dpe_123

GTTGCCTGCCTGCCGTGCACCAAATCTTCACTAATCCACAATGAAATTCCTTTCGCTTGCCTTTGTCCTGGGCCTGATGGCGGCTCTGGCTAACGGTGAGTTGAGACAAAAATATATAAAAGTGTATTTAAATTTAATTATTATATTTATTTGTGT **********************************..............(((((((((((.(((.((.(((((.......))))).)).))).)))))).)))))..............**********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V057 head	M042 female body	V111 male body	V050 head	V042 embryo	M021 embryo
....................................................................................TCTGGCTAACGGTGAGTTGAG...................................................	21	0	1	28.00	28	13	3	11	1	0	0
....................................................................................TCTGGCTAACGGTGAGTTGAGA..................................................	22	0	1	17.00	17	6	3	6	2	0	0
....................................................................................TCTGGCTAACGGTGAGTTGA....................................................	20	0	1	6.00	6	2	2	1	1	0	0
....................................................................................TCTGGCTAACGGTGAGTTGAGAC.................................................	23	0	1	4.00	4	0	2	1	1	0	0
...................................................TTCGCTTGCCTTTGTCCTGGGC...................................................................................	22	0	1	3.00	3	0	2	0	1	0	0
....................................................................................TCTGGCTAACGGTGAGTTGAGT..................................................	22	1	1	2.00	2	1	0	1	0	0	0
...................................................TTCGCTTGCCTTTGTCCTGGG....................................................................................	21	0	1	2.00	2	0	2	0	0	0	0
....................................................................................TCTGGATAACGGTGAGTTGAGA..................................................	22	1	1	1.00	1	1	0	0	0	0	0
.....................................................................................CTGGCTAACGGTGAGTTGA....................................................	19	0	1	1.00	1	0	1	0	0	0	0
...................................................................................CTCTGGCTAACGGTGAGTTGAG...................................................	22	0	1	1.00	1	1	0	0	0	0	0
...................................................TTCGCTTGCCTTTGTCCTGGGCC..................................................................................	23	0	1	1.00	1	0	1	0	0	0	0
.....................................................................................CTGGCTAACGGTGAGTTGAG...................................................	20	0	1	1.00	1	0	1	0	0	0	0
................................................................GTCCTGGGCCTGATGGCGGCTC......................................................................	22	0	1	1.00	1	1	0	0	0	0	0
..................................................TTTCGCTTGCCTTTGTCCTG......................................................................................	20	0	1	1.00	1	0	0	0	0	0	1
........CCTGCCGTGCACCAAATCT.................................................................................................................................	19	0	1	1.00	1	1	0	0	0	0	0
...................................................TTCGCTTGACTTTGTCCTGGG....................................................................................	21	1	1	1.00	1	0	1	0	0	0	0
.............................................................TTTGTCCTGGGCCTGATGGCGGCTCT.....................................................................	26	0	1	1.00	1	0	1	0	0	0	0
....................................................................................TCTGGCTAACGGTGAGTTGCG...................................................	21	1	1	1.00	1	1	0	0	0	0	0
..................................................................CCTGGGCCTGATGGCGGCTC......................................................................	20	0	1	1.00	1	1	0	0	0	0	0
.....................................................CGCTTGCCTTTGTCCTGGG....................................................................................	19	0	1	1.00	1	0	1	0	0	0	0
....................................................................................TCTGGCTAACGGTGACTTGTGA..................................................	22	2	1	1.00	1	1	0	0	0	0	0
....................................................................................TCTGGCTAACGGTGAGTTGTG...................................................	21	1	1	1.00	1	1	0	0	0	0	0
....CCTGCCTGCCGTGCACCAAA....................................................................................................................................	20	0	1	1.00	1	0	1	0	0	0	0
....................................................................................TCTGGCTAGCGGTGAGTTGAGTC.................................................	23	2	1	1.00	1	0	1	0	0	0	0
....................................................................................TCTGGCTAACGGTGAGTTTAG...................................................	21	1	1	1.00	1	1	0	0	0	0	0
....................................................................................TCTGGCTAACGGTGAGTTGAGACC................................................	24	1	1	1.00	1	1	0	0	0	0	0
.........................................................................CTGATGGCGGCTCTGGCTA................................................................	19	0	1	1.00	1	0	0	0	0	1	0
....................................................................................TCGGGCTAACGGTGAGTTGAGA..................................................	22	1	1	1.00	1	1	0	0	0	0	0
....................................................................................TCGGGCTAACGGTGAGTTGAG...................................................	21	1	1	1.00	1	1	0	0	0	0	0
.........................CTTCACTAATCCACAATGA................................................................................................................	19	0	1	1.00	1	0	0	0	1	0	0
....................................................TCGCTTGCCTTTGTCCTGGGCCTG................................................................................	24	0	1	1.00	1	0	0	0	0	0	1
....................................................................................TCTGGCTAACGGAGAGCTGAGAC.................................................	23	2	1	1.00	1	1	0	0	0	0	0
....................................................................................TCTGGCTAACGGTGAGTTGAGACA................................................	24	0	1	1.00	1	1	0	0	0	0	0
...................................................................................CTCTGGCTAACGGTGAGTTGA....................................................	21	0	1	1.00	1	0	0	1	0	0	0
...................................................TTCGCTTGCCTTTGTCCTGG.....................................................................................	20	0	1	1.00	1	0	1	0	0	0	0
............................................................CTTTGTCCTGGGCCTGATGG............................................................................	20	0	1	1.00	1	0	0	0	0	1	0
....................................................................................TCTGGCTAGCGGTGAGTTGA....................................................	20	1	1	1.00	1	0	1	0	0	0	0
..............................................................TTGTCCTGGGCCTGATGGCGGCTCT.....................................................................	25	0	1	1.00	1	0	1	0	0	0	0
...........................................................................GATGGCGGCTATCGCGAACGGT...........................................................	22	3	2	0.50	1	0	0	1	0	0	0
......................................................................GGACTGATGGCGGATGTGGCT.................................................................	21	3	6	0.17	1	0	0	0	0	1	0
.............................................................TTTGTCCTCGGCCGGATGTC...........................................................................	20	3	10	0.10	1	0	1	0	0	0	0

CAACGGACGGACGGCACGTGGTTTAGAAGTGATTAGGTGTTACTTTAAGGAAAGCGAACGGAAACAGGACCCGGACTACCGCCGAGACCGATTGCCACTCAACTCTGTTTTTATATATTTTCACATAAATTTAAATTAATAATATAAATAAACACA **********************************..............(((((((((((.(((.((.(((((.......))))).)).))).)))))).)))))..............**********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M042 female body	V050 head	V057 head	V111 male body
..........ACGGGACGTGGTCTAGAAGTTATT..........................................................................................................................	24	3	1	1.00	1	1	0	0	0
.....................................................................................................GCTCTGTTTTTATATTTTTTC..................................	21	2	5	0.20	1	0	1	0	0
...................................................................GAGCCGGACGACCGCGGAGAC....................................................................	21	3	14	0.14	2	0	0	2	0
............GGGACGTGGTCTAGAAGT..............................................................................................................................	18	2	20	0.10	2	0	0	0	2

Species	Coordinate	ID	Type	Alignment
droPer2	scaffold_4:6935834-6935989 +	dpe_123	confident	GTTGCCTGCCTGC-CGTGCACC----AAAT----------------CTT---CACTAATCC---------------------ACAATGAAATTCCTTTCGCTTGCCTTTGTCCTGGGCCTGATGGCGGCTCTGGCTAACGGTGAGTTGAGACAAA----A---------ATATA------TAAAAGTGTAT----------TT--A---AATTTAATTATTATA-----------TTTATTTG-----TGT
dp5	3:11535110-11535265 +	dps_88	confident	GTTGTCTGCCTGC-CGTGCACC----AAAT----------------CTT---CACTAATCC---------------------ACAATGAAATTCCTTTCCCTTGCCTTTGTCCTGGGCCTGATGGCGGCTCTGGCTAACGGTGAGTTGAGACAAA----A---------ATACA------TAAAAGTGTAT----------TT--A---AATTTAATTATGATA-----------TTTATTTG-----TGT
droWil2	scf2_1100000004954:3517015-3517155 -			GTTTTCCGC-AACAAC---------GACAA----------------CTA---CAACAAACCACA----------------AAAACATGAAATTCCTTTCGGTTGCTTTCGTTCTGGGTCTGCTGGCGGCTTTGGCCAATGGTGAGTTCTCCA----------------------------CTAA------TTTAT------ATATACTGTATATACTTA------------TGA--------AT-----CT
droVir3	scaffold_12963:5776869-5777023 +			GTTC--AGC-TTA-AGTTCTA------CAA----------------GCTTACCAATTAACTA---------AC--TAA--ACAAAATGAAATTCCTGTCGGTTGCATTTCTGCTGGGTCTGCTGG---CTTTGGCTAGTGGTGAGTACTTAAAGA----A---------GATCA------TAATGC-------AA------AA--ATAATATTTAACAC---------------TTTCTTTTT-----TGT
droMoj3	scaffold_6496:6196795-6196970 +			GTG--CAAT-CGCAAGTGCTCCAGAGTCTTCACAGCAGTCGTGCAAACCCA-------------AAAACAAAG--CCAAGTCAATATGAAATTCCTGTCGCTCGCTTTTCTGCTCGGCCTGCTCG---CTCTGGCCAGTGGTAAGTCG----AAC----TATTCAAGAGATTTC------GCAATT-------GA-------------GCATTCAACTA-------------AATTTTAATC-------CT
droGri2	scaffold_15252:7673893-7674052 -			GTTC--AGC-TTT--ATTCGCACAAGCAAT----------------ACT---AATTAACCC-----------A--CTA--AGAAAATGAAATTCCTATCGATTGGATTTGTGCTCGCACTTCTGG---CACTTGCAAGTGGTAAGTTTTGTAAAC----A----------TA--------CGAA------T----------TC--A---AATTAATTGGCTGTACTAATCGTC-TACTATTTG-----TGG
droAna3	scaffold_12916:10236226-10236369 -			GTTCAGTTCTCGCTTCTG--TTCCAGCC--------------------------------------------A--CTT--GCAAGATGAAATTCCTCTCGGTTGCCTTCCTCCTCGGCCTCCTGG---CTCTGGCCAGTGGTGAGTGTTACCC----------------------------CAAAT-------GAGTTTATTT--TAGTAATTTAACTA------------TTTTATTGCTCAAA-----T
droBip1	scf7180000396769:1103296-1103437 -			GTTCAGTACTCGCTTCTG--TTCCAGCC--------------------------------------------A--CTT--GCAAGATGAAGTTCCTCTCGGTTGCCTTCCTCCTCGGCCTCTTGG---CTCTGGCCAGCGGTGAGTGTTATCT-C----T---------GTTAG------TCAA----------T------TT--AAGCCTTTTATCTA------------TT-TTTTCTTTATA-----T
droKik1	scf7180000302471:64179-64358 -			GTTGTCAGC-TGCCAATCCACCAGAGTTCAC---------------TCGCCGAGTTCCTTAAAAAAAACAAAA--CTATTTCAACATGAAATTCCTGTCGCTCGCCTTCGTCTTGGGTCTGGTTG---CCCTCGCCAGCGGTCAGTAAAAAAAAG----T---------CTATA------TAAATTAATA---TT------AT--AAATTAATAAATTG----A-----------ATTATTTT-----TTA
droFic1	scf7180000453851:9436-9605 -			GTTGTCTTC-TGAAAATCCTCTTGCTTCAA----------------CCGCAACAACAAACCACA------AAA--CCA--ACAACATGAAATTCCTGTCGCTTGCCTTTGTTTTGGGTCTGCTGG---CTCTGGCCAACGGTAAGTAAATTAAATAA--------AACTATTTG------AGAACT-------GT------A--------TTTTATTTATATTG-----------TCAATGTT-----TGC
droEle1	scf7180000489694:114611-114786 +			GTTGTCACC-TGCA-ATCCTCTCGAGTCAA----------------CCGCAAAAACAAACCACA------AAA--TCA--ACAACATGAAATTCCTGTCGCTTGCCTTTGTTTTGGGACTGCTGG---CTCTGGCCAATGGTGAGTGAACTCAACTAAAT---------ATTTG------CAAACA-------AC------GT--AAGTCATTTAACTC------------TGATTTCCATTCTA--CAGT
droRho1	scf7180000771278:4938-5116 -			GTTCTCACT-GGCAAATCCTCTCGAGTCAA----------------CCGCAAAAACAAACCACAAA-----AA--TCA--ACAACATGAAGTTCCTGTCGCTTGCCTTTGTTTTGGGTCTGCTGG---CTCTGGCCAATGGTGAGTAAACTAAAC----T---------ATATATTTAACTAAACA-------AT------AT--CTGTCATTTAATC-------------TTATTTCAATCCTT--TAGT
droBia1	scf7180000302292:2305401-2305580 +			GTTGTCGGC-TGCAAATCCCCTCGAGTCAA----------------CCTCAAAAACCAACCACA------AAA--CCA--AGAAAATGAAATTCCTGTCGCTTGCCTTTGTCTTGGGTCTGCTGGCTGCTGTGGCCAATGGTGAGTAAATTGAACGAACT---------GTCTG------CGAACT-------GC------AT--AAGTTATTTAATTA------------TTATCACAACTATT--TTCC
droTak1	scf7180000416016:451699-451873 -			GTTGTCAGC-TGCAAATCCTCTCGAGTCAA----------------CCTCAAAAACAAACCACA------AAA--TCAAAACAACATGAAATTCCTGTCGCTTGCCTTTGTCTTGGGTTTGCTGG---CTCTGGCCAACGGTGAGTAAACAGAAC----T---------ATTTG------CAAACT-------AC------AT--AAGTTATTTAATTG------------TGATTTTAATTATA--TTTC
droEug1	scf7180000409672:3286465-3286632 +			GTTGTCAGC-TGCAAATCCTACCGAGTCAA----------------CCTCA------AACCACAAA-----AACATCA--ACAACATGAAATTCCTGTCGCTTGCCTTTGTCTTGGGTCTGGTGG---CTCTGGCTAATGGTGAGTTAACTAAAC----T---------ATTTA------CGAACT-------TT------AT--AAGTTATTAAATGA------------TTATATTAATTTC----CTT
dm3	chr2R:14275631-14275801 +			GTTGTCAAC-GGCTAATACGCGGGAGTCAA----------------GCTCAGAATTCAACCACAAA-----AA--CCA--ACAACATGAAATTCCTATCACTCGCCTTCGTTTTGGGTCTGCTGG---CTCTGGCCAACGGTGAGTAATGCCAAC----T---------ATTTA------CAAACT-------AA------AT--AAGTTATTTAATTA------------TGATTTTAATTATA-----T
droSim2	2r:14943075-14943245 +			GTTGTCAAC-TGCAAATTCTTTGGAGTCAA----------------GCTCAGCATTCAACCACAAA-----AA--CCA--ACAACATGAAATTCCTATCACTCGCCTTCGTTCTGGGTCTGCTGG---CTCTGGCCAACGGTGAGTAATGCCAAC----T---------ATTCA------CCAACT-------AA------AT--AAGTTATTTAATTA------------TGATTTTAATTATA-----T
droSec2	scaffold_1:11750839-11751014 +			GTTGTCAAC-TGCAAATTCTCTGGAGTCAA----------------GCTCAGCATTCAACCACAAA-----AA--CCA--ACAACATGAAATTCCTATCACTCGCCTTCGTTCTGGGTCTGCTGG---CTCTGGCCAACGGTGAGTAATGCCAAC----T---------ATTCA------CCAACT-------AC------AT--AAGTTATTTAATTA------------TGATTTAAATTATATTTCCA
droYak3	2R:14912646-14912815 -			GTTGTTAGC-TGCATATCCTCTGGAGTCAA----------------GCTCAGAAACCAACCACA------AAA--CCA--AAAACATGAAATTCCTATCAGTTGCCTTTGTTCTGGGTCTGCTGG---CCCTGGCCAACGGTGAGTAATCCCAGA----T---------ATTCG------CAAGCT-------AA------AT--ATGTTATTTAATTA------------TGATTTCAATTATA-----T
droEre2	scaffold_4845:8481608-8481755 +			GT-------------------------CAA----------------GCTCAGAATCCAACCACA------AAA--CCA--ACAACATGAAATTCCTATCAGTTGCCTTCGTTCTGGGTCTGCTGG---CTCTGGCCAACGGTGAGTAATCCCAGC----T---------ATTCC------CAAACT-------AT------ATATATGTTATTTAATTA------------TGATTTCATTTATA-----T

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droPer2

GTTGCCTGCCTGC-CGTGCACC----AAAT----------------CTT---CACTAATCC---------------------ACAATGAAATTCCTTTCGCTTGCCTTTGTCCTGGGCCTGATGGCGGCTCTGGCTAACGGTGAGTTGAGACAAA----A---------ATATA------TAAAAGTGTAT----------TT--A---AATTTAATTATTATA-----------TTTATTTG-----TGT	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
.................................................................................................................................TCTGGCTAACGGTGAGTTGAG.....................................................................................................	21	1	28.00	28	0	3	0	1	13	11
.................................................................................................................................TCTGGCTAACGGTGAGTTGAGA....................................................................................................	22	1	17.00	17	0	3	0	2	6	6
.................................................................................................................................TCTGGCTAACGGTGAGTTGA......................................................................................................	20	1	6.00	6	0	2	0	1	2	1
.................................................................................................................................TCTGGCTAACGGTGAGTTGAGAC...................................................................................................	23	1	4.00	4	0	2	0	1	0	1
................................................................................................TTCGCTTGCCTTTGTCCTGGGC.....................................................................................................................................	22	1	3.00	3	0	2	0	1	0	0
.................................................................................................................................TCTGGCTAACGGTGAGTTGAGT....................................................................................................	22	1	2.00	2	0	0	0	0	1	1
................................................................................................TTCGCTTGCCTTTGTCCTGGG......................................................................................................................................	21	1	2.00	2	0	2	0	0	0	0
..................................................................................................................................CTGGCTAACGGTGAGTTGA......................................................................................................	19	1	1.00	1	0	1	0	0	0	0
................................................................................................................................CTCTGGCTAACGGTGAGTTGAG.....................................................................................................	22	1	1.00	1	0	0	0	0	1	0
................................................................................................TTCGCTTGCCTTTGTCCTGGGCC....................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0
..................................................................................................................................CTGGCTAACGGTGAGTTGAG.....................................................................................................	20	1	1.00	1	0	1	0	0	0	0
.............................................................................................................GTCCTGGGCCTGATGGCGGCTC........................................................................................................................	22	1	1.00	1	0	0	0	0	1	0
...............................................................................................TTTCGCTTGCCTTTGTCCTG........................................................................................................................................	20	1	1.00	1	1	0	0	0	0	0
........CCTGC-CGTGCACC----AAAT----------------CT...........................................................................................................................................................................................................	19	1	1.00	1	0	0	0	0	1	0
..........................................................................................................TTTGTCCTGGGCCTGATGGCGGCTCT.......................................................................................................................	26	1	1.00	1	0	1	0	0	0	0
...............................................................................................................CCTGGGCCTGATGGCGGCTC........................................................................................................................	20	1	1.00	1	0	0	0	0	1	0
..................................................................................................CGCTTGCCTTTGTCCTGGG......................................................................................................................................	19	1	1.00	1	0	1	0	0	0	0
....CCTGCCTGC-CGTGCACC----AAA..............................................................................................................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0
.................................................................................................................................TCTGGCTAACGGTGAGTTGAGACC..................................................................................................	24	1	1.00	1	0	0	0	0	1	0
......................................................................................................................CTGATGGCGGCTCTGGCTA..................................................................................................................	19	1	1.00	1	0	0	1	0	0	0
..............................................CTT---CACTAATCC---------------------ACAATGA..................................................................................................................................................................	19	1	1.00	1	0	0	0	1	0	0
.................................................................................................TCGCTTGCCTTTGTCCTGGGCCTG..................................................................................................................................	24	1	1.00	1	1	0	0	0	0	0
.................................................................................................................................TCTGGCTAACGGTGAGTTGAGACA..................................................................................................	24	1	1.00	1	0	0	0	0	1	0
................................................................................................................................CTCTGGCTAACGGTGAGTTGA......................................................................................................	21	1	1.00	1	0	0	0	0	0	1
................................................................................................TTCGCTTGCCTTTGTCCTGG.......................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0
.........................................................................................................CTTTGTCCTGGGCCTGATGG..............................................................................................................................	20	1	1.00	1	0	0	1	0	0	0
...........................................................................................................TTGTCCTGGGCCTGATGGCGGCTCT.......................................................................................................................	25	1	1.00	1	0	1	0	0	0	0

dp5

GTTGTCTGCCTGC-CGTGCACC----AAAT----------------CTT---CACTAATCC---------------------ACAATGAAATTCCTTTCCCTTGCCTTTGTCCTGGGCCTGATGGCGGCTCTGGCTAACGGTGAGTTGAGACAAA----A---------ATACA------TAAAAGTGTAT----------TT--A---AATTTAATTATGATA-----------TTTATTTG-----TGT	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
.................................................................................................................................TCTGGCTAACGGTGAGTTGAG.....................................................................................................	21	1	20.00	20	1	10	0	0	0	1	8	0	0	0
.................................................................................................................................TCTGGCTAACGGTGAGTTGAGA....................................................................................................	22	1	19.00	19	0	12	0	0	0	3	4	0	0	0
.................................................................................................................................TCTGGCTAACGGTGAGTTGAGAC...................................................................................................	23	1	10.00	10	1	7	0	0	0	1	1	0	0	0
.................................................................................................................................TCTGGCTAACGGTGAGTTGA......................................................................................................	20	1	10.00	10	0	5	0	0	0	1	4	0	0	0
.................................................................................................TCCCTTGCCTTTGTCCTGGGC.....................................................................................................................................	21	1	2.00	2	0	1	0	0	0	1	0	0	0	0
................................................................................................................................CTCTGGCTAACGGTGAGTTGA......................................................................................................	21	1	2.00	2	0	1	0	0	0	0	1	0	0	0
..................................................................................................................................CTGGCTAACGGTGAGTTGAG.....................................................................................................	20	1	2.00	2	0	1	0	0	0	0	1	0	0	0
.TTGTCTGCCTGC-CGTGCAC......................................................................................................................................................................................................................................	19	1	1.00	1	0	0	0	1	0	0	0	0	0	0
.................................................................................................................................TCTGGCTAACGGTGAGTTG.......................................................................................................	19	1	1.00	1	0	1	0	0	0	0	0	0	0	0
............................................................................................................TGTCCTGGGCCTGATGGCGGC..........................................................................................................................	21	1	1.00	1	0	1	0	0	0	0	0	0	0	0
..................................................................................................................GGGCCTGATGGCGGCTCTGGCTAACG...............................................................................................................	26	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.......GCCTGC-CGTGCACC----AAAT----------------CTT---C......................................................................................................................................................................................................	22	1	1.00	1	0	1	0	0	0	0	0	0	0	0
................................................................................................................................CTCTGGCTAACGGTGAGTTG.......................................................................................................	20	1	1.00	1	0	0	0	0	0	0	1	0	0	0
............................................................................................................TGTCCTGGGCCTGATGGCG............................................................................................................................	19	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.....................................................................................................TTGCCTTTGTCCTGGGCCT...................................................................................................................................	19	1	1.00	1	0	1	0	0	0	0	0	0	0	0
................................................................................................................CTGGGCCTGATGGCGGCTC........................................................................................................................	19	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.................................................................................................................................TCTGGCTAACGGTGAGTTGAGACA..................................................................................................	24	1	1.00	1	0	1	0	0	0	0	0	0	0	0
..TGTCTGCCTGC-CGTGCACC----AAA..............................................................................................................................................................................................................................	22	1	1.00	1	0	1	0	0	0	0	0	0	0	0
...............................................................................................................................GCTCTGGCTAACGGTGAGTTGAG.....................................................................................................	23	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.................................................................................................................................TCTGGCTAACGGTGAGTTGAGAA...................................................................................................	23	1	1.00	1	0	1	0	0	0	0	0	0	0	0
............................................................................................................TGTCCTGGGCCTGATGGCGG...........................................................................................................................	20	1	1.00	1	0	1	0	0	0	0	0	0	0	0
...........................................................................................................TTGTCCTGGGCCTGATGGCGGCTC........................................................................................................................	24	1	1.00	1	0	0	0	1	0	0	0	0	0	0
................................................................................................................................CTCTGGCTAACGGTGAGTTGAG.....................................................................................................	22	1	1.00	1	0	1	0	0	0	0	0	0	0	0
...............................................................................................................CCTGGGCCTGATGGCGGCTCTGGC....................................................................................................................	24	1	1.00	1	0	0	0	1	0	0	0	0	0	0
.................................................................................................................................TCTGGCTAACGGTGAGTTGAGT....................................................................................................	22	1	1.00	1	0	1	0	0	0	0	0	0	0	0

droWil2

GTTTTCCGC-AACAAC---------GACAA----------------CTA---CAACAAACCACA----------------AAAACATGAAATTCCTTTCGGTTGCTTTCGTTCTGGGTCTGCTGGCGGCTTTGGCCAATGGTGAGTTCTCCA----------------------------CTAA------TTTAT------ATATACTGTATATACTTA------------TGA--------AT-----CT	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
...................................................................................ACATGAAATTCCTTTCGGTTG...................................................................................................................................................	21	1	2.00	2	1	1	0	0	0
.................................................................................................TCGGTTGCTTTCGTTCTGGGTCT...................................................................................................................................	23	1	1.00	1	1	0	0	0	0
....................................................................................................GTTGCTTTCGTTCTGGGTCTG..................................................................................................................................	21	1	1.00	1	0	0	0	0	1
......................................................................................TGAAATTCCTTTCGGTTGCT.................................................................................................................................................	20	1	1.00	1	0	0	0	0	1
...................................................................................................GGTTGCTTTCGTTCTGGGTC....................................................................................................................................	20	1	1.00	1	0	0	0	1	0
..........................................................................................................TTCGTTCTGGGTCTGCTGGC.............................................................................................................................	20	1	1.00	1	0	0	0	0	1
...................................................................................................GGTTGCTTTCGTTCTGGGTCT...................................................................................................................................	21	1	1.00	1	1	0	0	0	0
................................................................................................................CTGGGTCTGCTGGCGGCT.........................................................................................................................	18	1	1.00	1	1	0	0	0	0
............................................................................................TCCTTTCGGTTGCTTTCGTTC..........................................................................................................................................	21	1	1.00	1	0	1	0	0	0
.........................GACAA----------------CTA---CAACAAACCA.............................................................................................................................................................................................	18	1	1.00	1	0	1	0	0	0

droVir3

GTTC--AGC-TTA-AGTTCTA------CAA----------------GCTTACCAATTAACTA---------AC--TAA--ACAAAATGAAATTCCTGTCGGTTGCATTTCTGCTGGGTCTGCTGG---CTTTGGCTAGTGGTGAGTACTTAAAGA----A---------GATCA------TAATGC-------AA------AA--ATAATATTTAACAC---------------TTTCTTTTT-----TGT	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	SRR2096013 Ovary_Strain_9_oxidized	SRR2096014 Ovary_Strain_160_oxidized	SRR2096026 embryo_0-2h from 14 day old Strain 9 mothers	SRR2096038 embryo_0-2h from 14 day old Strain 9 mothers	SRR2096050 embryo_0-2h from 14 day old Strain 160 mothers	SRR2096055 Ovary_Min_43	SRR2096056 Ovary_Min_46	SRR2096057 Ovary_Min_50	SRR2096058 Ovary_Min_98	SRR2096059 Ovary_Min_164	SRR2096060 Ovary_Min_193	SRR2096061 embryo_0-2h from 14 day old Strain 160 mothers	SRR2096072 embryo_0-2h from 15to16 day old dysgenic mothers	SRR2096079 embryo_0-2h from 15to16 day old dysgenic mothers	SRR2096080 embryo_0-2h from 15to16 day old nondysgenic mothers	SRR2096081 embryo_0-2h from 15to16 day old nondysgenic mothers
...C--AGC-TTA-AGTTCTA------CAA----------------GCT..........................................................................................................................................................................................................	20	1	2.00	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	0
..................CTA------CAA----------------GCTTACCAATTAACTA---------AC--T...............................................................................................................................................................................	25	1	2.00	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
.........................................................................................AATTCCTGTCGGTTGCATTT..............................................................................................................................................	20	1	2.00	2	0	0	1	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
....................................................................................AATGAAATTCCTGTCGGTTGC..................................................................................................................................................	21	1	1.00	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.....................................................................................ATGAAATTCCTGTCGGTTGCATTTC.............................................................................................................................................	25	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.TTC--AGC-TTA-AGTTCTA------CAA----------------GCTTAC.......................................................................................................................................................................................................	25	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
........................................................................C--TAA--ACAAAATGAAATTCC............................................................................................................................................................	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	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
.........................................................................................................ATTTCTGCTGGGTCTGCT................................................................................................................................	18	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
GTTC--AGC-TTA-AGTTCTA------CAA----------------GCT..........................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................................................................AA--ACAAAATGAAATTCCTGTCGGTTGC..................................................................................................................................................	27	1	1.00	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.......................................................................................GAAATTCCTGTCGGTTGCATT...............................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
....................A------CAA----------------GCTTACCAATTAACTA---------AC--TAA--AC.........................................................................................................................................................................	27	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.....................................................................................................TTGCATTTCTGCTGGGTCTGC.................................................................................................................................	21	1	1.00	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
......................................................................................................TGCATTTCTGCTGGGTCTGC.................................................................................................................................	20	1	1.00	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
......................................................................................TGAAATTCCTGTCGGTTGCA.................................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..................................................................................................................................................ACTTAAAGA----A---------GATCA------TAATGC-------AA------AA--A.............................................	26	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...............................................................................................................GCTGGGTCTGCTGG---CTTT.......................................................................................................................	18	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droMoj3

GTG--CAAT-CGCAAGTGCTCCAGAGTCTTCACAGCAGTCGTGCAAACCCA-------------AAAACAAAG--CCAAGTCAATATGAAATTCCTGTCGCTCGCTTTTCTGCTCGGCCTGCTCG---CTCTGGCCAGTGGTAAGTCG----AAC----TATTCAAGAGATTTC------GCAATT-------GA-------------GCATTCAACTA-------------AATTTTAATC-------CT	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
..............AGTGCTCCAGAGTCTTCACA.........................................................................................................................................................................................................................	20	1	2.00	2	2	0	0	0	0	0
.TG--CAAT-CGCAAGTGCTCCAGAG.................................................................................................................................................................................................................................	22	1	2.00	2	1	0	1	0	0	0
..G--CAAT-CGCAAGTGCTCCAGAGTC...............................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	1
......................AGAGTCTTCACAGCAGTCGTGCA..............................................................................................................................................................................................................	23	1	1.00	1	0	0	0	1	0	0
................................................................................TCAATATGAAATTCCTGTCGCTCGC..................................................................................................................................................	25	1	1.00	1	1	0	0	0	0	0
.TG--CAAT-CGCAAGTGCTCCAGC..................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	1	0	0
..................................................................AACAAAG--CCAAGTCAATATGA..................................................................................................................................................................	21	1	1.00	1	1	0	0	0	0	0
GTG--CAAT-CGCAAGTGCTCCAG...................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	1	0	0
.....................................GTCGTGCAAACCCA-------------AAAACAAAG--CCA.............................................................................................................................................................................	26	1	1.00	1	1	0	0	0	0	0
.......................GAGTCTTCACAGCAGTCGTGCAAA............................................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	1
...............................................................................................................GCTCGGCCTGCTCG---CTCTGGCCA..................................................................................................................	23	1	1.00	1	1	0	0	0	0	0
.......AT-CGCAAGTGCTCCAGAGTCTT.............................................................................................................................................................................................................................	22	1	1.00	1	0	0	0	1	0	0
........T-CGCAAGTGCTCCAGAGTCT..............................................................................................................................................................................................................................	20	1	1.00	1	0	0	0	1	0	0
..................................GCAGTCGTGCAAACCCA-------------AAAA.......................................................................................................................................................................................	21	1	1.00	1	1	0	0	0	0	0
.....................................................................................................................................................................AGAGATTTC------GCAATT-------GA-------------GCAC.......................................	21	1	1.00	1	1	0	0	0	0	0
.........................GTCTTCACAGCAGTCGTGC...............................................................................................................................................................................................................	19	1	1.00	1	1	0	0	0	0	0
..................CTCCAGAGTCTTCACAGCAG.....................................................................................................................................................................................................................	20	1	1.00	1	0	0	0	1	0	0
.......AT-CGCAAGTGCTCCAGAGTCT..............................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	1	0	0
................................CAGCAGTCGTGCAAACCCA-------------...........................................................................................................................................................................................	19	1	1.00	1	0	0	0	1	0	0
........................................................................................................................GCTCG---CTCTGGCCAGTGGTAAGTCG----AA.................................................................................................	27	1	1.00	1	0	0	0	0	0	1

droGri2

GTTC--AGC-TTT--ATTCGCACAAGCAAT----------------ACT---AATTAACCC-----------A--CTA--AGAAAATGAAATTCCTATCGATTGGATTTGTGCTCGCACTTCTGG---CACTTGCAAGTGGTAAGTTTTGTAAAC----A----------TA--------CGAA------T----------TC--A---AATTAATTGGCTGTACTAATCGTC-TACTATTTG-----TGG	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
...................................................................................................GATTGGATTTGTGCTCGCA.....................................................................................................................................	19	1	24.00	24	17	7
................................................................................................ATCGATTGGATTTGTGCTCGCA.....................................................................................................................................	22	1	18.00	18	5	13
.....................................................ATTAACCC-----------A--CTA--AGAAAATG...................................................................................................................................................................	20	1	12.00	12	12	0
..............................................................................................CTATCGATTGGATTTGTGCTCGCA.....................................................................................................................................	24	1	10.00	10	9	1
................................................................................................ATCGATTGGATTTGTGCTCG.......................................................................................................................................	20	1	9.00	9	4	5
....................................................................................................ATTGGATTTGTGCTCGCA.....................................................................................................................................	18	1	8.00	8	8	0
..............................................................................................CTATCGATTGGATTTGTGCTCG.......................................................................................................................................	22	1	8.00	8	6	2
........................................................................................................GATTTGTGCTCGCACTTCTGG---CA.........................................................................................................................	23	1	8.00	8	7	1
.............................................................................................CCTATCGATTGGATTTGTG...........................................................................................................................................	19	1	7.00	7	1	6
.......................................................................................................GGATTTGTGCTCGCACTTCTGG---CA.........................................................................................................................	24	1	7.00	7	7	0
.............................................................................................CCTATCGATTGGATTTGTGCTCGCA.....................................................................................................................................	25	1	6.00	6	4	2
....................................................................................................ATTGGATTTGTGCTCGCACTTCTGG---CA.........................................................................................................................	27	1	6.00	6	4	2
....................................................................................................ATTGGATTTGTGCTCGCACTTCTG...............................................................................................................................	24	1	5.00	5	4	1
................................................................................................ATCGATTGGATTTGTGCTC........................................................................................................................................	19	1	5.00	5	2	3
..............................................................................................CTATCGATTGGATTTGTGCTC........................................................................................................................................	21	1	5.00	5	2	3
..............................................................................................CTATCGATTGGATTTGTGCT.........................................................................................................................................	20	1	5.00	5	1	4
...............................................................................................TATCGATTGGATTTGTGCTCGCA.....................................................................................................................................	23	1	5.00	5	3	2
....................................................................................................ATTGGATTTGTGCTCGCACT...................................................................................................................................	20	1	5.00	5	4	1
...................................................................................................GATTGGATTTGTGCTCGCACT...................................................................................................................................	21	1	4.00	4	2	2
......................................................TTAACCC-----------A--CTA--AGAAAATG...................................................................................................................................................................	19	1	4.00	4	4	0
................................................................................................ATCGATTGGATTTGTGCT.........................................................................................................................................	18	1	4.00	4	4	0
...................................................................................................GATTGGATTTGTGCTCGCACTTCTG...............................................................................................................................	25	1	4.00	4	2	2
................................................................................................ATCGATTGGATTTGTGCTCGC......................................................................................................................................	21	1	3.00	3	0	3
................................................................................................................CTCGCACTTCTGG---CACTTG.....................................................................................................................	19	1	3.00	3	3	0
..........................................................................................ATTCCTATCGATTGGATTTGTGCTC........................................................................................................................................	25	1	3.00	3	1	2
.......................................................................................................GGATTTGTGCTCGCACTTCTGG---CACTT......................................................................................................................	27	1	3.00	3	3	0
.............................................................................................................GTGCTCGCACTTCTGG---CA.........................................................................................................................	18	1	3.00	3	3	0
.........................................................................................AATTCCTATCGATTGGATTTGTGCT.........................................................................................................................................	25	1	3.00	3	0	3
.........................................................................................................ATTTGTGCTCGCACTTCTG...............................................................................................................................	19	1	3.00	3	3	0
...........................................................................CTA--AGAAAATGAAATTCCT...........................................................................................................................................................	19	1	3.00	3	3	0
........................................................................................AAATTCCTATCGATTGGATTTGTGCTC........................................................................................................................................	27	1	3.00	3	0	3
..............................................................................................CTATCGATTGGATTTGTG...........................................................................................................................................	18	1	3.00	3	3	0
................................................................................................ATCGATTGGATTTGTGCTCGCACT...................................................................................................................................	24	1	3.00	3	3	0
.........................................................................................AATTCCTATCGATTGGATTTGTGCTC........................................................................................................................................	26	1	3.00	3	0	3
....................................................................................................ATTGGATTTGTGCTCGCACTT..................................................................................................................................	21	1	3.00	3	1	2
..........................................................................................................TTTGTGCTCGCACTTCTGG---CA.........................................................................................................................	21	1	3.00	3	3	0
.................................................................................................TCGATTGGATTTGTGCTCGCA.....................................................................................................................................	21	1	3.00	3	3	0
..........................................................................................ATTCCTATCGATTGGATTTGTG...........................................................................................................................................	22	1	3.00	3	1	2
...................................................................................................GATTGGATTTGTGCTCGCACTTC.................................................................................................................................	23	1	3.00	3	2	1
........................................................................................................GATTTGTGCTCGCACTTCTG...............................................................................................................................	20	1	3.00	3	3	0
....................................................................................................ATTGGATTTGTGCTCGCACTTCTGG---C..........................................................................................................................	26	1	3.00	3	2	1
...................................................................................................GATTGGATTTGTGCTCGC......................................................................................................................................	18	1	2.00	2	2	0
.................................................................................................TCGATTGGATTTGTGCTC........................................................................................................................................	18	1	2.00	2	2	0
....................................................AATTAACCC-----------A--CTA--AGAAAATG...................................................................................................................................................................	21	1	2.00	2	2	0
........................................................................................................GATTTGTGCTCGCACTTCTGG---C..........................................................................................................................	22	1	2.00	2	2	0
GTTC--AGC-TTT--ATTCGCACA...................................................................................................................................................................................................................................	19	1	2.00	2	2	0
................................................................................................ATCGATTGGATTTGTGCTCGCACTTCTG...............................................................................................................................	28	1	2.00	2	1	1
...............................................................................................................GCTCGCACTTCTGG---CACTT......................................................................................................................	19	1	2.00	2	2	0
.....................................................................................................................ACTTCTGG---CACTTGCAAGT................................................................................................................	19	1	2.00	2	2	0
.................TCGCACAAGCAAT----------------ACT---AATTAACC...............................................................................................................................................................................................	24	1	2.00	2	2	0
.........................................................................................AATTCCTATCGATTGGATTTGTG...........................................................................................................................................	23	1	2.00	2	1	1
...............................................................................................TATCGATTGGATTTGTGCTC........................................................................................................................................	20	1	2.00	2	1	1
....................................................................................AATGAAATTCCTATCGATTG...................................................................................................................................................	20	1	2.00	2	1	1
..............................................................................................CTATCGATTGGATTTGTGCTCGCACTT..................................................................................................................................	27	1	2.00	2	2	0
.................................................................................................TCGATTGGATTTGTGCTCGCACTTCTG...............................................................................................................................	27	1	2.00	2	1	1
.....................................................ATTAACCC-----------A--CTA--AGAAAATGAAATTC.............................................................................................................................................................	26	1	2.00	2	2	0
...............ATTCGCACAAGCAAT----------------ACT---A......................................................................................................................................................................................................	19	1	2.00	2	2	0
..............................................................................................CTATCGATTGGATTTGTGCTCGCACT...................................................................................................................................	26	1	2.00	2	1	1
...............................................................................................TATCGATTGGATTTGTGCTCGC......................................................................................................................................	22	1	2.00	2	1	1
....................................................................................................ATTGGATTTGTGCTCGCACTTC.................................................................................................................................	22	1	2.00	2	1	1
........................................................................................................GATTTGTGCTCGCACTTC.................................................................................................................................	18	1	2.00	2	2	0
................TTCGCACAAGCAAT----------------ACT---AATTAACC...............................................................................................................................................................................................	25	1	2.00	2	2	0
.....................................................ATTAACCC-----------A--CTA--AGAAAATGAA.................................................................................................................................................................	22	1	2.00	2	2	0
....................................................AATTAACCC-----------A--CTA--AGAAAATGAAATTC.............................................................................................................................................................	27	1	2.00	2	2	0
................................................................................................................CTCGCACTTCTGG---CACTTGCA...................................................................................................................	21	1	2.00	2	2	0
...................................................................................................GATTGGATTTGTGCTCGCACTT..................................................................................................................................	22	1	2.00	2	0	2
.............................................................................................................GTGCTCGCACTTCTGG---CACTTGCA...................................................................................................................	24	1	2.00	2	2	0
...................................................................................................GATTGGATTTGTGCTCGCACTTCTGG---...........................................................................................................................	26	1	2.00	2	1	1
.....................................................................................................................ACTTCTGG---CACTTGCAAGTG...............................................................................................................	20	1	2.00	2	2	0
.........................................................................................................ATTTGTGCTCGCACTTCTGG---CA.........................................................................................................................	22	1	2.00	2	2	0
........................................................................................AAATTCCTATCGATTGGATTTGTGCT.........................................................................................................................................	26	1	2.00	2	0	2
GTTC--AGC-TTT--ATTCGCACAAGCAAT----------------A............................................................................................................................................................................................................	26	1	2.00	2	2	0
....................................................AATTAACCC-----------A--CTA--AGAAAATGAAATTCC............................................................................................................................................................	28	1	2.00	2	2	0
................................................................................................ATCGATTGGATTTGTGCTCGCAC....................................................................................................................................	23	1	1.00	1	1	0
....................CACAAGCAAT----------------ACT---AATTAACCC-----------A--CT..............................................................................................................................................................................	25	1	1.00	1	1	0
.......................................................................................................GGATTTGTGCTCGCACTTCTGG---C..........................................................................................................................	23	1	1.00	1	1	0
........................................................AACCC-----------A--CTA--AGAAAATGAAATT..............................................................................................................................................................	22	1	1.00	1	1	0
.............................................................................................................GTGCTCGCACTTCTGG---CACTT......................................................................................................................	21	1	1.00	1	1	0
................................................................................................................CTCGCACTTCTGG---CACTTGCAAGTG...............................................................................................................	25	1	1.00	1	1	0
......................CAAGCAAT----------------ACT---AATTAACC...............................................................................................................................................................................................	19	1	1.00	1	1	0
..........................................................................................................TTTGTGCTCGCACTTCTGG---CACTT......................................................................................................................	24	1	1.00	1	1	0
...................GCACAAGCAAT----------------ACT---AATTAACCC-----------G--................................................................................................................................................................................	24	1	1.00	1	1	0
...............................................................................................TATCGATTGGATTTGTGCT.........................................................................................................................................	19	1	1.00	1	1	0
............................................................................TA--AGAAAATGAAATTCCTATCGATTG...................................................................................................................................................	26	1	1.00	1	1	0
...........................................................................................TTCCTATCGATTGGATTTGTGCTCGCA.....................................................................................................................................	27	1	1.00	1	1	0
.....................................................................................ATGAAATTCCTATCGATT....................................................................................................................................................	18	1	1.00	1	1	0
........................................................AACCC-----------A--CTA--AGAAAATGAA.................................................................................................................................................................	19	1	1.00	1	1	0
...........TT--ATTCGCACAAGCAAT----------------ACT---AATTAACCC-----------...................................................................................................................................................................................	29	1	1.00	1	1	0
.........................................................ACCC-----------A--CTA--AGAAAATGAA.................................................................................................................................................................	18	1	1.00	1	1	0
.......................AAGCAAT----------------ACT---AATTAACCC-----------A--CT..............................................................................................................................................................................	22	1	1.00	1	1	0
..................................................................................................CGATTGGATTTGTGCTCGCA.....................................................................................................................................	20	1	1.00	1	1	0
........................................................................................AAATTCCTATCGATTGGATTTGTGCTCG.......................................................................................................................................	28	1	1.00	1	1	0
..........................................................................................ATTCCTATCGATTGGATTTGTGCTCG.......................................................................................................................................	26	1	1.00	1	1	0
..........................................................................................ATTCCTATCGATTGGATTTGTGCTCGC......................................................................................................................................	27	1	1.00	1	0	1
...........TT--ATTCGCACAAGCAAT----------------ACT---.......................................................................................................................................................................................................	20	1	1.00	1	1	0
................TTCGCACAAGCAAT----------------ACT---AATT...................................................................................................................................................................................................	21	1	1.00	1	1	0
.......................................................................................................GGATTTGTGCTCGCACTTCTGG---CACTTG.....................................................................................................................	28	1	1.00	1	1	0
........................................................................................AAATTCCTATCGATTGGATT...............................................................................................................................................	20	1	1.00	1	1	0
.....................................................................................ATGAAATTCCTATCGATTGGATTTGTG...........................................................................................................................................	27	1	1.00	1	1	0
................................................T---AATTAACCC-----------A--CTA--AGAAAATGAA.................................................................................................................................................................	24	1	1.00	1	1	0
........C-TTT--ATTCGCACAAGCAAT----------------A............................................................................................................................................................................................................	20	1	1.00	1	0	1
........................................................................A--CTA--AGAAAATGAAATTCCTATCGATTG...................................................................................................................................................	28	1	1.00	1	1	0
............................................................................................TCCTATCGATTGGATTTGTGCTCGCA.....................................................................................................................................	26	1	1.00	1	1	0
.........................GCAAT----------------ACT---AATTAACCC-----------A--CT..............................................................................................................................................................................	20	1	1.00	1	1	0
.........................................................ACCC-----------A--CTA--AGAAAATGAAATTCCTA..........................................................................................................................................................	25	1	1.00	1	1	0
......AGC-TTT--ATTCGCACAAGCAAT----------------ACT---A......................................................................................................................................................................................................	25	1	1.00	1	1	0
.....................................................................................................TTGGATTTGTGCTCGCACTTCTGG---C..........................................................................................................................	25	1	1.00	1	0	1
.............................................................................................CCTATCGATTGGATTTGTGCTC........................................................................................................................................	22	1	1.00	1	1	0
.............................................................................................................GTGCTCGCACTTCTGG---CACTTGCAAGT................................................................................................................	27	1	1.00	1	1	0
....................................................................................AATGAAATTCCTATCGATTGGATTTGTG...........................................................................................................................................	28	1	1.00	1	0	1
........................................................................................................GATTTGTGCTCGCACTTCT................................................................................................................................	19	1	1.00	1	1	0
...................................................................................................................GCACTTCTGG---CACTTGCAAGT................................................................................................................	21	1	1.00	1	1	0
................................................................................................................CTCGCACTTCTGG---CACTTGC....................................................................................................................	20	1	1.00	1	1	0
...................................................................................AAATGAAATTCCTATCGATTG...................................................................................................................................................	21	1	1.00	1	1	0
........................................................................................................GATTTGTGCTCGCACTTCTGG---...........................................................................................................................	21	1	1.00	1	1	0
...............................................................................................TATCGATTGGATTTGTGCTCGCACTTC.................................................................................................................................	27	1	1.00	1	0	1
...........................AAT----------------ACT---AATTAACCC-----------A--CTA--AG.........................................................................................................................................................................	21	1	1.00	1	1	0
...................................................................................AAATGAAATTCCTATCGATTGG..................................................................................................................................................	22	1	1.00	1	1	0
......................................................................................................................CTTCTGG---CACTTGCAAGTG...............................................................................................................	19	1	1.00	1	1	0
.TTC--AGC-TTT--ATTCGCACAAGCAAT----------------ACT---.......................................................................................................................................................................................................	27	1	1.00	1	1	0
............................................................................................................TGTGCTCGCACTTCTGG---CAC........................................................................................................................	20	1	1.00	1	1	0
...................GCACAAGCAAT----------------ACT---AATTAACCC-----------...................................................................................................................................................................................	23	1	1.00	1	1	0
...........................................................................................TTCCTATCGATTGGATTTGTGCTCG.......................................................................................................................................	25	1	1.00	1	1	0
........................................................AACCC-----------A--CTA--AGAAAATGAAATTCCTATCG.......................................................................................................................................................	29	1	1.00	1	1	0
...............................................CT---AATTAACCC-----------A--CTA--AGAAAATG...................................................................................................................................................................	23	1	1.00	1	1	0
......................................................TTAACCC-----------A--CTA--AGAAAATGAAATTCCT...........................................................................................................................................................	27	1	1.00	1	1	0
.................................................................................................................TCGCACTTCTGG---CACTTG.....................................................................................................................	18	1	1.00	1	1	0
................................................................................................ATCGATTGGATTTGTGCTCGCACTTCT................................................................................................................................	27	1	1.00	1	1	0
...................................................................................................GATTGGATTTGTGCTCGCAC....................................................................................................................................	20	1	1.00	1	1	0
..................CGCACAAGCAAT----------------ACT---AATT...................................................................................................................................................................................................	19	1	1.00	1	1	0
..............................................................................................CTATCGATTGGATTTGTGCTCGC......................................................................................................................................	23	1	1.00	1	0	1
...........................................................................................................TTGTGCTCGCACTTCTGG---CACT.......................................................................................................................	22	1	1.00	1	1	0
...............................................................................................TATCGATTGGATTTGTGCTCGCACT...................................................................................................................................	25	1	1.00	1	1	0
GTTC--AGC-TTT--ATTCGCACAAGCAAT----------------ACT---.......................................................................................................................................................................................................	28	1	1.00	1	1	0
..................................................................................................CGATTGGATTTGTGCTCG.......................................................................................................................................	18	1	1.00	1	0	1
........................................................................................AAATTCCTATCGATTGGATTTGTG...........................................................................................................................................	24	1	1.00	1	0	1
...........................................................................CTA--AGAAAATGAAATTCCTAT.........................................................................................................................................................	21	1	1.00	1	1	0
.......................................................TAACCC-----------A--CTA--AGAAAATGAAATT..............................................................................................................................................................	23	1	1.00	1	1	0
..................................................................................................................CGCACTTCTGG---CACTTGCAAGT................................................................................................................	22	1	1.00	1	1	0
GTTC--AGC-TTT--ATTCGCACAAGCA...............................................................................................................................................................................................................................	23	1	1.00	1	1	0
...........................................................................................................TTGTGCTCGCACTTCTGG---C..........................................................................................................................	19	1	1.00	1	1	0
......................................................................................................................CTTCTGG---CACTTGCAAGT................................................................................................................	18	1	1.00	1	1	0
....................................................................................................................CACTTCTGG---CACTTGCAAGTG...............................................................................................................	21	1	1.00	1	1	0
.................TCGCACAAGCAAT----------------ACT---AA.....................................................................................................................................................................................................	18	1	1.00	1	1	0
...............................................................................................TATCGATTGGATTTGTGCTCGCACTT..................................................................................................................................	26	1	1.00	1	0	1
....................................................................................................................CACTTCTGG---CACTTGCAAGTGC..............................................................................................................	22	1	1.00	1	1	0
.................................................................................................TCGATTGGATTTGTGCTCG.......................................................................................................................................	19	1	1.00	1	1	0
...............................................................................................................GCTCGCACTTCTGG---CACTTGC....................................................................................................................	21	1	1.00	1	1	0
...............................................CT---AATTAACCC-----------A--CTA--AGAAAAT....................................................................................................................................................................	22	1	1.00	1	1	0
...C--AGC-TTT--ATTCGCACAAGCA...............................................................................................................................................................................................................................	20	1	1.00	1	0	1
...............................................................................................................GCTCGCACTTCTGG---CACTTG.....................................................................................................................	20	1	1.00	1	1	0
...................................................................................................................GCACTTCTGG---CACTTGCAAGTG...............................................................................................................	22	1	1.00	1	1	0
....................CACAAGCAAT----------------ACT---AATTAACCC-----------A--................................................................................................................................................................................	23	1	1.00	1	1	0
...............................................................................................................GCTCGCACTTCTGG---CACTTGCAAGT................................................................................................................	25	1	1.00	1	1	0
............................................................................................TCCTATCGATTGGATTTGTG...........................................................................................................................................	20	1	1.00	1	0	1
.................................................................................................................TCGCACTTCTGG---CACTTGCAAGTG...............................................................................................................	24	1	1.00	1	1	0
.....................................................ATTAACCC-----------A--CTA--AGAAAAT....................................................................................................................................................................	19	1	1.00	1	1	0
..................CGCACAAGCAAT----------------ACT---AATTAACCC-----------...................................................................................................................................................................................	24	1	1.00	1	1	0
............................................................................................................TGTGCTCGCACTTCTGG---CACTTGCA...................................................................................................................	25	1	1.00	1	1	0
.......................AAGCAAT----------------ACT---AATTAACCC-----------...................................................................................................................................................................................	19	1	1.00	1	1	0
.............................................................................A--AGAAAATGAAATTCCTATCGATTG...................................................................................................................................................	25	1	1.00	1	1	0
..........................................................................................................TTTGTGCTCGCACTTCTGG---C..........................................................................................................................	20	1	1.00	1	1	0
.......GC-TTT--ATTCGCACAAGCAAT----------------A............................................................................................................................................................................................................	21	1	1.00	1	1	0
......................CAAGCAAT----------------ACT---AATTAACCC-----------A--CTA--AGA........................................................................................................................................................................	27	1	1.00	1	1	0
.........................................................................................AATTCCTATCGATTGGATTTGTGCTCG.......................................................................................................................................	27	1	1.00	1	1	0
..................................................................................................CGATTGGATTTGTGCTCGC......................................................................................................................................	19	1	1.00	1	1	0
...............................................................................................TATCGATTGGATTTGTGCTCG.......................................................................................................................................	21	1	1.00	1	0	1
.....................................................................................................TTGGATTTGTGCTCGCAC....................................................................................................................................	18	1	1.00	1	1	0
.....................................................................................................TTGGATTTGTGCTCGCACTTCTG...............................................................................................................................	23	1	1.00	1	1	0
........................AGCAAT----------------ACT---AATTAACCC-----------A--................................................................................................................................................................................	19	1	1.00	1	1	0
.........................................................................................................ATTTGTGCTCGCACTTCTGG---CACTTGCA...................................................................................................................	28	1	1.00	1	1	0
............................................................C-----------A--CTA--AGAAAATGAAATTC.............................................................................................................................................................	19	1	1.00	1	1	0
......................................................TTAACCC-----------A--CTA--AGAAAATGAAATTCC............................................................................................................................................................	26	1	1.00	1	1	0

droAna3

GTTCAGTTCTCGCTTCTG--TTCCAGCC--------------------------------------------A--CTT--GCAAGATGAAATTCCTCTCGGTTGCCTTCCTCCTCGGCCTCCTGG---CTCTGGCCAGTGGTGAGTGTTACCC----------------------------CAAAT-------GAGTTTATTT--TAGTAATTTAACTA------------TTTTATTGCTCAAA-----T	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
.................G--TTCCAGCC--------------------------------------------A--CTT--GCAAGA.....................................................................................................................................................................	19	1	2.00	2	0	0	0	0	0	2
....AGTTCTCGCTTCTG--TTCCAGCC--------------------------------------------A--CTT--...........................................................................................................................................................................	26	1	1.00	1	1	0	0	0	0	0
.......................................................................................GAAATTCCTCTCGGTTGCC.................................................................................................................................................	19	1	1.00	1	0	0	0	0	0	1
...........................................................................................TTCCTCTCGGTTGCCTTCCTCC..........................................................................................................................................	22	1	1.00	1	0	0	0	0	0	1
......................................................................................TGAAATTCCTCTCGGTTGC..................................................................................................................................................	19	1	1.00	1	0	0	0	0	0	1
................................................................................GCAAGATGAAATTCCTCTCGGT.....................................................................................................................................................	22	1	1.00	1	0	0	0	0	0	1
.......TCTCGCTTCTG--TTCCAGCC--------------------------------------------A--................................................................................................................................................................................	20	1	1.00	1	0	0	0	0	0	1
.........................GCC--------------------------------------------A--CTT--GCAAGATGAAATTC.............................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	1
.....GTTCTCGCTTCTG--TTCCAGC................................................................................................................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0
........................AGCC--------------------------------------------A--CTT--GCAAGATGAAA................................................................................................................................................................	19	1	1.00	1	0	0	0	0	0	1

droBip1

GTTCAGTACTCGCTTCTG--TTCCAGCC--------------------------------------------A--CTT--GCAAGATGAAGTTCCTCTCGGTTGCCTTCCTCCTCGGCCTCTTGG---CTCTGGCCAGCGGTGAGTGTTATCT-C----T---------GTTAG------TCAA----------T------TT--AAGCCTTTTATCTA------------TT-TTTTCTTTATA-----T	Size	Hit Count	Total Norm	Total
No Reads

droKik1

GTTGTCAGC-TGCCAATCCACCAGAGTTCAC---------------TCGCCGAGTTCCTTAAAAAAAACAAAA--CTATTTCAACATGAAATTCCTGTCGCTCGCCTTCGTCTTGGGTCTGGTTG---CCCTCGCCAGCGGTCAGTAAAAAAAAG----T---------CTATA------TAAATTAATA---TT------AT--AAATTAATAAATTG----A-----------ATTATTTT-----TTA	Size	Hit Count	Total Norm	Total
No Reads

droFic1

GTTGTCTTC-TGAAAATCCTCTTGCTTCAA----------------CCGCAACAACAAACCACA------AAA--CCA--ACAACATGAAATTCCTGTCGCTTGCCTTTGTTTTGGGTCTGCTGG---CTCTGGCCAACGGTAAGTAAATTAAATAA--------AACTATTTG------AGAACT-------GT------A--------TTTTATTTATATTG-----------TCAATGTT-----TGC	Size	Hit Count	Total Norm	Total
No Reads

droEle1

GTTGTCACC-TGCA-ATCCTCTCGAGTCAA----------------CCGCAAAAACAAACCACA------AAA--TCA--ACAACATGAAATTCCTGTCGCTTGCCTTTGTTTTGGGACTGCTGG---CTCTGGCCAATGGTGAGTGAACTCAACTAAAT---------ATTTG------CAAACA-------AC------GT--AAGTCATTTAACTC------------TGATTTCCATTCTA--CAGT	Size	Hit Count	Total Norm	Total
No Reads

droRho1

GTTCTCACT-GGCAAATCCTCTCGAGTCAA----------------CCGCAAAAACAAACCACAAA-----AA--TCA--ACAACATGAAGTTCCTGTCGCTTGCCTTTGTTTTGGGTCTGCTGG---CTCTGGCCAATGGTGAGTAAACTAAAC----T---------ATATATTTAACTAAACA-------AT------AT--CTGTCATTTAATC-------------TTATTTCAATCCTT--TAGT	Size	Hit Count	Total Norm	Total
No Reads

droBia1

GTTGTCGGC-TGCAAATCCCCTCGAGTCAA----------------CCTCAAAAACCAACCACA------AAA--CCA--AGAAAATGAAATTCCTGTCGCTTGCCTTTGTCTTGGGTCTGCTGGCTGCTGTGGCCAATGGTGAGTAAATTGAACGAACT---------GTCTG------CGAACT-------GC------AT--AAGTTATTTAATTA------------TTATCACAACTATT--TTCC	Size	Hit Count	Total Norm	Total
No Reads

droTak1

GTTGTCAGC-TGCAAATCCTCTCGAGTCAA----------------CCTCAAAAACAAACCACA------AAA--TCAAAACAACATGAAATTCCTGTCGCTTGCCTTTGTCTTGGGTTTGCTGG---CTCTGGCCAACGGTGAGTAAACAGAAC----T---------ATTTG------CAAACT-------AC------AT--AAGTTATTTAATTG------------TGATTTTAATTATA--TTTC	Size	Hit Count	Total Norm	Total
No Reads

droEug1

GTTGTCAGC-TGCAAATCCTACCGAGTCAA----------------CCTCA------AACCACAAA-----AACATCA--ACAACATGAAATTCCTGTCGCTTGCCTTTGTCTTGGGTCTGGTGG---CTCTGGCTAATGGTGAGTTAACTAAAC----T---------ATTTA------CGAACT-------TT------AT--AAGTTATTAAATGA------------TTATATTAATTTC----CTT	Size	Hit Count	Total Norm	Total
No Reads

dm3

GTTGTCAAC-GGCTAATACGCGGGAGTCAA----------------GCTCAGAATTCAACCACAAA-----AA--CCA--ACAACATGAAATTCCTATCACTCGCCTTCGTTTTGGGTCTGCTGG---CTCTGGCCAACGGTGAGTAATGCCAAC----T---------ATTTA------CAAACT-------AA------AT--AAGTTATTTAATTA------------TGATTTTAATTATA-----T	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	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
.......AC-GGCTAATACGCGGGAGTCAA----------------GCT..........................................................................................................................................................................................................	25	1	6.00	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...................GCGGGAGTCAA----------------GCTCAGAAT....................................................................................................................................................................................................	20	1	2.00	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	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
...........GCTAATACGCGGGAGTCA..............................................................................................................................................................................................................................	18	1	2.00	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	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
.......AC-GGCTAATACGCGGGAGTC...............................................................................................................................................................................................................................	20	1	2.00	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	1	0	0	0	0	0	0	0	0	0	0	0	0
..............AATACGCGGGAGTCAA----------------GCTCA........................................................................................................................................................................................................	21	1	2.00	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	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
...................GCGGGAGTCAA----------------GCTCAGAATTCA.................................................................................................................................................................................................	23	1	2.00	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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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GTTGTCAAC-GGCTAATACGCGGGA..................................................................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
......................................................................................................................CTGCTGG---CTCTGGCCAAC................................................................................................................	18	3	0.67	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	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
...................................................................................................................GGTCTGCTGG---CTCTGGCCAAC................................................................................................................	21	2	0.50	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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

droSim2

GTTGTCAAC-TGCAAATTCTTTGGAGTCAA----------------GCTCAGCATTCAACCACAAA-----AA--CCA--ACAACATGAAATTCCTATCACTCGCCTTCGTTCTGGGTCTGCTGG---CTCTGGCCAACGGTGAGTAATGCCAAC----T---------ATTCA------CCAACT-------AA------AT--AAGTTATTTAATTA------------TGATTTTAATTATA-----T	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
..........TGCAAATTCTTTGGAGTC...............................................................................................................................................................................................................................	18	1	5.00	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
................TTCTTTGGAGTCAA----------------GCTC.........................................................................................................................................................................................................	18	1	3.00	3	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.......................................................................................GAAATTCCTATCACTCGCCTT...............................................................................................................................................	21	1	2.00	2	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0
.......AC-TGCAAATTCTTTGGAG.................................................................................................................................................................................................................................	18	1	2.00	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
GTTGTCAAC-TGCAAATTCTTTGG...................................................................................................................................................................................................................................	23	1	2.00	2	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.............................................................................................................GTTCTGGGTCTGCTGG---CTCTGGC....................................................................................................................	23	1	2.00	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..................................................................................................CACTCGCCTTCGTTCTGGGTC....................................................................................................................................	21	1	2.00	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.........................................................................................................CTTCGTTCTGGGTCTGCTGG---CTCTGGC....................................................................................................................	27	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................AT--AAGTTATTTAATTA------------TGATT...............	21	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................AA----------------GCTCAGCATTCAACCAC............................................................................................................................................................................................	19	1	1.00	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
...............ATTCTTTGGAGTCAA----------------GCT..........................................................................................................................................................................................................	18	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
................................................................................................................CTGGGTCTGCTGG---CTCTGGC....................................................................................................................	20	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
GTTGTCAAC-TGCAAATTCT.......................................................................................................................................................................................................................................	19	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
........................................................................................................................GCTGG---CTCTGGCCAACGGTGAGTAATGC....................................................................................................	28	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0
.........................GTCAA----------------GCTCAGCATTCAACCACAAA-----....................................................................................................................................................................................	25	1	1.00	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0
.TTGTCAAC-TGCAAATTCTTTGGAGTCAA----------------G............................................................................................................................................................................................................	29	1	1.00	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0
......................................................................................................CGCCTTCGTTCTGGGTCTGCTGG---CTCTGG.....................................................................................................................	29	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
......AAC-TGCAAATTCTTTGGAG.................................................................................................................................................................................................................................	19	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.....................................................ATTCAACCACAAA-----AA--CCA--ACAAC......................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
..............................................................................................CTATCACTCGCCTTCGTTCTGGGT.....................................................................................................................................	24	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
......................................................................................................CGCCTTCGTTCTGGGTCTGCT................................................................................................................................	21	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.........................GTCAA----------------GCTCAGCATTCAACC..............................................................................................................................................................................................	20	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
................................................................................................ATCACTCGCCTTCGTTCTGGGTCTGCT................................................................................................................................	27	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.....................................................................................................TCGCCTTCGTTCTGGGTCTGCT................................................................................................................................	22	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.......................................................................................................GCCTTCGTTCTGGGTCTGCT................................................................................................................................	20	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.............................A----------------GCTCAGCATTCAACCACAA..........................................................................................................................................................................................	20	1	1.00	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
.............................................................................................................GTTCTGGGTCTGCTGG---CT.........................................................................................................................	18	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
................................................................................................ATCACTCGCCTTCGTTCTGGGTC....................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
....................................................................................................................GTCTGCTGG---CTCTGGCCAA.................................................................................................................	19	2	1.00	2	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0
....................................................................................................CTCGCCTTCGTTCTGGGTC....................................................................................................................................	19	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..TGTCAAC-TGCAAATTCTTTGGA..................................................................................................................................................................................................................................	22	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..........................................................................................ATTCCTATCACTCGCCTTCGTTCTG........................................................................................................................................	25	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
................................................................................................................CTGGGTCTGCTGG---CTCTG......................................................................................................................	18	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................................................................................................CGTTCTGGGTCTGCTGG---CTCTGG.....................................................................................................................	23	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..................................................................................................................GGGTCTGCTGG---CTCTGGCCAACGCC.............................................................................................................	25	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.TTGTCAAC-TGCAAATTCTTTGG...................................................................................................................................................................................................................................	22	1	1.00	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0
............CAAATTCTTTGGAGTCAA----------------GCTCAGC......................................................................................................................................................................................................	25	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0
...................................................................................................................GGTCTGCTGG---CTCTGGCCAA.................................................................................................................	20	2	0.50	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droSec2

GTTGTCAAC-TGCAAATTCTCTGGAGTCAA----------------GCTCAGCATTCAACCACAAA-----AA--CCA--ACAACATGAAATTCCTATCACTCGCCTTCGTTCTGGGTCTGCTGG---CTCTGGCCAACGGTGAGTAATGCCAAC----T---------ATTCA------CCAACT-------AC------AT--AAGTTATTTAATTA------------TGATTTAAATTATATTTCCA	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
...........GCAAATTCTCTGGAGTCAA----------------G............................................................................................................................................................................................................	20	1	1.00	1	0	1	0	0
............................................................................................................CGTTCTGGGTCTGCTGG---CTCT.......................................................................................................................	21	1	1.00	1	1	0	0	0
........C-TGCAAATTCTCTGGAGTCAA----------------GC...........................................................................................................................................................................................................	23	1	1.00	1	0	1	0	0
..................................................................................................CACTCGCCTTCGTTCTGGGTCTGCT................................................................................................................................	25	1	1.00	1	0	0	1	0
............................................................................................TCCTATCACTCGCCTTCGTTCTGGGT.....................................................................................................................................	26	1	1.00	1	0	0	0	1
..................................................................................................CACTCGCCTTCGTTCTGGGTCT...................................................................................................................................	22	1	1.00	1	0	1	0	0
..............................................................................................CTATCACTCGCCTTCGTTCTG........................................................................................................................................	21	1	1.00	1	0	1	0	0
...........GCAAATTCTCTGGAGTCAA----------------GC...........................................................................................................................................................................................................	21	1	1.00	1	0	0	0	1
.........................................................................................................CTTCGTTCTGGGTCTGCTGG---CTCTG......................................................................................................................	25	1	1.00	1	0	0	1	0

droYak3

GTTGTTAGC-TGCATATCCTCTGGAGTCAA----------------GCTCAGAAACCAACCACA------AAA--CCA--AAAACATGAAATTCCTATCAGTTGCCTTTGTTCTGGGTCTGCTGG---CCCTGGCCAACGGTGAGTAATCCCAGA----T---------ATTCG------CAAGCT-------AA------AT--ATGTTATTTAATTA------------TGATTTCAATTATA-----T	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
....................CTGGAGTCAA----------------GCTCAGAAACC..................................................................................................................................................................................................	21	1	6.00	6	6	0	0	0	0	0	0	0	0	0	0
..........................................................................................ATTCCTATCAGTTGCCTTTGTTCT.........................................................................................................................................	24	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
.............ATATCCTCTGGAGTCAA----------------GCTC.........................................................................................................................................................................................................	21	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0
...............ATCCTCTGGAGTCAA----------------GCTC.........................................................................................................................................................................................................	19	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0
....................................................................................................................GTCTGCTGG---CCCTGGCCAACGCC.............................................................................................................	23	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0
...............ATCCTCTGGAGTCAA----------------GCTCAGAAACCAA................................................................................................................................................................................................	28	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
..................CTCTGGAGTCAA----------------GCTCAGAAACC..................................................................................................................................................................................................	23	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0
..........TGCATATCCTCTGGAGTCAA----------------G............................................................................................................................................................................................................	21	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
.TTGTTAGC-TGCATATCCTCTG....................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
GTTGTTAGC-TGCATATCCTCTGGAGTC...............................................................................................................................................................................................................................	27	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0

droEre2

GT-------------------------CAA----------------GCTCAGAATCCAACCACA------AAA--CCA--ACAACATGAAATTCCTATCAGTTGCCTTCGTTCTGGGTCTGCTGG---CTCTGGCCAACGGTGAGTAATCCCAGC----T---------ATTCC------CAAACT-------AT------ATATATGTTATTTAATTA------------TGATTTCATTTATA-----T	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
.....................................................................................................TTGCCTTCGTTCTGGGTCT...................................................................................................................................	19	1	1.00	1	1	0	0	0	0	0	0
.T-------------------------CAA----------------GCTCAGAATCCAACCA.............................................................................................................................................................................................	20	1	1.00	1	0	0	0	0	0	1	0
................................................................................................ATCAGTTGCCTTCGTTCT.........................................................................................................................................	18	1	1.00	1	0	0	0	0	0	1	0
.................................................................................................................TGGGTCTGCTGG---CTCTGGCC...................................................................................................................	20	1	1.00	1	1	0	0	0	0	0	0

dpe_123

scaffold_4:6935884-6935939 +

confident

Canonical miRNA

intron

Predicted structure

Flybase annnotation

Sense Strand Reads

Anti-sense strand reads

Re-alignment of all predicted orthologs

Re-alignment of all predicted orthologs with sRNA reads

-21.5	-20.9	-20.7