dya_64

TGAAATTAGATCTATGCTAAATACAAGTGATTATTGATATCAAAATGTCCCGGGGAAGTTACCTGGTGTATTGTTTTTAATCAACCAATCACTGGATAGCTTTCCTAGAACAAAATGACAGTGCCTTTACATAAACAGTAAATATATAATTTCCGTCCAC *********************************....(((...(((...((((((((((.((((((.((((.((......)).)))))))))).))))))))))...)))...)))......**********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M056 embryo	V120 male body	M043 female body	V058 head	V046 embryo	V052 head
.......................................................................................ATCACTGGATAGCTTTCCTAGA...................................................	22	0	1	119.00	119	73	27	11	3	5	0
.......................................................................................ATCACTGGATAGCTTTCCTAG....................................................	21	0	1	33.00	33	5	20	3	2	1	2
.......................................................................................AGCACTGGATAGCTTTCCTAGA...................................................	22	1	1	12.00	12	12	0	0	0	0	0
.......................................................................................ATCACTGGATAGCTTTCCTA.....................................................	20	0	1	11.00	11	0	10	0	0	0	1
..................................................CGGGGAAGTTACCTGGTGTATTG.......................................................................................	23	0	1	5.00	5	1	3	0	0	1	0
.......................................................................................ATCACTGGATAGCTTTCCTAGT...................................................	22	1	1	5.00	5	0	5	0	0	0	0
.......................................................................................ATCACTGGATAGCTTTCCTAT....................................................	21	1	1	4.00	4	0	2	2	0	0	0
.......................................................................................ATCTCTGGATAGCTTTCCTAGA...................................................	22	1	1	4.00	4	4	0	0	0	0	0
..................................................CGGGGAAGTTACCTGGTGTAT.........................................................................................	21	0	1	3.00	3	0	3	0	0	0	0
.......................................................................................ATAACTGGATAGCTTTCCTAGA...................................................	22	1	1	3.00	3	3	0	0	0	0	0
.......................................................................................AGCACTGGATAGCTTTCCTAG....................................................	21	1	1	2.00	2	2	0	0	0	0	0
.......................................................................................ATCACTGGATAGCTTTCCTAGAA..................................................	23	0	1	2.00	2	1	1	0	0	0	0
.......................................................................................ATCACTGGATAGCTTTCCTT.....................................................	20	1	1	2.00	2	1	1	0	0	0	0
.......................................................................................ATCCCTGGAGAGCGTTCCTAGA...................................................	22	3	1	2.00	2	0	0	0	2	0	0
.......................................................................................AGAACTGGATAGCTTTCCTAGA...................................................	22	2	1	1.00	1	1	0	0	0	0	0
..........................................................................................GCTGGATAGCTTTCCTAG....................................................	18	1	1	1.00	1	0	1	0	0	0	0
.......................................................................................ATCACTGGATAGCTTTCCTAGAGA.................................................	24	2	1	1.00	1	1	0	0	0	0	0
..................................................CGGGGAAGTTACCTGGTGTATT........................................................................................	22	0	1	1.00	1	0	1	0	0	0	0
.......................................................................................ATTACTGGATAGCTTTCCTAGA...................................................	22	1	1	1.00	1	1	0	0	0	0	0
..................................................CGGGGAAGTTACCTGGTGTA..........................................................................................	20	0	1	1.00	1	0	1	0	0	0	0
.......................................................................................TGCACTGGATAGCTTTCCTAGA...................................................	22	2	1	1.00	1	1	0	0	0	0	0
........................................................................................TCACTGGATAGCTTTCCTAG....................................................	20	0	1	1.00	1	0	0	1	0	0	0
.......................................................................................ATCACTGGATAGCTTTCCTAGAAA.................................................	24	1	1	1.00	1	1	0	0	0	0	0
.......................................................................................ATCACTGGATAACTTTCCTAGA...................................................	22	1	1	1.00	1	0	1	0	0	0	0
.......................................................................................ATCTCTGGATAGCTTTCCTAGAA..................................................	23	1	1	1.00	1	1	0	0	0	0	0
.......................................................................................AGCACTGGATAGCTTTCCTAGAAA.................................................	24	2	1	1.00	1	1	0	0	0	0	0
.......................................................................................ATCACGGGATAGCTTTCCTAGA...................................................	22	1	1	1.00	1	0	0	0	1	0	0
.......................................................................................ATCACTGCATAGCTTTCCTA.....................................................	20	1	1	1.00	1	0	1	0	0	0	0
.......................................................................................ATCACTTGATAGCTTTCCTAGA...................................................	22	1	1	1.00	1	1	0	0	0	0	0
.......................................................................................ATCGCTGGATAGCTTTCCTAGA...................................................	22	1	1	1.00	1	0	0	0	0	1	0
...............................................TCCCGGGGACCTTACCTTGTGT...........................................................................................	22	3	1	1.00	1	0	0	0	1	0	0
..................................................CGGGGAAGTTACCTGGTGT...........................................................................................	19	0	1	1.00	1	0	0	0	0	1	0
.......................................................................................ATCACTGGATAGCTTTCCTTT....................................................	21	2	1	1.00	1	0	1	0	0	0	0
.......................................................................................ATCACTGGATAGCTTTCCATGC...................................................	22	3	2	0.50	1	0	0	0	1	0	0
................................................CGCAGGGAGGTTACCTGGT.............................................................................................	19	3	5	0.20	1	0	0	0	1	0	0
...............................................TTCCGGAGAGGTTACCTGG..............................................................................................	19	3	9	0.11	1	0	0	0	1	0	0
.............................................CGTCCCGGGGAGCTTACC.................................................................................................	18	3	20	0.05	1	0	0	1	0	0	0
.............ATGCTAAATACTACTGACT................................................................................................................................	19	3	20	0.05	1	1	0	0	0	0	0

ACTTTAATCTAGATACGATTTATGTTCACTAATAACTATAGTTTTACAGGGCCCCTTCAATGGACCACATAACAAAAATTAGTTGGTTAGTGACCTATCGAAAGGATCTTGTTTTACTGTCACGGAAATGTATTTGTCATTTATATATTAAAGGCAGGTG **********************************....(((...(((...((((((((((.((((((.((((.((......)).)))))))))).))))))))))...)))...)))......*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V052 head
..........................................TGTACAGGGCTCCTTCAAAGG.................................................................................................	21	3	3	0.33	1	1

Species	Coordinate	ID	Alignment
droYak3	X:4178168-4178327 +	dya_64	TGAAATTAGATCTATGCTAAATACAAGTGATTATTGATATCAAAATGTCCC-GGGGAAGTTACCTGGTGTATTGTTTTTAATCAACCAATCACTGGAT-AGCT-TTCCTAGAACAAAATGACAGTGCC-------------------------TTTACATAAAC--AGTAAATATAT-----------------------------------------------AATT----TCCGTCCA-C
droEre2	scaffold_4690:1630697-1630838 -	der_46	TGGAC-----------------ACAAGAGATTTTTAATGTCGAAGTGTTCT-AGGGAGGATACCTGGTGTGTTGTATTTTAAAAATCAATCATCGGCT-ATCT-TTCCTAGAATAATATGACATAGAC--------------------------ACACGTAATA--ATAAAGTATTA-----------------------------------------------CATT----TTAGTCCA-C
droSec2	scaffold_4:2465126-2465268 +	dse_38	TTAAGA-----------ATATTACAAATTATTAC---CATT--CATATCCT-GGACAGTGTTCCTAATAGTCTGTTATTATTACA-CAAACCTTGGGA-ATAC-TTTCGAGATAAGGATGGCATAACG--------------------------CTGCAAAAA-TAAGTATAAACA------------------------------------------------TATC----CCTATCCATC
droSim2	x:3953597-3953737 -	dsi-mir-2582b	TTAAGA-----------ATATTACAAATTATTAC---CATT--CATATCCT-GGAGAGTGTTCTTAATAGTCTGTTATTATTACA-CAAACTTTGGGA-ATAC-TTTCGAGAT-ATGATGGCATAACG--------------------------CTGCAAAAA-TAAGTATAAACA------------------------------------------------TATC----CCTATCCA-T
dm3	chrX:4259685-4259804 -		A-------------------TTACGAATGATTAC---CATT--CATATCCT-TGGAACAATTCCTAATAGAATGTTATTATTACAACAATCTTTAGCA-AGAC-TTTCGAGATAAGGATGGCATAACG--------------------------CTGCAAAAAAAAAATATAA---------------------------------------------------------------------
droTak1	scf7180000415394:1164905-1165029 +		TAGACA------------------------------------------------------------GCAGCATTTTTTTA-TAAATAAATCTGTTGTCTATAT-TTCTGACAC-ACGATGGTATTTTTCAACAATCAATAGATTACCAAAATCATTATATAAAT--AGTAAATATAT-----------------------------------------------AATT----AACTTTCA-T
droRho1	scf7180000779334:418684-418885 +		CGACTTTTTATCAAT----AAAATATGAAAAAAT---CATG--CATGTTTTTTGGGGTGATATGCATTAGATTGCTTTTA-TATATCAATCTTTTGCT-TATTCTCCTAAAAACAAGATTGTATTACT-------------------------TCTGCAATAA-TGCATAT--ATGAAATTAAATTATTAAGAAAGATTATACTGTTTGTATTCTATACAATAAAATCCAAATCCATCCA-A

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droYak3

TGAAATTAGATCTATGCTAAATACAAGTGATTATTGATATCAAAATGTCCC-GGGGAAGTTACCTGGTGTATTGTTTTTAATCAACCAATCACTGGAT-AGCT-TTCCTAGAACAAAATGACAGTGCC-------------------------TTTACATAAAC--AGTAAATATAT-----------------------------------------------AATT----TCCGTCCA-C	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
........................................................................................ATCACTGGAT-AGCT-TTCCTAGA..................................................................................................................................	22	1	119.00	119	0	11	73	5	0	3	27	0	0	0	0
........................................................................................ATCACTGGAT-AGCT-TTCCTAG...................................................................................................................................	21	1	33.00	33	0	3	5	1	2	2	20	0	0	0	0
........................................................................................ATCACTGGAT-AGCT-TTCCTA....................................................................................................................................	20	1	11.00	11	0	0	0	0	1	0	10	0	0	0	0
..................................................C-GGGGAAGTTACCTGGTGTATTG........................................................................................................................................................................	23	1	5.00	5	0	0	1	1	0	0	3	0	0	0	0
........................................................................................ATCACTGGAT-AGCT-TTCCTAGT..................................................................................................................................	22	1	5.00	5	0	0	0	0	0	0	5	0	0	0	0
........................................................................................ATCACTGGAT-AGCT-TTCCTAT...................................................................................................................................	21	1	4.00	4	0	2	0	0	0	0	2	0	0	0	0
..................................................C-GGGGAAGTTACCTGGTGTAT..........................................................................................................................................................................	21	1	3.00	3	0	0	0	0	0	0	3	0	0	0	0
........................................................................................ATCACTGGAT-AGCT-TTCCTAGAA.................................................................................................................................	23	1	2.00	2	0	0	1	0	0	0	1	0	0	0	0
........................................................................................ATCACTGGAT-AGCT-TTCCTT....................................................................................................................................	20	1	2.00	2	0	0	1	0	0	0	1	0	0	0	0
........................................................................................ATCACTGGAT-AGCT-TTCCTAGAGA................................................................................................................................	24	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0
..................................................C-GGGGAAGTTACCTGGTGTATT.........................................................................................................................................................................	22	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
..................................................C-GGGGAAGTTACCTGGTGTA...........................................................................................................................................................................	20	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
.........................................................................................TCACTGGAT-AGCT-TTCCTAG...................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
........................................................................................ATCACTGGAT-AGCT-TTCCTAGAAA................................................................................................................................	24	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0
..................................................C-GGGGAAGTTACCTGGTGT............................................................................................................................................................................	19	1	1.00	1	0	0	0	1	0	0	0	0	0	0	0
........................................................................................ATCACTGGAT-AGCT-TTCCTTT...................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0

droEre2

TGGAC-----------------ACAAGAGATTTTTAATGTCGAAGTGTTCT-AGGGAGGATACCTGGTGTGTTGTATTTTAAAAATCAATCATCGGCT-ATCT-TTCCTAGAATAATATGACATAGAC--------------------------ACACGTAATA--ATAAAGTATTA-----------------------------------------------CATT----TTAGTCCA-C	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
..................................................T-AGGGAGGATACCTGGTGTGTTG........................................................................................................................................................................	23	1	627.00	627	12	1	7	1	549	46	11
..................................................T-AGGGAGGATACCTGGTGTGT..........................................................................................................................................................................	21	1	588.00	588	6	0	10	1	549	22	0
..................................................T-AGGGAGGATACCTGGTGTGTT.........................................................................................................................................................................	22	1	238.00	238	1	0	4	2	215	16	0
..................................................T-AGGGAGGATACCTGGTGTG...........................................................................................................................................................................	20	1	181.00	181	1	0	3	0	147	30	0
........................................................................................ATCATCGGCT-ATCT-TTCCTAGA..................................................................................................................................	22	1	75.00	75	8	0	2	0	42	22	1
..................................................T-AGGGAGGATACCTGGTGTGTTT........................................................................................................................................................................	23	1	55.00	55	3	0	1	0	48	3	0
..................................................T-AGGGAGGATACCTGGTGT............................................................................................................................................................................	19	1	46.00	46	0	0	0	0	42	4	0
..................................................T-AGGGAGGATACCTGGTGTGTTGT.......................................................................................................................................................................	24	1	42.00	42	2	0	1	0	36	3	0
..................................................T-AGGGAGGATACCTGGTGTGA..........................................................................................................................................................................	21	1	20.00	20	0	0	0	0	17	3	0
..................................................T-AGGGAGGATACCTGGTGTGTTA........................................................................................................................................................................	23	1	12.00	12	0	0	0	0	10	2	0
........................................................................................ATCATCGGCT-ATCT-TTCCTAG...................................................................................................................................	21	1	9.00	9	4	0	0	0	4	1	0
........................................................................................ATCATCGGCT-ATCT-TTCCTAGAA.................................................................................................................................	23	1	8.00	8	0	0	0	0	8	0	0
..................................................T-AGGGAGGATACCTGGTGTGTTGA.......................................................................................................................................................................	24	1	8.00	8	0	0	0	0	8	0	0
..................................................T-AGGGAGGATACCTGGTGTT...........................................................................................................................................................................	20	1	7.00	7	1	0	0	0	5	1	0
..................................................T-AGGGAGGATACCTGGTGTGTA.........................................................................................................................................................................	22	1	6.00	6	0	0	0	0	6	0	0
........................................................................................ATCATCGGCT-ATCT-TTCCTAGT..................................................................................................................................	22	1	5.00	5	1	0	0	0	4	0	0
..................................................T-AGGGAGGATACCTGGTGTGTAT........................................................................................................................................................................	23	1	5.00	5	0	0	0	0	5	0	0
..................................................T-AGGGAGGATACCTGGTG.............................................................................................................................................................................	18	1	4.00	4	0	0	0	0	0	4	0
..................................................T-AGGGAGGATACCTGGTGTGTTGTT......................................................................................................................................................................	25	1	4.00	4	0	0	0	0	4	0	0
........................................................................................ATCATCGGCT-ATCT-TTCCTAGAT.................................................................................................................................	23	1	3.00	3	1	0	0	0	1	1	0
..................................................T-AGGGAGGATACCTGGTGTGTTAA.......................................................................................................................................................................	24	1	3.00	3	0	0	0	0	3	0	0
..................................................T-AGGGAGGATACCTGGTGTA...........................................................................................................................................................................	20	1	2.00	2	0	0	0	0	2	0	0
..................................................T-AGGGAGGATACCTGGTGTGTAA........................................................................................................................................................................	23	1	2.00	2	0	0	0	0	2	0	0
..................................................T-AGGGAGGATACCTGGTGTTG..........................................................................................................................................................................	21	1	2.00	2	0	0	0	0	2	0	0
..................................................T-AGGGAGGATACCTGGTGTGTTGTAT.....................................................................................................................................................................	26	1	2.00	2	0	0	0	0	2	0	0
..................................................T-AGGGAGGATACCTGGTGTGTTTC.......................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	1	0
..................................................T-AGGGAGGATACCTGGTGTGTATA.......................................................................................................................................................................	24	1	1.00	1	0	0	0	0	1	0	0
..................................................T-AGGGAGGATACCTGGTGA............................................................................................................................................................................	19	1	1.00	1	0	0	0	0	1	0	0
..................................................T-AGGGAGGATACCTGGTGTGAAT........................................................................................................................................................................	23	1	1.00	1	0	0	0	0	1	0	0
........................................................................................ATCATCGGCT-ATCT-TTCCTAGAG.................................................................................................................................	23	1	1.00	1	0	0	0	0	1	0	0
.......................................................................................AATCATCGGCT-ATCT-TTCCTAG...................................................................................................................................	22	1	1.00	1	0	0	0	0	0	1	0
................................................TCT-AGGGAGGATACCTGGTGTG...........................................................................................................................................................................	22	1	1.00	1	0	0	0	0	1	0	0
..................................................T-AGGGAGGATACCTGGTGTGTTGTTAA....................................................................................................................................................................	27	1	1.00	1	0	0	0	0	1	0	0
..................................................T-AGGGAGGATACCTGGTGTGG..........................................................................................................................................................................	21	1	1.00	1	1	0	0	0	0	0	0
..................................................T-AGGGAGGATACCTGGTGTGTTAAT......................................................................................................................................................................	25	1	1.00	1	0	0	0	0	1	0	0
..................................................T-AGGGAGGATACCTGGTGTGTTGTA......................................................................................................................................................................	25	1	1.00	1	0	0	0	0	1	0	0
.........................................................................................TCATCGGCT-ATCT-TTCCTAG...................................................................................................................................	20	1	1.00	1	1	0	0	0	0	0	0
..................................................T-AGGGAGGATACCTGGTGTGTTGTAA.....................................................................................................................................................................	26	1	1.00	1	0	0	0	0	1	0	0
..................................................T-AGGGAGGATACCTGGTGTGTTGC.......................................................................................................................................................................	24	1	1.00	1	0	0	0	0	1	0	0
..................................................T-AGGGAGGATACCTGGTA.............................................................................................................................................................................	18	1	1.00	1	0	0	0	0	1	0	0
..................................................T-AGGGAGGATACCTGGTGTGTC.........................................................................................................................................................................	22	1	1.00	1	0	0	0	0	1	0	0
........................................................................................ATCATCGGCT-ATCT-TTCCTAGAAA................................................................................................................................	24	1	1.00	1	0	0	0	0	1	0	0
..................................................T-AGGGAGGATACCTGGTGTGTTTAG......................................................................................................................................................................	25	1	1.00	1	0	0	0	0	1	0	0

droSec2

TTAAGA-----------ATATTACAAATTATTAC---CATT--CATATCCT-GGACAGTGTTCCTAATAGTCTGTTATTATTACA-CAAACCTTGGGA-ATAC-TTTCGAGATAAGGATGGCATAACG--------------------------CTGCAAAAA-TAAGTATAAACA------------------------------------------------TATC----CCTATCCATC	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
.......................................................................................AAACCTTGGGA-ATAC-TTTCGAG...................................................................................................................................	22	2	448.00	896	28	769	58	41
........................................................................................AACCTTGGGA-ATAC-TTTCGAG...................................................................................................................................	21	2	182.00	364	1	342	4	17
.......................................................................................AAACCTTGGGA-ATAC-TTTCGA....................................................................................................................................	21	2	80.00	160	1	144	8	7
........................................................................................AACCTTGGGA-ATAC-TTTCGAGT..................................................................................................................................	22	2	50.00	100	1	89	5	5
.......................................................................................AAACCTTGGGA-ATAC-TTTCG.....................................................................................................................................	20	2	28.00	56	0	51	2	3
........................................................................................AACCTTGGGA-ATAC-TTTCGAGA..................................................................................................................................	22	2	26.50	53	0	48	2	3
..................................................T-GGACAGTGTTCCTAATAGTCTGT.......................................................................................................................................................................	24	2	21.00	42	7	13	12	10
........................................................................................AACCTTGGGA-ATAC-TTTCGA....................................................................................................................................	20	2	13.50	27	1	25	0	1
.......................................................................................AAACCTTGGGA-ATAC-TTTCGAGA..................................................................................................................................	23	2	10.50	21	0	17	2	2
..................................................T-GGACAGTGTTCCTAATAGTCTG........................................................................................................................................................................	23	2	4.00	8	6	0	1	1
.......................................................................................AAACCTTGGGA-ATAC-TTTCGAGT..................................................................................................................................	23	2	3.00	6	0	6	0	0
........................................................................................AACCTTGGGA-ATAC-TTTCGAGC..................................................................................................................................	22	2	3.00	6	0	6	0	0
.........................................................................................ACCTTGGGA-ATAC-TTTCGAG...................................................................................................................................	20	2	2.00	4	0	4	0	0
.......................................................................................AAACCTTGGGA-ATAC-TTTCGAGTAT................................................................................................................................	25	2	1.50	3	0	3	0	0
........................................................................................AACCTTGGGA-ATAC-TTTCGAGTAT................................................................................................................................	24	2	1.50	3	0	3	0	0
.......................................................................................AAACCTTGGGA-ATAC-TTTCGAT...................................................................................................................................	22	2	1.00	2	0	2	0	0
..................................................T-GGACAGTGTTCCTAATAGTCT.........................................................................................................................................................................	22	2	1.00	2	0	1	0	1
........................................................................................AACCTTGGGA-ATAC-TTTCGAA...................................................................................................................................	21	2	1.00	2	0	2	0	0
.......................................................................................AAACCTTGGGA-ATAC-TTTCGAGTA.................................................................................................................................	24	2	0.50	1	0	1	0	0
........................................................................................AACCTTGGGA-ATAC-TTTCGAT...................................................................................................................................	21	2	0.50	1	0	1	0	0
..................................................T-GGACAGTGTTCCTAATAGTC..........................................................................................................................................................................	21	2	0.50	1	0	1	0	0
.........................................................................................ACCTTGGGA-ATAC-TTTCGAGT..................................................................................................................................	21	2	0.50	1	0	1	0	0
...........................................................................................CTTGGGA-ATAC-TTTCGAGA..................................................................................................................................	19	2	0.50	1	0	1	0	0
........................................................................................AACCTTGGGA-ATAC-TTTCGATT..................................................................................................................................	22	2	0.50	1	0	1	0	0
........................................................................................AACCTTGGGA-ATAC-TTTCGT....................................................................................................................................	20	2	0.50	1	0	1	0	0
..................................................T-GGACAGTGTTCCTAATAGTCTGTTT.....................................................................................................................................................................	26	2	0.50	1	0	1	0	0
........................................................................................AACCTTGGGA-ATAC-TTTCGAGTC.................................................................................................................................	23	2	0.50	1	0	1	0	0
........................................................................................AACCTTGGGA-ATAC-TTTCGAGAT.................................................................................................................................	23	2	0.50	1	0	1	0	0
....................................................GGACAGTGTTCCTAATAGTCTGT.......................................................................................................................................................................	23	2	0.50	1	1	0	0	0
.......................................................................................AAACCTTGGGA-ATAC-TTTCGACT..................................................................................................................................	23	2	0.50	1	0	1	0	0
..................................................T-GGACAGTGTTCCTAATAGTCTGTC......................................................................................................................................................................	25	2	0.50	1	0	1	0	0
..................................................T-GGACAGTGTTCCTAATAGTCTGTTAAA...................................................................................................................................................................	28	2	0.50	1	0	1	0	0
..................................................T-GGACAGTGTTCCTAATAGTCTGTT......................................................................................................................................................................	25	2	0.50	1	0	0	0	1
.......................................................................................AAACCTTGGGA-ATAC-TTTCGAGC..................................................................................................................................	23	2	0.50	1	0	1	0	0
........................................................................................AACCTTGGGA-ATAC-TTTCG.....................................................................................................................................	19	2	0.50	1	0	1	0	0

droSim2

TTAAGA-----------ATATTACAAATTATTAC---CATT--CATATCCT-GGAGAGTGTTCTTAATAGTCTGTTATTATTACA-CAAACTTTGGGA-ATAC-TTTCGAGAT-ATGATGGCATAACG--------------------------CTGCAAAAA-TAAGTATAAACA------------------------------------------------TATC----CCTATCCA-T	Size	Hit Count	Total Norm	Total	M023 Head	M024 Male-body	M025 Embryo	M053 Female-body	O001 Testis	O002 Head	SRR553485 Ovary	SRR553486 Ovary	SRR553487 Ovary	SRR553488 Ovary	SRR618934 Ovary	V044 Embryo	SRR902008 Ovary	SRR902009 Testis	SRR1275487 Male larvae	SRR1275485 Male prepupae	SRR1275483 Male prepupae
.......................................................................................AAACTTTGGGA-ATAC-TTTCGAG...................................................................................................................................	22	1	1810.00	1810	0	2	0	4	424	6	41	49	42	31	858	12	1	340	0	0	0
.......................................................................................AAACTTTGGGA-ATAC-TTTCGA....................................................................................................................................	21	1	549.00	549	0	0	0	1	167	3	7	19	10	8	121	0	0	213	0	0	0
..................................................T-GGAGAGTGTTCTTAATAGTCTG........................................................................................................................................................................	23	1	327.00	327	0	6	0	1	234	2	1	0	6	0	77	0	0	0	0	0	0
..................................................T-GGAGAGTGTTCTTAATAGTCT.........................................................................................................................................................................	22	1	232.00	232	0	0	0	1	155	2	0	0	0	0	66	8	0	0	0	0	0
..................................................T-GGAGAGTGTTCTTAATAGTCTGT.......................................................................................................................................................................	24	1	223.00	223	0	1	0	1	143	3	5	0	3	2	65	0	0	0	0	0	0
.......................................................................................AAACTTTGGGA-ATAC-TTTC......................................................................................................................................	19	1	159.00	159	0	0	0	0	140	0	0	0	0	0	19	0	0	0	0	0	0
..................................................T-GGAGAGTGTTCTTAATA.............................................................................................................................................................................	18	1	159.00	159	0	0	0	0	143	1	0	0	0	0	15	0	0	0	0	0	0
..................................................T-GGAGAGTGTTCTTAATAG............................................................................................................................................................................	19	1	155.00	155	0	0	0	0	150	4	0	0	0	0	1	0	0	0	0	0	0
........................................................................................AACTTTGGGA-ATAC-TTTCGAGA..................................................................................................................................	22	1	152.00	152	0	0	0	2	36	0	8	4	4	4	83	0	0	11	0	0	0
.......................................................................................AAACTTTGGGA-ATAC-TTTCG.....................................................................................................................................	20	1	140.00	140	0	0	0	0	60	3	0	1	0	0	29	0	0	47	0	0	0
........................................................................................AACTTTGGGA-ATAC-TTTCGAG...................................................................................................................................	21	1	128.00	128	0	0	0	0	47	0	0	3	2	0	32	0	0	44	0	0	0
..................................................T-GGAGAGTGTTCTTAATAGTC..........................................................................................................................................................................	21	1	101.00	101	0	0	0	0	93	2	0	0	0	0	6	0	0	0	0	0	0
.......................................................................................AAACTTTGGGA-ATAC-TTT.......................................................................................................................................	18	1	73.00	73	0	0	0	0	63	2	0	0	0	0	8	0	0	0	0	0	0
.......................................................................................AAACTTTGGGA-ATAC-TTTCGAGA..................................................................................................................................	23	1	66.00	66	0	3	1	0	16	0	1	0	4	0	25	1	0	15	0	0	0
..................................................T-GGAGAGTGTTCTTAATAGT...........................................................................................................................................................................	20	1	50.00	50	0	0	0	0	42	1	0	0	0	0	7	0	0	0	0	0	0
............................................................................................TTGGGA-ATAC-TTTCGAG...................................................................................................................................	17	1	31.00	31	0	0	0	0	0	0	0	0	0	0	31	0	0	0	0	0	0
.......................................................................................AAACTTTGGGA-ATAC-T.........................................................................................................................................	16	1	31.00	31	0	0	0	0	0	0	0	0	0	0	31	0	0	0	0	0	0
........................................................................................AACTTTGGGA-ATAC-TTTCGA....................................................................................................................................	20	1	26.00	26	0	0	0	0	14	0	0	1	1	0	5	0	0	5	0	0	0
........................................................................................AACTTTGGGA-ATAC-TTTC......................................................................................................................................	18	1	20.00	20	0	0	0	0	13	2	0	0	0	0	5	0	0	0	0	0	0
........................................................................................AACTTTGGGA-ATAC-TTTCGAGAA-................................................................................................................................	23	1	14.00	14	0	1	0	0	0	0	0	0	1	0	9	0	0	3	0	0	0
.......................................................................................AAACTTTGGGA-ATAC-TTTCGAGT..................................................................................................................................	23	1	14.00	14	0	0	0	0	0	0	0	0	0	0	3	0	0	11	0	0	0
.......................................................................................AAACTTTGGGA-ATAC-TT........................................................................................................................................	17	1	13.00	13	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0
...........................................................................................TTTGGGA-ATAC-TTTCGAG...................................................................................................................................	18	1	12.00	12	0	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0
........................................................................................AACTTTGGGA-ATAC-TTTCG.....................................................................................................................................	19	1	12.00	12	0	0	0	0	9	1	0	0	0	0	2	0	0	0	0	0	0
.......................................................................................AAACTTTGGGA-ATAC-TTTCGAA...................................................................................................................................	22	1	11.00	11	0	0	0	0	0	0	0	1	0	0	8	0	0	2	0	0	0
.......................................................................................AAACTTTGGGA-ATAC-TTTCGAT...................................................................................................................................	22	1	10.00	10	0	0	0	0	0	0	0	0	0	0	6	0	0	4	0	0	0
...........................................................GTTCTTAATAGTCTGT.......................................................................................................................................................................	16	1	8.00	8	0	0	0	0	0	0	0	0	0	0	8	0	0	0	0	0	0
.......................................................................................AAACTTTGGGA-ATAC-TTTCGAGAA-................................................................................................................................	24	1	7.00	7	0	0	0	0	0	0	0	0	0	0	5	0	0	2	0	0	0
........................................................................................AACTTTGGGA-ATAC-TTTCGAGT..................................................................................................................................	22	1	7.00	7	0	0	0	0	0	0	0	0	0	0	4	0	1	2	0	0	0
..................................................T-GGAGAGTGTTCTTAATAGTCTGTT......................................................................................................................................................................	25	1	6.00	6	0	0	0	0	2	0	2	0	0	0	2	0	0	0	0	0	0
....................................................GGAGAGTGTTCTTAATAGTCTG........................................................................................................................................................................	22	1	6.00	6	0	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0
.........................................................GTGTTCTTAATAGTCTG........................................................................................................................................................................	17	1	6.00	6	0	0	0	0	0	0	0	0	0	0	6	0	0	0	0	0	0
......................................................................................CAAACTTTGGGA-ATAC-TTTCGAG...................................................................................................................................	23	1	5.00	5	0	0	0	0	0	0	0	0	0	0	1	0	0	4	0	0	0
.........................................................GTGTTCTTAATAGTCTGT.......................................................................................................................................................................	18	1	5.00	5	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0
..................................................T-GGAGAGTGTTCTTA................................................................................................................................................................................	15	2	4.50	9	0	0	0	0	0	0	0	0	0	0	9	0	0	0	0	0	0
.............................................................................................TGGGA-ATAC-TTTCGAG...................................................................................................................................	16	1	4.00	4	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0
.......................................................GAGTGTTCTTAATAGTCTG........................................................................................................................................................................	19	1	3.00	3	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0
.......................................................................................AAACTTTGGGA-ATAC-..........................................................................................................................................	15	1	3.00	3	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0
............................................................................................TTGGGA-ATAC-TTTCGAGA..................................................................................................................................	18	1	3.00	3	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0
..............................................................................................GGGA-ATAC-TTTCGAGA..................................................................................................................................	16	1	3.00	3	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0
........................................................................................AACTTTGGGA-ATAC-TTTCGAGAT-................................................................................................................................	23	1	3.00	3	0	0	0	0	2	0	0	0	0	0	1	0	0	0	0	0	0
..................................................T-GGAGAGTGTTCTTAAT..............................................................................................................................................................................	17	1	3.00	3	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0
.........................................................................................ACTTTGGGA-ATAC-TTTCGAG...................................................................................................................................	20	1	3.00	3	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	0
........................................................................................AACTTTGGGA-ATAC-TTTCGAGC..................................................................................................................................	22	1	2.00	2	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0
......................................................................................CAAACTTTGGGA-ATAC-TTTCGA....................................................................................................................................	22	1	2.00	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0
........................................................................................AACTTTGGGA-ATAC-TTTCGAGG..................................................................................................................................	22	1	2.00	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................................................................................TTGGGA-ATAC-TTTCGAGAT-ATGATGGCA.......................................................................................................................	28	1	2.00	2	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0
.......................................................................................AAACTTTGGGA-ATAC-TTTCGAGG..................................................................................................................................	23	1	2.00	2	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
.......................................................................................AAACTTTGGGA-ATAC-TTTCGT....................................................................................................................................	21	1	2.00	2	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0
..................................................T-GGAGAGTGTTCTTAATAGTCTGA.......................................................................................................................................................................	24	1	2.00	2	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0
..........................................................TGTTCTTAATAGTCTGT.......................................................................................................................................................................	17	1	2.00	2	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0
.......................................................................................AAACTTTGGGA-ATAC-TTTCGAGAT-A...............................................................................................................................	25	1	2.00	2	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0
........................................................AGTGTTCTTAATAGTCTGT.......................................................................................................................................................................	19	1	2.00	2	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0
...........................................................................................TTTGGGA-ATAC-TTTCGAGA..................................................................................................................................	19	1	2.00	2	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0
.........................................................GTGTTCTTAATAGTCT.........................................................................................................................................................................	16	1	2.00	2	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0
........................................................................................AACTTTGGGA-ATAC-T.........................................................................................................................................	15	1	2.00	2	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0
..................................................T-GGAGAGTGTTCTTAATAGTCTGTA......................................................................................................................................................................	25	1	2.00	2	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0
..................................................T-GGAGAGTGTTCTTAATAGTCA.........................................................................................................................................................................	22	1	2.00	2	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0
......................................................................................CAAACTTTGGGA-ATAC-TTTCG.....................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
...........................................................GTTCTTAATAGTCTG........................................................................................................................................................................	15	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
..................................................T-GGAGAGTGTTCTTAATAGTCTGC.......................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
..................................................T-GGAGAGTGTTCTTAATAGTCTGTTAAA...................................................................................................................................................................	28	1	1.00	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
.......................................................................................AAACTTTGGGA-ATAC-TTTCGAC...................................................................................................................................	22	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
............................................................................................TTGGGA-ATAC-TTTCG.....................................................................................................................................	15	2	1.00	2	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0
.............................................................................................TGGGA-ATAC-TTTCGAGA..................................................................................................................................	17	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
......................................................AGAGTGTTCTTAATAGTCTGT.......................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
.......................................................GAGTGTTCTTAATAGTCT.........................................................................................................................................................................	18	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
..................................................T-GGAGAGTGTTCTTAA...............................................................................................................................................................................	16	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
........................................................AGTGTTCTTAATAGTCTG........................................................................................................................................................................	18	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
..................................................T-GGAGAGTGTTCTTAATAGTCTGTTA.....................................................................................................................................................................	26	1	1.00	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
.......................................................................................AAACTTTGGGA-ATAC-TTTCGAGGA-................................................................................................................................	24	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
.......................................................................................AAACTTTGGGA-ATAC-TTTCGC....................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
..................................................T-GGAGAGTGTTCTTAATAGTCTA........................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
........................................................AGTGTTCTTAATAGTCT.........................................................................................................................................................................	17	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
........................................................................................AACTTTGGGA-ATAC-TTTCGAGAT-A...............................................................................................................................	24	1	1.00	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
.......................................................................................AAACTTTGGGA-ATAC-TTTCGAGGG-................................................................................................................................	24	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
............................................................................................TTGGGA-ATAC-TTTCGA....................................................................................................................................	16	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
.......................................................GAGTGTTCTTAATAGTCTGT.......................................................................................................................................................................	20	1	1.00	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
.......................................................................................AAACTTTGGGA-ATAC-TTTCGTT...................................................................................................................................	22	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
..................................................T-GGAGAGTGTTCTTAATAGTCTTC.......................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
.......................................................................................AAACTTTGGGA-ATAC-TTTCGAGGG-T...............................................................................................................................	25	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
...........................................................................................TTTGGGA-ATAC-TTTCGA....................................................................................................................................	17	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
.......................................................................................AAACTTTGGGA-ATAC-TTTCA.....................................................................................................................................	20	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
..................................................T-GGAGAGTGTTCTTAATAGTCTAA.......................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
.................................................CT-GGAGAGTGTTCTTAATAG............................................................................................................................................................................	20	1	1.00	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
....................................................GGAGAGTGTTCTTAATAGTCT.........................................................................................................................................................................	21	1	1.00	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
........................................................................................AACTTTGGGA-ATAC-TTT.......................................................................................................................................	17	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
.......................................................................................AAACTTTGGGA-ATAC-G.........................................................................................................................................	16	4	0.25	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
............................................................................................TTGGGA-ATAC-TTTCGAA...................................................................................................................................	17	5	0.20	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
.......................................................................................AAACTTTGGGA-ATAC-TTTGAG....................................................................................................................................	21	7	0.14	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
............................................................................................TTGGGA-ATAC-TTTCGC....................................................................................................................................	16	11	0.09	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0

dm3

A-------------------TTACGAATGATTAC---CATT--CATATCCT-TGGAACAATTCCTAATAGAATGTTATTATTACAACAATCTTTAGCA-AGAC-TTTCGAGATAAGGATGGCATAACG--------------------------CTGCAAAAAAAAAATATAA---------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	GSM154618 Ovary	GSM154620 Ovary	GSM154621 Ovary	GSM154622 Ovary	GSM180328 Head	GSM180329 Mixed-body	GSM180330 Embryo	GSM180331 Embryo	GSM180332 Embryo	GSM180333 Embryo	GSM180334 Larvae	GSM180335 Disc	GSM180336 Pupae	GSM180337 S2	GSM231091 Ovary	GSM239041 Head	GSM239050 Head	GSM239051 S2	GSM239052 S2	GSM246084 Head	GSM266765 S2	GSM280082 Ovary	GSM280083 Ovary	GSM280084 Ovary	GSM280085 Testis	GSM280086 Ovary	GSM280087 S2-NP	GSM280088 S2-NP	GSM312995 Head	GSM313160 Head	GSM313161 Head	GSM313162 Head	GSM313163 Head	GSM313164 Head	GSM313165 Head	GSM343287 Embryo	GSM379050 Ovary	GSM379051 Ovary	GSM379052 Ovary	GSM379053 Ovary	GSM379054 Ovary	GSM379055 Ovary	GSM379056 Ovary	GSM379057 Ovary	GSM379058 Ovary	GSM379059 Ovary	GSM379060 Ovary	GSM379061 Ovary	GSM379062 Ovary	GSM379063 Ovary	GSM379064 Ovary	GSM379065 Ovary	GSM379066 Ovary	GSM379067 Ovary	GSM424739 S2	GSM424740 S2	GSM424741 S2	GSM467729 Female-body	GSM467730 Female-body	GSM467731 Female-body	M002 CS	M003 Male-body	M004 Male-body	M005 ML-DmD32	M006 ML-DmD32	M029 OSC	M030 OSC	M031 OSC	M032 S2-R+	M033 S2-R+	M034 S2-R+	M035 S2-R+	M036 S2-R+	M037 S2-R+	M038 S2-R+	M039 S2-R+	M048 S2-R+	OSS2 OSS	OSS6 OSS	OSS7 OSS	OSS8 OSS	S1 Head	S10 Embryo	S11 Embryo	S12 Embryo	S13 Embryo	S14 Embryo	S15 S2-GMR	S16 Kc	S17 Larvae	S18 Larvae	S19 Pupae	S2 Head	S20 Pupae	S21 Disc	S22 Head	S23 Female-body	S24 Male-body	S25 Larvae	S26 Larvae	S27 Pupae	S28 Pupae	S29 Head	S3 Male-body	S30 S2-GMR	S31 S2	S32 S2	S33 Kc	S34 Kc	S35 Kc	S4 Female-body	S5 Disc	S6 Embryo	S7 Embryo	S8 S2	S9 Embryo	SRR001337 Head	SRR001338 Head	SRR001339 Head	SRR001340 Head	SRR001341 Head	SRR001342 Head	SRR001343 Head	SRR001344 Head	SRR001345 Head	SRR001346 Head	SRR001347 Head	SRR001348 Head	SRR001349 Head	SRR001664 Head	SRR010951 Ovary	SRR010952 Ovary	SRR010953 Ovary	SRR010954 Ovary	SRR010955 Ovary	SRR010956 Ovary	SRR010957 Ovary	SRR010958 Ovary	SRR010959 Ovary	SRR010960 Ovary	SRR014268 Embryo	SRR014269 Embryo	SRR014270 Embryo	SRR014271 Embryo	SRR014272 Embryo	SRR014273 Ovary	SRR014274 Ovary	SRR014275 Ovary	SRR014276 Ovary	SRR014277 Ovary	SRR014278 Ovary	SRR014279 Ovary	SRR014280 Ovary	SRR014281 Ovary	SRR014282 Ovary	SRR023197 S2	SRR023399 S2	SRR023400 S2	SRR023402 S2	SRR023407 S2	SRR029028 S2	SRR029029 S2	SRR029030 S2	SRR029031 S2	SRR029032 S2	SRR029033 S2	SRR029608 Head	SRR029633 Head	SRR030145 gb3	SRR031692 Head	SRR031693 Head	SRR031694 Head	SRR031696 Head	SRR031697 Head	SRR031698 Head	SRR031699 Head	SRR031700 Head	SRR031701 Head	SRR031702 Head	SRR031703 Head	SRR031704 Head	SRR032092 S2	SRR032093 S2	SRR032094 S2	SRR032095 S2-NP	SRR032096 S2-NP	SRR032152 Head	SRR060643 Testis	SRR060644 Ovary	SRR060645 Testis	SRR060646 Ovary	SRR060647 Ovary	SRR060648 Ovary	SRR060649 Ovary	SRR060650 Testis	SRR060651 Ovary	SRR060652 Testis	SRR060653 Ovary	SRR065151 Ovary	SRR065152 Ovary	SRR065153 Ovary	SRR065154 Ovary	SRR065155 Ovary	SRR065800 Ovary	SRR065801 Ovary	SRR065802 Ovary	SRR065803 Ovary	SRR065804 Ovary	SRR065805 Ovary	SRR065806 Ovary	SRR065807 Ovary	SRR097865 S2-NP	SRR097866 S2-NP	SRR097867 S2-NP	SRR298536 Ovary	SRR298537 Ovary	SRR298711 Ovary	SRR298712 Ovary	SRR317110 Ovary	SRR317111 Ovary	SRR317112 Ovary	SRR317113 Ovary	SRR317114 Ovary	SRR317115 Ovary	SRR317116 Ovary	SRR317117 Ovary	SRR341115 S2	SRR341116 S2	SRR341117 S2	SRR341118 S2	SRR351332 Mixed-body	SRR351333 Mixed-body	T004 OSC	T005 CME-L1	V001 Embryo	V002 Embryo	V003 S2	V006 Female-body	V007 Head	V008 S2	V009 CME-L1	V010 ML-DmD20-C5	V011 Sg4	V012 Male-body	V013 Head	V014 DTT	V015 DreRFHV	V018 Kc167	V019 GM2	V020 S2-R+	V021 ML-DmD21	V022 ML-DmD32	V023 Head	V024 Kc167	V025 S2-R+	V026 1182-2H	V027 ML-DmD21	V028 CME-W1-Cl.8+	V029 ML-DmD9	V030 ML-DmD8	V031 GM2	V032 S1	V033 CME-W1-Cl.8+	V034 ML-DmD16-C3	V035 ML-DmD32	V036 ML-DmD20-C5	V037 S2	V038 S2	V063 Ovary	V0632 Ovary	V064 Ovary	V0642 Ovary	V065 Ovary	V0652 Ovary	V066 Ovary	V0662 Ovary	V067 S2-NP	V073 mbn2	V074 S3	V075 ML-DmBG1-C1	V076 ML-DmBG3-C2	V077 Head	V078 Head	V079 Head	V080 Head	V081 Embryo	V082 Embryo	V083 Male-body	V084 Female-body	V085 CME-W2	V086 Female-body	V088 Ovary	V0882 Ovary	V089 Ovary	V0892 Ovary	V090 Male-body	V091 fGS/OSS	V092 Male-body	V093 Male-body	V094 S2-R+	V095 S2-R+	V096 Ovary	V097 Ovary	V098 Ovary	V125 ML-DmD9	V126 CME-L1	V127 G2	V128 S3	V129 ML-DmBG1-C1	V130 ML-DmBG3-C2	V131 ML-DmD16-C3	V132 ML-DmD32	V133 Sg4	V134 ML-DmD8	V135 CME-W2	V136 Male-body	V137 Head	V138 Male-body	V139 Female-body	V140 Female-body	V141 Female-body	V142 Female-body	V144 OSC	V145 S2	V146 S1	V147 1182-2H	V148 mbn2	GSM1528798 follicle cells
......................................................................................................C-TTTCGAGATAAGGATGG.........................................................................................................................	18	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.........................................................................................................TTCGAGATAAGGATC..........................................................................................................................	15	12	0.08	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droTak1

TAGACA------------------------------------------------------------GCAGCATTTTTTTA-TAAATAAATCTGTTGTCTATAT-TTCTGACAC-ACGATGGTATTTTTCAACAATCAATAGATTACCAAAATCATTATATAAAT--AGTAAATATAT-----------------------------------------------AATT----AACTTTCA-T	Size	Hit Count	Total Norm	Total
No Reads

droRho1

CGACTTTTTATCAAT----AAAATATGAAAAAAT---CATG--CATGTTTTTTGGGGTGATATGCATTAGATTGCTTTTA-TATATCAATCTTTTGCT-TATTCTCCTAAAAACAAGATTGTATTACT-------------------------TCTGCAATAA-TGCATAT--ATGAAATTAAATTATTAAGAAAGATTATACTGTTTGTATTCTATACAATAAAATCCAAATCCATCCA-A	Size	Hit Count	Total Norm	Total
No Reads

dya_64

X:4178218-4178277 +

Known Ortholog

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

-21.9	-21.1	-21.0