	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................................................................................................................................................CAAGA---------GAACGGGCAGTAC.....	18	17	0.06	1	0	1	0	0	0	0	0	0	0	0
................................................................................................................................................AT------------------------------------------CAGCAGCA---CCA---G----CAGCA...........................................................................................................................................................................	19	17	0.06	1	0	1	0	0	0	0	0	0	0	0
..............................CAACAT------------------CAGCA---GCCGC---AG..........................................................................................................................................................................................................................................................................................................................	18	17	0.06	1	0	1	0	0	0	0	0	0	0	0
..........................................................................................................................................................................................................................................................................................CAGCAG---CAGCAGCA--GCAG-------------------------------------------------CAAGA---------GAA...............	26	18	0.06	1	0	1	0	0	0	0	0	0	0	0
..........................................................................................................................................................................................................................................................................................CAGCAG---CAGCAGCA--GCAG-------------------------------------------------CAAGA---------GA................	25	18	0.06	1	0	1	0	0	0	0	0	0	0	0
..........................................................................................................GCAG---------------CAG---CAGCAGCACCAACAT------------------------------------------C.....................................................................................................................................................................................................	23	20	0.05	1	0	1	0	0	0	0	0	0	0	0
............................................................................................................................................................................................................................................................CAGCAGCAGCAGC---------AGCAGCAGCAGCAG---...............................................................................................	27	20	0.05	1	0	1	0	0	0	0	0	0	0	0
............................................................................................................................................................................................CAGCAGCA---CCA---G----CAGCAGCAGCA.....................................................................................................................................................................	23	20	0.05	1	0	1	0	0	0	0	0	0	0	0
.........................................................................AGCAG-----------C---------AGC---AGCAG---------------CAG---CAGCA..........................................................................................................................................................................................................................................................	22	20	0.05	1	0	0	0	0	0	1	0	0	0	0
..............................................................................................................................................................................................................................................................................................AG---CAGCAGCA--GCAG-------------------------------------------------CAAGA---------..................	19	20	0.05	1	0	1	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................................................CAGCAGCAGCA---GCAGCAG---------------CAGCAGCA.................................................................................................................................	26	20	0.05	1	0	0	0	0	1	0	0	0	0	0
.........................................................................................................................................................................................................................................................CAGCAGCAGCAGCAGC---------AGCAGCAGCAG.....................................................................................................	27	20	0.05	1	0	1	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................................................................CAG---------------CAGCAGCAGCAGCAGC---------AGCAGCAG........................................................................................................	27	20	0.05	1	0	1	0	0	0	0	0	0	0	0
........................................................................................................................................................................................................................................................................C---------AGCAGCAGCAGCAG---CAGCAGCA--GCAG-------------------------------------------------................................	27	20	0.05	1	0	1	0	0	0	0	0	0	0	0
...............................................................................................................................................................................................................................................................CAGCAGCAGC---------AGCAGCAGCAGCAG---CAG............................................................................................	27	20	0.05	1	0	1	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................................................CAGCAGC---------AGCAGCAGCAGCAG---CAGCAG.........................................................................................	27	20	0.05	1	0	1	0	0	0	0	0	0	0	0
.............................................................................................................................CAG---CAGCAGCACCAACAT------------------------------------------CAGCAG................................................................................................................................................................................................	24	20	0.05	1	0	1	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................................AGCAGCA---GCAGCAG---------------CAGCAGC..................................................................................................................................	21	20	0.05	1	0	0	1	0	0	0	0	0	0	0
.....................................................................................................................................................................................................................................................................CAGC---------AGCAGCAGCAGCAG---CAGCAGCA--G....................................................................................	27	20	0.05	1	0	1	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................GCAGCAGCAGCA---GCAGCAG---------------CAGCA....................................................................................................................................	24	20	0.05	1	0	1	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................................................................................................................................................CAAGA---------GAACGGGCAGTCTA....	19	20	0.05	1	0	1	0	0	0	0	0	0	0	0
....................................................................................................GC---AGCAG---------------CAG---CAGCAGCA.......................................................................................................................................................................................................................................................	18	20	0.05	1	0	1	0	0	0	0	0	0	0	0
......................................................CAGCA---GCCGC---AGCAGCAG-----------C---------A..............................................................................................................................................................................................................................................................................................	20	20	0.05	1	0	1	0	0	0	0	0	0	0	0

droPer2

AGG-----AGGAGCAG--------------CAGCAG------------------CAGCA---CCAGCAGCAGC--------------AGCAGCCGCAGCAGC---AGC------------------------------AGCAGCAG------------------------------------------CAGCTCCA---GCA---T----CAGCAGCACCAGCAGCAGCAGCCG---------CAGCAGCAGCAGCAGCACCAGC---------ATCAGCAGCGC------CAGCAGCA--TCAG-------------------------------------------------CAGGA---------GAAGGGGCAGTGGCAGCA	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
......................................................................................................................................................................................................................................................................AGC---------ATCAGCAGCGC------CAGCAGC........................................................................................	21	3	0.33	1	0	1	0	0	0	0
....................................................................................................................................................................................................................................................................CCAGC---------ATCAGCAGCGC------CAGCAG.........................................................................................	22	3	0.33	1	0	1	0	0	0	0
....................................................................................................................................................................................................................................................................CCAGC---------ATCAGCAGCGC------CAGCAGC........................................................................................	23	3	0.33	1	0	0	1	0	0	0
....................................................................................................................................................................................................................................................AGCAGCAGCAGCAGCACCAGC---------AT..............................................................................................................	23	5	0.20	1	0	1	0	0	0	0
.......................................................................................................................................................................................................................................................AGCAGCAGCAGCACCAGC---------ATCAGCA.........................................................................................................	25	5	0.20	1	0	1	0	0	0	0
........................................................................................................................................................................................................................................................................C---------ATCAGCAGCGC------CAGCAG.........................................................................................	18	6	0.17	1	0	1	0	0	0	0
.......................................................................................................................................................................................................................................CCG---------CAGCAGCAGCAGCAGCACCAGC---------................................................................................................................	25	6	0.17	1	0	1	0	0	0	0
..................................................................................................................................................................................................CA---GCA---T----CAGCAGCACCAGCAGC................................................................................................................................................................	22	8	0.13	1	0	0	1	0	0	0
...........................................................................................................................................................................................................................CAGCAGCAGCAGCCG---------CAGCAGCA.......................................................................................................................................	23	20	0.05	1	0	1	0	0	0	0
.....................................................................CAGC--------------AGCAGCCGCAGCAGC---AGC------------------------------A.......................................................................................................................................................................................................................................................	23	20	0.05	1	0	1	0	0	0	0
..............................................................................................................................................................................................................................CAGCAGCAGCCG---------CAGCAGCAGCA....................................................................................................................................	23	20	0.05	1	0	1	0	0	0	0
..................................................................CAGCAGC--------------AGCAGCCGCAGCAGC---A........................................................................................................................................................................................................................................................................................	23	20	0.05	1	0	1	0	0	0	0

droAna3

AGC-----AACTGTTG--------------CACGAATCGCAGCAG---CA---GC---A------------ACAGCAGC--------------------------AGC------------------------AGCA------GCAA----------TACCA-----------------T---------CCGCATCACCTGCATCCGCAC-AGTCTGCC---------GCACCAG---------------CAGCAGCAGCAGCAGC---------AACAGCAGCAA------CAACAGCA--GCAG-------------------------------------------------CAGCA---------ACTGGCCGAGCAGCAGCT	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
.....................................................................................................................................................................................................................................................................CAGC---------AACAGCAGCAA------CAACAGCA--GCAG-------------------------------------------------C...............................	28	10	0.10	1	0	0	0	0	0	1
....................................................................................................................................................................................................................................CACCAG---------------CAGCAGCAGCAGCAGC---------AAC.............................................................................................................	25	14	0.07	1	0	1	0	0	0	0
........................................................................................................................................................................................................................................................................C---------AACAGCAGCAA------CAACAGCA--GCAG-------------------------------------------------C...............................	25	15	0.07	1	0	1	0	0	0	0
.....................................................................................................................................................................................................................................ACCAG---------------CAGCAGCAGCAGCAGC---------AAC.............................................................................................................	24	19	0.05	1	1	0	0	0	0	0
.............................................................................................................................................................................................................................................................AGCAGCAGCAGC---------AACAGC..........................................................................................................	18	20	0.05	1	0	0	0	0	0	1
.........................................................................................................................................................................................................................................................CAGCAGCAGCAGCAGC---------AACAGCAGCA......................................................................................................	26	20	0.05	1	1	0	0	0	0	0
......................................GCAGCAG---CA---GC---A------------ACAGCAGC--------------------------.........................................................................................................................................................................................................................................................................................	20	20	0.05	1	0	0	0	0	1	0
......................................................................................................................................................................................................................................................................AGC---------AACAGCAGCAA------CAACAGC........................................................................................	21	20	0.05	1	0	1	0	0	0	0
....................................................................................................................................................................................................................................CACCAG---------------CAGCAGCAGCAGCAGC---------A...............................................................................................................	23	20	0.05	1	1	0	0	0	0	0
........................................................................................................................................................................................................................................................................C---------AACAGCAGCAA------CAACAGCA--GCA..................................................................................	23	20	0.05	1	0	1	0	0	0	0
............................................G---CA---GC---A------------ACAGCAGC--------------------------AGC------------------------AGCA------GCA.................................................................................................................................................................................................................................................	24	20	0.05	1	0	1	0	0	0	0
..........................................................................................................................................................................................................................................................................................CAA------CAACAGCA--GCAG-------------------------------------------------CAGC............................	19	20	0.05	1	1	0	0	0	0	0
................................................................................................................................................................................................................................................................AGCAGCAGC---------AACAGCAGC.......................................................................................................	18	20	0.05	1	0	1	0	0	0	0
...........................................AG---CA---GC---A------------ACAGCAGC--------------------------AGC------------------------AGCA------GCA.................................................................................................................................................................................................................................................	25	20	0.05	1	0	0	0	0	0	1
....................................................................................................................................................................................................................................CACCAG---------------CAGCAGCAGCAGCAGC---------................................................................................................................	22	20	0.05	1	0	1	0	0	0	0
.......................................................................................................................................................................................................................................................................................CAGCAA------CAACAGCA--GCAG-------------------------------------------------C...............................	19	20	0.05	1	1	0	0	0	0	0
.........................................GCAG---CA---GC---A------------ACAGCAGC--------------------------AGC------------------------A.............................................................................................................................................................................................................................................................	21	20	0.05	1	0	0	0	0	0	1
.......................................................................................................................................................................................................................................................................................................AGCA--GCAG-------------------------------------------------CAGCA---------ACTGGG............	19	20	0.05	1	1	0	0	0	0	0
.........................................................................................................................................................................................................................................................................................GCAA------CAACAGCA--GCAG-------------------------------------------------CAGCA---------..................	21	20	0.05	1	0	0	0	0	0	1

droBip1

AGC-----AACCGCAT--------------TCACTG------------------CATCA---GCAGCATGGACAGCAGCAACTC--------------------------------------CACGGCCATACACAGCACCAACAT------------------------------------------CATTCCCA---CCA---G----CAGCAGCAGCAACAGCAGCAGCAG---------CAACAACAGCAGCAGCAGCAAC---------ACCATCATCAG------CAGCAGCA--GCAA-------------------------------------------------CACGC---------TCAGCAGCAGCAGCAGCA	Size	Hit Count	Total Norm	Total
No Reads

droKik1

CAG-----C-----A--------------CCAGC------------AGCA---GCAGCA---CC------AGCAGCAGC--------AGC---------------TCCAG---------------CAG---CAGCAGCACCAGCAG------------------------------------------CAGCACCA---CCA---G----CAGCAGCA------------GCAC---------CAGCAGCAGCAGCACCAGCAGC---------AGCAGCACCAG------CAGCAGCAGC-ACA-------------------------------------------------CAGCA---------GCAGCAGCAACAGCAGCA	Size	Hit Count	Total Norm	Total
No Reads

droFic1

AAT-----CTCTGCCC--------------CGCGAGCAGCAGCAA---------CAGCA------------ACAGCAGC--------------------------AGCAA---------------CAG---CAG----------------------CAGCA-----------------ACAGCAA---CATC---A---GCAACAGCGA-CAGCAGCA---------GCAGCAG---------------CAGCAGCAACAGCAGC---------AACAGCAACAG------CAGCAGCA--GCAG-------------------------------------------------CAACA---------CGAGGAGGAGATGATGAT	Size	Hit Count	Total Norm	Total
No Reads

droEle1

AGG-----ATCTGGTCAATGCCTCAATTC--------------AG---CAGGAACAGGA---A---------AAGAAGC-----CGCCGC---------AGCC---GC------------------------A---------G---CC------------------------------ACAGCCGCAGCCGC-------------------------------------AACCC---------AAGCTGCAGTTGGAGGTGGAGG---------AGGAGGAGCAG------AAGCAGCA--GCAG-------------------------------------------------GAGGA---------GGAGGAGGAGACGCTGCT	Size	Hit Count	Total Norm	Total
No Reads

droRho1

CAA-----C-----A--------------ACAGC------------ACCA---GC---A------------ACAGCAG-----------C---------AGCAGCAACAA---------------C------A---------ACAA------------------------------------------CACA---C---CCAACAGTGCGCAGCAG------------CAGCAG---------CAGCAACATCAGCAGCAGCAAC---------ACCATCAGCAG------CAGCAGCA--GCAGCA---------------------------------TCACCAGC----AGCAA--------------------CGTGTTGTT	Size	Hit Count	Total Norm	Total
No Reads

droBia1

AGG-----TCTTCATCATCACACGCAATC-AGGGAGC------AGCAGC---------------------AGCAGCAGC--------------------------AGCGGCGGCAG---------CTG---CA------GCAGGAG------------------------------------------GAGCC--G---GCAAC-G----GAGGAG------------CACCAGCAGCAGCAGC---TGCAGGAGGAGGAGGAGG---------AGATGGAGGAG------GAGCAGGA--GCCG-------------------------------------------------TTG-G---------CCAGCAGGCGTCCATGCA	Size	Hit Count	Total Norm	Total
No Reads

droTak1

AGCAT----ATCGCCACAGGCCCTTGGC---------------CA---------CAGCA--------------------------GCAGC---------AGCA---GC------------------------A---------A---CAACA----------ACGGCAGCAA-----------------CTCG---C---CCAAGAG----------------------CACCAGCAGCAGCAGC---AGCAGCAGTAGTAGCAGC---------AGCAGCAGCAG------CAGCAGCA--GCGACC---------------------------------A-GCCGACACACAGC-----------------------AACATTCC	Size	Hit Count	Total Norm	Total
No Reads

droEug1

AGC-----GTCTGCAG--------------CAGCAG------------------CAGGC---CATG---------CAGC-----AGCAGC---------AACA---GC------------------------A---------A---CAACA---------------------------ACAGCAG---CAGC---A---GCAA-------------------------------------------------------CAACAAC---------ACCATCAGCAG------CAGCAGCA--GCAGCAACCCAAAATGGGAGGTGTGCCCAACTTCAATAAGCAA----------CAGCA---------GCAACAGGTGCCGCAGCA	Size	Hit Count	Total Norm	Total
No Reads

dm3

CAA-----C-----A--------------ACAGC------------AGCA---GC---A------------GC--------------------------AGCA---GC------AGCAACAGCAGGCCTCGCCGCATCTCTC---------------------------------------------------------GCT------T-AGCTCACC---------GCACCAGCAGCAGCAGC---AGCAGCAGGGACAGCACC---------AAA------ACCACCACCAGCAAC----AAG-------------------------------------------------GTGGG---------GGTGGCGGAGGAGCTGGT	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
..............................................................................................................................................................................................................................................................................................................AAG-------------------------------------------------GTGGG---------GGTGGCGGAGGAG.....	21	1	3.00	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...........................................................................................................................................................................................................................................................................................ACCACCACCAGCAAC----AAG-------------------------------------------------G...............................	19	2	2.50	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.........................................................................................................................GCAGGCCTCGCCGCATCTCTC---------------------------------------------------------GCT------..................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
..........................................................A------------GC--------------------------AGCA---GC------AGCAACAGCAGGCCTCG...............................................................................................................................................................................................................................................................	26	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	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
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........................................................................................................................................................................................................................................AGCAGCAGCAGC---AGCAGCAGG..................................................................................................................................	21	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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

droSim2

AGC-----AGCAGCTG--------------------------------------CAGTT---GC------AACAACA--------GCAGC---------AGCA---GC------------------------A---------G---CA------------------------------ACAGTTGCAGCTGCAACA---CCAACAG-------CATCA---------GCAGCAG---------CAGCAGCATCAACAGCAACATC---------AACAGCAGCAG------CAGCAGCA--GCAA-------------------------------------------------CAACA---------TCAGGCGCTGCAGCTGTC	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
..............................................................GC------AACAACA--------GCAGC---------AGCA---G.......................................................................................................................................................................................................................................................................................	19	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0

droSec2

CAG-----T-----A--------------CCAGC------------AACC---GC---AACAGC------AACAACAAC--------------------------AACAG---------------CAA---CAGCTACTGCAACAG------------------------------------------GAGCAGCA---CCA---G----CAACTGCAACAGCA------------------------------ACAGCAGCAGCATCAGCAGCTACTGCAGCAA------CAGCTGCC--ACAG------------------------------------------C----AGCGACGGCAAACGTACAAGGAATACTTGCAGCA	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
........................................................................................................................................................................................................CA---G----CAACTGCAACAGCA------------------------------AC..................................................................................................................................	19	5	0.20	1	0	0	1	0
...........................................................................................................................................................................................................................CAGCA------------------------------ACAGCAGCAGCATCAG....................................................................................................................	21	17	0.06	1	0	0	0	1
...............................................................................................................................................................................................................................A------------------------------ACAGCAGCAGCATCAGCAGC................................................................................................................	21	20	0.05	1	1	0	0	0

droYak3

GCT-TAGCGCCAGCAG--------------CAGCAG------------------CAGCA---GCAGCAACAGCAACAGC--------AG------------------------------------CAGCAGCAGCAGCAGCAGCAG------------------------------------------CAGCAGCA---ACA---G----CAGCAACAACAGCAGCAGCAGCAA---------CAGCAGCAGCAGCAGCAGCAGC---------AGCAGCAGCAG------CAGCAGCA--GCAG-------------------------------------------------CAGCA---------ACAGCAGCAGCAGCAGCA	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
...................................................................................................................................................................................................................................................CAGCAGCAGCAGCAGCAGCAGC---------AGCAGC..........................................................................................................	28	20	0.75	15	0	0	0	0	0	0	0	0	0	0	15
...........................................................................CAGC--------AG------------------------------------CAGCAGCAGCAGCAGCAGCAG------------------------------------------C.....................................................................................................................................................................................................	28	20	0.75	15	0	0	0	0	0	0	0	0	0	0	15
......................................................................................................................................................................................................................................................................................................CAGCA--GCAG-------------------------------------------------CAGCA---------ACAGCAGCAGC.......	25	20	0.30	6	0	0	0	0	0	0	0	0	0	0	6
...................................................................................................................................................................................................................................GCAGCAA---------CAGCAGCAGCAGCAGCA..............................................................................................................................	24	20	0.10	2	0	2	0	0	0	0	0	0	0	0	0
................................GCAG------------------CAGCA---GCAGCAACAGCAAC......................................................................................................................................................................................................................................................................................................................	23	20	0.10	2	0	2	0	0	0	0	0	0	0	0	0
.............................................................................................................................................................................................AGCAGCA---ACA---G----CAGCAACAACAGCAGC................................................................................................................................................................	27	15	0.07	1	0	0	1	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................AGCAACAACAGCAGCAGCAGCAA---------CAGC...........................................................................................................................................	27	17	0.06	1	0	0	1	0	0	0	0	0	0	0	0
.....................................................................................................................................GCAGCAGCAGCAG------------------------------------------CAGCAGCA---AC.........................................................................................................................................................................................	23	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
...................................................................AACAGCAACAGC--------AG------------------------------------CAGCAGCAGCAG.........................................................................................................................................................................................................................................................	26	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
........................................................GCA---GCAGCAACAGCAACAGC--------AG------------------------------------CAGCA................................................................................................................................................................................................................................................................	27	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................................................................................AGCAGCA--GCAG-------------------------------------------------CAGCA---------ACAGCAGCA.........	25	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
................................................................................................................................................................................................................................................................................................................G-------------------------------------------------CAGCA---------ACAGCAGCAGCAGCAGC.	23	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................................................................................................GCAG------CAGCAGCA--GCAG-------------------------------------------------CAGCA---------ACAGC.............	26	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
..........................................................................................................................................................................................................................ACAGCAGCAGCAGCAA---------CAGCAGCA.......................................................................................................................................	24	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
....................................................................ACAGCAACAGC--------AG------------------------------------CAGCAGC..............................................................................................................................................................................................................................................................	20	20	0.05	1	0	0	1	0	0	0	0	0	0	0	0
.................................................................GCAACAGCAACAGC--------AG------------------------------------CAGCAGCAGCA..........................................................................................................................................................................................................................................................	27	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
............GCAG--------------CAGCAG------------------CAGCA---GCAGCAACAGC.........................................................................................................................................................................................................................................................................................................................	26	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
................................................................................................................................................................................................................................................................................................................G-------------------------------------------------CAGCA---------ACAGCAGCAGCAGCAGCA	24	20	0.05	1	0	0	0	0	0	0	1	0	0	0	0
............GCAG--------------CAGCAG------------------CAGCA---GCAGCAAC............................................................................................................................................................................................................................................................................................................................	23	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
................................................................................................................................................................................................................................GCAGCAGCAA---------CAGCAGCAG......................................................................................................................................	19	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................A---ACA---G----CAGCAACAACAGCAGCAGC.............................................................................................................................................................	24	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
..........................................................................................................................................AGCAGCAG------------------------------------------CAGCAGCA---ACA---G----CAGCA...........................................................................................................................................................................	25	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
..........................................................A---GCAGCAACAGCAACAGC--------AG------------------------------------C....................................................................................................................................................................................................................................................................	21	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
.....................................................................................................................................GCAGCAGCAGCAG------------------------------------------CAGCAGCA---ACA---G----C...............................................................................................................................................................................	26	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
....................................................................ACAGCAACAGC--------AG------------------------------------CAGCAGCAGCA..........................................................................................................................................................................................................................................................	24	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................................................................................................GCAG------CAGCAGCA--GCAG-------------------------------------------------CAGCA---------AC................	23	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0

droEre2

AGC-----TAATGCTG--------------CAGCAA------------------CAGCA---GCAGCAACAGCAGCAGCAACAA--------------------------------------CAGCAGCTGCAGCAGCAGCAACAA------------------------------------------CAGCAGCT---ACA---G----CAGCAGCAACAACAGCAGCTGCAG---------CAGCAGCAACAACAGCAGCTGC---------AGCAGCAACAA------CTGCAGCA--GCAA-------------------------------------------------CTGCA---------ACAACAGCAGCTGCAACT	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
..........................................................................................................................................AGCAACAA------------------------------------------CAGCAGCT---ACA---G----CA..............................................................................................................................................................................	22	2	0.50	1	0	0	0	0	1	0	0
...................................................................................................................................................................................................................................................................................................................................................................TGCA---------ACAACAGCAGCTGCA...	19	2	0.50	1	1	0	0	0	0	0	0
.........................................................................................................................................CAGCAACAA------------------------------------------CAGCAGCT---ACA---G----CAGCA...........................................................................................................................................................................	26	2	0.50	1	0	0	0	0	0	1	0
......................................................................AGCAGCAGCAACAA--------------------------------------CAGC....................................................................................................................................................................................................................................................................	18	20	0.15	3	0	0	0	0	0	3	0
..............................................................................CAACAA--------------------------------------CAGCAGCTGCAGCA..........................................................................................................................................................................................................................................................	20	7	0.14	1	0	0	0	0	1	0	0
........................................................................................................................................................................................................................CAACAACAGCAGCTGCAG---------CA.............................................................................................................................................	20	7	0.14	1	0	0	0	0	1	0	0
.........................................................................................................................................................................................................................................................CAACAACAGCAGCTGC---------AGCA............................................................................................................	20	7	0.14	1	0	0	0	0	1	0	0
...................................................................AACAGCAGCAGCAACAA--------------------------------------CAGCA...................................................................................................................................................................................................................................................................	22	20	0.10	2	0	0	0	0	2	0	0
.............................................................................................................................................................................................................................................................AACAGCAGCTGC---------AGCAGCA.........................................................................................................	19	13	0.08	1	0	0	0	1	0	0	0
..................................................................................AA--------------------------------------CAGCAGCTGCAGCAGCA.......................................................................................................................................................................................................................................................	19	13	0.08	1	0	0	0	1	0	0	0
............................................................................................................................................................................................................................AACAGCAGCTGCAG---------CAGCA..........................................................................................................................................	19	13	0.08	1	0	0	0	1	0	0	0
...............G--------------CAGCAA------------------CAGCA---GCAGCAACAGCAGCAGC...................................................................................................................................................................................................................................................................................................................	29	20	0.05	1	0	1	0	0	0	0	0
..................................................................................................................................GCAGCAGCAGCAACAA------------------------------------------CAGCAGC...............................................................................................................................................................................................	23	20	0.05	1	0	0	0	0	1	0	0
.................................CAA------------------CAGCA---GCAGCAACAGC.........................................................................................................................................................................................................................................................................................................................	19	20	0.05	1	0	1	0	0	0	0	0
................................................................AGCAACAGCAGCAGCAACA...............................................................................................................................................................................................................................................................................................................	19	20	0.05	1	0	0	0	1	0	0	0
...................................................................AACAGCAGCAGCAACAA--------------------------------------CAGCAGC.................................................................................................................................................................................................................................................................	24	20	0.05	1	1	0	0	0	0	0	0
......................................................................................................................................................................................................................................GCAG---------CAGCAGCAACAACAGCAGC............................................................................................................................	23	20	0.05	1	0	0	0	0	1	0	0

dmo_464

scaffold_6328:598807-598872 +

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