dpe_322

TCTTGTTAACAGCTTTTGCTTTTTTGTTTACCTCACTCGCAATTTGTCTGTACTTAAAACCATTTGTTCGTTTTTATTGTTCTTATTGTGTTTATTATTATTGCATTTTTAATGACGAACTGATGGTTTAAAGTACAAGCAAAGTGCAAGTTTCACCTTTTTCGAAATTGCCAATTATTATGAAAATA *********************************((.(((.(((((.(((((((.((((((((.(((((((.(((...........((((...........))))...))).))))))).)))))))).))))))).))))).))).))...*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V057 head	V050 head	M042 female body	M021 embryo	V042 embryo	V111 male body
..................................................TACTTAAAACCATTTGTTCGTT....................................................................................................................	22	0	1	31.00	31	6	7	14	1	2	1
..................................................TACTTGAAACCATTTGTTCGTT....................................................................................................................	22	1	1	24.00	24	12	10	1	0	0	1
..................................................TACTTGAAACCATTTGTTCGT.....................................................................................................................	21	1	1	7.00	7	4	3	0	0	0	0
..................................................TACTTAAAACCATTTGTTCGT.....................................................................................................................	21	0	1	7.00	7	4	0	2	1	0	0
..................................................TGCTTGAAACCATTTGTTCGTT....................................................................................................................	22	2	1	3.00	3	2	1	0	0	0	0
..................................................TACTTAAAACCATTTGTTCGTTT...................................................................................................................	23	0	1	1.00	1	0	0	1	0	0	0
..................................................TACTTGAAACCATTTGCTCGTT....................................................................................................................	22	2	1	1.00	1	1	0	0	0	0	0
..................................................TACTTGAAACCATTTGTTCTTT....................................................................................................................	22	2	1	1.00	1	0	1	0	0	0	0
..................................................TACTTGGAACCATTTGTTCGTT....................................................................................................................	22	2	1	1.00	1	0	1	0	0	0	0
..................................................TACTTAAAGCCCTTTGTTCGTTC...................................................................................................................	23	3	1	1.00	1	1	0	0	0	0	0
..................................................GACTTAAAACCATTTGTTCGTT....................................................................................................................	22	1	1	1.00	1	0	0	1	0	0	0
..................................................TAATTGAAACCATTTGTTCGTT....................................................................................................................	22	2	2	0.50	1	1	0	0	0	0	0
..................................................TACCTAAAACCATTTGTGCGTG....................................................................................................................	22	3	2	0.50	1	1	0	0	0	0	0
..................................................TAAGTAAAACCATTTGTTCGTT....................................................................................................................	22	2	2	0.50	1	1	0	0	0	0	0
.................................................................................................TTATTGCACTGTTAATGACGG......................................................................	21	3	3	0.33	1	1	0	0	0	0	0

AGAACAATTGTCGAAAACGAAAAAACAAATGGAGTGAGCGTTAAACAGACATGAATTTTGGTAAACAAGCAAAAATAACAAGAATAACACAAATAATAATAACGTAAAAATTACTGCTTGACTACCAAATTTCATGTTCGTTTCACGTTCAAAGTGGAAAAAGCTTTAACGGTTAATAATACTTTTAT *********************************((.(((.(((((.(((((((.((((((((.(((((((.(((...........((((...........))))...))).))))))).)))))))).))))))).))))).))).))...*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V111 male body
...............................GATTGAGCTTTATACAGACAT........................................................................................................................................	21	3	2	0.50	1	1

Species	Coordinate	ID	Type	Alignment
droPer2	scaffold_1:1709209-1709396 +	dpe_322	candidate-rescued	T-----CTTGTTAACAGCTTT-TGCT------------TTTTTG-----TTTACCTCAC--TCGC------AATTTGTCTGTACTTAAAACCATTTG-TTCGTTT------TTATTGTTCTTA-TTGTGTTTATT--AT--TAT---T-G--CAT-------------------------T--TTTAATGACGAACTGATGGTT--TAAAGTACAAGCAAAGTGCA-------AGTTTCA------------------------------------------------------------------------CCT--TTTTCGAAATTGCCAATTATT--------------------------ATGAAAATA--
dp5	4_group3:234371-234558 +	dps_243	confident	T-----CTTGTTAACAGCTTT-TGCT------------TTTTTG-----TTTACCTCAC--TCGC------AATTTGTCTGTACTTAAAACCATTTG-TTCGTTT------TTATTGTTCTTA-TTGTGTTTATT--AT--TAT---T-G--CAT-------------------------T--TTTAATGACGAACTGATGGTT--TAAAGTACAAGCAAAGTGCA-------AGTTTCA------------------------------------------------------------------------CCT--TTTTCGAAATTGCCAATTATT--------------------------ATGAAAATA--
droWil2	scf2_1100000004521:12231584-12231847 -			C-----CTTGTTAATAGCTTTTTGCT------------TT---------TTTACCTCAT--CAAC------ACTTTGATTGTAATTGAAACTGTTTAAAGCATTT------CCCTTGTTGTCAATAGTGTTCA-T--TT--TCTTTTT-T--TACTTAATTTAATTTAATTATTTTTTGCA--TATAACGCTTAAC-GTGGTCG--TCAAAAGCAATCAAAGTGTTTTTG---GGGTTCT---ACGTTTTCATTGTA-TACATATATATTTATAC--------------------TATTATAAAATAGTTTAAATTTTTTTCAAAATTGCCAATTATT--------------------------C---GGACA--
droVir3	scaffold_12723:4015059-4015324 +	dvi_23304		T-----TTTTTTG----GTTT-TATT------------TTTTTTCT---TAAACCACGTTTTGTC------GCCTTGCTTGCGATTAAAAGCAGTCGAACGGGTT------TCATTGTTGTAA-TTATATTTTAT--TT--------------GT-T-----------------------T--TTGAAAAGCGTTT-GATTGTT--TTGAATGCAAGCAAGGTGTTATTA----GGTTGACCCATGTTTTTAACATACTACATACACATGCAGACATCCAGACAGGCAAACATAAATTTATAAAC-------------------TAGTTTTGTTTATTGAATGAAAAACAAATGGCCAACTTCTT---CGATTTA
droMoj3	scaffold_6500:14710021-14710198 -			TTCTGCCTTGTTGACAGCTTTGTGCTTTTCATTTTCTTACATTTGT---TTGATCACGAATTGGC------GCTTTGCTTGCGCTTAAAACTAATTGAACGGGTT------TCATTGTTGTAG-TTATATATTTT--AT--TTG---TTTAATTTTA-----------------------TTTTTGAAATGCGTTC-AATAGAGGTTTGCCAGCAAGCAAGGTGC------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	scaffold_15252:3644378-3644525 -			T-----CTTGTTAACAGCTTT-TGCT------------CTTTTT-----TTTACCTCGATTCAGC------GCTTTGCTTGCGCTTAAAGCCATTTAAACGGGTT------TCATTGTTGTAA-TTATATTATAT--TT--TAT---T-T---GT-T-----------------------T--TTGAAGTGCGTTT-AATAGTT--TTGGATGCAAGCAAGGTG-------------------------------------------------------------------------------------------------------------------------------------------------------
droAna3	scaffold_12916:13774631-13774831 -	dan_4040	confident	T-----CTTGTTAACAGCTTT-TGCT------------TTTTTTTTTTATGTACCTCAG--AGGCG----TTTTTTGTGTGTGCCTAAGACTAC-CG-CCCGGTT------TGCTTGTTGTAA-TTGTGTGTTT-GTAT--TAT---TTT--TATTA-----------------------TTTTTTAAGAACTGGC-GGAAGTT--TTAGGGGCAGACAAAGCTATGCCA-ACAGATTCA------------------------------------------------------------------------ACT--TTTTCAAAATTGCCAACTTGT------------------------------GAACA--
droBip1	scf7180000396535:738654-738840 -			T-----CTTGTTAACAGCTTT-TGCT------------TTTTTT-----TGTACCTCAT--AGGC------CCTTTGTTTGCGCCCAAGACTACCTC-CCCGATT------TGCTTGTTGTCA-TTGTGTTCTTT-TAT--TAT---T-T--TATTTTTTTTT-----------------G--TTTAAGTACGGGC-GGCAGTT--TTTAGCGCAGACAAA-------------GATTCA------------------------------------------------------------------------AGT-TTTTTCAAAATTGCCAATTTAT------------------------------GAAGA--
droKik1	scf7180000302677:189885-190085 +			T-----CTTGTTAACTGCTTT-TGCT------------TATT-T-----TATACCTCAC--TGGCCCC---TGTTTGTCTGTGCCTAAGATCATCGC-GTCGCCTTGATTATCATTGTTGTCA-TTGTGTTGTGT--AT--TAT---T-T--TAGTT-----------------------T--TTTAAGGACGAAC-GATAATG--TTAGGTGCAGGCAAGGCAAAGCCAAATAGATTCA------------------------------------------------------------------------CCC--TTTTCG-AATTGCCAATAATT------------------------------GAACATA
droFic1	scf7180000454144:360272-360465 -			T-----CTTGTTAACAGCTTT-TGCT------------TTTTTT-----TTTACCTCAG--TGGC------TTTTTGCCTGCGCCAAAGATCGTCCA-CTCGTTT------TGATTGTTGTCA-TTGTGTTCTATATAT--TAT---T-T--TATTA-----------------------T--TTTAAGGACGAGCCAATGGTG--TTCGGGGCAGGCAAAGCGAGGCCA-ATAGATTCA------------------------------------------------------------------------CCG--TTTTCAAAATTGCCAATTATT------------------------------GAACA--
droEle1	scf7180000491186:2985986-2986176 -			T-----CTTGTTAACAGCTTT-TGCT------------TTTT-T-----TTTACCTCAG--TGGCT-----GCTGTGCCTGCGCCAAAGACCATCCA-CTCGTTT------TCATTGTTGTAA-TTGTGTTCTAT--AT--TGT---T-T--TATTA--------------------------TTTAAGGACGAGC-AATGGTG-TTTGGGGGCAGGCAAAGCGAAGCCA-ATAGATTCA------------------------------------------------------------------------CCG--TTTTCAAAATTGCCAATTACT------------------------------GAACA--
droRho1	scf7180000779234:260078-260265 +			T-----CTTGTTAACAGCTTT-TGCT------------TTT--T-----TTTACCTCAC--TGGC------TTTTTGCCTGCGCCAAAGATCATTCA-CTCGTTT------TCATTGTTGTAA-TTGTGTTCTAT--AT--TAT---T-T--TATT------------------------T--TTTAAGGACGAGC-AATGGTG--TTAGGGGCAGGCAAAGCGGAGCCA-ATAGATTCA------------------------------------------------------------------------CCG--TTTTCAAAATTGCCAATTACT------------------------------GAACA--
droBia1	scf7180000301468:35129-35329 -			T-----CTTGTTAACAGCTTT-TGCT------------TTT--T-----TTTACCTCAG--CGGCTTGCATTTGCTGCCTGCGCCCAAGATCATCCA-CTCGTTT------TCATTGTTGTCA-TTGTGTTCTATATAT--TAT---T-T--TATTA-----------------------G--TTTAAGGACGAGC-GGAGGTG--TTAGGGGCAGGCAAGGCGAAGCCT-ATAGATTCA------------------------------------------------------------------------AAGTTTTTTCAAAATTGCCAATTACT------------------------------GAACATA
droTak1	scf7180000415667:579347-579537 +			T-----CTTGTTAACAGCTTT-TGCT------------TTT--T-----TTTACCTCAG--CGGC------TTTTTGCCTGCCCCAAAGATCATCCA-CTCGTTT------TGATTGTTGTAA-TTGTGTTCTAT--ATTATAT---T-T--TATTA-----------------------T--TTTAAGGACGAGC-GATGATG--TTCGGAGCAGGCAAGGCAAGGCCT-ATAGATTCA------------------------------------------------------------------------ACG--TTTTCAAAATTGCCAATTACT------------------------------GAACA--
droEug1	scf7180000409554:4977650-4977841 +			T-----CTTGTTAACAGCTTT-TGCT------------TTT--T-----TTTACCTCAG--TGGC------TTTTTGCCTGCGCCAAAGATCATGCA-CTCGATT------TCATTGTTGTAA-TTGTGTTCCAT--ATTTTTT---A-T--TATTA-----------------------T--TTTAAGGGCGAGC-AATGGTG--TTAGGAGCAGGCAAAGCGAAGCCAAATAGATTCA------------------------------------------------------------------------ACG--TTTTCAAAATTGCCAATTACT------------------------------GAACA--
dm3	chr2L:9935027-9935218 -			T-----CTTGTTAACAGCTTT-TGCT------------TTTTTT-----TTTACCTCAG--TGGC------TATTTGCCTGCGACACAGACCATGCA-CTCGTTT------TCATTGTTGTAA-TTGTGTTCTAT--AT--TAT---TTT--TATTA-----------------------T--TTTAAGGACGAGC-TGTGGTG--CTGAGAGCAGGCAAAGCACAGCCA-ATAGATTCA------------------------------------------------------------------------ACG--TTTTCAAAATTGCCAATTACT------------------------------GAACA--
droSim2	2l:9633178-9633370 -			T-----CTTGTTAACAGCTTT-TGCT------------TTTTTTT----TTTACCTCAG--TGGC------TATTTGCCTGCGCCACAGACCATGCA-CTCGTTT------ATATTGTTGTAA-TTGTGTTCTAT--AT--TAT---TTT--TATTA-----------------------T--TTTAAGGACGAGC-TGTGGTG--CTGGGAGCAGGCAAAGCGCAGCCA-ATAGATTCA------------------------------------------------------------------------ACG--TTTTCAAAATTGCCAATTACT------------------------------GAACA--
droSec2	scaffold_3:5381854-5382047 -			T-----CTTGTTAACAGCTTT-TGCT------------TTTTTTTT---TTTACCTCAG--TGGC------TATTTGCCTGCGCCACAGACCATGCA-CTCGTTT------ATATTGTTGTAA-TTGTGTTCTAT--AT--TAT---TTT--TATTA-----------------------T--TTTAAGGACGAGC-TGTGGTG--CTGGGAGCAGGCAAAGCGCAGCCA-ATAGATTCA------------------------------------------------------------------------ACG--TTTTCAAAATTGCCAATTACT------------------------------GAACA--
droYak3	2L:12625727-12625915 -			T-----CTTGTTAACAGCTTT-TGCT------------TTT--T-----TTTACCTCAG--TGGC------TTTTTGCCTGCGCCAAAGACCATGCA-CTCGTTT------TCATTGTTGTAA-TTGTGTTCTAT--AT--TAT---T-T--TATTA-----------------------T--TTTAAGGACGAGC-AATGGTG--TTGGGGGCAGGCAAAGCGCAGCCA-ATAGATTCA------------------------------------------------------------------------ACG--TTTTCAAAATTGCCAATTACT------------------------------GAACA--
droEre2	scaffold_4929:10555277-10555465 -			T-----CTTGTTAACAGCTTT-TGCT------------TTT--T-----TTTACCTCAG--TGGC------TTTTTGCCTGCGCCAAAGACCATGCA-CTCGTTT------TAATTGTTGTAA-TTGTGTTCTAT--AT--TAG---T-T--TATTA-----------------------T--TTTAAAGACGAGC-AATGGTG--TTGGGTGCAGGCAATGCGTAGCCA-ATAGATTCA------------------------------------------------------------------------ACG--TTTTCGAAATTGCCAATTACT------------------------------GAACA--

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droPer2

T-----CTTGTTAACAGCTTT-TGCT------------TTTTTG-----TTTACCTCAC--TCGC------AATTTGTCTGTACTTAAAACCATTTG-TTCGTTT------TTATTGTTCTTA-TTGTGTTTATT--AT--TAT---T-G--CAT-------------------------T--TTTAATGACGAACTGATGGTT--TAAAGTACAAGCAAAGTGCA-------AGTTTCA------------------------------------------------------------------------CCT--TTTTCGAAATTGCCAATTATT--------------------------ATGAAAATA--	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
.................................................................................TACTTAAAACCATTTG-TTCGTT...............................................................................................................................................................................................................................................................................	22	1	31.00	31	1	14	2	7	6	1
.................................................................................TACTTAAAACCATTTG-TTCGT................................................................................................................................................................................................................................................................................	21	1	7.00	7	1	2	0	0	4	0
.................................................................................TACTTAAAACCATTTG-TTCGTTT------........................................................................................................................................................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0

dp5

T-----CTTGTTAACAGCTTT-TGCT------------TTTTTG-----TTTACCTCAC--TCGC------AATTTGTCTGTACTTAAAACCATTTG-TTCGTTT------TTATTGTTCTTA-TTGTGTTTATT--AT--TAT---T-G--CAT-------------------------T--TTTAATGACGAACTGATGGTT--TAAAGTACAAGCAAAGTGCA-------AGTTTCA------------------------------------------------------------------------CCT--TTTTCGAAATTGCCAATTATT--------------------------ATGAAAATA--	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
.................................................................................TACTTAAAACCATTTG-TTCGTT...............................................................................................................................................................................................................................................................................	22	1	111.00	111	0	59	12	2	12	4	18	2	0	2
.................................................................................TACTTAAAACCATTTG-TTCGT................................................................................................................................................................................................................................................................................	21	1	7.00	7	0	4	1	1	1	0	0	0	0	0
.................................................................................TACTTAAAACCATTTG-TTCGTTA------........................................................................................................................................................................................................................................................................	23	1	3.00	3	0	3	0	0	0	0	0	0	0	0
.................................................................................TACTTAAAACCATTTG-TTCG.................................................................................................................................................................................................................................................................................	20	1	2.00	2	0	2	0	0	0	0	0	0	0	0
.................................................................................TACTTAAAACCATTTG-TTCGTTA------AA......................................................................................................................................................................................................................................................................	25	1	2.00	2	0	2	0	0	0	0	0	0	0	0
.............................................................................................................................................................................................GACGAACTGATGGTT--TAAAGTAC.................................................................................................................................................................	23	1	2.00	2	0	0	1	1	0	0	0	0	0	0
.................................................................................TACTTAAAACCATTTG-TTCGC................................................................................................................................................................................................................................................................................	21	1	2.00	2	0	0	0	2	0	0	0	0	0	0
..................................................................................ACTTAAAACCATTTG-TTCGTT...............................................................................................................................................................................................................................................................................	21	1	2.00	2	0	2	0	0	0	0	0	0	0	0
.........................................................................................................................................................AT-------------------------T--TTTAATGACGAACTGATGGT............................................................................................................................................................................	23	1	2.00	2	0	2	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................ACTGATGGTT--TAAAGTACAAGC.............................................................................................................................................................	22	1	1.00	1	0	0	1	0	0	0	0	0	0	0
...............................................................................................................................................................................................CGAACTGATGGTT--TAAAGTACA................................................................................................................................................................	22	1	1.00	1	0	1	0	0	0	0	0	0	0	0
............................................................................GTCTGTACTTAAAACCATTT.......................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0	0	0	0	0
........................................................................ATTTGTCTGTACTTAAAACCATT........................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0	0	0	0	0
...............................................................................................................................................................................................CGAACTGATGGTT--TAAAGT...................................................................................................................................................................	19	1	1.00	1	0	1	0	0	0	0	0	0	0	0
...........................................................................................................................................................................................ATGACGAACTGATGGTT--TAAAGT...................................................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.........................................................................................................................................................AT-------------------------T--TTTAATGACGAACTGATG..............................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	1	0	0	0
...............................................................................TGTACTTAAAACCATTTG-TTCG.................................................................................................................................................................................................................................................................................	22	1	1.00	1	0	1	0	0	0	0	0	0	0	0
....................................................ACCTCAC--TCGC------AATTTGTCTG......................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	1	0	0	0	0	0	0	0
.............................................................................TCTGTACTTAAAACCATTTG-TTCGTTT------T.......................................................................................................................................................................................................................................................................	28	1	1.00	1	0	0	1	0	0	0	0	0	0	0
.......................................................................AATTTGTCTGTACTTAAAACCA..........................................................................................................................................................................................................................................................................................	22	1	1.00	1	0	1	0	0	0	0	0	0	0	0
................................................................................GTACTTAAAACCATTTG-TTCGTT...............................................................................................................................................................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.................................................................................TACTTAAAACCATTTG-TTCGTTT------........................................................................................................................................................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0	0	0	0	0
...................................................................................CTTAAAACCATTTG-TTCGTT...............................................................................................................................................................................................................................................................................	20	1	1.00	1	0	0	0	0	0	0	1	0	0	0
.................................................................................TACTTAAAACCATTTG-TTCGTC...............................................................................................................................................................................................................................................................................	22	1	1.00	1	0	0	1	0	0	0	0	0	0	0

droWil2

C-----CTTGTTAATAGCTTTTTGCT------------TT---------TTTACCTCAT--CAAC------ACTTTGATTGTAATTGAAACTGTTTAAAGCATTT------CCCTTGTTGTCAATAGTGTTCA-T--TT--TCTTTTT-T--TACTTAATTTAATTTAATTATTTTTTGCA--TATAACGCTTAAC-GTGGTCG--TCAAAAGCAATCAAAGTGTTTTTG---GGGTTCT---ACGTTTTCATTGTA-TACATATATATTTATAC--------------------TATTATAAAATAGTTTAAATTTTTTTCAAAATTGCCAATTATT--------------------------C---GGACA--	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
................................................................................................................................................................................................................................TTTTTG---GGGTTCT---ACGTTTT.............................................................................................................................	20	1	1.00	1	0	0	0	0	1
..........................................................T--CAAC------ACTTTGATTGTAATTGAAACTGT.........................................................................................................................................................................................................................................................................................	28	1	1.00	1	1	0	0	0	0
.......................................T---------TTTACCTCAT--CAAC------ACTTTGATT.......................................................................................................................................................................................................................................................................................................	24	1	1.00	1	0	1	0	0	0
................................................................................GTAATTGAAACTGTTTAAAGC..................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	1	0

droVir3

T-----TTTTTTG----GTTT-TATT------------TTTTTTCT---TAAACCACGTTTTGTC------GCCTTGCTTGCGATTAAAAGCAGTCGAACGGGTT------TCATTGTTGTAA-TTATATTTTAT--TT--------------GT-T-----------------------T--TTGAAAAGCGTTT-GATTGTT--TTGAATGCAAGCAAGGTGTTATTA----GGTTGACCCATGTTTTTAACATACTACATACACATGCAGACATCCAGACAGGCAAACATAAATTTATAAAC-------------------TAGTTTTGTTTATTGAATGAAAAACAAATGGCCAACTTCTT---CGATTTA	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
.....................................................................................TAAAAGCAGTCGAACGGGTT------TC......................................................................................................................................................................................................................................................................	22	1	5.00	5	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
....................................................................................................................................................................................................................................TA----GGTTGACCCATGTTTTTAACATAC.....................................................................................................................	26	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	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.....................................................................................TAAAAGCAGTCGAACGGGTT------TCA.....................................................................................................................................................................................................................................................................	23	1	3.00	3	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	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
.......................................................................................................................................................................................................................................................TTTTAACATACTACATACACATGCAGA.....................................................................................................	27	1	2.00	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..................................................................................GATTAAAAGCAGTCGAAC...................................................................................................................................................................................................................................................................................	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	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
.............................................T---TAAACCACGTTTTGTC------GCCTTG..........................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...................................................AACCACGTTTTGTC------GCC.............................................................................................................................................................................................................................................................................................................	17	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.......................................TTTTTCT---TAAACCACGTTTTGTC------GCCT............................................................................................................................................................................................................................................................................................................	27	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..............................................................................TTGCGATTAAAAGCAGTCGAACGGG................................................................................................................................................................................................................................................................................	25	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	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
.........................................................................................................................................................................................................................................................TTAACATACTACATACACATGC........................................................................................................	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
............................................................................................................................................................................................AAGCGTTT-GATTGTT--TTGAAT...................................................................................................................................................................	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	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
..............................................................................TTGCGATTAAAAGCAGTCGAACGGGT...............................................................................................................................................................................................................................................................................	26	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
......................................TTTTTTCT---TAAACCACGTTTTGTC------GCCT............................................................................................................................................................................................................................................................................................................	28	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	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
...........................................................................................................................................................................................................................AGGTGTTATTA----GGTTGACCCATGTT...............................................................................................................................	25	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	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
..........................................TTCT---TAAACCACGTTTTGT.......................................................................................................................................................................................................................................................................................................................	19	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
...........................................TCT---TAAACCACGTTTTGTC------GCCTTGCT........................................................................................................................................................................................................................................................................................................	27	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	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
.................................................................................................................................................................................................................................................CCATGTTTTTAACATACTACATACA.............................................................................................................	25	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.....................................................................................TAAAAGCAGTCGAACGGGTT------TCAA....................................................................................................................................................................................................................................................................	24	1	1.00	1	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
...............................................................................TGCGATTAAAAGCAGTCGAACGGG................................................................................................................................................................................................................................................................................	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	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
......................................................................................................................................................................................................................................................................TACACATGCAGACATCCAGACAG..........................................................................................	23	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	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
...............................................................................................................................................................................................................................GTTATTA----GGTTGACCCATGT................................................................................................................................	20	1	1.00	1	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
............................................................................................................................................................T-----------------------T--TTGAAAAGCGTTT-GATT..............................................................................................................................................................................	19	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
...................................................................................................................................................................................................................TGCAAGCAAGGTGTTATTA----GG...........................................................................................................................................	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	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
.....................................................................................TAAAAGCAGTCGAACGGGTT------T.......................................................................................................................................................................................................................................................................	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	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
............................................................................................................................................................................................AAGCGTTT-GATTGTT--.........................................................................................................................................................................	15	2	0.50	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................................................................................................................................................................................AAGCGTTT-GATTGTT--C........................................................................................................................................................................	16	16	0.06	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	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droMoj3

TTCTGCCTTGTTGACAGCTTTGTGCTTTTCATTTTCTTACATTTGT---TTGATCACGAATTGGC------GCTTTGCTTGCGCTTAAAACTAATTGAACGGGTT------TCATTGTTGTAG-TTATATATTTT--AT--TTG---TTTAATTTTA-----------------------TTTTTGAAATGCGTTC-AATAGAGGTTTGCCAGCAAGCAAGGTGC------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
.................................................................................................................ATTGTTGTAG-TTATATATTTT--AT--TT........................................................................................................................................................................................................................................	25	1	1.00	1	0	0	0	0	0	1

droGri2

T-----CTTGTTAACAGCTTT-TGCT------------CTTTTT-----TTTACCTCGATTCAGC------GCTTTGCTTGCGCTTAAAGCCATTTAAACGGGTT------TCATTGTTGTAA-TTATATTATAT--TT--TAT---T-T---GT-T-----------------------T--TTGAAGTGCGTTT-AATAGTT--TTGGATGCAAGCAAGGTG-------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

droAna3

T-----CTTGTTAACAGCTTT-TGCT------------TTTTTTTTTTATGTACCTCAG--AGGCG----TTTTTTGTGTGTGCCTAAGACTAC-CG-CCCGGTT------TGCTTGTTGTAA-TTGTGTGTTT-GTAT--TAT---TTT--TATTA-----------------------TTTTTTAAGAACTGGC-GGAAGTT--TTAGGGGCAGACAAAGCTATGCCA-ACAGATTCA------------------------------------------------------------------------ACT--TTTTCAAAATTGCCAACTTGT------------------------------GAACA--	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
................................................................................................................................................................................................TGGC-GGAAGTT--TTAGGGGCAG...............................................................................................................................................................	21	1	127.00	127	57	1	0	7	5	57
................................................................................................................................................................................................TGGC-GGAAGTT--TTAGGGGCAGA..............................................................................................................................................................	22	1	100.00	100	28	5	1	10	12	44
...............................................................................................................................................................................................CTGGC-GGAAGTT--TTAGGGGCAG...............................................................................................................................................................	22	1	45.00	45	24	2	0	4	2	13
...............................................................................TGTGCCTAAGACTAC-CG-CCCGG................................................................................................................................................................................................................................................................................	22	1	42.00	42	41	1	0	0	0	0
................................................................................................................................................................................................TGGC-GGAAGTT--TTAGGGGCA................................................................................................................................................................	20	1	30.00	30	6	0	0	4	5	15
...............................................................................................................................................................................................CTGGC-GGAAGTT--TTAGGGGCAGA..............................................................................................................................................................	23	1	30.00	30	11	2	0	2	5	10
...............................................................................TGTGCCTAAGACTAC-CG-CCCGGT...............................................................................................................................................................................................................................................................................	23	1	24.00	24	21	3	0	0	0	0
...............................................................................................................................................................................................CTGGC-GGAAGTT--TTAGGGGCA................................................................................................................................................................	21	1	18.00	18	5	0	0	1	2	10
................................................................................................................................................................................................TGGC-GGAAGTT--TTAGGGGCAGT..............................................................................................................................................................	22	1	17.00	17	6	0	1	0	0	10
...............................................................................TGTGCCTAAGACTAC-CG-CCCGGTT------........................................................................................................................................................................................................................................................................	24	1	17.00	17	16	1	0	0	0	0
...............................................................................TGTGCCTAAGACTAC-CG-CCCG.................................................................................................................................................................................................................................................................................	21	1	13.00	13	11	0	0	0	0	2
...............................................................................................................................................................................................CTGGC-GGAAGTT--TTAGGGGC.................................................................................................................................................................	20	1	8.00	8	2	0	0	0	0	6
................................................................................................................................................................................................TGGC-GGAAGTT--TTAGGGGC.................................................................................................................................................................	19	1	7.00	7	2	0	0	1	1	3
...............................................................................TGTGCCTAAGACTAC-CG-CC...................................................................................................................................................................................................................................................................................	19	1	7.00	7	7	0	0	0	0	0
................................................................................................................................................................................................TGGC-GGAAGTT--TTAGGGGCAGAT.............................................................................................................................................................	23	1	7.00	7	2	0	0	1	1	3
................................................................................................................................................................................................TGGC-GGAAGTT--TTAGGGG..................................................................................................................................................................	18	1	6.00	6	4	0	0	0	0	2
................................................................................GTGCCTAAGACTAC-CG-CCCGGT...............................................................................................................................................................................................................................................................................	22	1	5.00	5	5	0	0	0	0	0
................................................................................GTGCCTAAGACTAC-CG-CCCGG................................................................................................................................................................................................................................................................................	21	1	4.00	4	4	0	0	0	0	0
...............................................................................TGTGCCTAAGACTAC-CG-CCC..................................................................................................................................................................................................................................................................................	20	1	4.00	4	4	0	0	0	0	0
...............................................................................................................................................................................................CTGGC-GGAAGTT--TTAGGGGCAGT..............................................................................................................................................................	23	1	4.00	4	1	0	0	2	1	0
.................................................................................TGCCTAAGACTAC-CG-CCCGGTT------........................................................................................................................................................................................................................................................................	22	1	4.00	4	3	1	0	0	0	0
................................................................................................................................................................................................TGGC-GGAAGTT--TTAGGGGT.................................................................................................................................................................	19	1	3.00	3	1	0	0	0	1	1
................................................................................................................................................................................................TGGC-GGAAGTT--TTAGGGGCAGTT.............................................................................................................................................................	23	3	3.00	9	3	0	0	1	2	3
.................................................................................................................................................................................................GGC-GGAAGTT--TTAGGGGCAGA..............................................................................................................................................................	21	1	3.00	3	3	0	0	0	0	0
...............................................................................................................................................................................................CTGGC-GGAAGTT--TTAGGG...................................................................................................................................................................	18	1	2.00	2	1	0	0	0	1	0
...............................................................................................................................................................................................CTGGC-GGAAGTT--TTAGGGG..................................................................................................................................................................	19	1	2.00	2	0	0	0	1	1	0
................................................................................................................................................................................................TGGC-GGAAGTT--TTAGGGGCAGAA.............................................................................................................................................................	23	1	2.00	2	2	0	0	0	0	0
................................................................................................................................................................................................TGGC-GGAAGTT--TTAGGGGCAT...............................................................................................................................................................	21	1	2.00	2	0	0	0	0	1	1
...............................................................................TGTGCCTAAGACTAC-CG-CCCGGTT------A.......................................................................................................................................................................................................................................................................	25	1	2.00	2	2	0	0	0	0	0
.................................................................................................................................................................................................GGC-GGAAGTT--TTAGGGGCAG...............................................................................................................................................................	20	1	2.00	2	2	0	0	0	0	0
.................................................................................TGCCTAAGACTAC-CG-CCCGG................................................................................................................................................................................................................................................................................	20	1	2.00	2	2	0	0	0	0	0
...............................................................................................................................................................................................CTGGC-GGAAGTT--TTAGGGGCAGAT.............................................................................................................................................................	24	1	1.00	1	0	0	0	0	1	0
...............................................................................TGTGCCTAAGACTAC-CG-CCCT.................................................................................................................................................................................................................................................................................	21	1	1.00	1	1	0	0	0	0	0
................................................ATGTACCTCAG--AGGCG----TTTTTTGTGT.......................................................................................................................................................................................................................................................................................................	26	1	1.00	1	0	0	0	0	1	0
...............................................................................................................................................................................................CTGGC-GGAAGTT--TTAGGGGT.................................................................................................................................................................	20	1	1.00	1	0	0	0	0	0	1
................................................................................................................................................................................................TGGC-GGAAGTT--TTAGGGGCAC...............................................................................................................................................................	21	1	1.00	1	0	0	0	0	1	0
................................................................................................................................................................................................TGGC-GGAAGTT--TTAGGGGCAGGT.............................................................................................................................................................	23	1	1.00	1	0	0	0	1	0	0
...............................................................................................................................................................................................CTGGC-GGAAGTT--TTAGGGGCAT...............................................................................................................................................................	22	1	1.00	1	1	0	0	0	0	0
...............................................................................................................TGCTTGTTGTAA-TTGTGTGT...................................................................................................................................................................................................................................................	20	1	1.00	1	0	0	0	1	0	0
...............................................................................................................................................................................................CTGGC-GGAAGTT--TTAGGT...................................................................................................................................................................	18	1	1.00	1	1	0	0	0	0	0
...............................................................................TGTGCCTAAGACTAC-CG-CCCGGTT------T.......................................................................................................................................................................................................................................................................	25	1	1.00	1	1	0	0	0	0	0
..................................................GTACCTCAG--AGGCG----TTTTTTGTG........................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	1
................................................................................GTGCCTAAGACTAC-CG-CCCG.................................................................................................................................................................................................................................................................................	20	1	1.00	1	1	0	0	0	0	0
................................................................................GTGCCTAAGACTAC-CG-CCCGGTT------........................................................................................................................................................................................................................................................................	23	1	1.00	1	1	0	0	0	0	0
.................................................................................................................................................................................................GGC-GGAAGTT--TTAGGGGC.................................................................................................................................................................	18	1	1.00	1	1	0	0	0	0	0
..................................................................................................................................................................................................GC-GGAAGTT--TTAGGGGCAGATTT...........................................................................................................................................................	23	1	1.00	1	1	0	0	0	0	0
.............................................................................TGTGTGCCTAAGACTAC-CG-CCC..................................................................................................................................................................................................................................................................................	22	1	1.00	1	1	0	0	0	0	0
...............................................................................TGTGCCTAAGACTAC-CG-CA...................................................................................................................................................................................................................................................................................	19	1	1.00	1	1	0	0	0	0	0
...............................................................................................................................................................................................CTGGC-GGAAGTT--TTAGGGGCT................................................................................................................................................................	21	1	1.00	1	1	0	0	0	0	0
................................................................................................................................................................................................TGGC-GGAAGTT--TTAGGGGCAGTAT............................................................................................................................................................	24	1	1.00	1	0	0	0	0	1	0
..................................................................................GCCTAAGACTAC-CG-CCCGGTT------........................................................................................................................................................................................................................................................................	21	1	1.00	1	1	0	0	0	0	0
...............................................................................................................................................................................................CTGGC-GGAAGTT--TTAGGGGCATT..............................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	1
................................................................................................................................................................................................TGGC-GGAAGTT--TTAGGGGCAGATTT...........................................................................................................................................................	25	1	1.00	1	0	0	0	0	0	1
...............................................................................................................................................................................................CTGGC-GGAAGTT--TTAGGGGCAGTA.............................................................................................................................................................	24	1	1.00	1	0	0	0	1	0	0
...............................................................................TGTGCCTAAGACTAC-CG-CCCGGTA------........................................................................................................................................................................................................................................................................	24	1	1.00	1	0	1	0	0	0	0
................................................................................................................................................................................................TGGC-GGAAGTT--TTAGGGGCAGTTT............................................................................................................................................................	24	4	0.50	2	0	0	0	0	0	2
...............................................................................................................................................................................................CTGGC-GGAAGTT--TTAGGGGCAGTTT............................................................................................................................................................	25	3	0.33	1	0	0	0	0	0	1

droBip1

T-----CTTGTTAACAGCTTT-TGCT------------TTTTTT-----TGTACCTCAT--AGGC------CCTTTGTTTGCGCCCAAGACTACCTC-CCCGATT------TGCTTGTTGTCA-TTGTGTTCTTT-TAT--TAT---T-T--TATTTTTTTTT-----------------G--TTTAAGTACGGGC-GGCAGTT--TTTAGCGCAGACAAA-------------GATTCA------------------------------------------------------------------------AGT-TTTTTCAAAATTGCCAATTTAT------------------------------GAAGA--	Size	Hit Count	Total Norm	Total
No Reads

droKik1

T-----CTTGTTAACTGCTTT-TGCT------------TATT-T-----TATACCTCAC--TGGCCCC---TGTTTGTCTGTGCCTAAGATCATCGC-GTCGCCTTGATTATCATTGTTGTCA-TTGTGTTGTGT--AT--TAT---T-T--TAGTT-----------------------T--TTTAAGGACGAAC-GATAATG--TTAGGTGCAGGCAAGGCAAAGCCAAATAGATTCA------------------------------------------------------------------------CCC--TTTTCG-AATTGCCAATAATT------------------------------GAACATA	Size	Hit Count	Total Norm	Total
No Reads

droFic1

T-----CTTGTTAACAGCTTT-TGCT------------TTTTTT-----TTTACCTCAG--TGGC------TTTTTGCCTGCGCCAAAGATCGTCCA-CTCGTTT------TGATTGTTGTCA-TTGTGTTCTATATAT--TAT---T-T--TATTA-----------------------T--TTTAAGGACGAGCCAATGGTG--TTCGGGGCAGGCAAAGCGAGGCCA-ATAGATTCA------------------------------------------------------------------------CCG--TTTTCAAAATTGCCAATTATT------------------------------GAACA--	Size	Hit Count	Total Norm	Total
No Reads

droEle1

T-----CTTGTTAACAGCTTT-TGCT------------TTTT-T-----TTTACCTCAG--TGGCT-----GCTGTGCCTGCGCCAAAGACCATCCA-CTCGTTT------TCATTGTTGTAA-TTGTGTTCTAT--AT--TGT---T-T--TATTA--------------------------TTTAAGGACGAGC-AATGGTG-TTTGGGGGCAGGCAAAGCGAAGCCA-ATAGATTCA------------------------------------------------------------------------CCG--TTTTCAAAATTGCCAATTACT------------------------------GAACA--	Size	Hit Count	Total Norm	Total
No Reads

droRho1

T-----CTTGTTAACAGCTTT-TGCT------------TTT--T-----TTTACCTCAC--TGGC------TTTTTGCCTGCGCCAAAGATCATTCA-CTCGTTT------TCATTGTTGTAA-TTGTGTTCTAT--AT--TAT---T-T--TATT------------------------T--TTTAAGGACGAGC-AATGGTG--TTAGGGGCAGGCAAAGCGGAGCCA-ATAGATTCA------------------------------------------------------------------------CCG--TTTTCAAAATTGCCAATTACT------------------------------GAACA--	Size	Hit Count	Total Norm	Total
No Reads

droBia1

T-----CTTGTTAACAGCTTT-TGCT------------TTT--T-----TTTACCTCAG--CGGCTTGCATTTGCTGCCTGCGCCCAAGATCATCCA-CTCGTTT------TCATTGTTGTCA-TTGTGTTCTATATAT--TAT---T-T--TATTA-----------------------G--TTTAAGGACGAGC-GGAGGTG--TTAGGGGCAGGCAAGGCGAAGCCT-ATAGATTCA------------------------------------------------------------------------AAGTTTTTTCAAAATTGCCAATTACT------------------------------GAACATA	Size	Hit Count	Total Norm	Total
No Reads

droTak1

T-----CTTGTTAACAGCTTT-TGCT------------TTT--T-----TTTACCTCAG--CGGC------TTTTTGCCTGCCCCAAAGATCATCCA-CTCGTTT------TGATTGTTGTAA-TTGTGTTCTAT--ATTATAT---T-T--TATTA-----------------------T--TTTAAGGACGAGC-GATGATG--TTCGGAGCAGGCAAGGCAAGGCCT-ATAGATTCA------------------------------------------------------------------------ACG--TTTTCAAAATTGCCAATTACT------------------------------GAACA--	Size	Hit Count	Total Norm	Total
No Reads

droEug1

T-----CTTGTTAACAGCTTT-TGCT------------TTT--T-----TTTACCTCAG--TGGC------TTTTTGCCTGCGCCAAAGATCATGCA-CTCGATT------TCATTGTTGTAA-TTGTGTTCCAT--ATTTTTT---A-T--TATTA-----------------------T--TTTAAGGGCGAGC-AATGGTG--TTAGGAGCAGGCAAAGCGAAGCCAAATAGATTCA------------------------------------------------------------------------ACG--TTTTCAAAATTGCCAATTACT------------------------------GAACA--	Size	Hit Count	Total Norm	Total
No Reads

dm3

T-----CTTGTTAACAGCTTT-TGCT------------TTTTTT-----TTTACCTCAG--TGGC------TATTTGCCTGCGACACAGACCATGCA-CTCGTTT------TCATTGTTGTAA-TTGTGTTCTAT--AT--TAT---TTT--TATTA-----------------------T--TTTAAGGACGAGC-TGTGGTG--CTGAGAGCAGGCAAAGCACAGCCA-ATAGATTCA------------------------------------------------------------------------ACG--TTTTCAAAATTGCCAATTACT------------------------------GAACA--	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
..........................................................................................................................................................TTA-----------------------T--TTTAAGGACGAGC-TGTGGTG--C........................................................................................................................................................................	25	1	22.00	22	0	0	0	0	0	0	0	0	0	0	0	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	3	0	0	0	0	0	0	0	0	0	1	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	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	1	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	3	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	3	0	0	0	0	0
....................................................................................................................................................................................T--TTTAAGGACGAGC-TGTGGTG--CTGA.....................................................................................................................................................................	25	1	12.00	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	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	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	1	0	1	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	3	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0
..........................................................................................................................................................................................................TG--CTGAGAGCAGGCAAAGCACAGCCA-A...............................................................................................................................................	27	1	11.00	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	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	2	2	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	1	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	2	0	0	0	0	0
...........................................................................................................................................................TA-----------------------T--TTTAAGGACGAGC-TGTGGTG--CT.......................................................................................................................................................................	25	1	11.00	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	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	1	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	1	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
........................................................................................................................................................................................TTAAGGACGAGC-TGTGGTG--CTGA.....................................................................................................................................................................	23	1	11.00	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	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	8	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.........................................................................................................................................................ATTA-----------------------T--TTTAAGGACGAGC-TGTGGTG--C........................................................................................................................................................................	26	1	10.00	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	2	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	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	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
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................................................................................................................................................................................................GAGC-TGTGGTG--CTGAGAGC.................................................................................................................................................................	19	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	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	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	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
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...........................................................................................................................................................TA-----------------------T--TTTAAGGACGAGC-TGTGGTG--C........................................................................................................................................................................	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	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	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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................................................................C------TATTTGCCTGCGACACA...............................................................................................................................................................................................................................................................................................	18	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
............................................................................................................................................................A-----------------------T--TTTAAGGACGAGC-TGTGGT............................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
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...................................................................................................................................................................................................C-TGTGGTG--CTGAGAGCAGGC.............................................................................................................................................................	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
.................................................................................................................ATTGTTGTAA-TTGTGTTCTAT--AT--TAT---T...................................................................................................................................................................................................................................	27	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
......................................................................................................................................T--AT--TAT---TTT--TATTA-----------------------T--TTTAAGGACGAGC-..................................................................................................................................................................................	28	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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

droSim2

T-----CTTGTTAACAGCTTT-TGCT------------TTTTTTT----TTTACCTCAG--TGGC------TATTTGCCTGCGCCACAGACCATGCA-CTCGTTT------ATATTGTTGTAA-TTGTGTTCTAT--AT--TAT---TTT--TATTA-----------------------T--TTTAAGGACGAGC-TGTGGTG--CTGGGAGCAGGCAAAGCGCAGCCA-ATAGATTCA------------------------------------------------------------------------ACG--TTTTCAAAATTGCCAATTACT------------------------------GAACA--	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
..........................................................................................................................................................TTA-----------------------T--TTTAAGGACGAGC-TGTGGTG--CT.......................................................................................................................................................................	26	1	3.00	3	0	0	0	0	0	0	2	1	0	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................................TGTGGTG--CTGGGAGCAGGCAAAGCG.......................................................................................................................................................	25	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
.................................................................................CGCCACAGACCATGCA-CTC..................................................................................................................................................................................................................................................................................	19	1	1.00	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0
....................................................................................................................................................................................T--TTTAAGGACGAGC-TGTGGTG--CTGGG....................................................................................................................................................................	26	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
..........................................................................................................................................................TTA-----------------------T--TTTAAGGACGAGC-TGTGGTG--C........................................................................................................................................................................	25	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
...............................................................................................................................................T---TTT--TATTA-----------------------T--TTTAAGGACGAGC-TGT...............................................................................................................................................................................	26	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
.................................................TTTACCTCAG--TGGC------TATTTGCCTG......................................................................................................................................................................................................................................................................................................	24	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
T-----CTTGTTAACAGCTTT-TGC..............................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
........................................................................................................................................................................................TTAAGGACGAGC-TGTGGTG--CTGGGA...................................................................................................................................................................	25	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
..............................................................................................................................................................................................ACGAGC-TGTGGTG--CTGGGAGCAGGCAA...........................................................................................................................................................	27	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
....................................................................................................................................................................................T--TTTAAGGACGAGC-TGTGGTG--CT.......................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0

droSec2

T-----CTTGTTAACAGCTTT-TGCT------------TTTTTTTT---TTTACCTCAG--TGGC------TATTTGCCTGCGCCACAGACCATGCA-CTCGTTT------ATATTGTTGTAA-TTGTGTTCTAT--AT--TAT---TTT--TATTA-----------------------T--TTTAAGGACGAGC-TGTGGTG--CTGGGAGCAGGCAAAGCGCAGCCA-ATAGATTCA------------------------------------------------------------------------ACG--TTTTCAAAATTGCCAATTACT------------------------------GAACA--	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
...............................................................................................CA-CTCGTTT------ATATTGTTGTA.............................................................................................................................................................................................................................................................	20	1	1.00	1	0	0	0	1
.............................................................................................................................................................................................GACGAGC-TGTGGTG--CTGGGAGCAGGC.............................................................................................................................................................	26	1	1.00	1	0	0	1	0
.................................................................................................................................................................................................AGC-TGTGGTG--CTGGGAGCAGG..............................................................................................................................................................	21	1	1.00	1	0	1	0	0
.......................................................................................................TT------ATATTGTTGTAA-TTGTGTT....................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	1	0
.....................................................................................................................................................................................................TGTGGTG--CTGGGAGCAGG..............................................................................................................................................................	18	1	1.00	1	0	0	0	1
...........................................................................................................................................................................................................G--CTGGGAGCAGGCAAAGC........................................................................................................................................................	18	1	1.00	1	0	0	1	0
..................................................TTACCTCAG--TGGC------TATTTGCCTG......................................................................................................................................................................................................................................................................................................	23	1	1.00	1	1	0	0	0

droYak3

T-----CTTGTTAACAGCTTT-TGCT------------TTT--T-----TTTACCTCAG--TGGC------TTTTTGCCTGCGCCAAAGACCATGCA-CTCGTTT------TCATTGTTGTAA-TTGTGTTCTAT--AT--TAT---T-T--TATTA-----------------------T--TTTAAGGACGAGC-AATGGTG--TTGGGGGCAGGCAAAGCGCAGCCA-ATAGATTCA------------------------------------------------------------------------ACG--TTTTCAAAATTGCCAATTACT------------------------------GAACA--	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
.................................................................................................................................................................................................AGC-AATGGTG--TTGGGGGCAGGCA............................................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
..............................................................................................................................................AT---T-T--TATTA-----------------------T--TTTAAGGACGAG....................................................................................................................................................................................	22	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
.............................................................................................................................................................................................GACGAGC-AATGGTG--TTGGGGGCA................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
.............................................................................................................................................................................................GACGAGC-AATGGTG--TTGGGG...................................................................................................................................................................	20	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0

droEre2

T-----CTTGTTAACAGCTTT-TGCT------------TTT--T-----TTTACCTCAG--TGGC------TTTTTGCCTGCGCCAAAGACCATGCA-CTCGTTT------TAATTGTTGTAA-TTGTGTTCTAT--AT--TAG---T-T--TATTA-----------------------T--TTTAAAGACGAGC-AATGGTG--TTGGGTGCAGGCAATGCGTAGCCA-ATAGATTCA------------------------------------------------------------------------ACG--TTTTCGAAATTGCCAATTACT------------------------------GAACA--	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
.............................................................................................................................................................................................GACGAGC-AATGGTG--TTGGGTGCAGGC.............................................................................................................................................................	26	1	2.00	2	0	0	0	0	1	1	0
.............................................................................................................................................................................................GACGAGC-AATGGTG--TTGG.....................................................................................................................................................................	18	1	1.00	1	0	0	0	1	0	0	0
...............................................................................................................................................................................................CGAGC-AATGGTG--TTGGGTGC.................................................................................................................................................................	20	1	1.00	1	0	0	0	0	0	1	0
.................................................................................................................................................................................................................................AGCCA-ATAGATTCA------------------------------------------------------------------------ACG--TT........................................................	19	1	1.00	1	0	0	0	0	1	0	0
...............................................................................................................................................................................................CGAGC-AATGGTG--TTGGGTGCA................................................................................................................................................................	21	1	1.00	1	1	0	0	0	0	0	0
...............................................................................................................................................................................................CGAGC-AATGGTG--TTGGGTGCAG...............................................................................................................................................................	22	1	1.00	1	0	0	0	0	1	0	0
.........................................................................................................................................................................................TAAAGACGAGC-AATGGTG--TTGGGTGCA................................................................................................................................................................	27	1	1.00	1	0	0	0	0	0	1	0
.................................................................................................................................................................................................AGC-AATGGTG--TTGGGTGCAGGT.............................................................................................................................................................	22	1	1.00	1	0	0	0	0	1	0	0
........................................................................................................................................................................................................GGTG--TTGGGTGCAGGCAATGCGT......................................................................................................................................................	23	1	1.00	1	0	0	0	0	1	0	0

dpe_322

scaffold_1:1709259-1709346 +

candidate-rescued

Canonical miRNA

intergenic

Predicted structure

Flybase annnotation

Sense Strand Reads

Anti-sense strand reads

Re-alignment of all predicted orthologs

Re-alignment of all predicted orthologs with sRNA reads

-35.9	-35.6	-35.5