dya_34

ATTTTCTCTTTGTTATTCTGCAATGGATTTATTTGCTTTAGGATTTATTTTTTCGGACAATTCAATCTGGGCGTTGCTTTCGCTGAGGTAGTATTGTTTGGAAGACTAAGTTAACGAGCATTCATCTCATTTTTGAAATTTTGTGTTCATGAGTG *********************************(((...((((((.(((((((((((((...((((.((((.......)))).))))...))))))))))))).))))))...))).**********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V120 male body	M026 head	M056 embryo	M043 female body	V046 embryo	SRR1275484 Male prepupae	V058 head	SRR1275488 Male larvae	V052 head
...................................................................................TGAGGTAGTATTGTTTGGAAG...................................................	21	0	1	348.00	348	300	16	12	14	2	2	2	0	0
...................................................................................TGAGGTAGTATTGTTTGGAAGA..................................................	22	0	1	333.00	333	263	23	25	13	8	1	0	0	0
..................................................TTTCGGACAATTCAATCTGGGC...................................................................................	22	0	1	81.00	81	16	29	19	8	8	0	0	0	1
...................................................................................TGAGGTAGTATTGTTTGGAAGAT.................................................	23	1	1	53.00	53	42	8	1	2	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGAA....................................................	20	0	1	51.00	51	49	1	1	0	0	0	0	0	0
..................................................TTTCGGACAATTCAATCTGGGCG..................................................................................	23	0	1	43.00	43	8	16	9	9	1	0	0	0	0
..................................................TTTCGGACAATTCAATCTGGG....................................................................................	21	0	1	32.00	32	8	15	2	6	1	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGAAA...................................................	21	1	1	32.00	32	30	1	0	1	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGA.....................................................	19	0	1	29.00	29	26	2	1	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGAAGAA.................................................	23	1	1	24.00	24	24	0	0	0	0	0	0	0	0
..................................................TTTCGGACAATTCAATCTGGGT...................................................................................	22	1	1	23.00	23	8	14	1	0	0	0	0	0	0
..................................................TTTCGGACAATTCAATCTGGGCGT.................................................................................	24	0	1	18.00	18	4	12	1	1	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGAAT...................................................	21	1	1	17.00	17	15	2	0	0	0	0	0	0	0
..................................................TTTCGGACAATTCAATCTGGGCT..................................................................................	23	1	1	15.00	15	2	13	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGAT....................................................	20	1	1	12.00	12	9	3	0	0	0	0	0	0	0
...................................................................................TTAGGTAGTATTGTTTGGAAGA..................................................	22	1	1	11.00	11	0	0	11	0	0	0	0	0	0
..................................................................................CTGAGGTAGTATTGTTTGGAAGA..................................................	23	0	1	10.00	10	9	0	1	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGAAGT..................................................	22	1	1	10.00	10	7	0	1	0	0	0	2	0	0
..................................................TTTCGGACAATTCAATCTGGGTT..................................................................................	23	2	1	9.00	9	2	7	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGAAAA..................................................	22	1	1	8.00	8	7	1	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGAAGATT................................................	24	1	1	8.00	8	8	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGAAGAAA................................................	24	2	1	8.00	8	6	0	0	0	0	2	0	0	0
..................................................TTTCGGACAATTCAATCTGGGCTT.................................................................................	24	1	1	8.00	8	2	4	2	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGT.....................................................	19	1	1	7.00	7	7	0	0	0	0	0	0	0	0
..................................................TTTCGGACAATTCAATCTGGGA...................................................................................	22	1	1	5.00	5	5	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGAAGAAT................................................	24	1	1	5.00	5	5	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGAAGTA.................................................	23	2	1	5.00	5	3	2	0	0	0	0	0	0	0
..................................................TTTCGGACAATTCAATCTGGGCAT.................................................................................	24	1	1	5.00	5	1	4	0	0	0	0	0	0	0
..................................GCTTTAGGATTTGTTTTTT......................................................................................................	19	1	2	4.00	8	2	3	0	1	1	0	1	0	0
...................................................................................TTAGGTAGTATTGTTTGGAAG...................................................	21	1	1	4.00	4	0	0	4	0	0	0	0	0	0
..................................................TTTCGGACAATTCAATCTGG.....................................................................................	20	0	1	4.00	4	1	2	0	1	0	0	0	0	0
..................................................TTTCGGACAATTCAATC........................................................................................	17	0	1	4.00	4	0	0	0	0	0	3	0	1	0
..................................................................................CTGAGGTAGTATTGTTTGGA.....................................................	20	0	1	4.00	4	4	0	0	0	0	0	0	0	0
...................................................................................TGAGGGAGTATTGTTTGGAAG...................................................	21	1	1	3.00	3	3	0	0	0	0	0	0	0	0
..................................................TTTCGGACAATTCAATCTGGGCGG.................................................................................	24	1	1	3.00	3	0	3	0	0	0	0	0	0	0
..................................................TTTCGGACAATTCAATCTGGGCGC.................................................................................	24	1	1	3.00	3	0	1	2	0	0	0	0	0	0
..................................................TTTCGGACAATTCAATCTGGGCGTTT...............................................................................	26	1	1	3.00	3	1	0	0	1	0	1	0	0	0
..................................................TTTCGGACAATTCAATCTGGGCC..................................................................................	23	1	1	3.00	3	0	3	0	0	0	0	0	0	0
..................................................TTTCGGACAATTCAATCTGGGTTT.................................................................................	24	2	1	3.00	3	3	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGAAGTT.................................................	23	2	1	3.00	3	3	0	0	0	0	0	0	0	0
..................................................................................CTGAGGTAGTATTGTTTGGAA....................................................	21	0	1	3.00	3	3	0	0	0	0	0	0	0	0
..................................................................................CTGAGGTAGTATTGTTTGGAAG...................................................	22	0	1	3.00	3	1	0	1	1	0	0	0	0	0
...................................................................................TGAGGGAGTATTGTTTGGAAGA..................................................	22	1	1	3.00	3	2	0	1	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGATT...................................................	21	2	1	2.00	2	2	0	0	0	0	0	0	0	0
..................................................TTTCGGACAATTCAATCTGGAC...................................................................................	22	1	1	2.00	2	0	2	0	0	0	0	0	0	0
....................................................................................GAGGTAGTATTGTTTGGAAGA..................................................	21	0	1	2.00	2	0	0	0	2	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGAAGAATT...............................................	25	2	1	2.00	2	2	0	0	0	0	0	0	0	0
..................................................TGTCGGACAATTCAATCTGGGC...................................................................................	22	1	1	2.00	2	0	0	2	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGAAAAA.................................................	23	2	1	2.00	2	2	0	0	0	0	0	0	0	0
..................................................................................CTGAGGTAGTATTGTTTGGAAA...................................................	22	1	1	2.00	2	2	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGCAAG...................................................	21	1	1	2.00	2	2	0	0	0	0	0	0	0	0
..................................................TTTTGGACAATTCAATCTGGGC...................................................................................	22	1	1	2.00	2	0	0	2	0	0	0	0	0	0
..................................................TGTTGGACAATTCAATCTGGGC...................................................................................	22	2	1	2.00	2	0	0	2	0	0	0	0	0	0
..................................................TTTCGGACAATTCAATCTGGGCGTT................................................................................	25	0	1	2.00	2	0	2	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGTT....................................................	20	2	1	2.00	2	2	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGAAGG..................................................	22	1	1	2.00	2	0	2	0	0	0	0	0	0	0
..................................................TTTCGGACAATTCAATCTGGGGG..................................................................................	23	1	1	1.00	1	0	0	0	1	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGAAAAAAAA..............................................	26	3	1	1.00	1	1	0	0	0	0	0	0	0	0
..................................................TTTCGGACAATTCAATCTGGGTC..................................................................................	23	2	1	1.00	1	0	1	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTCGAAG...................................................	21	1	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TAAGGTAGTATTGTTTGGAAA...................................................	21	2	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGAAGCA.................................................	23	2	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGCAGTATTGTTTGGAT....................................................	20	2	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................TTCGGACAATTCAATCTGGGCG..................................................................................	22	0	1	1.00	1	0	0	0	1	0	0	0	0	0
...................................................................................TAAGGTAGTATTGTTTGGAA....................................................	20	1	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGTAA...................................................	21	2	1	1.00	1	1	0	0	0	0	0	0	0	0
..................................................TTTCGGACAATTCAATCT.......................................................................................	18	0	1	1.00	1	0	0	0	0	0	1	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGAAATT.................................................	23	3	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGCATTGTTTGGAAGA..................................................	22	1	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGCAAGAAAA...............................................	25	3	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTAGAAGA..................................................	22	1	1	1.00	1	1	0	0	0	0	0	0	0	0
...............................................................................................CTTTGGAAGACTAATTTAACG.......................................	21	2	1	1.00	1	0	0	0	1	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTAGAAG...................................................	21	1	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGAAGTATTGTTTGGAAG...................................................	21	1	1	1.00	1	0	0	0	1	0	0	0	0	0
..................................................TATCGGACAATTCAATCTGGGC...................................................................................	22	1	1	1.00	1	0	0	1	0	0	0	0	0	0
..................................................TTTCGGACAATTCAATCTGGGAGGT................................................................................	25	2	1	1.00	1	1	0	0	0	0	0	0	0	0
....................................................TCGGACAATTCAATCTGGGC...................................................................................	20	0	1	1.00	1	1	0	0	0	0	0	0	0	0
..................................................TGTCGGACAATTCAATCTGGGCG..................................................................................	23	1	1	1.00	1	0	0	1	0	0	0	0	0	0
..................................................TTTCGGACAATTCAATCTTGGCG..................................................................................	23	1	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGCTTGGAAG...................................................	21	1	1	1.00	1	1	0	0	0	0	0	0	0	0
..................................................TCTCGGACAATTCAATCTGGGC...................................................................................	22	1	1	1.00	1	0	0	0	0	0	0	1	0	0
...................................................................................TGAGGTAGTATTGTTTGGAAGAAAA...............................................	25	2	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGAAAT..................................................	22	2	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGAATAAA................................................	24	3	1	1.00	1	1	0	0	0	0	0	0	0	0
.....................................................................................AGGAAGTATTGTTTGGAAGA..................................................	20	1	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGATA...................................................	21	2	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGATGTAGTATTGTTTGGAAGA..................................................	22	1	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGCATTGTTTGGAAG...................................................	21	1	1	1.00	1	1	0	0	0	0	0	0	0	0
..................................................TTTCGGGCAATTCAATCTGGGCGT.................................................................................	24	1	1	1.00	1	0	1	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGCTTGGAAGA..................................................	22	1	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGAAGATAT...............................................	25	3	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGAAGAC.................................................	23	0	1	1.00	1	1	0	0	0	0	0	0	0	0
..................................................CTTCGGACAATTCAATCTGGGC...................................................................................	22	1	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGTATTATTGTTTGGAAT...................................................	21	2	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................TTCGGACAATTCAATCTGGGCGT.................................................................................	23	0	1	1.00	1	0	0	0	1	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGTAAA..................................................	22	2	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGAGGA..................................................	22	1	1	1.00	1	0	1	0	0	0	0	0	0	0
...................................................................................TGAGGGAGTATTGTTTGGAAGT..................................................	22	2	1	1.00	1	1	0	0	0	0	0	0	0	0
..................................................TTTCGGACAATTCAATCTGGGCGA.................................................................................	24	1	1	1.00	1	0	1	0	0	0	0	0	0	0
..................................................TTTCGGACATTTCAATCTGGGC...................................................................................	22	1	1	1.00	1	0	0	1	0	0	0	0	0	0
..................................................CTTCGGACAATTCAATCTGGGCGTCT...............................................................................	26	3	1	1.00	1	1	0	0	0	0	0	0	0	0
..................................................TTTCGGACCATTCAATCTGGGC...................................................................................	22	1	1	1.00	1	0	1	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGGTTGGAAG...................................................	21	1	1	1.00	1	1	0	0	0	0	0	0	0	0
....................................................................................GAGGTAGTATTGTTTGGAAG...................................................	20	0	1	1.00	1	0	0	1	0	0	0	0	0	0
...................................................................................TTAGTTAGTATTGTTTGGAAG...................................................	21	2	1	1.00	1	0	0	1	0	0	0	0	0	0
..................................................................................CTGAGGTAGTATTGTTTGGAAGAA.................................................	24	1	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TTAGGGAGTATTGTTTGGAAGA..................................................	22	2	1	1.00	1	0	0	1	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGA......................................................	18	1	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGT......................................................	18	1	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGCGGTAGTATTGTTTGGAAG...................................................	21	1	1	1.00	1	0	0	1	0	0	0	0	0	0
..................................................TTTCGGACAATTCAATCTGGTC...................................................................................	22	1	1	1.00	1	0	0	0	0	0	0	1	0	0
...................................................................................TGAGGTAGCATTGTTTGGAA....................................................	20	1	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGAAGAAG................................................	24	2	1	1.00	1	1	0	0	0	0	0	0	0	0
..................................................TGTCGGACAATTCAATCTGG.....................................................................................	20	1	1	1.00	1	0	0	1	0	0	0	0	0	0
...................................................................................TGAGGGAGTATTGTTTGGAA....................................................	20	1	1	1.00	1	1	0	0	0	0	0	0	0	0
..................................................TTTCGGACAATTCAATCTGGGCAAT................................................................................	25	2	1	1.00	1	0	1	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGGAG...................................................	21	1	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGAAGC..................................................	22	1	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGAATT..................................................	22	2	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTTTTTGGAAG...................................................	21	1	1	1.00	1	0	1	0	0	0	0	0	0	0
..................................................TTTCAGACAATTCAATCTGGGCG..................................................................................	23	1	1	1.00	1	0	0	0	0	1	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGC......................................................	18	1	1	1.00	1	1	0	0	0	0	0	0	0	0
..................................................TGTCGGACAATTCAATCTGGG....................................................................................	21	1	1	1.00	1	0	0	1	0	0	0	0	0	0
..................................................TTTCGGACAGTTCAATCTGGGC...................................................................................	22	1	1	1.00	1	0	0	0	1	0	0	0	0	0
..................................................TTTCGGACAATTCAATCTGGGCTTAT...............................................................................	26	3	1	1.00	1	0	1	0	0	0	0	0	0	0
...................................................TTCGGACAATTCAATCTGGGC...................................................................................	21	0	1	1.00	1	0	0	0	1	0	0	0	0	0
...................................................................................TGAGGTAGTATTTATTGGAAG...................................................	21	2	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGAAATA.................................................	23	3	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGAAAGA..................................................	22	1	1	1.00	1	1	0	0	0	0	0	0	0	0
..................................................TGTCGGACAATTCAATCTGGAC...................................................................................	22	2	1	1.00	1	0	0	1	0	0	0	0	0	0
..................................................TTTCGGACTATTCAATCTGGG....................................................................................	21	1	1	1.00	1	0	0	0	1	0	0	0	0	0
...................................................................................TGAGGTAGTATTATTTGGAAA...................................................	21	2	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGG......................................................	18	0	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGCTTGGAA....................................................	20	1	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGAAGATTTT..............................................	26	3	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGATGTAGTATTGTTTGGAAGT..................................................	22	2	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGCAG...................................................	21	1	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGTGGTATTGTTTGGAAGA..................................................	22	1	1	1.00	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTGGAAG....................................................	20	3	3	0.67	2	2	0	0	0	0	0	0	0	0
...................................CTTTAGGATTTGTTTTTT......................................................................................................	18	1	4	0.50	2	0	2	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTATAG......................................................	18	2	2	0.50	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGATAT..................................................	22	3	2	0.50	1	1	0	0	0	0	0	0	0	0
............................TTATTAGCTTTAGGATTTGTTTTTT......................................................................................................	25	2	2	0.50	1	0	0	0	1	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGTTT...................................................	21	3	5	0.40	2	2	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGTT.....................................................	19	2	3	0.33	1	1	0	0	0	0	0	0	0	0
..................................GCTTTAGGATTTGTTTTT.......................................................................................................	18	1	3	0.33	1	0	1	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTAAAA....................................................	20	2	3	0.33	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTTTGGTTA...................................................	21	3	4	0.25	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGAAGTATTGTTTGGAT....................................................	20	2	8	0.13	1	1	0	0	0	0	0	0	0	0
......................................................................................................AAACTAAGATTACGAGCATT.................................	20	3	19	0.05	1	1	0	0	0	0	0	0	0	0
...................................................................................TGAGGTAGTATTGTATAGT.....................................................	19	3	20	0.05	1	1	0	0	0	0	0	0	0	0

Species	Coordinate	ID	Type	Alignment
droYak3	2R:12724086-12724240 +	dya_34	confident	AT----TTTCTCTTTGTTATT-------------CTGCAATGGATTTATTT--------GCTTTAGGATTTA-------TTTTTTCGGACAATTCAATCTGGGCGTTGCTTTCGCTGAGGTAGTATTGTTTGGAAGACTAAGTTAACGAGC-------------------------------------------------------------------------------------------------------------------------------------------------------------ATTCATCTCATTT-TTGAAAT---------------------------------------------TTTGTGTTCATGAGTG
droEre2	scaffold_4845:10618676-10618838 -	der_25	confident	GT----TTTCT----GTTATTTTACTATATAA------------CTTATTTATGAAGAAGCTTTAGGATTTA-------ATTTTTCCGACAATGCGATCTAGGCGTTTCTATCGCTGAGGTAGTATTGTTTGAAAGATTAAGTTAAAGCGT-------------------------------------------------------------------------------------------------------------------------------------------------------------AATCATCAAAATT-TTAAAATGTG------------------------------------------AATAAGTACATAAGTG
droSec2	scaffold_1:14026259-14026320 -			GT----ATTCTTTTTGCTATT-------------CTA-----------------------------------------------------------------------------------------------------TAGGCTAACGAGC-------------------------------------------------------------------------------------------------------------------------------------------------------------ATTCCTTAAAAT-------A----------------------------------------------CATATGTACATAAGTG
droSim2	2r:17041524-17041580 -			AAT-TTATTCTTTTTGCTATT-------------CTA-----------------------------------------------------------------------------------------------------TAGGCTAATGAGC-------------------------------------------------------------------------------------------------------------------------------------------------------------ATTCCTTAAAAT-------------------------------------------------------------ACATATGTG
dm3	chr2R:16472054-16472133 -			TATGGTATTCTGTTTGCTATT-------------ATA-----------------------------------------------------------------------------------------------------AAAGTTCACGAGC--------------------TAA-----------------------------------------------GCTAACG--------------------------------------------------------------------------------ATTCATTAAAAT-------ATGTA------------------------------------------CATACATATTTAAGTG
droEug1	scf7180000409474:1489443-1489655 +			TT----TTGGC------AATT-------------AC------------------------------------------------ATATAAAG---------------------------------------------GTAAAATAAAGTGCCTTTCTTAAAAATCAAGTGCTTAATATTGAAAGTATGATTATTAAAATAATATTTATTTACATTTAAAGCACTTTCGAATTTTTAAGATAACTCAATGGGTGTACATTTTTAAATAATTATTGTTCGAGCGTTGAGTTATTTTAAGAATTAATGTGTAAGTCGCAATAA-------------------------------------------------------------GTGAAAATG
droTak1	scf7180000415401:100735-100900 -			AC----CTTCG-TTTATTACT---CTTGATAATTCTGTAAAAGAA--------------ATTAAAACATCTTTTATTGATTTATACAGAGAA---------------------------------------------ATAAGTTTAAGTGA-------------------------------------------------------------------------------------------------------------------------------------------------------------ATTCGCCAAAAATGGTTAAAGCTAAAAAAGTGCGTGTTTAAGTTCCTATCGGAATCAGTACTTTTATTTGCTTTTCTGGATT
droRho1	scf7180000780104:83008-83037 -			AT----TATTTATTTGTTAGT-------------ATAT------TTTATTT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AC-----------

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droYak3

AT----TTTCTCTTTGTTATT-------------CTGCAATGGATTTATTT--------GCTTTAGGATTTA-------TTTTTTCGGACAATTCAATCTGGGCGTTGCTTTCGCTGAGGTAGTATTGTTTGGAAGACTAAGTTAACGAGC-------------------------------------------------------------------------------------------------------------------------------------------------------------ATTCATCTCATTT-TTGAAAT---------------------------------------------TTTGTGTTCATGAGTG	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
...................................................................................................................TGAGGTAGTATTGTTTGGAAG..............................................................................................................................................................................................................................................................	21	1	348.00	348	16	14	12	2	0	2	300	0	0	2	0
...................................................................................................................TGAGGTAGTATTGTTTGGAAGA.............................................................................................................................................................................................................................................................	22	1	333.00	333	23	13	25	8	0	0	263	0	0	1	0
..................................................................................TTTCGGACAATTCAATCTGGGC..............................................................................................................................................................................................................................................................................................	22	1	81.00	81	29	8	19	8	1	0	16	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGGAAGAT............................................................................................................................................................................................................................................................	23	1	53.00	53	8	2	1	0	0	0	42	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGGAA...............................................................................................................................................................................................................................................................	20	1	51.00	51	1	0	1	0	0	0	49	0	0	0	0
..................................................................................TTTCGGACAATTCAATCTGGGCG.............................................................................................................................................................................................................................................................................................	23	1	43.00	43	16	9	9	1	0	0	8	0	0	0	0
..................................................................................TTTCGGACAATTCAATCTGGG...............................................................................................................................................................................................................................................................................................	21	1	32.00	32	15	6	2	1	0	0	8	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGGAAA..............................................................................................................................................................................................................................................................	21	1	32.00	32	1	1	0	0	0	0	30	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGGA................................................................................................................................................................................................................................................................	19	1	29.00	29	2	0	1	0	0	0	26	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGGAAGAA............................................................................................................................................................................................................................................................	23	1	24.00	24	0	0	0	0	0	0	24	0	0	0	0
..................................................................................TTTCGGACAATTCAATCTGGGT..............................................................................................................................................................................................................................................................................................	22	1	23.00	23	14	0	1	0	0	0	8	0	0	0	0
..................................................................................TTTCGGACAATTCAATCTGGGCGT............................................................................................................................................................................................................................................................................................	24	1	18.00	18	12	1	1	0	0	0	4	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGGAAT..............................................................................................................................................................................................................................................................	21	1	17.00	17	2	0	0	0	0	0	15	0	0	0	0
..................................................................................TTTCGGACAATTCAATCTGGGCT.............................................................................................................................................................................................................................................................................................	23	1	15.00	15	13	0	0	0	0	0	2	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGGAT...............................................................................................................................................................................................................................................................	20	1	12.00	12	3	0	0	0	0	0	9	0	0	0	0
..................................................................................................................CTGAGGTAGTATTGTTTGGAAGA.............................................................................................................................................................................................................................................................	23	1	10.00	10	0	0	1	0	0	0	9	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGGAAGT.............................................................................................................................................................................................................................................................	22	1	10.00	10	0	0	1	0	0	2	7	0	0	0	0
..................................................................................TTTCGGACAATTCAATCTGGGTT.............................................................................................................................................................................................................................................................................................	23	1	9.00	9	7	0	0	0	0	0	2	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGGAAGAAA...........................................................................................................................................................................................................................................................	24	1	8.00	8	0	0	0	0	0	0	6	0	0	2	0
...................................................................................................................TGAGGTAGTATTGTTTGGT................................................................................................................................................................................................................................................................	19	1	7.00	7	0	0	0	0	0	0	7	0	0	0	0
..................................................................................TTTCGGACAATTCAATCTGGGA..............................................................................................................................................................................................................................................................................................	22	1	5.00	5	0	0	0	0	0	0	5	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGGAAGTA............................................................................................................................................................................................................................................................	23	1	5.00	5	2	0	0	0	0	0	3	0	0	0	0
..................................................................................TTTCGGACAATTCAATCTGG................................................................................................................................................................................................................................................................................................	20	1	4.00	4	2	1	0	0	0	0	1	0	0	0	0
..................................................................................TTTCGGACAATTCAATC...................................................................................................................................................................................................................................................................................................	17	1	4.00	4	0	0	0	0	0	0	0	1	0	3	0
..................................................................................................................CTGAGGTAGTATTGTTTGGA................................................................................................................................................................................................................................................................	20	1	4.00	4	0	0	0	0	0	0	4	0	0	0	0
..................................................................................TTTCGGACAATTCAATCTGGGCGG............................................................................................................................................................................................................................................................................................	24	1	3.00	3	3	0	0	0	0	0	0	0	0	0	0
..................................................................................TTTCGGACAATTCAATCTGGGCGC............................................................................................................................................................................................................................................................................................	24	1	3.00	3	1	0	2	0	0	0	0	0	0	0	0
..................................................................................TTTCGGACAATTCAATCTGGGCGTTT..........................................................................................................................................................................................................................................................................................	26	1	3.00	3	0	1	0	0	0	0	1	0	0	1	0
..................................................................................TTTCGGACAATTCAATCTGGGCC.............................................................................................................................................................................................................................................................................................	23	1	3.00	3	3	0	0	0	0	0	0	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGGAAGTT............................................................................................................................................................................................................................................................	23	1	3.00	3	0	0	0	0	0	0	3	0	0	0	0
..................................................................................................................CTGAGGTAGTATTGTTTGGAA...............................................................................................................................................................................................................................................................	21	1	3.00	3	0	0	0	0	0	0	3	0	0	0	0
..................................................................................................................CTGAGGTAGTATTGTTTGGAAG..............................................................................................................................................................................................................................................................	22	1	3.00	3	0	1	1	0	0	0	1	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGGATT..............................................................................................................................................................................................................................................................	21	1	2.00	2	0	0	0	0	0	0	2	0	0	0	0
....................................................................................................................GAGGTAGTATTGTTTGGAAGA.............................................................................................................................................................................................................................................................	21	1	2.00	2	0	2	0	0	0	0	0	0	0	0	0
..................................................................................................................CTGAGGTAGTATTGTTTGGAAA..............................................................................................................................................................................................................................................................	22	1	2.00	2	0	0	0	0	0	0	2	0	0	0	0
..................................................................................TTTCGGACAATTCAATCTGGGCGTT...........................................................................................................................................................................................................................................................................................	25	1	2.00	2	2	0	0	0	0	0	0	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGGTT...............................................................................................................................................................................................................................................................	20	1	2.00	2	0	0	0	0	0	0	2	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGGAAGG.............................................................................................................................................................................................................................................................	22	1	2.00	2	2	0	0	0	0	0	0	0	0	0	0
..................................................................................TTTCGGACAATTCAATCTGGGTC.............................................................................................................................................................................................................................................................................................	23	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGGAAGCA............................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
...................................................................................TTCGGACAATTCAATCTGGGCG.............................................................................................................................................................................................................................................................................................	22	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
..................................................................................TTTCGGACAATTCAATCT..................................................................................................................................................................................................................................................................................................	18	1	1.00	1	0	0	0	0	0	0	0	0	0	1	0
...................................................................................................................TGAGGTAGTATTGTTTGGAAATT............................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
....................................................................................TCGGACAATTCAATCTGGGC..............................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGGAAAT.............................................................................................................................................................................................................................................................	22	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGGATA..............................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGGAAGATAT..........................................................................................................................................................................................................................................................	25	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGGAAGAC............................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
...................................................................................TTCGGACAATTCAATCTGGGCGT............................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
..................................................................................TTTCGGACAATTCAATCTGGGCGA............................................................................................................................................................................................................................................................................................	24	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0
....................................................................................................................GAGGTAGTATTGTTTGGAAG..............................................................................................................................................................................................................................................................	20	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0
..................................................................................................................CTGAGGTAGTATTGTTTGGAAGAA............................................................................................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGA.................................................................................................................................................................................................................................................................	18	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGT.................................................................................................................................................................................................................................................................	18	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGGAAGAAG...........................................................................................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGGAAGC.............................................................................................................................................................................................................................................................	22	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGGAATT.............................................................................................................................................................................................................................................................	22	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGC.................................................................................................................................................................................................................................................................	18	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
...................................................................................TTCGGACAATTCAATCTGGGC..............................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGGAAATA............................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGG.................................................................................................................................................................................................................................................................	18	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGGATAT.............................................................................................................................................................................................................................................................	22	2	0.50	1	0	0	0	0	0	0	1	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGGTTT..............................................................................................................................................................................................................................................................	21	5	0.40	2	0	0	0	0	0	0	2	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGTT................................................................................................................................................................................................................................................................	19	3	0.33	1	0	0	0	0	0	0	1	0	0	0	0
...................................................................................................................TGAGGTAGTATTGTTTGGTTA..............................................................................................................................................................................................................................................................	21	4	0.25	1	0	0	0	0	0	0	1	0	0	0	0

droEre2

GT----TTTCT----GTTATTTTACTATATAA------------CTTATTTATGAAGAAGCTTTAGGATTTA-------ATTTTTCCGACAATGCGATCTAGGCGTTTCTATCGCTGAGGTAGTATTGTTTGAAAGATTAAGTTAAAGCGT-------------------------------------------------------------------------------------------------------------------------------------------------------------AATCATCAAAATT-TTAAAATGTG------------------------------------------AATAAGTACATAAGTG	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
...................................................................................................................TGAGGTAGTATTGTTTGAAAGA.............................................................................................................................................................................................................................................................	22	1	5023.00	5023	22	0	19	5	4474	503	0
...................................................................................................................TGAGGTAGTATTGTTTGAAAG..............................................................................................................................................................................................................................................................	21	1	1087.00	1087	8	0	4	1	958	116	0
...................................................................................................................TGAGGTAGTATTGTTTGAAAGAA............................................................................................................................................................................................................................................................	23	1	725.00	725	5	0	1	0	654	65	0
...................................................................................................................TGAGGTAGTATTGTTTGAAAGAT............................................................................................................................................................................................................................................................	23	1	392.00	392	5	0	2	0	344	38	3
..................................................................................TTTCCGACAATGCGATCTAGG...............................................................................................................................................................................................................................................................................................	21	1	369.00	369	11	0	8	1	297	52	0
...................................................................................................................TGAGGTAGTATTGTTTGAAA...............................................................................................................................................................................................................................................................	20	1	203.00	203	2	0	3	1	171	26	0
...................................................................................................................TGAGGTAGTATTGTTTGAAAGAAA...........................................................................................................................................................................................................................................................	24	1	145.00	145	1	0	1	0	127	16	0
....................................................................................................................GAGGTAGTATTGTTTGAAAGA.............................................................................................................................................................................................................................................................	21	1	133.00	133	0	0	0	0	115	18	0
...................................................................................................................TGAGGTAGTATTGTTTGAAAA..............................................................................................................................................................................................................................................................	21	1	55.00	55	0	0	0	1	47	7	0
..................................................................................TTTCCGACAATGCGATCTAGGC..............................................................................................................................................................................................................................................................................................	22	1	51.00	51	1	0	3	2	37	8	0
..................................................................................TTTCCGACAATGCGATCTAG................................................................................................................................................................................................................................................................................................	20	1	40.00	40	4	0	1	0	33	2	0
...................................................................................................................TGAGGTAGTATTGTTTGAAAGT.............................................................................................................................................................................................................................................................	22	1	39.00	39	0	0	0	1	33	5	0
...................................................................................................................TGAGGTAGTATTGTTTGAA................................................................................................................................................................................................................................................................	19	1	36.00	36	0	0	0	0	30	6	0
...................................................................................................................TGAGGTAGTATTGTTTGAAAGAC............................................................................................................................................................................................................................................................	23	1	22.00	22	0	0	0	0	19	3	0
...................................................................................................................TGAGGTAGTATTGTTTGAAAGATA...........................................................................................................................................................................................................................................................	24	1	17.00	17	1	0	0	0	13	3	0
...................................................................................................................TGAGGTAGTATTGTTTGAAAGACA...........................................................................................................................................................................................................................................................	24	1	12.00	12	0	0	0	0	10	2	0
...................................................................................................................TGAGGTAGTATTGTTTGAAAGC.............................................................................................................................................................................................................................................................	22	1	11.00	11	0	0	0	0	11	0	0
....................................................................................................................GAGGTAGTATTGTTTGAAAGAA............................................................................................................................................................................................................................................................	22	1	11.00	11	0	0	1	0	10	0	0
.................................................................................TTTTCCGACAATGCGATCTAGG...............................................................................................................................................................................................................................................................................................	22	1	11.00	11	2	0	0	0	7	2	0
....................................................................................................................GAGGTAGTATTGTTTGAAAG..............................................................................................................................................................................................................................................................	20	1	10.00	10	1	0	0	0	8	1	0
...................................................................................................................TGAGGTAGTATTGTTTGAAAGATT...........................................................................................................................................................................................................................................................	24	1	9.00	9	0	0	0	0	9	0	0
...................................................................................................................TGAGGTAGTATTGTTTGAAAGAG............................................................................................................................................................................................................................................................	23	1	8.00	8	0	0	0	0	8	0	0
...................................................................................................................TGAGGTAGTATTGTTTGAAGA..............................................................................................................................................................................................................................................................	21	1	7.00	7	0	0	1	0	6	0	0
...................................................................................................................TGAGGTAGTATTGTTTGAAAGATAT..........................................................................................................................................................................................................................................................	25	1	5.00	5	0	0	0	0	4	1	0
..................................................................................TTTCCGACAATGCGATCTAGGCGT............................................................................................................................................................................................................................................................................................	24	1	5.00	5	0	0	0	0	5	0	0
..................................................................................TTTCCGACAATGCGATCTAGGA..............................................................................................................................................................................................................................................................................................	22	1	5.00	5	0	0	1	0	4	0	0
..................................................................................TTTCCGACAATGCGATCTAGGT..............................................................................................................................................................................................................................................................................................	22	1	5.00	5	0	0	0	0	4	1	0
....................................................................................................................GAGGTAGTATTGTTTGAAAGAAA...........................................................................................................................................................................................................................................................	23	1	4.00	4	0	0	0	0	4	0	0
...................................................................................................................TGAGGTAGTATTGTTTGAAAGCA............................................................................................................................................................................................................................................................	23	1	4.00	4	0	0	0	0	3	1	0
....................................................................................................................GAGGTAGTATTGTTTGAAAGAT............................................................................................................................................................................................................................................................	22	1	4.00	4	1	0	0	0	2	1	0
...................................................................................................................TGAGGTAGTATTGTTTGAAAGTA............................................................................................................................................................................................................................................................	23	1	3.00	3	0	0	0	0	3	0	0
..................................................................................TTTCCGACAATGCGATCTAGGCA.............................................................................................................................................................................................................................................................................................	23	1	3.00	3	0	0	0	0	1	2	0
...................................................................................................................TGAGGTAGTATTGTTTGAAAGTAA...........................................................................................................................................................................................................................................................	24	1	3.00	3	0	0	0	0	3	0	0
..................................................................................TTTCCGACAATGCGATCTAGGCT.............................................................................................................................................................................................................................................................................................	23	1	2.00	2	0	0	0	0	2	0	0
...................................................................................................................TGAGGTAGTATTGTTTGA.................................................................................................................................................................................................................................................................	18	1	2.00	2	0	0	0	0	2	0	0
...................................................................................................................TGAGGTAGTATTGTTTGAAT...............................................................................................................................................................................................................................................................	20	1	2.00	2	0	0	0	0	2	0	0
...................................................................................................................TGAGGTAGTATTGTTTGAAAGG.............................................................................................................................................................................................................................................................	22	1	2.00	2	0	0	0	0	2	0	0
....................................................................................................................GAGGTAGTATTGTTTGAAA...............................................................................................................................................................................................................................................................	19	1	2.00	2	0	0	0	0	1	1	0
...................................................................................................................TGAGGTAGTATTGTTTGAAAT..............................................................................................................................................................................................................................................................	21	1	2.00	2	0	0	0	0	1	1	0
..................................................................................................................CTGAGGTAGTATTGTTTGAAAGA.............................................................................................................................................................................................................................................................	23	1	2.00	2	0	0	0	0	1	1	0
...................................................................................TTCCGACAATGCGATCTAGG...............................................................................................................................................................................................................................................................................................	20	1	2.00	2	0	0	0	0	0	2	0
..................................................................................TTTCCGACAATGCGATCTAGGCG.............................................................................................................................................................................................................................................................................................	23	1	2.00	2	0	0	0	0	1	1	0
...................................................................................................................TGAGGTAGTATTGTTTGAAAGAAGT..........................................................................................................................................................................................................................................................	25	1	1.00	1	0	0	0	0	1	0	0
........................................................................................................................TAGTATTGTTTGAAAGAA............................................................................................................................................................................................................................................................	18	2	1.00	2	0	0	0	0	2	0	0
..................................................................................TTTCCGACAATGCGATCTAGGCAAA...........................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	0	0	0	1	0	0
....................................................................................................................GAGGTAGTATTGTTTGAAAT..............................................................................................................................................................................................................................................................	20	1	1.00	1	1	0	0	0	0	0	0
..................................................................................................................CTGAGGTAGTATTGTTTGAAAGAT............................................................................................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	1	0	0
..................................................................................TTTCCGACAATGCGATCTAGGCGTT...........................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	0	0	0	1	0	0
..................................................................................TTTCCGACAATGCGATCTAGGAT.............................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	1	0	0
...................................................................................................................TGAGGTAGTATTGTTTGAAAC..............................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	1	0	0
....................................................................................................................GAGGTAGTATTGTTTGAAAGT.............................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	1	0	0
...................................................................................................................TGAGGTAGTATTGTTTGAAAAT.............................................................................................................................................................................................................................................................	22	1	1.00	1	0	0	0	0	1	0	0
...................................................................................................................TGAGGTAGTATTGTTTGAAAGAAAT..........................................................................................................................................................................................................................................................	25	1	1.00	1	0	0	0	0	1	0	0
...................................................................................................................TGAGGTAGTATTGTTTGAAAGAGA...........................................................................................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	1	0
...................................................................................................................TGAGGTAGTATTGTTTGAT................................................................................................................................................................................................................................................................	19	1	1.00	1	0	0	0	0	1	0	0
..................................................................................TTTCCGACAATGCGATCTAT................................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	0	0	0	1	0	0
...................................................................................................................TGAGGTAGTATTGTTTGAAAGCC............................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	1	0	0
..................................................................................................................CTGAGGTAGTATTGTTTGAAAGAA............................................................................................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	1	0
.......................................................................................................................GTAGTATTGTTTGAAAGA.............................................................................................................................................................................................................................................................	18	1	1.00	1	0	0	0	0	1	0	0

droSec2

GT----ATTCTTTTTGCTATT-------------CTA-----------------------------------------------------------------------------------------------------TAGGCTAACGAGC-------------------------------------------------------------------------------------------------------------------------------------------------------------ATTCCTTAAAAT-------A----------------------------------------------CATATGTACATAAGTG	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
.T----ATTCTTTTTGCTATT-------------CTA-----------------------------------------------------------------------------------------------------TA..........................................................................................................................................................................................................................................................	21	1	1.00	1	1	0	0	0

droSim2

AAT-TTATTCTTTTTGCTATT-------------CTA-----------------------------------------------------------------------------------------------------TAGGCTAATGAGC-------------------------------------------------------------------------------------------------------------------------------------------------------------ATTCCTTAAAAT-------------------------------------------------------------ACATATGTG	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
.....TATTCTTTTTGCTATT-------------CTA-----------------------------------------------------------------------------------------------------TAGG........................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0

dm3

TATGGTATTCTGTTTGCTATT-------------ATA-----------------------------------------------------------------------------------------------------AAAGTTCACGAGC--------------------TAA-----------------------------------------------GCTAACG--------------------------------------------------------------------------------ATTCATTAAAAT-------ATGTA------------------------------------------CATACATATTTAAGTG

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

No Reads

droEug1

TT----TTGGC------AATT-------------AC------------------------------------------------ATATAAAG---------------------------------------------GTAAAATAAAGTGCCTTTCTTAAAAATCAAGTGCTTAATATTGAAAGTATGATTATTAAAATAATATTTATTTACATTTAAAGCACTTTCGAATTTTTAAGATAACTCAATGGGTGTACATTTTTAAATAATTATTGTTCGAGCGTTGAGTTATTTTAAGAATTAATGTGTAAGTCGCAATAA-------------------------------------------------------------GTGAAAATG	Size	Hit Count	Total Norm	Total
No Reads

droTak1

AC----CTTCG-TTTATTACT---CTTGATAATTCTGTAAAAGAA--------------ATTAAAACATCTTTTATTGATTTATACAGAGAA---------------------------------------------ATAAGTTTAAGTGA-------------------------------------------------------------------------------------------------------------------------------------------------------------ATTCGCCAAAAATGGTTAAAGCTAAAAAAGTGCGTGTTTAAGTTCCTATCGGAATCAGTACTTTTATTTGCTTTTCTGGATT	Size	Hit Count	Total Norm	Total
No Reads

droRho1

AT----TATTTATTTGTTAGT-------------ATAT------TTTATTT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AC-----------	Size	Hit Count	Total Norm	Total
No Reads

dya_34

2R:12724136-12724190 +

confident

Testes-restricted

intergenic

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