dse_66

CGCCGCGTTGTTTCGCTGCATGTGAGAGAATTCCGTGGCTGGCATCGCTCGCTGTAAATTGTAATCATCAAAGCGTTTTCTCAGAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTCCGTACACAGAAAGAAAACCCCTTTTGAAAAAACCATTTAA *********************************.((((((((.((((((((((((...((((.((((((.(((((((...)))).)))))))))))))...))))))))))))))))))))....**********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V115 head	V114 embryo	M054 female body	V113 male body
..........................................................................................TTGGTGTTACTTCTTGCAGTGA...................................................	22	1	1	264.00	264	175	45	34	10
..........................................................................................TTGGTGTTACTTCTTACAGTGA...................................................	22	0	1	177.00	177	45	126	6	0
..........................................................................................TTGGTGTTACTTCTTGCAGTG....................................................	21	1	1	34.00	34	30	1	2	1
..................................................GCTGTAAATTGTAATCATCA.............................................................................................	20	0	1	28.00	28	25	1	1	1
..........................................................................................TTGGTGTTACTTCTTGCGGTGA...................................................	22	2	1	14.00	14	9	1	3	1
..................................................GCTGTAAATTGTAATCATCAA............................................................................................	21	0	1	12.00	12	12	0	0	0
..........................................................................................TTGGTGTTACTTCTTGCAGTGT...................................................	22	2	1	8.00	8	8	0	0	0
..........................................................................................TTGGTGTTACTTCTTGCAGT.....................................................	20	1	1	8.00	8	7	1	0	0
..................................................GCTGTAAATTGTAATCATCAAA...........................................................................................	22	0	1	7.00	7	7	0	0	0
..........................................................................................TTGGTGTTACTTCTTACAGTG....................................................	21	0	1	6.00	6	1	5	0	0
..................................................GCTGTAAATTGTAATCATC..............................................................................................	19	0	1	5.00	5	5	0	0	0
.........................................................................................CTTGGTGTTACTTCTTACAGTGA...................................................	23	0	1	5.00	5	0	5	0	0
..........................................................................................TTGGTGTTACTTCTTGCAGTGAA..................................................	23	2	1	5.00	5	5	0	0	0
..................................................GCTGTAAATTGTAATCATCAAAGC.........................................................................................	24	0	1	5.00	5	3	1	1	0
..........................................................................................TTGGTGTTACTTCTTGCGGTG....................................................	21	2	1	4.00	4	2	0	1	1
..........................................................................................TTGGTGTTACTTCTTGTAGTGA...................................................	22	2	1	4.00	4	0	4	0	0
..................................................GCTGTAAATTGTAATCATCAAAG..........................................................................................	23	0	1	3.00	3	2	0	1	0
..........................................................................................TTGGTGTTACTTCTTGCAGTGAT..................................................	23	2	1	3.00	3	2	1	0	0
.........................................................................................CTTGGTGTTACTTCTTGCAGTGA...................................................	23	1	1	3.00	3	2	1	0	0
...........................................................................................TTGTGTTACTTCTTGCAGTGA...................................................	21	2	1	2.00	2	1	1	0	0
..........................................................................................TTGGTGTTACTTCTTACGGTGA...................................................	22	1	1	2.00	2	0	2	0	0
..........................................................................................TTTGTGTTACTTCTTGCAGTGA...................................................	22	2	1	2.00	2	1	0	1	0
..........................................................................................TTGGTGTTACTTCTTACAGTGT...................................................	22	1	1	2.00	2	0	2	0	0
..........................................................................................TTGGTGTTACTTCTTATAGTGA...................................................	22	1	1	2.00	2	1	1	0	0
...........................................................................................TGGTGTTACTTCTTGCAGTGA...................................................	21	1	1	2.00	2	0	0	2	0
..........................................................................................TTGGTGTTGCTTCTTGCAGTGA...................................................	22	2	2	2.00	4	4	0	0	0
..........................................................................................TTGCTGTTACTTCTTGCAGTGA...................................................	22	2	1	2.00	2	2	0	0	0
..........................................................................................TTGGTGTTACTTCTTGCAGTTA...................................................	22	2	2	1.50	3	0	1	2	0
...........................................................................................TGGTGTTACTTCTTGCAGTGAA..................................................	22	2	1	1.00	1	0	0	1	0
..............................TTCCGTGGCTGGCATCGCTC.................................................................................................................	20	0	1	1.00	1	0	1	0	0
..........................................................................................TTGGTGTTACTTCTCGCAGTG....................................................	21	2	1	1.00	1	1	0	0	0
..........................................................................................TTGGTGCTACTTCTTACAGTGA...................................................	22	1	1	1.00	1	0	1	0	0
..........................................................................................TTGGTGTTACTTCTTGCAGTGAAA.................................................	24	3	1	1.00	1	1	0	0	0
..........................................................................................TTGGTGTTACTTCTTACACTGA...................................................	22	1	1	1.00	1	1	0	0	0
..........................................................................................TTGGTGTTACATCTTACAGTGA...................................................	22	1	1	1.00	1	0	1	0	0
..........................................................................................TTGGTGTTACTTTTTACAGTGA...................................................	22	1	1	1.00	1	0	1	0	0
.................................................CGCTGTAAATTGTAATCATCAA............................................................................................	22	0	1	1.00	1	1	0	0	0
..........................................................................................TTGGTGCTACTTCTTGCAGTG....................................................	21	2	1	1.00	1	1	0	0	0
.........................................................................................TTTGGTGTTACTTCTTGCAGTGA...................................................	23	2	1	1.00	1	0	0	1	0
..........................................................................................TTGGTGTTACTTCTTGCGGT.....................................................	20	2	1	1.00	1	1	0	0	0
..........................................................................................TTGGTGTTACTTCTTGCAGTGAG..................................................	23	1	1	1.00	1	0	1	0	0
..........................................................................................TTGGTGTTCCTTCTTGCAGTGA...................................................	22	2	1	1.00	1	1	0	0	0
..........................................................................................TTGGTCTTACTTCTTGCAGTGA...................................................	22	2	1	1.00	1	1	0	0	0
..........................................................................................TTGGTGTTTCTTCTTGCAGTGA...................................................	22	2	1	1.00	1	0	1	0	0
.........................................................................................CTTGGTGTTATTTCTTGCAGTGA...................................................	23	2	1	1.00	1	0	1	0	0
..........................................................................................TTGGTGTTACTTCTTACAGCGA...................................................	22	1	1	1.00	1	0	1	0	0
..................................................GCTGTAAATTGTAATCATCAAAGCG........................................................................................	25	0	1	1.00	1	0	1	0	0
.........................................................................................CTTGGTGTTACTTCTTACAGTG....................................................	22	0	1	1.00	1	0	1	0	0
..........................................................................................TTGGTGTTATTTCTTACAGTGA...................................................	22	1	1	1.00	1	0	1	0	0
..........................................................................................TTGGTGTTACTTTTTGCAGTGA...................................................	22	2	1	1.00	1	0	1	0	0
..........................................................................................TTGGTGTTACTTCATGTAGTGA...................................................	22	3	1	1.00	1	0	1	0	0
..........................................................................................TTGGTGTTACTTCTTGCGGTGAA..................................................	23	3	1	1.00	1	1	0	0	0
...........................................................................................TGGTGTTACTTCTTACAGTGA...................................................	21	0	1	1.00	1	0	0	1	0
..........................................................................................TTGGTGTTGCTTCTTACAGTG....................................................	21	1	1	1.00	1	1	0	0	0
.........................................................................................CTTGGTGTTACTTCTTGCAGT.....................................................	21	1	1	1.00	1	1	0	0	0
..........................................................................................TTGGTGTTATTTCTTGCAGTGA...................................................	22	2	2	1.00	2	0	2	0	0
..........................................................................................TTGGTGTTACTTCTTACAGT.....................................................	20	0	1	1.00	1	1	0	0	0
..........................................................................................TTGGGGTTACTTCTTGCAGTGA...................................................	22	2	1	1.00	1	0	0	1	0
..................................................GCTGTAAATTGTAATAATCAAAGC.........................................................................................	24	1	1	1.00	1	0	1	0	0
..........................................................................................TTGGTTTTACTTCTTGCAGTGA...................................................	22	2	1	1.00	1	1	0	0	0
...........................................................................................TTGTGTTACTTCTTACAGTGA...................................................	21	1	1	1.00	1	0	1	0	0
..........................................................................................TCGGTGTTACTTCTTGCAGTG....................................................	21	2	1	1.00	1	1	0	0	0
..........................................................................................TTGGCGTTACTTCTTACAGTGA...................................................	22	1	1	1.00	1	0	0	1	0
..........................................................................................TTGGCGTTACTTCTTGCCGTGA...................................................	22	3	1	1.00	1	0	0	1	0
..........................................................................................TTGGTGTTACTTCTTGTAGTGT...................................................	22	3	1	1.00	1	1	0	0	0
..........................................................................................TTGGTGTTACTTCTTACTGTGA...................................................	22	1	1	1.00	1	0	1	0	0
..........................................................................................TTGGTGTTACTTCTTGCATTGA...................................................	22	2	1	1.00	1	1	0	0	0
..........................................................................................TTGGTGTTACTTCTTGCAGTGAC..................................................	23	2	1	1.00	1	0	1	0	0
..........................................................................................TTGGTGTTACTTCTTACAGTGG...................................................	22	1	1	1.00	1	0	1	0	0
.............................................................................................CTGTTACTTCTTGCAGTGA...................................................	19	2	2	0.50	1	1	0	0	0
..........................................................................................TTGGTGTTCCTTCTTGCAGGGA...................................................	22	3	2	0.50	1	0	0	1	0
..........................................................................................TTGGTGTTATTTCTTGCGGTGA...................................................	22	3	3	0.33	1	0	1	0	0
..................................................GCTGTAAATTTTAATCCTC..............................................................................................	19	2	4	0.25	1	1	0	0	0
....................................................................CAAAGCGTTTTCTCAGGC.............................................................................	18	2	8	0.13	1	0	0	1	0
............................................................................................TTGGTTACTTCTTACAGTGA...................................................	20	3	9	0.11	1	0	1	0	0
..........................................................................................TTGGTGTTACTTCTCAGTGT.....................................................	20	3	10	0.10	1	0	1	0	0
.............................................................TAATCATCAAAACGTTGT....................................................................................	18	2	11	0.09	1	0	1	0	0

GCGGCGCAACAAAGCGACGTACACTCTCTTAAGGCACCGACCGTAGCGAGCGACATTTAACATTAGTAGTTTCGCAAAAGAGTCTCGGCGAACCACAATGAAGAATGTCACTCACACGGTCAGGCATGTGTCTTTCTTTTGGGGAAAACTTTTTTGGTAAATT **********************************.((((((((.((((((((((((...((((.((((((.(((((((...)))).)))))))))))))...))))))))))))))))))))....*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V113 male body	V114 embryo	M054 female body	V115 head
..........................................................................................................................................TTGCGGAATACTTCTTTGGTA....	21	3	5	0.60	3	2	1	0	0
........................................................................................................................................TTTTGCGGAATACTTCTTTGGTA....	23	3	2	0.50	1	1	0	0	0
...........................................................................................................................................TGCGGAATACTTCTTTGGTA....	20	3	8	0.50	4	3	0	1	0
.........................................................................................................................................TTTGCGGAATACTTCTTTGGTA....	22	3	4	0.25	1	1	0	0	0
..............................................................................................................ATCACGCGGTCCGGCATGT..................................	19	3	10	0.20	2	0	1	1	0
............................................................................................................................................GCGGAATACTTCTTTGGTA....	19	3	20	0.10	2	0	0	1	1

Species	Coordinate	ID	Type	Alignment
droSec2	scaffold_21:701202-701364 +	dse_66	confident	CGCCGCGTTGTTTCGCTGCATGTGAGAG---AA--------TTCCGTGGCTGGCAT--CGCTCGCTGTAAATTGTAATCATCAAAGCGTT-TT-C-TCA--GAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTC---CGTACACA--GAAAGAAAA-----CCCC-TT-----------TTG----------------------AAA---AAACCA------------------------------------TTTAA---
droSim2	x:12305303-12305465 +	dsi_358	confident	CGCCGCGTTGTTTCGCTGCATGTGAGAG---AA--------TTCCGTGGCTGGCAT--CGCTCGCTGTAAATTGTAATCATCAAAGCGTT-TT-C-TCA--GAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTC---CGTACACA--GAAAGAAAA-----CCCC-TT-----------TTG----------------------AAA---AAACCA------------------------------------TTTAA---
dm3	chrX:12956074-12956239 +	dme-mir-971	Known_mirbase	CGCCGCGTTGTTTCGCTGCATGTGAGAG---AA--------TTCCGTGGCTGGCAT--CGCTCGCTGTAAATTGTAATCATCAAAGCGTT-TT-C-TCA--GAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTC---CGTACACA--GAAAGAAAA-----CCCC-TA-----------TTG----------------------ATA---TAACCA------------------------------------TTTAATTT
droEre2	scaffold_4690:13914701-13914875 -	der_60	confident	CGCCGCGTTGTTTCGCTGCATGTGAGAG---AA--------TTCCGTGGCTGGCAT--CGCCCGCTGTAAATTGTAATCATCAAAGCGTT-TT-C-TCA--GAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTC---CGTACACA--GAAAGAAAA-----CCCC-TT----------------------------------------------CC------------TT--TGGTACATAACAAAAAAATAAATAA---
droYak3	X:7229754-7229917 +	dya_52	confident	CGCCGCGTTGTTTCGCTGCATGTGAGAG---AA--------TTCCGTGGCTGGCAT--CGCTCGCTGTAAATTGTAATCATCAAAGCGTT-TT-C-TCA--GAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTC---CGTACACA--GAAAGAAAA-----ACCCCTT-----------TAA----------------------GAA---AAAACA------------------------------------CAAAA---
droEug1	scf7180000409110:1404448-1404611 +			CGCCGCGTTGTTTCGCTGCATGTGAGAG---AA--------TTCCGTGGCTGGCAT--CGCTCGCTGTAAATTGTAATCATCAAAGCGTT-TT-C-TCA--GAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTC---CGTACACACAGAAAGAAAA-----------T-----------ATGAAGAAG------------------A---AGAACC------------------------------------CTAAA---
droBia1	scf7180000298389:643165-643333 +			CGCCGCGTTGTTTCGCTGCATGTGAGAG---AA--------TTCCGTGGCTGGCAT--CGCCCGCTGTAAATTGTAATCATCAAAGCGTT-TTTC-TCA--GAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTC---CGTACACA--CAGAGAAAA-----CCCC-TT-----------TT-----------------CCCCTGGAA---AAACCA------------------------------------ATTGA---
droTak1	scf7180000413998:42792-42984 +			CGCCGCGTTGTTTCGCTGCATGTGAGAG---AA--------TTCCGTGGCTGGCAT--CGCTCGCTGTAAATTGTAATCATCAAAGCGTT-TT-C-TCA--GAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTC---CGTACACA--GAAAGAAAAAAATAACCC-TT-----------TTGCCGAAAAAGAAAAAATCCCCTGAAAACCAAACCA------------------------------------TTCGA---
droEle1	scf7180000490546:934528-934694 -			CGCCGCGTTGTTTCGCTGCATGTGAGAG---AA--------TTCCGTGGCTGGCAT--CGCTCGCTGTAAATTGTAATCATCAAAGCGTT-TTTC-TCA--GAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGCC---CGTACACA--GAAAGAAAT-----A--------------------------------------------A---AAACTCATTGAAATATCCC-----------------------TTGAA---
droRho1	scf7180000779914:464120-464290 -			CGCCGCGTTGTTTCGCTGCATGTGAGAG---AA--------TTCCGTGGCTGGCAT--CGTTCGCTGTAAATTGTAATCATCAAAGCGTT-TTTT-TCA--GAACCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTC---CGTACACA--GAAAGAAAA-----CTCC-CT-----------TTG----------------------AAA----GCTCC------------TTAA-GGC------------A---ATAAA---
droFic1	scf7180000454050:893092-893253 +			CGCCGCGTTGTTTCGCTGCATGTGAGAG---AA--------TTCCGTGGCTGGCAT--CGCCCGCTGTAAATTGTAATCATCAAAGCGTT-TT-C-TCA--GAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTC---CGTACACA--AAGAGAAAA-----CCCC-AT-----------ATG----------------------AAA----CCCCC------------------------------------TTTGA---
droKik1	scf7180000302544:775439-775606 -			CGCCGCGTTC--------------AGAGCGAAA--------TTCCTTGGCTGGCAG--CGCACACTGTAAATTGTAATCATCAAAGCGTT-TTTC-TCA--GAGCCGCTTGGTGTTACTTCTTACAGTGAGTGCGCCAGTA-CACGTACACACGGCAAGAAAG-----AACC-TTAAAAAGTATATTTG----------------------AAA---AAAAAA------------------------------------TATAA---
droAna3	scaffold_13117:3891768-3891909 +	dan_51	confident	CGCCACGTTGTTTCGCTGCATGTGAGAA---AA--------TTCCGTGGCTGGCAT--CGTTCACTGTAAATTGTAACCATCAAAGCGTT-TTTTATCA--GAGCCGCTTGGTGTTACTTCTTACAGTGAGTGAGCCAGCT---GGAGCACA--TATTAAAAA--------------------------------------------------------------------------------------------------------
droBip1	scf7180000396383:483170-483307 -			CGCCACGTTGTTTCGCTGCATGTGAGAA---AA--------TTCCGTGGCTGGCAT--CGTTCACTGTAAATTGTAACCATCAAAGCGTT-TTTTATCA--GAGCCGCTTGGTGTTACTTCTTACAGTGAGTGAGCCAGCT---GGAGCACA--CA-------------------------------------------------------------------------------------------------------TTT-----
dp5	XL_group3a:1391638-1391761 -	dps-mir-971	Known_mirbase	CGCCGCGT---GTCTCAGCATGTGAGAG---AGCGGCTCCTTTCCCTGGACCCCAT--CGCTCGCTGTAAATTGTAATGGCCAAAGCTTT-TTTGTTGG--TAGCAGCTTGGTGTTACTTCTTACAGTGAGTGTG------------------------------------------------------------------------------------------------------------------------------------
droPer2	scaffold_52:413294-413417 +	dpe_90	confident	CGCCGCGT---GTCTCAGCATGTGAGAG---AGCGGCTCCTTTCCCTGGACCCCAT--CGCTCGCTGTAAATTGTAATGGCCAAAGCTTT-TTTGTTGG--TAGCAGCTTGGTGTTACTTCTTACAGTGAGTGTG------------------------------------------------------------------------------------------------------------------------------------
droWil2	scf2_1100000004909:6691507-6691611 -	dwi_36	confident	CGCCGCGTTATAC-------------------A--------TTAAACGGCCCAATA--CGCTCGCTGTAAATTGTAGCAATCAAAGCGTTGCCTT-TTGCCTCACAGCTTGGTGTTACTTCTTACAGTGAGTGTG------------------------------------------------------------------------------------------------------------------------------------
droVir3	scaffold_12928:4279775-4279879 -	dvi-mir-971	Known_mirbase	CAACACGTCACA-AGCTGA-----------------------------AATGACGTCACGCCCGCTGTAAAATGTAATCATCAGAGCGTC-CT-C-TC----AACCGCTTGGTGTTACTTCTTACAGTGAGTGCGACGGCC---C--------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6328:350122-350197 +	dmo_78	confident	CGA----------------------------------------------------------CCGCTGTAAATTGTAATCATCAAAGCGTC-TG-C-TA----AATCGCTTGGTGTTACTTCTTACAGTGAGCGCGGCGCTC------------------------------------------------------------------------------------------------------------------------------
droGri2	scaffold_14853:994400-994545 -	dgr_60	candidate-rescued	AGATGCCACG---------------------AA-----------CTTGAATGACGTCACGCCCGCTGTAATATGTAATCATCAAAGCGTG-TATT-TT----ACTCGCTTGGTGTTACTTCTTACAGTGAGTGCGACGGCCACACGTCCAGC--GGAGGAGAG-----TGAA-TC-----------TAG----------------------CGC---AGAGAA------------------------------------TTCAA---

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droSec2

CGCCGCGTTGTTTCGCTGCATGTGAGAG---AA--------TTCCGTGGCTGGCAT--CGCTCGCTGTAAATTGTAATCATCAAAGCGTT-TT-C-TCA--GAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTC---CGTACACA--GAAAGAAAA-----CCCC-TT-----------TTG----------------------AAA---AAACCA------------------------------------TTTAA---	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
............................................................................................................TTGGTGTTACTTCTTACAGTGA.........................................................................................................................................	22	1	177.00	177	6	0	126	45
...............................................................GCTGTAAATTGTAATCATCA........................................................................................................................................................................................	20	1	28.00	28	1	1	1	25
...............................................................GCTGTAAATTGTAATCATCAA.......................................................................................................................................................................................	21	1	12.00	12	0	0	0	12
...............................................................GCTGTAAATTGTAATCATCAAA......................................................................................................................................................................................	22	1	7.00	7	0	0	0	7
............................................................................................................TTGGTGTTACTTCTTACAGTG..........................................................................................................................................	21	1	6.00	6	0	0	5	1
...............................................................GCTGTAAATTGTAATCATC.........................................................................................................................................................................................	19	1	5.00	5	0	0	0	5
...........................................................................................................CTTGGTGTTACTTCTTACAGTGA.........................................................................................................................................	23	1	5.00	5	0	0	5	0
...............................................................GCTGTAAATTGTAATCATCAAAGC....................................................................................................................................................................................	24	1	5.00	5	1	0	1	3
...............................................................GCTGTAAATTGTAATCATCAAAG.....................................................................................................................................................................................	23	1	3.00	3	1	0	0	2
............................................................................................................TTGGTGTTACTTCTTACAGTGT.........................................................................................................................................	22	1	2.00	2	0	0	2	0
.........................................TTCCGTGGCTGGCAT--CGCTC............................................................................................................................................................................................................	20	1	1.00	1	0	0	1	0
..............................................................CGCTGTAAATTGTAATCATCAA.......................................................................................................................................................................................	22	1	1.00	1	0	0	0	1
...............................................................GCTGTAAATTGTAATCATCAAAGCG...................................................................................................................................................................................	25	1	1.00	1	0	0	1	0
...........................................................................................................CTTGGTGTTACTTCTTACAGTG..........................................................................................................................................	22	1	1.00	1	0	0	1	0
.............................................................................................................TGGTGTTACTTCTTACAGTGA.........................................................................................................................................	21	1	1.00	1	1	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGT...........................................................................................................................................	20	1	1.00	1	0	0	0	1
............................................................................................................TTGGTGTTACTTCTTACAGTGG.........................................................................................................................................	22	1	1.00	1	0	0	1	0
.................................................................................CAAAGCGTT-TT-C-TCA--GGC...................................................................................................................................................................	18	8	0.13	1	1	0	0	0

droSim2

CGCCGCGTTGTTTCGCTGCATGTGAGAG---AA--------TTCCGTGGCTGGCAT--CGCTCGCTGTAAATTGTAATCATCAAAGCGTT-TT-C-TCA--GAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTC---CGTACACA--GAAAGAAAA-----CCCC-TT-----------TTG----------------------AAA---AAACCA------------------------------------TTTAA---	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
............................................................................................................TTGGTGTTACTTCTTACAGTGA.........................................................................................................................................	22	1	285.00	285	52	0	62	7	0	0	0	0	18	13	0	133	0	0	0	0	0
...............................................................GCTGTAAATTGTAATCATCAAAGC....................................................................................................................................................................................	24	1	96.00	96	61	1	33	0	0	0	0	0	0	1	0	0	0	0	0	0	0
...............................................................GCTGTAAATTGTAATCATCAAAG.....................................................................................................................................................................................	23	1	90.00	90	76	1	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGTGG.........................................................................................................................................	22	1	26.00	26	9	0	16	0	0	0	0	0	0	0	0	1	0	0	0	0	0
.........................................TTCCGTGGCTGGCAT--CGCTC............................................................................................................................................................................................................	20	1	16.00	16	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...............................................................GCTGTAAATTGTAATCATC.........................................................................................................................................................................................	19	1	16.00	16	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGTG..........................................................................................................................................	21	1	5.00	5	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0
................................A--------TTCCGTGGCTGGCAT--CGCTC............................................................................................................................................................................................................	21	1	4.00	4	3	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
................................................................................................................TGTTACTTCTTACAGTGA.........................................................................................................................................	18	1	2.00	2	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAG............................................................................................................................................	19	1	2.00	2	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...............................................................GCTGTAAATTGTAATCATCAAAGA....................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGTGAA........................................................................................................................................	23	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...............................................................GCTGTAAATTGTAATCATCAAA......................................................................................................................................................................................	22	1	1.00	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
...............................AA--------TTCCGTGGCTGGCAT--CGCTC............................................................................................................................................................................................................	22	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

dm3

CGCCGCGTTGTTTCGCTGCATGTGAGAG---AA--------TTCCGTGGCTGGCAT--CGCTCGCTGTAAATTGTAATCATCAAAGCGTT-TT-C-TCA--GAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTC---CGTACACA--GAAAGAAAA-----CCCC-TA-----------TTG----------------------ATA---TAACCA------------------------------------TTTAATTT	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
............................................................................................................TTGGTGTTACTTCTTACAGTGA.........................................................................................................................................	22	1	4185.00	4185	0	0	0	0	18	0	0	0	0	18	5	9	1	0	1	0	1	0	8	0	0	0	0	28	0	0	0	0	1	5	117	103	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	11	11	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	25	9	1	1	1	1	0	28	10	7	27	67	2	41	81	8	17	75	102	15	16	358	4	1	0	6	44	0	5	1	52	0	85	2	23	9	29	95	0	49	0	27	44	169	1	48	2	43	59	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	93	132	0	156	2	0	119	132	6	132	1	168	6	259	30	0	0	0	0	0	407	0	0	0	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	16	0	3	2	4	0	26	1	0	0	1	0	0	0	0	22	17	0	3	14	0	0	0	0	2	8	0	3	0	0	0	1	1	65	0	0	3	0	0	0	0	0	7	1	0	1	0	0	0	0	0	0	0	0	0	1	0	0	3	0	0	1	11	13	6	37	1	40	1	1	1	0	0	1	0	0	6	0	0	3	3	0	1	0	0	0	0	12	0	0	0	0	4	0	0	0	2	84	3	1	9	1	0	0	0	7	51	2	0
...............................................................GCTGTAAATTGTAATCATCA........................................................................................................................................................................................	20	1	359.00	359	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	1	1	0	3	1	8	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	28	0	16	0	0	3	17	0	20	1	31	0	31	5	0	0	0	0	0	18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	2	3	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	25	22	44	38	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	1	0	0	0	1	0	0	0	1	0	0	0
...............................................................GCTGTAAATTGTAATCATCAAAGC....................................................................................................................................................................................	24	1	280.00	280	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	18	21	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	1	0	0	6	0	0	1	0	0	0	16	0	0	0	0	0	1	0	0	1	0	1	0	0	0	1	3	0	1	0	1	2	2	0	5	1	8	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	21	0	13	0	0	4	26	0	18	0	18	2	37	10	0	0	0	0	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	1	0	0	0	2	2	2	2	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0
...............................................................GCTGTAAATTGTAATCATCAAAG.....................................................................................................................................................................................	23	1	229.00	229	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	8	14	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	2	2	7	0	4	2	9	3	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	11	12	0	4	0	0	6	15	1	8	1	30	2	38	6	0	0	0	0	0	14	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	3	1	0	1	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	1	6	1	5	0	2	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
...............................................................GCTGTAAATTGTAATCATCAA.......................................................................................................................................................................................	21	1	174.00	174	0	0	0	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	1	0	0	0	0	0	0	0	0	0	25	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	2	1	7	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	10	0	13	0	1	6	8	0	6	0	13	0	20	0	0	0	0	0	0	15	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	1	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	8	4	10	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
............................................................................................................TTGGTGTTACTTCTTACAGTG..........................................................................................................................................	21	1	163.00	163	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	5	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	1	3	1	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	6	0	0	0	2	0	1	8	3	0	2	2	0	1	30	2	0	0	0	2	0	0	0	1	0	2	0	3	0	0	2	0	0	0	0	0	1	0	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	3	0	0	0	0	2	3	0	1	0	5	0	5	4	0	0	0	0	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	2	0	1	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	7	0	0	1	0	0	0	0	4	5	2	0
...............................................................GCTGTAAATTGTAATCATCAAA......................................................................................................................................................................................	22	1	78.00	78	0	0	0	0	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	1	0	0	0	2	0	2	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	9	9	0	7	0	0	1	5	1	5	1	7	0	14	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	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	1	3	3	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
...............................................................GCTGTAAATTGTAATCATC.........................................................................................................................................................................................	19	1	73.00	73	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	3	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	1	1	3	8	0	3	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	3	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	9	3	10	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0
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.............................................................................................................TGGTGTTACTTCTTACAGTGA.........................................................................................................................................	21	1	8.00	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGTGG.........................................................................................................................................	22	1	8.00	8	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	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	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	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGTGAG........................................................................................................................................	23	1	5.00	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...............................................................GCTGTAAATTGTAATCATCAAAGA....................................................................................................................................................................................	24	1	5.00	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	1	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACA.............................................................................................................................................	18	1	5.00	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	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	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...........................................................................................................CTTGGTGTTACTTCTTACAGTGT.........................................................................................................................................	23	1	4.00	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...............................................................GCTGTAAATTGTAATCATCAAAGG....................................................................................................................................................................................	24	1	4.00	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGT...........................................................................................................................................	20	1	4.00	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	1	0	0	0	0	0	0	0	0	0	1	0
...............................................................GCTGTAAATTGTAATCATCAAAGCG...................................................................................................................................................................................	25	1	4.00	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droEre2

CGCCGCGTTGTTTCGCTGCATGTGAGAG---AA--------TTCCGTGGCTGGCAT--CGCCCGCTGTAAATTGTAATCATCAAAGCGTT-TT-C-TCA--GAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTC---CGTACACA--GAAAGAAAA-----CCCC-TT----------------------------------------------CC------------TT--TGGTACATAACAAAAAAATAAATAA---	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
............................................................................................................TTGGTGTTACTTCTTACAGTGA.........................................................................................................................................	22	1	231.00	231	39	45	1	66	1	79	0
...............................................................GCTGTAAATTGTAATCATCA........................................................................................................................................................................................	20	1	45.00	45	0	0	6	0	1	38	0
...............................................................GCTGTAAATTGTAATCATCAAAGC....................................................................................................................................................................................	24	1	29.00	29	1	12	0	1	1	14	0
...............................................................GCTGTAAATTGTAATCATCAAAG.....................................................................................................................................................................................	23	1	26.00	26	0	1	2	1	0	22	0
...............................................................GCTGTAAATTGTAATCATCAA.......................................................................................................................................................................................	21	1	22.00	22	0	0	0	0	0	22	0
...............................................................GCTGTAAATTGTAATCATCAAA......................................................................................................................................................................................	22	1	22.00	22	1	0	0	0	0	21	0
............................................................................................................TTGGTGTTACTTCTTACAGTG..........................................................................................................................................	21	1	15.00	15	2	4	0	5	0	4	0
.............................................................................................................TGGTGTTACTTCTTACAGTGA.........................................................................................................................................	21	1	5.00	5	5	0	0	0	0	0	0
...........................................................................................................CTTGGTGTTACTTCTTACAGTGA.........................................................................................................................................	23	1	5.00	5	0	4	0	0	0	1	0
............................................................................................................TTGGTGTTACTTCTTACAGTGT.........................................................................................................................................	22	1	2.00	2	0	0	1	1	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGTGAA........................................................................................................................................	23	1	2.00	2	0	0	0	0	0	2	0
............................................................................................................TTGGTGTTACTTCTTACAGT...........................................................................................................................................	20	1	2.00	2	0	0	0	0	0	2	0
................................................................CTGTAAATTGTAATCATCAAAG.....................................................................................................................................................................................	22	1	2.00	2	2	0	0	0	0	0	0
...............................................................GCTGTAAATTGTAATCATCAAAGCG...................................................................................................................................................................................	25	1	2.00	2	0	0	0	0	0	2	0
............................................................................................................TTGGTGTTACTTCTTACAGTGC.........................................................................................................................................	22	1	2.00	2	0	0	1	1	0	0	0
...............................................................GCTGTAAATTGTAATCAT..........................................................................................................................................................................................	18	1	2.00	2	0	0	0	0	0	2	0
...............................................................GCTGTAAATTGTAATCATCAAAA.....................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	1	0
............................................................................................................TTGGTGTTACTTCTTACAGTGTA........................................................................................................................................	23	1	1.00	1	0	0	0	1	0	0	0
..............................................................CGCTGTAAATTGTAATCATCA........................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	1	0
...............................................................GCTGTAAATTGTAATCATC.........................................................................................................................................................................................	19	1	1.00	1	0	0	0	0	0	1	0
...............................................................GCTGTAAATTGTAATCATCG........................................................................................................................................................................................	20	1	1.00	1	0	0	0	0	0	1	0
..............................................................CGCTGTAAATTGTAATCATCAAAG.....................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	1	0
.........................................TTCCGTGGCTGGCAT--CGCCC............................................................................................................................................................................................................	20	1	1.00	1	1	0	0	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGTGAC........................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0	0
...............................AA--------TTCCGTGGCTGGCAT--CGCCC............................................................................................................................................................................................................	22	1	1.00	1	0	0	0	0	0	1	0
...........................................................................................................CTTGGTGTTACTTCTTACAGTG..........................................................................................................................................	22	1	1.00	1	1	0	0	0	0	0	0
................................................................................................................TGTTACTTCTTACAGTGA.........................................................................................................................................	18	1	1.00	1	0	0	0	1	0	0	0
........................................................................................................................................CAGTC---CGTACACA--GAAAGAAAA-----...................................................................................................	22	1	1.00	1	0	0	0	0	0	1	0

droYak3

CGCCGCGTTGTTTCGCTGCATGTGAGAG---AA--------TTCCGTGGCTGGCAT--CGCTCGCTGTAAATTGTAATCATCAAAGCGTT-TT-C-TCA--GAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTC---CGTACACA--GAAAGAAAA-----ACCCCTT-----------TAA----------------------GAA---AAAACA------------------------------------CAAAA---	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
............................................................................................................TTGGTGTTACTTCTTACAGTGA.........................................................................................................................................	22	1	227.00	227	11	11	138	63	0	2	2	0	0	0	0
...............................................................GCTGTAAATTGTAATCATCAAAGC....................................................................................................................................................................................	24	1	69.00	69	28	1	39	0	1	0	0	0	0	0	0
...............................................................GCTGTAAATTGTAATCATCAAAG.....................................................................................................................................................................................	23	1	36.00	36	29	2	4	1	0	0	0	0	0	0	0
...............................................................GCTGTAAATTGTAATCATCA........................................................................................................................................................................................	20	1	10.00	10	0	1	0	0	5	4	0	0	0	0	0
.........................................TTCCGTGGCTGGCAT--CGCTC............................................................................................................................................................................................................	20	1	10.00	10	9	0	1	0	0	0	0	0	0	0	0
................................A--------TTCCGTGGCTGGCAT--CGCTC............................................................................................................................................................................................................	21	1	6.00	6	5	0	1	0	0	0	0	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAG............................................................................................................................................	19	1	6.00	6	0	0	6	0	0	0	0	0	0	0	0
...............................................................GCTGTAAATTGTAATCATC.........................................................................................................................................................................................	19	1	4.00	4	3	1	0	0	0	0	0	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGTG..........................................................................................................................................	21	1	4.00	4	0	0	4	0	0	0	0	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGTGAA........................................................................................................................................	23	1	4.00	4	1	1	1	1	0	0	0	0	0	0	0
.............................................................................................................TGGTGTTACTTCTTACAGTGA.........................................................................................................................................	21	1	4.00	4	0	4	0	0	0	0	0	0	0	0	0
...........................................................................................................CTTGGTGTTACTTCTTACAGTGA.........................................................................................................................................	23	1	3.00	3	0	0	2	1	0	0	0	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGTGG.........................................................................................................................................	22	1	2.00	2	1	0	0	1	0	0	0	0	0	0	0
...............................................................GCTGTAAATTGTAATCATCAAAGCG...................................................................................................................................................................................	25	1	2.00	2	1	0	0	1	0	0	0	0	0	0	0
...............................................................GCTGTAAATTGTAATCATCAA.......................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	1	0	0	0	0	0
..........................................TCCGTGGCTGGCAT--CGCTC............................................................................................................................................................................................................	19	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0
.............................................................................................................TGGTGTTACTTCTTACAGTG..........................................................................................................................................	20	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0

droEug1

CGCCGCGTTGTTTCGCTGCATGTGAGAG---AA--------TTCCGTGGCTGGCAT--CGCTCGCTGTAAATTGTAATCATCAAAGCGTT-TT-C-TCA--GAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTC---CGTACACACAGAAAGAAAA-----------T-----------ATGAAGAAG------------------A---AGAACC------------------------------------CTAAA---	Size	Hit Count	Total Norm	Total
No Reads

droBia1

CGCCGCGTTGTTTCGCTGCATGTGAGAG---AA--------TTCCGTGGCTGGCAT--CGCCCGCTGTAAATTGTAATCATCAAAGCGTT-TTTC-TCA--GAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTC---CGTACACA--CAGAGAAAA-----CCCC-TT-----------TT-----------------CCCCTGGAA---AAACCA------------------------------------ATTGA---	Size	Hit Count	Total Norm	Total
No Reads

droTak1

CGCCGCGTTGTTTCGCTGCATGTGAGAG---AA--------TTCCGTGGCTGGCAT--CGCTCGCTGTAAATTGTAATCATCAAAGCGTT-TT-C-TCA--GAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTC---CGTACACA--GAAAGAAAAAAATAACCC-TT-----------TTGCCGAAAAAGAAAAAATCCCCTGAAAACCAAACCA------------------------------------TTCGA---	Size	Hit Count	Total Norm	Total
No Reads

droEle1

CGCCGCGTTGTTTCGCTGCATGTGAGAG---AA--------TTCCGTGGCTGGCAT--CGCTCGCTGTAAATTGTAATCATCAAAGCGTT-TTTC-TCA--GAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGCC---CGTACACA--GAAAGAAAT-----A--------------------------------------------A---AAACTCATTGAAATATCCC-----------------------TTGAA---	Size	Hit Count	Total Norm	Total
No Reads

droRho1

CGCCGCGTTGTTTCGCTGCATGTGAGAG---AA--------TTCCGTGGCTGGCAT--CGTTCGCTGTAAATTGTAATCATCAAAGCGTT-TTTT-TCA--GAACCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTC---CGTACACA--GAAAGAAAA-----CTCC-CT-----------TTG----------------------AAA----GCTCC------------TTAA-GGC------------A---ATAAA---	Size	Hit Count	Total Norm	Total
No Reads

droFic1

CGCCGCGTTGTTTCGCTGCATGTGAGAG---AA--------TTCCGTGGCTGGCAT--CGCCCGCTGTAAATTGTAATCATCAAAGCGTT-TT-C-TCA--GAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTC---CGTACACA--AAGAGAAAA-----CCCC-AT-----------ATG----------------------AAA----CCCCC------------------------------------TTTGA---	Size	Hit Count	Total Norm	Total
No Reads

droKik1

CGCCGCGTTC--------------AGAGCGAAA--------TTCCTTGGCTGGCAG--CGCACACTGTAAATTGTAATCATCAAAGCGTT-TTTC-TCA--GAGCCGCTTGGTGTTACTTCTTACAGTGAGTGCGCCAGTA-CACGTACACACGGCAAGAAAG-----AACC-TTAAAAAGTATATTTG----------------------AAA---AAAAAA------------------------------------TATAA---	Size	Hit Count	Total Norm	Total
No Reads

droAna3

CGCCACGTTGTTTCGCTGCATGTGAGAA---AA--------TTCCGTGGCTGGCAT--CGTTCACTGTAAATTGTAACCATCAAAGCGTT-TTTTATCA--GAGCCGCTTGGTGTTACTTCTTACAGTGAGTGAGCCAGCT---GGAGCACA--TATTAAAAA--------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
............................................................................................................TTGGTGTTACTTCTTACAGTGA.........................................................................................................................................	22	1	223.00	223	18	78	12	10	4	101
...............................................................ACTGTAAATTGTAACCATCAAAGC....................................................................................................................................................................................	24	1	29.00	29	1	15	0	1	0	12
............................................................................................................TTGGTGTTACTTCTTACAGTG..........................................................................................................................................	21	1	26.00	26	1	3	1	1	1	19
...............................................................ACTGTAAATTGTAACCATCAAAG.....................................................................................................................................................................................	23	1	6.00	6	0	1	0	0	0	5
.............................................................................................................TGGTGTTACTTCTTACAGTGA.........................................................................................................................................	21	1	5.00	5	4	0	0	0	0	1
...............................................................ACTGTAAATTGTAACCATCA........................................................................................................................................................................................	20	1	4.00	4	1	0	0	0	0	3
............................................................................................................TTGGTGTTACTTCTTACAGTGAA........................................................................................................................................	23	1	3.00	3	1	2	0	0	0	0
...........................................................................................................CTTGGTGTTACTTCTTACAGTGA.........................................................................................................................................	23	1	3.00	3	0	3	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGTGAAA.......................................................................................................................................	24	1	3.00	3	0	2	0	0	0	1
...............................................................ACTGTAAATTGTAACCATCAAA......................................................................................................................................................................................	22	1	3.00	3	0	0	0	0	0	3
...........................................................................................................CTTGGTGTTACTTCTTACAGTG..........................................................................................................................................	22	1	3.00	3	0	0	1	1	0	1
............................................................................................................TTGGTGTTACTTCTTACAGTGC.........................................................................................................................................	22	1	2.00	2	0	1	1	0	0	0
.......................................................................................GTT-TTTTATCA--GAGCCGC...............................................................................................................................................................	18	1	2.00	2	0	2	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGT...........................................................................................................................................	20	1	2.00	2	0	0	0	1	0	1
...........................................................................................................CTTGGTGTTACTTCTTACAGTGT.........................................................................................................................................	23	1	1.00	1	0	0	0	0	0	1
...............................................................ACTGTAAATTGTAACCATCAA.......................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	1
...............................................................ACTGTAAATTGTAACCATCAAAGT....................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	1
............................................................................................................TTGGTGTTACTTCTTACAGTA..........................................................................................................................................	21	1	1.00	1	0	0	1	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGTGT.........................................................................................................................................	22	1	1.00	1	0	0	0	0	0	1
............................................................................................................TTGGTGTTACTTCTTACAG............................................................................................................................................	19	1	1.00	1	1	0	0	0	0	0
...............................................................ACTGTAAATTGTAACCATCAAAGCT...................................................................................................................................................................................	25	1	1.00	1	0	0	0	0	0	1

droBip1

CGCCACGTTGTTTCGCTGCATGTGAGAA---AA--------TTCCGTGGCTGGCAT--CGTTCACTGTAAATTGTAACCATCAAAGCGTT-TTTTATCA--GAGCCGCTTGGTGTTACTTCTTACAGTGAGTGAGCCAGCT---GGAGCACA--CA-------------------------------------------------------------------------------------------------------TTT-----	Size	Hit Count	Total Norm	Total
No Reads

dp5

CGCCGCGT---GTCTCAGCATGTGAGAG---AGCGGCTCCTTTCCCTGGACCCCAT--CGCTCGCTGTAAATTGTAATGGCCAAAGCTTT-TTTGTTGG--TAGCAGCTTGGTGTTACTTCTTACAGTGAGTGTG------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M022 Male-body	M040 Female-body	M059 Embryo	M062 Head	V043 Embryo	V051 Head	V112 Male-body	SRR902010 Ovary	SRR902011 Testis	SRR902012 CNS imaginal disc
............................................................................................................TTGGTGTTACTTCTTACAGTGA.........................................................................................................................................	22	1	538.00	538	0	203	118	64	109	35	5	0	0	4
...............................................................GCTGTAAATTGTAATGGCCAAAGC....................................................................................................................................................................................	24	1	70.00	70	0	8	18	30	10	4	0	0	0	0
...........................................................................................................CTTGGTGTTACTTCTTACAGTGA.........................................................................................................................................	23	1	42.00	42	0	4	25	5	6	2	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGTG..........................................................................................................................................	21	1	24.00	24	0	10	4	1	2	6	1	0	0	0
...............................................................GCTGTAAATTGTAATGGCCAAAGCT...................................................................................................................................................................................	25	1	14.00	14	0	2	4	7	1	0	0	0	0	0
...............................................................GCTGTAAATTGTAATGGCCAAAG.....................................................................................................................................................................................	23	1	12.00	12	0	7	0	0	0	5	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGTGT.........................................................................................................................................	22	1	11.00	11	0	0	0	0	3	8	0	0	0	0
.............................................................................................................TGGTGTTACTTCTTACAGTGA.........................................................................................................................................	21	1	10.00	10	0	10	0	0	0	0	0	0	0	0
...............................................................GCTGTAAATTGTAATGGCCA........................................................................................................................................................................................	20	1	8.00	8	0	4	0	0	0	4	0	0	0	0
...............................................................GCTGTAAATTGTAATGGCCAAA......................................................................................................................................................................................	22	1	7.00	7	0	0	0	1	0	5	0	0	0	1
............................................................................................................TTGGTGTTACTTCTTACAGTGAA........................................................................................................................................	23	1	6.00	6	0	3	0	1	0	0	0	0	0	2
............................................................................................................TTGGTGTTACTTCTTACAG............................................................................................................................................	19	1	4.00	4	0	0	2	1	0	1	0	0	0	0
...............................................................GCTGTAAATTGTAATGGCCAA.......................................................................................................................................................................................	21	1	4.00	4	0	1	0	1	0	2	0	0	0	0
...........................................................................................................CTTGGTGTTACTTCTTACAGTG..........................................................................................................................................	22	1	3.00	3	0	1	1	0	1	0	0	0	0	0
...............................................................GCTGTAAATTGTAATGGCCAAAGCC...................................................................................................................................................................................	25	1	2.00	2	0	0	0	2	0	0	0	0	0	0
................................................................................................................TGTTACTTCTTACAGTGA.........................................................................................................................................	18	1	2.00	2	0	1	0	0	1	0	0	0	0	0
..........................................TCCCTGGACCCCAT--CGCTC............................................................................................................................................................................................................	19	1	2.00	2	0	0	0	2	0	0	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGTGAAA.......................................................................................................................................	24	1	1.00	1	0	1	0	0	0	0	0	0	0	0
...........................................................................................................CTTGGTGTTACTTCTTACAGC...........................................................................................................................................	21	1	1.00	1	0	0	0	1	0	0	0	0	0	0
...........................................................................................................CTTGGTGTTACTTCTTACAG............................................................................................................................................	20	1	1.00	1	0	0	1	0	0	0	0	0	0	0
................................................................CTGTAAATTGTAATGGCCAAAGCT...................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	1	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGTGC.........................................................................................................................................	22	1	1.00	1	0	0	0	0	0	1	0	0	0	0
................................................................CTGTAAATTGTAATGGCCAAAGA....................................................................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.............................................................................................................TGGTGTTACTTCTTACAGTG..........................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0	0	0	0	0
........................................TTTCCCTGGACCCCAT--CGCTC............................................................................................................................................................................................................	21	1	1.00	1	0	0	0	1	0	0	0	0	0	0
..............................................................................................................GGTGTTACTTCTTACAGTGA.........................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGTGG.........................................................................................................................................	22	1	1.00	1	0	0	1	0	0	0	0	0	0	0
...........................................................................................................CTTGGTGTTACTTCTTACAGT...........................................................................................................................................	21	1	1.00	1	0	0	0	0	1	0	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGT...........................................................................................................................................	20	1	1.00	1	0	0	0	0	1	0	0	0	0	0
.................................................................TGTAAATTGTAATGGCCAAAGCT...................................................................................................................................................................................	23	1	1.00	1	0	0	0	1	0	0	0	0	0	0
.......................................................................................TTT-TTTGTTGG--TAGCAGC...............................................................................................................................................................	18	2	1.00	2	0	0	2	0	0	0	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAC............................................................................................................................................	19	1	1.00	1	0	0	1	0	0	0	0	0	0	0

droPer2

CGCCGCGT---GTCTCAGCATGTGAGAG---AGCGGCTCCTTTCCCTGGACCCCAT--CGCTCGCTGTAAATTGTAATGGCCAAAGCTTT-TTTGTTGG--TAGCAGCTTGGTGTTACTTCTTACAGTGAGTGTG------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
............................................................................................................TTGGTGTTACTTCTTACAGTGA.........................................................................................................................................	22	1	192.00	192	24	23	46	53	42	4
............................................................................................................TTGGTGTTACTTCTTACAGTG..........................................................................................................................................	21	1	19.00	19	0	2	4	9	3	1
...............................................................GCTGTAAATTGTAATGGCCAAAG.....................................................................................................................................................................................	23	1	9.00	9	0	0	0	5	4	0
...............................................................GCTGTAAATTGTAATGGCCAAAGCT...................................................................................................................................................................................	25	1	9.00	9	0	0	1	2	6	0
...............................................................GCTGTAAATTGTAATGGCCA........................................................................................................................................................................................	20	1	8.00	8	0	2	0	2	4	0
...............................................................GCTGTAAATTGTAATGGCCAAA......................................................................................................................................................................................	22	1	7.00	7	0	0	0	3	4	0
...........................................................................................................CTTGGTGTTACTTCTTACAGTGA.........................................................................................................................................	23	1	6.00	6	0	1	1	3	1	0
............................................................................................................TTGGTGTTACTTCTTACAGTGG.........................................................................................................................................	22	1	5.00	5	5	0	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGTGT.........................................................................................................................................	22	1	5.00	5	0	0	0	2	3	0
...............................................................GCTGTAAATTGTAATGGCCAA.......................................................................................................................................................................................	21	1	4.00	4	0	1	0	0	3	0
.........................................TTCCCTGGACCCCAT--CGCTC............................................................................................................................................................................................................	20	1	4.00	4	0	0	0	2	2	0
...........................................................................................................CTTGGTGTTACTTCTTACAGTG..........................................................................................................................................	22	1	3.00	3	0	0	0	2	0	1
.......................................................................................TTT-TTTGTTGG--TAGCAGC...............................................................................................................................................................	18	2	3.00	6	3	0	0	0	3	0
.................................................................TGTAAATTGTAATGGCCAAAGCT...................................................................................................................................................................................	23	1	3.00	3	0	0	0	1	2	0
.............................................................................................................TGGTGTTACTTCTTACAGTGA.........................................................................................................................................	21	1	3.00	3	0	2	0	1	0	0
...........................................................................................................CTTGGTGTTACTTCTTACAGT...........................................................................................................................................	21	1	3.00	3	1	0	0	1	1	0
...............................................................GCTGTAAATTGTAATGGCCAAAT.....................................................................................................................................................................................	23	1	2.00	2	0	0	0	0	2	0
...............................................................GCTGTAAATTGTAATGGCCAAAGC....................................................................................................................................................................................	24	1	2.00	2	0	2	0	0	0	0
..........................................TCCCTGGACCCCAT--CGCTC............................................................................................................................................................................................................	19	1	1.00	1	0	0	0	0	1	0
............................................................................................................TTGGTGTTACTTCTTACAGTGAA........................................................................................................................................	23	1	1.00	1	0	0	0	0	1	0
...............................................................GCTGTAAATTGTAATGGCCAAT......................................................................................................................................................................................	22	1	1.00	1	0	0	0	0	0	1
............................................................................................................TTGGTGTTACTTCTTACAGT...........................................................................................................................................	20	1	1.00	1	0	0	0	0	1	0
............................................................................................................TTGGTGTTACTTCTTACA.............................................................................................................................................	18	1	1.00	1	0	1	0	0	0	0
...........................................................................................................CTTGGTGTTACTTCTTACAGTGT.........................................................................................................................................	23	1	1.00	1	0	0	1	0	0	0
...............................................................GCTGTAAATTGTAATGGCC.........................................................................................................................................................................................	19	1	1.00	1	0	0	0	0	1	0

droWil2

CGCCGCGTTATAC-------------------A--------TTAAACGGCCCAATA--CGCTCGCTGTAAATTGTAGCAATCAAAGCGTTGCCTT-TTGCCTCACAGCTTGGTGTTACTTCTTACAGTGAGTGTG------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
............................................................................................................TTGGTGTTACTTCTTACAGTGA.........................................................................................................................................	22	1	4923.00	4923	431	167	8	540	3777
............................................................................................................TTGGTGTTACTTCTTACAGTG..........................................................................................................................................	21	1	449.00	449	13	9	0	28	399
............................................................................................................TTGGTGTTACTTCTTACAGTGT.........................................................................................................................................	22	1	118.00	118	0	1	0	7	110
............................................................................................................TTGGTGTTACTTCTTACAGTGG.........................................................................................................................................	22	1	82.00	82	78	0	0	2	2
............................................................................................................TTGGTGTTACTTCTTACAGT...........................................................................................................................................	20	1	74.00	74	3	3	1	1	66
...............................................................GCTGTAAATTGTAGCAATCAAAGC....................................................................................................................................................................................	24	1	72.00	72	52	0	0	12	8
.............................................................................................................TGGTGTTACTTCTTACAGTGA.........................................................................................................................................	21	1	22.00	22	0	15	0	0	7
............................................................................................................TTGGTGTTACTTCTTACAGTGAA........................................................................................................................................	23	1	20.00	20	0	1	0	1	18
...........................................................................................................CTTGGTGTTACTTCTTACAGTGA.........................................................................................................................................	23	1	10.00	10	0	1	0	2	7
............................................................................................................TTGGTGTTACTTCTTACAG............................................................................................................................................	19	1	7.00	7	3	1	0	0	3
............................................................................................................TTGGTGTTACTTCTTACAGTGC.........................................................................................................................................	22	1	5.00	5	0	0	1	0	4
............................................................................................................TTGGTGTTACTTCTTACAGTGAT........................................................................................................................................	23	1	4.00	4	0	0	0	1	3
.............................................................................................................TGGTGTTACTTCTTACAGTG..........................................................................................................................................	20	1	3.00	3	1	1	0	0	1
..............................................................................................................GGTGTTACTTCTTACAGTGA.........................................................................................................................................	20	1	2.00	2	0	1	0	0	1
............................................................................................................TTGGTGTTACTTCTTACAGTA..........................................................................................................................................	21	1	2.00	2	0	0	0	0	2
..........................................TAAACGGCCCAATA--CGCTC............................................................................................................................................................................................................	19	1	2.00	2	2	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGTGAAA.......................................................................................................................................	24	1	2.00	2	0	1	1	0	0
...........................................................................................................CTTGGTGTTACTTCTTACAGTGT.........................................................................................................................................	23	1	1.00	1	0	0	0	0	1
............................................................................................................TTGGTGTTACTTCTTACAGTT..........................................................................................................................................	21	1	1.00	1	0	0	0	0	1
................................................................................................................TGTTACTTCTTACAGTGA.........................................................................................................................................	18	1	1.00	1	0	0	0	0	1
............................................................................................................TTGGTGTTACTTCTTACAGTGAGT.......................................................................................................................................	24	1	1.00	1	0	0	0	0	1
............................................................................................................TTGGTGTTACTTCTTACAC............................................................................................................................................	19	1	1.00	1	1	0	0	0	0
.................................................................................................................GTTACTTCTTACAGTGAA........................................................................................................................................	18	1	1.00	1	0	1	0	0	0
.............................................................................................................TGGTGTTACTTCTTACAGTGT.........................................................................................................................................	21	1	1.00	1	0	0	0	0	1
............................................................................................................TTGGTGTTACTTCTTACA.............................................................................................................................................	18	1	1.00	1	0	0	0	0	1
.............................................................................................................TGGTGTTACTTCTTACAGT...........................................................................................................................................	19	1	1.00	1	0	0	0	0	1
.............................................................................................................TGGTGTTACTTCTTACAGTGAAA.......................................................................................................................................	23	1	1.00	1	0	1	0	0	0
...............................................................GCTGTAAATTGTAGCAATCAAAG.....................................................................................................................................................................................	23	1	1.00	1	0	1	0	0	0
...........................................................................................................CTTGGTGTTACTTCTTACAGTG..........................................................................................................................................	22	1	1.00	1	0	0	0	0	1
............................................................................................................TTGGTGTTACTTCTTACAGTGAG........................................................................................................................................	23	1	1.00	1	0	0	0	0	1
...............................................................GCTGTAAATTGTAGCAATC.........................................................................................................................................................................................	19	1	1.00	1	1	0	0	0	0
.................................................................................................................GTTACTTCTTACAGTGAT........................................................................................................................................	18	10	0.10	1	0	0	0	0	1

droVir3

CAACACGTCACA-AGCTGA-----------------------------AATGACGTCACGCCCGCTGTAAAATGTAATCATCAGAGCGTC-CT-C-TC----AACCGCTTGGTGTTACTTCTTACAGTGAGTGCGACGGCC---C--------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M027 Male-body	M028 Head	M047 Female-body	M061 Embryo	SRR060654 Ovary	SRR060655 Testis	SRR060656 Ovary	SRR060657 Testis	SRR060658 Ovary	SRR060659 Testis	SRR060660 Ovary	SRR060661 Embryo	SRR060662 Embryo	SRR060663 Embryo	SRR060664 Male-body	SRR060665 Female-body	SRR060666 Male-body	SRR060667 Female-body	SRR060668 Male-body	SRR060669 Female-body	SRR060670 Testis	SRR060671 Male-body	SRR060672 Female-body	SRR060673 Ovary	SRR060674 Ovary	SRR060675 Ovary	SRR060676 Ovary	SRR060677 Ovary	SRR060678 Testis	SRR060679 Testis	SRR060680 Testis	SRR060681 Testis	SRR060682 Embryo	SRR060683 Testis	SRR060684 Embryo	SRR060685 Embryo	SRR060686 Embryo	SRR060687 Embryo	SRR060688 Ovary	SRR060689 Testis	SRR1106712 embryo_0-2h	SRR1106713 embryo_0-2h	SRR1106714 embryo_2-4h	SRR1106715 embryo_4-6h	SRR1106716 embryo_4-6h	SRR1106717 embryo_6-8h	SRR1106718 embryo_6-8h	SRR1106719 embryo_8-10h	SRR1106720 embryo_8-10h	SRR1106721 embryo_10-12h	SRR1106722 embryo_10-12h	SRR1106723 embryo_12-14h	SRR1106724 embryo_12-14h	SRR1106725 embryo_14-16h	SRR1106726 embryo_14-16h	SRR1106727 larvae	SRR1106728 larvae	SRR1106729 mixed whole adult body	SRR1106730 embryo_16-30h	V047 Embryo	V053 Head	V116 Male-body	GSM1528803 follicle cells	SRR2096013 Ovary_Strain_9_oxidized	SRR2096014 Ovary_Strain_160_oxidized	SRR2096026 embryo_0-2h from 14 day old Strain 9 mothers	SRR2096038 embryo_0-2h from 14 day old Strain 9 mothers	SRR2096050 embryo_0-2h from 14 day old Strain 160 mothers	SRR2096055 Ovary_Min_43	SRR2096056 Ovary_Min_46	SRR2096057 Ovary_Min_50	SRR2096058 Ovary_Min_98	SRR2096059 Ovary_Min_164	SRR2096060 Ovary_Min_193	SRR2096061 embryo_0-2h from 14 day old Strain 160 mothers	SRR2096072 embryo_0-2h from 15to16 day old dysgenic mothers	SRR2096079 embryo_0-2h from 15to16 day old dysgenic mothers	SRR2096080 embryo_0-2h from 15to16 day old nondysgenic mothers	SRR2096081 embryo_0-2h from 15to16 day old nondysgenic mothers
............................................................................................................TTGGTGTTACTTCTTACAGTGA.........................................................................................................................................	22	1	962.00	962	0	54	164	63	2	0	0	0	0	1	0	0	0	0	78	37	26	83	30	29	0	21	100	0	0	1	0	0	8	2	2	22	1	27	0	0	0	0	0	53	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	4	87	44	13	0	0	0	0	1	1	0	4	0	2	0	1	0	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGTG..........................................................................................................................................	21	1	175.00	175	1	3	15	3	0	0	0	0	0	0	0	0	0	0	5	2	7	3	0	2	1	1	7	0	0	0	0	0	7	1	1	14	0	17	0	0	0	0	0	71	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	3	4	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...............................................................GCTGTAAAATGTAATCATCAGAGC....................................................................................................................................................................................	24	1	44.00	44	1	5	0	9	0	0	0	0	0	0	0	0	0	0	6	2	2	1	1	1	0	2	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	6	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGTGT.........................................................................................................................................	22	1	35.00	35	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.............................................................................................................TGGTGTTACTTCTTACAGTGA.........................................................................................................................................	21	1	18.00	18	0	0	16	0	0	0	0	0	0	0	0	0	0	0	0	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	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGTGG.........................................................................................................................................	22	1	13.00	13	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
............................................................................................................TTGGTGTTACTTCTTACAGTGAA........................................................................................................................................	23	1	12.00	12	0	0	3	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	1	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGTGAT........................................................................................................................................	23	1	9.00	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...............................................................GCTGTAAAATGTAATCATCAGAG.....................................................................................................................................................................................	23	1	7.00	7	0	1	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...........................................................................................................CTTGGTGTTACTTCTTACAGTGA.........................................................................................................................................	23	1	7.00	7	0	0	2	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAG............................................................................................................................................	19	1	4.00	4	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
...........................................................................................................CTTGGTGTTACTTCTTACAGTG..........................................................................................................................................	22	1	3.00	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	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
...............................................................GCTGTAAAATGTAATCATCAGA......................................................................................................................................................................................	22	1	3.00	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.............................................................CCGCTGTAAAATGTAATCATCAGAGC....................................................................................................................................................................................	26	1	3.00	3	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	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGT...........................................................................................................................................	20	1	3.00	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGTT..........................................................................................................................................	21	1	2.00	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGTGC.........................................................................................................................................	22	1	2.00	2	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	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.............................................................................................................TGGTGTTACTTCTTACAGTGT.........................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
............................................................................................................TTGGTGTTACTTCTTACAGTGAAA.......................................................................................................................................	24	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
................................................................................................................TGTTACTTCTTACAGTGAAA.......................................................................................................................................	20	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
.................................................................................................................GTTACTTCTTACAGTGAA........................................................................................................................................	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	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
............................................................................................................TTGGTGTTACTTCTTACAGTC..........................................................................................................................................	21	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
................................................................................................................TGTTACTTCTTACAGTGA.........................................................................................................................................	18	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.............................................................................................................TGGTGTTACTTCTTACAGTG..........................................................................................................................................	20	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..............................................................................................................GGTGTTACTTCTTACAGTGA.........................................................................................................................................	20	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.............................................................................................................TGGTGTTACTTCTTACAGTGAA........................................................................................................................................	22	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
................................................................................................................TGTTACTTCTTACAGTGAA........................................................................................................................................	19	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
................TGA-----------------------------AATGACGTCACGCCC............................................................................................................................................................................................................	18	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAC............................................................................................................................................	19	1	1.00	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droMoj3

CGA----------------------------------------------------------CCGCTGTAAATTGTAATCATCAAAGCGTC-TG-C-TA----AATCGCTTGGTGTTACTTCTTACAGTGAGCGCGGCGCTC------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
............................................................................................................TTGGTGTTACTTCTTACAGTGA.........................................................................................................................................	22	1	543.00	543	190	51	43	56	189	14
...............................................................GCTGTAAATTGTAATCATCAAAGC....................................................................................................................................................................................	24	1	40.00	40	2	1	1	1	35	0
.............................................................................................................TGGTGTTACTTCTTACAGTGA.........................................................................................................................................	21	1	23.00	23	22	0	0	0	1	0
...........................................................................................................CTTGGTGTTACTTCTTACAGTGA.........................................................................................................................................	23	1	20.00	20	6	0	0	1	12	1
............................................................................................................TTGGTGTTACTTCTTACAGTG..........................................................................................................................................	21	1	18.00	18	7	2	2	3	4	0
...............................................................GCTGTAAATTGTAATCATCAAAG.....................................................................................................................................................................................	23	1	8.00	8	1	1	2	0	4	0
............................................................................................................TTGGTGTTACTTCTTACAGTGT.........................................................................................................................................	22	1	8.00	8	0	0	4	3	1	0
...............................................................GCTGTAAATTGTAATCATCA........................................................................................................................................................................................	20	1	7.00	7	1	0	3	3	0	0
............................................................................................................TTGGTGTTACTTCTTACAGTGAA........................................................................................................................................	23	1	3.00	3	2	0	0	0	0	1
............................................................................................................TTGGTGTTACTTCTTACAGTGAT........................................................................................................................................	23	1	3.00	3	2	1	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGT...........................................................................................................................................	20	1	3.00	3	0	0	2	0	1	0
............................................................................................................TTGGTGTTACTTCTTACAG............................................................................................................................................	19	1	3.00	3	0	0	0	0	3	0
..............................................................................................................GGTGTTACTTCTTACAGTGA.........................................................................................................................................	20	1	2.00	2	2	0	0	0	0	0
...........................................................................................................CTTGGTGTTACTTCTTACAGTG..........................................................................................................................................	22	1	2.00	2	0	1	0	1	0	0
...............................................................GCTGTAAATTGTAATCATC.........................................................................................................................................................................................	19	1	2.00	2	0	0	2	0	0	0
...........................................................................................................CTTGGTGTTACTTCTTACAGT...........................................................................................................................................	21	1	2.00	2	0	0	0	0	2	0
.............................................................................................................TGGTGTTACTTCTTACAGTG..........................................................................................................................................	20	1	1.00	1	1	0	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGTGAC........................................................................................................................................	23	1	1.00	1	0	0	0	0	1	0
..............................................................CGCTGTAAATTGTAATCATC.........................................................................................................................................................................................	20	1	1.00	1	0	0	0	1	0	0
..............................................................CGCTGTAAATTGTAATCATCA........................................................................................................................................................................................	21	1	1.00	1	0	0	0	1	0	0
...............................................................GCTGTAAATTGTAATCATCAAAGA....................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	1	0
................................................................................................................TGTTACTTCTTACAGTGA.........................................................................................................................................	18	1	1.00	1	0	1	0	0	0	0
............................................................................................................TTGGTGTTACTTCTTACAGTGATT.......................................................................................................................................	24	1	1.00	1	0	0	0	0	1	0
............................................................................................................TTGGTGTTACTTCTTACAGTGC.........................................................................................................................................	22	1	1.00	1	0	0	1	0	0	0
...............................................................GCTGTAAATTGTAATCATCAA.......................................................................................................................................................................................	21	1	1.00	1	0	0	0	1	0	0

droGri2

AGATGCCACG---------------------AA-----------CTTGAATGACGTCACGCCCGCTGTAATATGTAATCATCAAAGCGTG-TATT-TT----ACTCGCTTGGTGTTACTTCTTACAGTGAGTGCGACGGCCACACGTCCAGC--GGAGGAGAG-----TGAA-TC-----------TAG----------------------CGC---AGAGAA------------------------------------TTCAA---	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
............................................................................................................TTGGTGTTACTTCTTACAGTGA.........................................................................................................................................	22	1	11.00	11	11	0
..............................................................................................................GGTGTTACTTCTTACAGTGA.........................................................................................................................................	20	1	1.00	1	1	0
............................................................................................................TTGGTGTTACTTCTTACAGTGT.........................................................................................................................................	22	1	1.00	1	0	1
...........................................................................................................CTTGGTGTTACTTCTTACAGTGA.........................................................................................................................................	23	1	1.00	1	1	0
.............................................................................................................TGGTGTTACTTCTTACAGTGA.........................................................................................................................................	21	1	1.00	1	1	0

dse_66

scaffold_21:701252-701314 +

Known Ortholog

Canonical miRNA

5pUTR

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

-45.4	-45.4	-45.4