dvi_4599

Name	Class	Family	Strand
Helitron-2N1_DVir	RC	Helitron	-

##################################################--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- GTTCGCAGTGCTATCAAGTATTGGGTGGAGCGTCACAAGCACGTCGTCCGGTGAGCTAAAACTCAAATACAGTTTGTGTTTAACACGAAAATTAAACAACAAGAAAGCTAGGGCACAATATGTGTGTGTGTGTGCATTCTCCGACCCCATAAAGTATATATATATGAACAGTATCAACAGTCGACTCGATATAGCCATGTCCGTCTGTCTTTAAGAAAATAAAATTGTATTCAAAACTTTTTTGTTTTTCA ************************************************(((.((((...(((........(((((((((((........)))))).))))).......)))((((...))))(((((((((((..................)))))))))))(((......)))...((((...)))).)))))))...************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	SRR060680 9xArg_testes_total	M047 female body	SRR060683 160_testes_total
.........................................................................................................................................................................................TCGAAATAGCCATGTCCGTCAGTCTT........................................	26	2	5	0.20	1	1	0	0
..................................................................................................................................................................................................CCATGTCCGTCTGTCTTCA......................................	19	1	7	0.14	1	0	1	0
........................................................................................................................................................................................CTCGATATAGCCATGTCCGTCTGTC..........................................	25	0	7	0.14	1	0	0	1

Species	Coordinate	ID	Alignment
droVir3	scaffold_12855:9983610-9983860 -	dvi_4599	GTTCGCAGTGCTATCAAGTATTGGGTGGAGCGTCAC---AAGCACGTCGTCCGGTGAGCTAAAACTCAAATACAGTTTG-----------T--GTT--TAACACGAAAATTAAACAACA-------------------------------AGAAAG------------------------------------------CT----AGGGCACAATATGT-----------GTGTGTGTGTGC-----------------ATTCTCCGACCCCATAAAGTATATAT--------AT--ATGAACAGTATCAACAGTCGACTCGATATAGCCATGTCCGTCTGTCTTTAAGAAAAT--------AAAAT--------------------------TGTA--TTCAAAACTTTTTTGTTTTTCA
droMoj3	scaffold_6500:24611796-24611943 +		C----------------AAAT---------------ATAAT-----------------------------------TTG-----------TATACCC--------------------------------------------TGAACCCATTG----------------------------AAAATG-------GGAAATC----AGGGTATAATGGTTTTGT-------------------------GA-AAAGGAATCATCGCAGACCCCACAAAGTATATAT--------ATTCTTGATCAGGACGACGAGCTGAGTCGATATAGCCCTGTCCGTCTGTC------------------------------------------------------------------------------
droGri2	scaffold_15203:6079894-6080132 -		G----------------AAGC----------TTTCT---AAGTACTCCG--CAATGAACTTTAACTAA-ATATAAATTTTTTCAAATGCTT--GTT--TAACGCAATACTTAAATATCC----------------------TT---------A--AAACGGG----------------------------------------------GATAATGGTTT-----------------TGTGCAAAAGTAG-GAAGGAAGCATCTCCAATCCCATAAAGAAAATAT--------AGTCTTGATCAGCATCAAGAGACGAGTCGATATAGCCATGTCCGTCTGTCCATCTGTATAT--------CTCAG--------------------------AGTA----TATAAGAGTTAGAGACTT--
droWil2	scf2_1100000004624:19279-19437 -		C----------------GAAT---------------AAAGT-----------------------------------TTC-----------C--GCTCTTAACAC------------------------------------------G--------------------------------AACAAAC-------AAT-ATT----AG--TATATTAAAGTCGCCA-------AAATGTATGTAACAGGCA-GAAGGAAGCATCTCCGACCCCACAAAGTATATAT--------ATTCTTGATCAGGATCAACAACCGAGTCGATCTAGCCATGTCCGTCTGTC------------------------------------------------------------------------------
dp5	XL_group1a:575345-575507 +		A----------------ACCT--------------------------------------------------------------------------------------------------------------AATTATACCCGATACT--------------------------------CAAAATG-------AGT-ATT----GGGTTATATTAGATTTGTGGTAAATGTGGATGTGTGTAACGTCCA-GAAGGAATCGTTTCCGACCCCATAAAGTATATAT--------ATTCTTGATCAGCATCAATAGCCGAGTCGATTGAGCCATGTCTGTCTGTC------------------------------------------------------------------------------
droPer2	scaffold_2264:1656-1873 +		A----------------GTATCGGGTATAACTGTAG---AGTTGCGGTGTCC--------------------------------------------------GCAGCAACTCAAAAC--GTTCCCCCTCGTTTTTATACCCGATACT--------------------------------CAAAATG-------AGT-ATT----GGGGTATATTAGATTTGTGGTAAAAGTGGATGTGTGTAACGTCCA-GAAGGAATCGTTTCCGACCCCATAAAGTATATAT--------ATTCTTGATCAGCATCAATAGCCGAGTCGATTGAGCCATGTCTGTCTGTC------------------------------------------------------------------------------
droAna3	scaffold_13082:2550780-2550986 +		T----------------AAAA----------------------------------------------------------------------------------------CTGAGAG--------------------------------------------------------------------ACTAGTTTGCGT-AGAAAAC------GAACAGG----T-------GTGCAAGTGTGCAACGCAGT-GAAGGAGATATCTCCGACCCTATAAAGTATATAT--------ATTCTTGATCAGGATCACCTCCTGAGTCGATATAAGCATGTCCGTCTGTCTGTCGGTTTCT------------ACTTTTTTAAAGCTATCGAGTTAAAACTT--TGCACACATCCTTCTTTTGTTTGA
droBip1	scf7180000395876:19203-19371 +		A----------------AAT----------------ACAAT-----------------------------------TTG-----------TT----T-TGACTC--------------------------TATTTATA--------TCGTAGAGAACAAGGG----------------------------------------------TATATCACA----T-------GTAAATGTATGTAACATAGA-GAAGAAATCGTCTCCGACCCCATAAAGTACATATAT------ATTCTTGATCAGGATCAACAGCCGAGTCGATATAGCCATGTCCGTCTATTGGTACGAA----------------------------------------------------------------------
droKik1	scf7180000302802:34749-34956 +		A----------------ATCC---------------AAAA---------------------------------------------------------------------ATA------------------------------------------------------ATTTTTTTTTTTGAAAAAACAAATTTGGGC-ACTAGAG------------------GGTTAAGTCAGAAGCTTGCTATGCAGT-AAAAGAGTAATTTCGGATCAAATAAAGTATATAT--------ACTCTTGATCAGCATCAACAGCCGAGTCGATCTAGTCATGTCCGTCTGTCCGTCCGTCCATCTGTCTGTTTCTA------------------------------TGTAAACTAGTCCCTCAGTTTTCA
droFic1	scf7180000452189:13288-13400 -		C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTAGACCCCATAAAGTATATAT--------ATTCTTGATCAGCATCACCATCCGAATCGAAATATGTATGTACGTCTGTCCGTCTGTCTGT--------TTCTA------------------------------TGTAAACTAGTCTCTCAGTTTTAA
droEle1	scf7180000490008:660-840 -		A----------------CAAA--------------------------------------------------------------------------------------AATTAAAAAACA-------------------------------GAAAAG-----TTATAATTTTTT------------------------------------------TCA--------------------TTTATTTTTCC-GAAGGAGACGTCTCCGACCCTATAAAGTATATAT--------ATTCTTGATCAGCATCACTAGTAGAGTCGATCTAGCCATGTCCGTCTGTCCGTCCGTCTGTCCGTCCGTTTCTA------------------------------CGCAAACTTGTCTCTCAGTTTTAA
droRho1	scf7180000776778:13226-13430 -		T----------------ATT--GGGTCTAATT--AT---AAGCCAATCTTCAGATGGCTTGAAGTTTAATGACA-TTTG-----------T----------------------------------------ATTTATACCCGTTACTCGTATAGTAAAAGGG----------------------------------------------TATATTGTATTCGTG-------CAAAAGTATGTAACATGTA-GAAGGCAGCGTTTCCGACCCTATAAAGTATATAT--------ATTCTTGTTCAGGATCACTAGCCGAGTCGATCTAGCCATGTCCGTCTGTC------------------------------------------------------------------------------
droBia1	scf7180000302291:1352646-1352796 +		T----------------GTTT---------------AAAA---------------------------------------------------------------------TTAAAAAAAA-------------------------------------------------------------------------------------------------AAACAA-------ACAGAAGTTTGCAACACAGT-GAAGGTGACGTTTCCGATCCCATAAAGTATATAT--------ATTCTTGATCAGCATCACTAGACGAGTCGATCTAGCCATGTCCACTTGCCCAAA--------------------------------------------------------CTAGTCTCTCAGTTTTGA
droTak1	scf7180000413342:10035-10190 -		T----------------AAGT---------------TTAAA-----------------------------------TTG-----------TATTTTT--TGCAT---------------------------------------TTCT--------------------------------CAAAA--------------GT----TA--TGTAACAAAGTTAT-------GCAAAAGTATGTAACAGA-A-GAAGGAAGCATTTCCGACCCTATAAAGTATATAT--------ATTCTTGATTAGGGTCAGTAGCCGAGTTGATATAGCCATGTCCGTCTGTCT-----------------------------------------------------------------------------
droEug1	scf7180000409299:4536-4671 +		A----------------C--------------------------------------------------------------------------------------------------------------------------------TCGTAGATTAAAAGGA----------------------------------------------TATAA--------T-------GATAAAGTATGTAACAGGTA-TAAGGAGGCGTTTCCGAACCTATGAAGTATATATATAT----ATTCTTAATCAGTATCAATAGCGAAGTCGATTTAGCTATGTCTGTCTGTCCGTA--------------------------------------------------------------------------
dm3	chr3L:22956138-22956344 -		A----------------AAATAAT------------ATATA-----------------------------------TTG-----------TATATTT--T--------------------------------------------ACTCGTAGAGTAAAAGGG----------------------------------------------TATACTATATTCGTTG-------AAAAGTATGTAGCAGGCA-----GAAGCGTTTCCGGCTATATAAAGTATATATATATATATATTTTCGATCAGGATAAATAGCCGATTCGATTTGGCCCTGTCCGTCTGTCTGTATGAACGT--------CGAGA--------------------------TGAAC-GTCAGAAATTGTTGGATATTCA
droSim2	2l:21325814-21325944 +		T----------------AAC----------------------------------------------------------------------------------GCAAAAACTCAAGCCCG-------------------------------------------------------------------------------------------------------TG--------AAA--GTGTAATAGGCA-TAAGGAAGCGTTTCCGACTATATAAAGTATATAT--------ATTCGTGATCGGGATCAATAGTCGAGTCGATCTGACCATGCCCGTCTGTCCGTATGAG---------------------------------------------------------------------A
droSec2	scaffold_20:811956-812078 +		T----------------TTAA--------------------------------------------------------------------------------CA------TTAACA------------------TTATACTA---------------------------------------------------------------------------------------------GATAGATACTAGGTA-CTAGGAAGCGTTTCCGACCATATAAAGTATATAT--------ATTCTTGATTAGGATCAATAGCCGAGTCGATCTGGCCATGGCCATCTGTTTTT---------------------------------------------------------------------------
droYak3	v2_chrUn_1453:1169-1310 +		T----------------TTGA---------------------------------TCAGCTTGAACAAA---------------------------------------A-ATA------------------------------------------------------CTTTTTT------------------------------------------TAGTTTTTG-------AAAAGTATGTAACAGGCAGCGTTTCCGCGTTTCCGACCATATAAAGTATATAT--------ATTCTGGATCAGGATCAATAGCTAAGTCGATCTGGCCATGTCCGTCTGTC------------------------------------------------------------------------------
droEre2	scaffold_4845:7394362-7394538 -		C----------------TAAA------------------A------------------------TTTAATTTTGGTTT---------------GTTTTTAGTATAATAAAAATAA-------------------------------AGCTAGAATAAAACGG----------------------------------------------TATAATAGGTTCCTTG-------AAAATCATGTAACAGGTA--AAGGAAG------CGACCAAATAAAGTATGTATATACAT---ATCCTGATGAGGATCAATAGCCGAGTCGATCTGGCCATGTCTGTCCGTCTCT---------------------------------------------------------------------------

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droVir3

GTTCGCAGTGCTATCAAGTATTGGGTGGAGCGTCAC---AAGCACGTCGTCCGGTGAGCTAAAACTCAAATACAGTTTG-----------T--GTT--TAACACGAAAATTAAACAACA-------------------------------AGAAAG------------------------------------------CT----AGGGCACAATATGT-----------GTGTGTGTGTGC-----------------ATTCTCCGACCCCATAAAGTATATAT--------AT--ATGAACAGTATCAACAGTCGACTCGATATAGCCATGTCCGTCTGTCTTTAAGAAAAT--------AAAAT--------------------------TGTA--TTCAAAACTTTTTTGTTTTTCA	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
.............................................................................................................................................................................................................................................................................................................................CTCGATATAGCCATGTCCGTCTGTC..............................................................................	25	7	0.14	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	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

droMoj3

C----------------AAAT---------------ATAAT-----------------------------------TTG-----------TATACCC--------------------------------------------TGAACCCATTG----------------------------AAAATG-------GGAAATC----AGGGTATAATGGTTTTGT-------------------------GA-AAAGGAATCATCGCAGACCCCACAAAGTATATAT--------ATTCTTGATCAGGACGACGAGCTGAGTCGATATAGCCCTGTCCGTCTGTC------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
...........................................................................................................................................................................................................................................................................................T--------ATTCTTGATCAGGACGACGAGCT.........................................................................................................	24	20	0.10	2	1	0	0	0	1	0
........................................................................................................................................................................................................................................................A-AAAGGAATCATCGCAGACCC......................................................................................................................................................	21	11	0.09	1	1	0	0	0	0	0
..........................................................................................................................................................................................................................................................AAAGGAATCATCGCAGACCCC.....................................................................................................................................................	21	11	0.09	1	1	0	0	0	0	0
.....................................................................................................................................................................................................................................................................................................................CGAGCTGAGTCGATATAGCCC..........................................................................................	21	20	0.05	1	0	1	0	0	0	0
......................................................................................................................................................................................................................................................................................................TCTTGATCAGGACGACGAGCT.........................................................................................................	21	20	0.05	1	1	0	0	0	0	0
...................................................................................................................................................CATTG----------------------------AAAATG-------GGAAATC----AG......................................................................................................................................................................................................................	20	20	0.05	1	0	0	0	0	0	1
..................................................................................................................................................................................................GAAATC----AGGGTATAATGGTTTTGT-------------------------.............................................................................................................................................................................	24	20	0.05	1	1	0	0	0	0	0

droGri2

G----------------AAGC----------TTTCT---AAGTACTCCG--CAATGAACTTTAACTAA-ATATAAATTTTTTCAAATGCTT--GTT--TAACGCAATACTTAAATATCC----------------------TT---------A--AAACGGG----------------------------------------------GATAATGGTTT-----------------TGTGCAAAAGTAG-GAAGGAAGCATCTCCAATCCCATAAAGAAAATAT--------AGTCTTGATCAGCATCAAGAGACGAGTCGATATAGCCATGTCCGTCTGTCCATCTGTATAT--------CTCAG--------------------------AGTA----TATAAGAGTTAGAGACTT--	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

droWil2

C----------------GAAT---------------AAAGT-----------------------------------TTC-----------C--GCTCTTAACAC------------------------------------------G--------------------------------AACAAAC-------AAT-ATT----AG--TATATTAAAGTCGCCA-------AAATGTATGTAACAGGCA-GAAGGAAGCATCTCCGACCCCACAAAGTATATAT--------ATTCTTGATCAGGATCAACAACCGAGTCGATCTAGCCATGTCCGTCTGTC------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
.....................................................................................................................................................................................................................TAAAGTCGCCA-------AAATGTATGTAACA...............................................................................................................................................................................	25	20	3.90	78	0	0	0	78	0
............................................................................................................................................................................................................................................TATGTAACAGGCA-GAAGGAAGCAT...............................................................................................................................................................	24	20	0.25	5	0	5	0	0	0
...............................................................................................................................................................................................................................A-------AAATGTATGTAACAGGCA-GA........................................................................................................................................................................	21	20	0.10	2	0	0	0	2	0
........................................................................................................................................................................................................................................................A-GAAGGAAGCATCTCCGACCC......................................................................................................................................................	21	20	0.05	1	0	1	0	0	0
.......................................................................................................................................................................................................................................AAATGTATGTAACAGGCA-GAAGGA....................................................................................................................................................................	24	20	0.05	1	0	1	0	0	0
................................................................................................................................................................................................................................................TAACAGGCA-GAAGGAAGCATC..............................................................................................................................................................	21	20	0.05	1	0	0	1	0	0
....................................................................................................................................................................................................................TTAAAGTCGCCA-------AAATGTATGTAACAGG.............................................................................................................................................................................	28	20	0.05	1	0	0	0	1	0
..........................................................................................................................................................................................................................................................................................................................CGAGTCGATCTAGCCATGTC......................................................................................	20	20	0.05	1	0	1	0	0	0
..................................................................................................................................................................................................................................................................CATCTCCGACCCCACAAAGTATATAT--------ATT.............................................................................................................................	29	20	0.05	1	0	1	0	0	0

dp5

A----------------ACCT--------------------------------------------------------------------------------------------------------------AATTATACCCGATACT--------------------------------CAAAATG-------AGT-ATT----GGGTTATATTAGATTTGTGGTAAATGTGGATGTGTGTAACGTCCA-GAAGGAATCGTTTCCGACCCCATAAAGTATATAT--------ATTCTTGATCAGCATCAATAGCCGAGTCGATTGAGCCATGTCTGTCTGTC------------------------------------------------------------------------------	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
.................................................................................................................................................................................................................................AAATGTGGATGTGTGTAACGT..............................................................................................................................................................................	21	2	1.50	3	0	3	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................................TTTGTGGTAAATGTGGATGTG......................................................................................................................................................................................	21	4	1.50	6	0	4	0	0	0	0	1	0	1	0
.......................................................................................................................................................................................................................GATTTGTGGTAAATGTGGATG........................................................................................................................................................................................	21	3	1.33	4	0	4	0	0	0	0	0	0	0	0
........................................................................................................................................................................................................................................................................................................TTGATCAGCATCAATAGCCGAGTC....................................................................................................	24	20	0.85	17	0	0	0	0	0	0	0	0	17	0
..................................................................................................................................................................................................................................AATGTGGATGTGTGTAACGTC.............................................................................................................................................................................	21	4	0.75	3	1	1	0	0	0	0	1	0	0	0
............................................................................................................................................................................................................................................................................................................TCAGCATCAATAGCCGAGTCGA..................................................................................................	22	20	0.55	11	0	11	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................................................................................................................TGATCAGCATCAATAGCCG........................................................................................................	19	20	0.55	11	0	11	0	0	0	0	0	0	0	0
........................................................................................................................................................................................................................ATTTGTGGTAAATGTGGATG........................................................................................................................................................................................	20	4	0.50	2	0	1	0	0	0	0	1	0	0	0
.........................................................................................................................................................................................................................TTTGTGGTAAATGTGGATGTGTC....................................................................................................................................................................................	23	4	0.50	2	0	0	0	0	0	0	0	0	2	0
............................................................................................................................................................................................................................................................................................................................AGTCGATTGAGCCATGTCTG....................................................................................	20	20	0.45	9	0	9	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................................................................................TGAGCCATGTCTGTCTGTC------------------------------------------------------------------------------	19	20	0.35	7	0	0	0	0	0	0	0	0	7	0
...............................................................................................................................................................................................................................GTAAATGTGGATGTGTGTAA.................................................................................................................................................................................	20	3	0.33	1	0	0	0	0	0	0	1	0	0	0
...............................................................................................................................................................................................................................GTAAATGTGGATGTGTGTAAC................................................................................................................................................................................	21	3	0.33	1	0	1	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................TTAGATTTGTGGTAAATGTG............................................................................................................................................................................................	20	3	0.33	1	0	1	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................................ATGTGGATGTGTGTAACGTC.............................................................................................................................................................................	20	6	0.33	2	0	1	0	0	0	0	1	0	0	0
....................................................................................................................................................................................................................................TGTGGATGTGTGTAACGTC.............................................................................................................................................................................	19	6	0.33	2	0	2	0	0	0	0	0	0	0	0
.................................................................................................................................................................................................................................AAATGTGGATGTGTGTAACG...............................................................................................................................................................................	20	3	0.33	1	0	1	0	0	0	0	0	0	0	0
........................................................................................................................................................................................................................ATTTGTGGTAAATGTGGATGT.......................................................................................................................................................................................	21	4	0.25	1	0	1	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................................................................................ATTCTTGATCAGCATCAATAGCCGA.......................................................................................................	25	20	0.25	5	0	5	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................................TTTGTGGTAAATGTGGATGT.......................................................................................................................................................................................	20	4	0.25	1	0	1	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................AATGTGGATGTGTGTAACGT..............................................................................................................................................................................	20	4	0.25	1	0	0	0	0	0	0	1	0	0	0
........................................................................................................................................................................................................................ATTTGTGGTAAATGTGGAT.........................................................................................................................................................................................	19	4	0.25	1	0	1	0	0	0	0	0	0	0	0
.............................................................................................................................................................................................................................TGGTAAATGTGGATGTGTGTA..................................................................................................................................................................................	21	4	0.25	1	0	1	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................................TTTGTGGTAAATGTGGATG........................................................................................................................................................................................	19	4	0.25	1	0	0	0	0	0	0	1	0	0	0
.........................................................................................................................................................................................................................TTTGTGGTAAATGTGGATGTGT.....................................................................................................................................................................................	22	4	0.25	1	0	0	0	0	0	0	0	1	0	0
.................................................................................................................................................................................................................................................................TCGTTTCCGACCCCATAAAGTATATAT--------A...............................................................................................................................	28	20	0.20	4	0	0	0	0	0	0	0	0	4	0
......................................................................................................................................................................................................................................................................................................................TAGCCGAGTCGATTGAGCCATGTCTG....................................................................................	26	20	0.20	4	0	4	0	0	0	0	0	0	0	0
....................T--------------------------------------------------------------------------------------------------------------AATTATACCCGATACT--------------------------------CAAAATG-------...................................................................................................................................................................................................................................	24	20	0.20	4	0	4	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................................................................................CA-GAAGGAATCGTTTCCGACCCCA....................................................................................................................................................	24	20	0.20	4	0	4	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................................ATGTGGATGTGTGTAACGTCC............................................................................................................................................................................	21	6	0.17	1	0	1	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................TGTGGATGTGTGTAACGTCC............................................................................................................................................................................	20	6	0.17	1	0	1	0	0	0	0	0	0	0	0
................................................................................................................................................ACT--------------------------------CAAAATG-------AGT-ATT----GGGT....................................................................................................................................................................................................................	20	12	0.17	2	0	2	0	0	0	0	0	0	0	0
...............................................................................................................................................TACT--------------------------------CAAAATG-------AGT-ATT----GGGT....................................................................................................................................................................................................................	21	12	0.17	2	0	1	0	0	1	0	0	0	0	0
....................................................................................................................................................................................................................................TGTGGATGTGTGTAACGTCCA-..........................................................................................................................................................................	21	6	0.17	1	0	1	0	0	0	0	0	0	0	0
...........................................................................................................................................................................................................................................................................................T--------ATTCTTGATCAGCATCAATAG...........................................................................................................	22	20	0.15	3	0	3	0	0	0	0	0	0	0	0
......................................................................................................................................................................................................................................................................................................TCTTGATCAGCATCAATAGCCG........................................................................................................	22	20	0.15	3	0	3	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................AAATG-------AGT-ATT----GGGTTATATT..............................................................................................................................................................................................................	21	8	0.13	1	0	1	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................................T----GGGTTATATTAGATTTGTG.....................................................................................................................................................................................................	20	8	0.13	1	0	1	0	0	0	0	0	0	0	0
........................................................................................................................................................................................TG-------AGT-ATT----GGGTTATATTAGA...........................................................................................................................................................................................................	21	8	0.13	1	0	1	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................................ATT----GGGTTATATTAGATTTGT......................................................................................................................................................................................................	21	9	0.11	1	0	1	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................T-ATT----GGGTTATATTAGATTTG.......................................................................................................................................................................................................	21	9	0.11	1	0	0	0	0	0	1	0	0	0	0
...........................................................................................................................................................................................................................................................................................................ATCAGCATCAATAGCCGAGTC....................................................................................................	21	20	0.10	2	0	0	0	0	0	0	2	0	0	0
.....................................................................................................................................................................................................................................................................................................TTCTTGATCAGCATCAATAGCCGAG......................................................................................................	25	20	0.10	2	0	0	0	0	0	0	0	2	0	0
..........................................................................................................................................................................................................................................................GAAGGAATCGTTTCCGACCCCATA..................................................................................................................................................	24	20	0.10	2	0	0	0	0	0	0	0	0	2	0
..........................................................................................................................................................................................................................................................................................................GATCAGCATCAATAGCCGAGT.....................................................................................................	21	20	0.10	2	0	2	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................................GTCCA-GAAGGAATCGTTTCCG..........................................................................................................................................................	21	20	0.10	2	0	0	0	0	0	2	0	0	0	0
.............................................................................................................................................................................................................................................................................................................CAGCATCAATAGCCGAGTCGA..................................................................................................	21	20	0.10	2	0	0	0	0	0	0	1	0	1	0
................................................................................................................................................................................................................................................................................TAAAGTATATAT--------ATTCTTGATCAGCA..................................................................................................................	26	20	0.10	2	0	0	0	0	0	0	0	2	0	0
......................................................................................................................................................................................................................................................CCA-GAAGGAATCGTTTCCGACCCCAT...................................................................................................................................................	26	20	0.10	2	0	0	0	0	0	0	0	0	2	0
...............................................................................................................................................................................................................................................................................................................................CGATTGAGCCATGTCTGTCTG................................................................................	21	20	0.10	2	0	0	0	0	0	0	2	0	0	0
..........................................................................................................................................................................................................................................................GAAGGAATCGTTTCCGACCCCATAAAGTA.............................................................................................................................................	29	20	0.10	2	0	2	0	0	0	0	0	0	0	0
...............................................................................................................................................................................................................................................................................................................................CGATTGAGCCATGTCTGTCTGTC------------------------------------------------------------------------------	23	20	0.10	2	0	2	0	0	0	0	0	0	0	0
...........................................................................................................................................................................................................................................................AAGGAATCGTTTCCGACCCCAT...................................................................................................................................................	22	20	0.10	2	0	2	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................GTTTCCGACCCCATAAAGTA.............................................................................................................................................	20	20	0.05	1	0	1	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................................ACGTCCA-GAAGGAATCGTTTC............................................................................................................................................................	21	20	0.05	1	0	0	0	1	0	0	0	0	0	0
......................................................................................................................................................................................................................................................CCA-GAAGGAATCGTTTCCGACCCC.....................................................................................................................................................	24	20	0.05	1	0	0	0	0	0	0	0	1	0	0
........................................................................................................................................................................................................................................................................................................TTGATCAGCATCAATAGCCGAGTCGAT.................................................................................................	27	20	0.05	1	0	0	0	0	0	1	0	0	0	0
.......................................................................................................................................ATACCCGATACT--------------------------------CAAAATG-------AG.................................................................................................................................................................................................................................	21	20	0.05	1	0	0	0	0	0	0	1	0	0	0
..........................................................................................................................................................................................................................................TGTGTGTAACGTCCA-GAAGGA....................................................................................................................................................................	21	20	0.05	1	0	0	0	1	0	0	0	0	0	0
...................................................................................................................................AATTATACCCGATACT--------------------------------CAAA.............................................................................................................................................................................................................................................	20	20	0.05	1	0	0	0	0	0	0	0	1	0	0
..............................................................................................................................................................................................................................................................................................................AGCATCAATAGCCGAGTCGATTG...............................................................................................	23	20	0.05	1	0	0	0	0	0	0	0	0	1	0
..................................................................................................................................................................................................................................................................................................................TCAATAGCCGAGTCGATTGAGC............................................................................................	22	20	0.05	1	0	0	0	0	0	0	1	0	0	0
......................................................................................................................................................................................................................................................................................................................TAGCCGAGTCGATTGAGCCATGTCT.....................................................................................	25	20	0.05	1	0	0	1	0	0	0	0	0	0	0
............................................................................................................................................................................................................................................................................................................................AGTCGATTGAGCCATGTCT.....................................................................................	19	20	0.05	1	0	0	0	0	0	0	1	0	0	0
......................................................................................................................................................................................................................................................................................ATATAT--------ATTCTTGATCAGCATCAATAGCC.........................................................................................................	29	20	0.05	1	0	0	1	0	0	0	0	0	0	0
....................T--------------------------------------------------------------------------------------------------------------AATTATACCCGATACT--------------------------------CAAAATG-------A..................................................................................................................................................................................................................................	25	20	0.05	1	0	1	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................................................ATGTGTGTAACGTCCA-GAAG......................................................................................................................................................................	20	20	0.05	1	0	0	0	0	0	0	0	0	1	0

droPer2

A----------------GTATCGGGTATAACTGTAG---AGTTGCGGTGTCC--------------------------------------------------GCAGCAACTCAAAAC--GTTCCCCCTCGTTTTTATACCCGATACT--------------------------------CAAAATG-------AGT-ATT----GGGGTATATTAGATTTGTGGTAAAAGTGGATGTGTGTAACGTCCA-GAAGGAATCGTTTCCGACCCCATAAAGTATATAT--------ATTCTTGATCAGCATCAATAGCCGAGTCGATTGAGCCATGTCTGTCTGTC------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
.............................................................................................................................................................................................................................................GTGTAACGTCCA-GAAGGAA...................................................................................................................................................................	19	20	0.25	5	0	0	0	0	0	5
......................................................................................................................................................................................................................................................................................................................TAGCCGAGTCGATTGAGCCAT.........................................................................................	21	20	0.20	4	0	4	0	0	0	0
...........................................................................................................................................................................................................................................GTGTGTAACGTCCA-GAAGGAATC.................................................................................................................................................................	23	20	0.05	1	0	0	0	0	1	0
......................................................................................................................................................................................................................................................................................................TCTTGATCAGCATCAATAGCCGAG......................................................................................................	24	20	0.05	1	0	0	0	1	0	0
.................................................................................................................................................CT--------------------------------CAAAATG-------AGT-ATT----GGGGTATATTA.............................................................................................................................................................................................................	26	20	0.05	1	0	1	0	0	0	0
...................................................................................................................................................................................................................................................CGTCCA-GAAGGAATCGTTTCCGA.........................................................................................................................................................	23	20	0.05	1	0	1	0	0	0	0
..............................CTGTAG---AGTTGCGGTGTCC--------------------------------------------------GCAGC.........................................................................................................................................................................................................................................................................................................................	24	20	0.05	1	0	1	0	0	0	0
.......................................................................................................................................................................................................................................................CA-GAAGGAATCGTTTCCGACC.......................................................................................................................................................	21	20	0.05	1	0	0	0	0	0	1
...................................................................................................................................................................................................................................................................................................................................TGAGCCATGTCTGTCTGT...............................................................................	18	20	0.05	1	0	1	0	0	0	0

droAna3

T----------------AAAA----------------------------------------------------------------------------------------CTGAGAG--------------------------------------------------------------------ACTAGTTTGCGT-AGAAAAC------GAACAGG----T-------GTGCAAGTGTGCAACGCAGT-GAAGGAGATATCTCCGACCCTATAAAGTATATAT--------ATTCTTGATCAGGATCACCTCCTGAGTCGATATAAGCATGTCCGTCTGTCTGTCGGTTTCT------------ACTTTTTTAAAGCTATCGAGTTAAAACTT--TGCACACATCCTTCTTTTGTTTGA	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
..........................................................................................................................................................................................................................................................................................................................TGAGTCGATATAAGCATGTCCGTCT.................................................................................	25	20	0.95	19	19	0	0	0	0	0
..............................................................................................................TGAGAG--------------------------------------------------------------------ACTAGTTTGCGT-AGAAAAC------G.................................................................................................................................................................................................................	26	5	0.40	2	1	0	1	0	0	0
..............................................................................................................................................................................................................................................................................................................................TCGATATAAGCATGTCCGTCTGTCTGTC..........................................................................	28	20	0.25	5	5	0	0	0	0	0
............................................................................................................................................................................................................................................................................................................................AGTCGATATAAGCATGTCCGTCT.................................................................................	23	20	0.15	3	3	0	0	0	0	0
..................................................................................................................................................................................................................................................ACGCAGT-GAAGGAGATATCT.............................................................................................................................................................	20	20	0.15	3	0	0	0	0	0	3
.....................................................................................................................................................................................................................................................................................................................................AAGCATGTCCGTCTGTCTGTCGG........................................................................	23	20	0.10	2	2	0	0	0	0	0
................................................................................................................................................................................................................................................CAACGCAGT-GAAGGAGATATC..............................................................................................................................................................	21	20	0.10	2	1	0	0	0	1	0
....................................................................................................................................................................................................................................................................................................................................TAAGCATGTCCGTCTGTCTGTCGGT.......................................................................	25	20	0.10	2	2	0	0	0	0	0
.............................................................................................................................................................................................................................................................................................................................GTCGATATAAGCATGTCCGTCTGTCTGT...........................................................................	28	20	0.10	2	0	1	0	1	0	0
.............................................................................................................................................................................................................................................GTGCAACGCAGT-GAAGGAGAT.................................................................................................................................................................	21	20	0.05	1	0	0	0	0	1	0
..................................................................................................................................................................................................................................................ACGCAGT-GAAGGAGATATCTCCGAC........................................................................................................................................................	25	20	0.05	1	0	1	0	0	0	0
.....................................................................................................................................................................................................................................................................................................................................AAGCATGTCCGTCTGTCTGTCGGT.......................................................................	24	20	0.05	1	1	0	0	0	0	0
...................................................................................................................................................................................................................................................................................................................................ATAAGCATGTCCGTCTGTCTGTCGGTTT.....................................................................	28	20	0.05	1	1	0	0	0	0	0
...................................................................................................................................................................................................................................................................................................................................ATAAGCATGTCCGTCTGTCTGTC..........................................................................	23	20	0.05	1	1	0	0	0	0	0
...........................................................................................................................................................................................................................................................................................................................GAGTCGATATAAGCATGTCCGTC..................................................................................	23	20	0.05	1	1	0	0	0	0	0
.....................................................................................................................................................................................................................................................................................................................................................................................................AACTT--TGCACACATCCTTCTTTTGT....	25	20	0.05	1	0	1	0	0	0	0
......................................................................................................................................................................................................................................................................................................................................AGCATGTCCGTCTGTCTGTCGG........................................................................	22	20	0.05	1	0	0	0	0	0	1
.............................................................................................................................................................................................................................................................................................................................GTCGATATAAGCATGTCCGTCTGT...............................................................................	24	20	0.05	1	0	0	1	0	0	0
.........................................................................................................................................................................................................................................AAGTGTGCAACGCAGT-GAAGGAGATA................................................................................................................................................................	26	20	0.05	1	0	0	0	0	1	0
....................................................................................................................................................................................................................................................................................................................................................................................TAAAGCTATCGAGTTAAAACT...........................	21	20	0.05	1	0	0	0	0	0	1
.............................................................................................................CTGAGAG--------------------------------------------------------------------ACTAGTTTGCGT-AGA............................................................................................................................................................................................................................	22	20	0.05	1	0	1	0	0	0	0
.............................................................................................................................................................................................................................................GTGCAACGCAGT-GAAGGAGATATC..............................................................................................................................................................	24	20	0.05	1	0	0	1	0	0	0
..............................................................................................................TGAGAG--------------------------------------------------------------------ACTAGTTTGCGT-AGAAAA.........................................................................................................................................................................................................................	24	20	0.05	1	1	0	0	0	0	0
....................................................................................................................................................................................................................................................................................................................................TAAGCATGTCCGTCTGTCTGTCGGTTTC....................................................................	28	20	0.05	1	1	0	0	0	0	0
...................................................................................................................................................................................................................................................................................................................................ATAAGCATGTCCGTCTGTCTGTCGGTT......................................................................	27	20	0.05	1	1	0	0	0	0	0
......................................................................................................................................................................................................................................................................................................................................AGCATGTCCGTCTGTCTGTCGGTT......................................................................	24	20	0.05	1	1	0	0	0	0	0
..........................................................................................................................................................................................................................................................................................................................................................................................TATCGAGTTAAAACTT--TGCACACATCC.............	27	20	0.05	1	0	1	0	0	0	0
..................................................................................................................................................................................................................................................ACGCAGT-GAAGGAGATATCTC............................................................................................................................................................	21	20	0.05	1	1	0	0	0	0	0
.......................................................................................................................................................................................................................................................................................................................................GCATGTCCGTCTGTCTGTCGGTTTCT------------AC.....................................................	28	20	0.05	1	1	0	0	0	0	0
..................................................................................................................................................................................................................................................................................................................................TATAAGCATGTCCGTCTGTC..............................................................................	20	20	0.05	1	1	0	0	0	0	0
..............................................................................................................................................................................................................................................................................................................................................................................................GAGTTAAAACTT--TGCACAC.................	19	20	0.05	1	0	1	0	0	0	0
..................................................................................................................................................................................................................................................................................................................TCACCTCCTGAGTCGATATAAGC...........................................................................................	23	20	0.05	1	1	0	0	0	0	0

droBip1

A----------------AAT----------------ACAAT-----------------------------------TTG-----------TT----T-TGACTC--------------------------TATTTATA--------TCGTAGAGAACAAGGG----------------------------------------------TATATCACA----T-------GTAAATGTATGTAACATAGA-GAAGAAATCGTCTCCGACCCCATAAAGTACATATAT------ATTCTTGATCAGGATCAACAGCCGAGTCGATATAGCCATGTCCGTCTATTGGTACGAA----------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droKik1

A----------------ATCC---------------AAAA---------------------------------------------------------------------ATA------------------------------------------------------ATTTTTTTTTTTGAAAAAACAAATTTGGGC-ACTAGAG------------------GGTTAAGTCAGAAGCTTGCTATGCAGT-AAAAGAGTAATTTCGGATCAAATAAAGTATATAT--------ACTCTTGATCAGCATCAACAGCCGAGTCGATCTAGTCATGTCCGTCTGTCCGTCCGTCCATCTGTCTGTTTCTA------------------------------TGTAAACTAGTCCCTCAGTTTTCA	Size	Hit Count	Total Norm	Total
No Reads

droFic1

C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTAGACCCCATAAAGTATATAT--------ATTCTTGATCAGCATCACCATCCGAATCGAAATATGTATGTACGTCTGTCCGTCTGTCTGT--------TTCTA------------------------------TGTAAACTAGTCTCTCAGTTTTAA	Size	Hit Count	Total Norm	Total
No Reads

droEle1

A----------------CAAA--------------------------------------------------------------------------------------AATTAAAAAACA-------------------------------GAAAAG-----TTATAATTTTTT------------------------------------------TCA--------------------TTTATTTTTCC-GAAGGAGACGTCTCCGACCCTATAAAGTATATAT--------ATTCTTGATCAGCATCACTAGTAGAGTCGATCTAGCCATGTCCGTCTGTCCGTCCGTCTGTCCGTCCGTTTCTA------------------------------CGCAAACTTGTCTCTCAGTTTTAA	Size	Hit Count	Total Norm	Total
No Reads

droRho1

T----------------ATT--GGGTCTAATT--AT---AAGCCAATCTTCAGATGGCTTGAAGTTTAATGACA-TTTG-----------T----------------------------------------ATTTATACCCGTTACTCGTATAGTAAAAGGG----------------------------------------------TATATTGTATTCGTG-------CAAAAGTATGTAACATGTA-GAAGGCAGCGTTTCCGACCCTATAAAGTATATAT--------ATTCTTGTTCAGGATCACTAGCCGAGTCGATCTAGCCATGTCCGTCTGTC------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droBia1

T----------------GTTT---------------AAAA---------------------------------------------------------------------TTAAAAAAAA-------------------------------------------------------------------------------------------------AAACAA-------ACAGAAGTTTGCAACACAGT-GAAGGTGACGTTTCCGATCCCATAAAGTATATAT--------ATTCTTGATCAGCATCACTAGACGAGTCGATCTAGCCATGTCCACTTGCCCAAA--------------------------------------------------------CTAGTCTCTCAGTTTTGA	Size	Hit Count	Total Norm	Total
No Reads

droTak1

T----------------AAGT---------------TTAAA-----------------------------------TTG-----------TATTTTT--TGCAT---------------------------------------TTCT--------------------------------CAAAA--------------GT----TA--TGTAACAAAGTTAT-------GCAAAAGTATGTAACAGA-A-GAAGGAAGCATTTCCGACCCTATAAAGTATATAT--------ATTCTTGATTAGGGTCAGTAGCCGAGTTGATATAGCCATGTCCGTCTGTCT-----------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droEug1

A----------------C--------------------------------------------------------------------------------------------------------------------------------TCGTAGATTAAAAGGA----------------------------------------------TATAA--------T-------GATAAAGTATGTAACAGGTA-TAAGGAGGCGTTTCCGAACCTATGAAGTATATATATAT----ATTCTTAATCAGTATCAATAGCGAAGTCGATTTAGCTATGTCTGTCTGTCCGTA--------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

dm3

A----------------AAATAAT------------ATATA-----------------------------------TTG-----------TATATTT--T--------------------------------------------ACTCGTAGAGTAAAAGGG----------------------------------------------TATACTATATTCGTTG-------AAAAGTATGTAGCAGGCA-----GAAGCGTTTCCGGCTATATAAAGTATATATATATATATATTTTCGATCAGGATAAATAGCCGATTCGATTTGGCCCTGTCCGTCTGTCTGTATGAACGT--------CGAGA--------------------------TGAAC-GTCAGAAATTGTTGGATATTCA	Size	Hit Count	Total Norm	Total	GSM154618 Ovary	GSM154620 Ovary	GSM154621 Ovary	GSM154622 Ovary	GSM180328 Head	GSM180329 Mixed-body	GSM180330 Embryo	GSM180331 Embryo	GSM180332 Embryo	GSM180333 Embryo	GSM180334 Larvae	GSM180335 Disc	GSM180336 Pupae	GSM180337 S2	GSM231091 Ovary	GSM239041 Head	GSM239050 Head	GSM239051 S2	GSM239052 S2	GSM246084 Head	GSM266765 S2	GSM280082 Ovary	GSM280083 Ovary	GSM280084 Ovary	GSM280085 Testis	GSM280086 Ovary	GSM280087 S2-NP	GSM280088 S2-NP	GSM312995 Head	GSM313160 Head	GSM313161 Head	GSM313162 Head	GSM313163 Head	GSM313164 Head	GSM313165 Head	GSM343287 Embryo	GSM379050 Ovary	GSM379051 Ovary	GSM379052 Ovary	GSM379053 Ovary	GSM379054 Ovary	GSM379055 Ovary	GSM379056 Ovary	GSM379057 Ovary	GSM379058 Ovary	GSM379059 Ovary	GSM379060 Ovary	GSM379061 Ovary	GSM379062 Ovary	GSM379063 Ovary	GSM379064 Ovary	GSM379065 Ovary	GSM379066 Ovary	GSM379067 Ovary	GSM424739 S2	GSM424740 S2	GSM424741 S2	GSM467729 Female-body	GSM467730 Female-body	GSM467731 Female-body	M002 CS	M003 Male-body	M004 Male-body	M005 ML-DmD32	M006 ML-DmD32	M029 OSC	M030 OSC	M031 OSC	M032 S2-R+	M033 S2-R+	M034 S2-R+	M035 S2-R+	M036 S2-R+	M037 S2-R+	M038 S2-R+	M039 S2-R+	M048 S2-R+	OSS2 OSS	OSS6 OSS	OSS7 OSS	OSS8 OSS	S1 Head	S10 Embryo	S11 Embryo	S12 Embryo	S13 Embryo	S14 Embryo	S15 S2-GMR	S16 Kc	S17 Larvae	S18 Larvae	S19 Pupae	S2 Head	S20 Pupae	S21 Disc	S22 Head	S23 Female-body	S24 Male-body	S25 Larvae	S26 Larvae	S27 Pupae	S28 Pupae	S29 Head	S3 Male-body	S30 S2-GMR	S31 S2	S32 S2	S33 Kc	S34 Kc	S35 Kc	S4 Female-body	S5 Disc	S6 Embryo	S7 Embryo	S8 S2	S9 Embryo	SRR001337 Head	SRR001338 Head	SRR001339 Head	SRR001340 Head	SRR001341 Head	SRR001342 Head	SRR001343 Head	SRR001344 Head	SRR001345 Head	SRR001346 Head	SRR001347 Head	SRR001348 Head	SRR001349 Head	SRR001664 Head	SRR010951 Ovary	SRR010952 Ovary	SRR010953 Ovary	SRR010954 Ovary	SRR010955 Ovary	SRR010956 Ovary	SRR010957 Ovary	SRR010958 Ovary	SRR010959 Ovary	SRR010960 Ovary	SRR014268 Embryo	SRR014269 Embryo	SRR014270 Embryo	SRR014271 Embryo	SRR014272 Embryo	SRR014273 Ovary	SRR014274 Ovary	SRR014275 Ovary	SRR014276 Ovary	SRR014277 Ovary	SRR014278 Ovary	SRR014279 Ovary	SRR014280 Ovary	SRR014281 Ovary	SRR014282 Ovary	SRR023197 S2	SRR023399 S2	SRR023400 S2	SRR023402 S2	SRR023407 S2	SRR029028 S2	SRR029029 S2	SRR029030 S2	SRR029031 S2	SRR029032 S2	SRR029033 S2	SRR029608 Head	SRR029633 Head	SRR030145 gb3	SRR031692 Head	SRR031693 Head	SRR031694 Head	SRR031696 Head	SRR031697 Head	SRR031698 Head	SRR031699 Head	SRR031700 Head	SRR031701 Head	SRR031702 Head	SRR031703 Head	SRR031704 Head	SRR032092 S2	SRR032093 S2	SRR032094 S2	SRR032095 S2-NP	SRR032096 S2-NP	SRR032152 Head	SRR060643 Testis	SRR060644 Ovary	SRR060645 Testis	SRR060646 Ovary	SRR060647 Ovary	SRR060648 Ovary	SRR060649 Ovary	SRR060650 Testis	SRR060651 Ovary	SRR060652 Testis	SRR060653 Ovary	SRR065151 Ovary	SRR065152 Ovary	SRR065153 Ovary	SRR065154 Ovary	SRR065155 Ovary	SRR065800 Ovary	SRR065801 Ovary	SRR065802 Ovary	SRR065803 Ovary	SRR065804 Ovary	SRR065805 Ovary	SRR065806 Ovary	SRR065807 Ovary	SRR097865 S2-NP	SRR097866 S2-NP	SRR097867 S2-NP	SRR298536 Ovary	SRR298537 Ovary	SRR298711 Ovary	SRR298712 Ovary	SRR317110 Ovary	SRR317111 Ovary	SRR317112 Ovary	SRR317113 Ovary	SRR317114 Ovary	SRR317115 Ovary	SRR317116 Ovary	SRR317117 Ovary	SRR341115 S2	SRR341116 S2	SRR341117 S2	SRR341118 S2	SRR351332 Mixed-body	SRR351333 Mixed-body	T004 OSC	T005 CME-L1	V001 Embryo	V002 Embryo	V003 S2	V006 Female-body	V007 Head	V008 S2	V009 CME-L1	V010 ML-DmD20-C5	V011 Sg4	V012 Male-body	V013 Head	V014 DTT	V015 DreRFHV	V018 Kc167	V019 GM2	V020 S2-R+	V021 ML-DmD21	V022 ML-DmD32	V023 Head	V024 Kc167	V025 S2-R+	V026 1182-2H	V027 ML-DmD21	V028 CME-W1-Cl.8+	V029 ML-DmD9	V030 ML-DmD8	V031 GM2	V032 S1	V033 CME-W1-Cl.8+	V034 ML-DmD16-C3	V035 ML-DmD32	V036 ML-DmD20-C5	V037 S2	V038 S2	V063 Ovary	V0632 Ovary	V064 Ovary	V0642 Ovary	V065 Ovary	V0652 Ovary	V066 Ovary	V0662 Ovary	V067 S2-NP	V073 mbn2	V074 S3	V075 ML-DmBG1-C1	V076 ML-DmBG3-C2	V077 Head	V078 Head	V079 Head	V080 Head	V081 Embryo	V082 Embryo	V083 Male-body	V084 Female-body	V085 CME-W2	V086 Female-body	V088 Ovary	V0882 Ovary	V089 Ovary	V0892 Ovary	V090 Male-body	V091 fGS/OSS	V092 Male-body	V093 Male-body	V094 S2-R+	V095 S2-R+	V096 Ovary	V097 Ovary	V098 Ovary	V125 ML-DmD9	V126 CME-L1	V127 G2	V128 S3	V129 ML-DmBG1-C1	V130 ML-DmBG3-C2	V131 ML-DmD16-C3	V132 ML-DmD32	V133 Sg4	V134 ML-DmD8	V135 CME-W2	V136 Male-body	V137 Head	V138 Male-body	V139 Female-body	V140 Female-body	V141 Female-body	V142 Female-body	V144 OSC	V145 S2	V146 S1	V147 1182-2H	V148 mbn2	GSM1528798 follicle cells
..........................................................................................................................................................................................................................TCGTTG-------AAAAGTATGTAGCAGGCA-----GA....................................................................................................................................................................	26	2	5.00	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	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	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	2	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	1	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................................TTCGTTG-------AAAAGTATGTAGCAGG.............................................................................................................................................................................	23	6	4.33	26	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	1	0	1	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	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	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	2	1	2	0	1	0	0	0	0	4	4	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
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T----------------AAC----------------------------------------------------------------------------------GCAAAAACTCAAGCCCG-------------------------------------------------------------------------------------------------------TG--------AAA--GTGTAATAGGCA-TAAGGAAGCGTTTCCGACTATATAAAGTATATAT--------ATTCGTGATCGGGATCAATAGTCGAGTCGATCTGACCATGCCCGTCTGTCCGTATGAG---------------------------------------------------------------------A	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
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....................................................................................................................................................................................................................................................................................GTATATAT--------ATTCGTGATCGGGA..................................................................................................................	22	1	6.00	6	0	0	0	0	0	0	6	0	0	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................................................................AAGTATATAT--------ATTCGTGATCGGGA..................................................................................................................	24	1	5.00	5	0	0	0	0	0	0	4	0	0	1	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................................................................GTATATAT--------ATTCGTGATCGGGATCA...............................................................................................................	25	1	4.00	4	0	0	0	0	0	0	1	0	3	0	0	0	0	0	0	0	0
..................................................................................................................GCCCG-------------------------------------------------------------------------------------------------------TG--------AAA--GTGTAATAGGCA-TAAGGA....................................................................................................................................................................	28	1	2.00	2	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0
.............................................................................................................................................................................................................................................................................................................CGGGATCAATAGTCGAGTCGATCT...............................................................................................	24	1	2.00	2	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0
................................................................................................................................................................................................................................................................................TAAAGTATATAT--------ATTCGTGATCGGG...................................................................................................................	25	1	1.00	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
.............................................................................................................................................................................................................................................................................................................CGGGATCAATAGTCGAGTCGATCTGA.............................................................................................	26	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
..........................................................................................................................................................................................................................................................................................................................CGAGTCGATCTGACCATGCCCGTCT.................................................................................	25	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
..........................................................................................................................................................................................................................................................................................AT--------ATTCGTGATCGGGATCAA..............................................................................................................	20	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
....................................................................................................................................................................................................................................................................................GTATATAT--------ATTCGTGATCGGGATCAAT.............................................................................................................	27	1	1.00	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
T----------------AAC----------------------------------------------------------------------------------GCAAAAACTCAAGCCCG-------------------------------------------------------------------------------------------------------TG--------AAA--GTG....................................................................................................................................................................................	29	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
..............................................................................................................................................................................................................................TG--------AAA--GTGTAATAGGCA-TAAGGAAGC.................................................................................................................................................................	26	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................................................................GTATATAT--------ATTCGTGATCGGGATCAATA............................................................................................................	28	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................................................................GTATATAT--------ATTCGTGATCGGGATC................................................................................................................	24	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
...........................................................................................................................................................................................................................................................................................................ATCGGGATCAATAGTCGAGTT....................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
.........................................................................................................................................................................................................................................................................................................TGATCGGGATCAATAGTC.........................................................................................................	18	1	1.00	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................................................................................................................TCTGACCATGCCCGTCTGTCCGTA..........................................................................	24	2	0.50	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................................................................................................................TGACCATGCCCGTCTGTCCGTATGAG---------------------------------------------------------------------A	27	2	0.50	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
..........................................................................................................................................................................................................................................................TAAGGAAGCGTTTCCGACTATATA..................................................................................................................................................	24	3	0.33	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
.....................................................................................................................................................................................................................................................GGCA-TAAGGAAGCGTT..............................................................................................................................................................	16	8	0.13	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
..........................................................................................................................................................................................................................................................................................................................CGAGTCGATCTGACCAT.........................................................................................	17	13	0.08	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
..................................................................................................................................................................................................................................................................................................................TCAATAGTCGAGTCGAT.................................................................................................	17	14	0.07	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
..........................................................................................................................................................................................................................................................................................................................CGAGTCGATCTGACCA..........................................................................................	16	15	0.07	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
......................................................................................................................................................................................................................................................................TCCGACTATATAAAGTATATAT--------ATT.............................................................................................................................	25	20	0.05	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................................................................................................TTCCGACTATATAAAGTATATAT--------ATT.............................................................................................................................	26	20	0.05	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
...............................................................................................................................................................................................................................................................AAGCGTTTCCGACTATATAAAGT..............................................................................................................................................	23	20	0.05	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
....................................................................................................................................................................................................................................................................TTTCCGACTATATAAAGTATATAT--------ATT.............................................................................................................................	27	20	0.05	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0

droSec2

T----------------TTAA--------------------------------------------------------------------------------CA------TTAACA------------------TTATACTA---------------------------------------------------------------------------------------------GATAGATACTAGGTA-CTAGGAAGCGTTTCCGACCATATAAAGTATATAT--------ATTCTTGATTAGGATCAATAGCCGAGTCGATCTGGCCATGGCCATCTGTTTTT---------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
.........................................................................................................................................................................................................................................................................................................TGATTAGGATCAATAGCCGAGTCGAT.................................................................................................	26	6	0.17	1	0	0	1	0

droYak3

T----------------TTGA---------------------------------TCAGCTTGAACAAA---------------------------------------A-ATA------------------------------------------------------CTTTTTT------------------------------------------TAGTTTTTG-------AAAAGTATGTAACAGGCAGCGTTTCCGCGTTTCCGACCATATAAAGTATATAT--------ATTCTGGATCAGGATCAATAGCTAAGTCGATCTGGCCATGTCCGTCTGTC------------------------------------------------------------------------------

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

No Reads

droEre2

C----------------TAAA------------------A------------------------TTTAATTTTGGTTT---------------GTTTTTAGTATAATAAAAATAA-------------------------------AGCTAGAATAAAACGG----------------------------------------------TATAATAGGTTCCTTG-------AAAATCATGTAACAGGTA--AAGGAAG------CGACCAAATAAAGTATGTATATACAT---ATCCTGATGAGGATCAATAGCCGAGTCGATCTGGCCATGTCTGTCCGTCTCT---------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
...............................................................................................................................................................................................................................................................................................................GGATCAATAGCCGAGTCGATCTGGCCA..........................................................................................	27	20	0.10	2	2	0	0	0	0	0	0

dvi_4599

scaffold_12855:9983660-9983810 -

Candidate

Unknown

Predicted structure

Flybase annnotation

Repeatable elements

Sense Strand Reads

Anti-sense strand reads

Re-alignment of all predicted orthologs

Re-alignment of all predicted orthologs with sRNA reads

CAAGCGTCACGATAGTTCATAACCCACCTCGCAGTGTTCGTGCAGCAGGCCACTCGATTTTGAGTTTATGTCAAACACAAATTGTGCTTTTAATTTGTTGTTCTTTCGATCCCGTGTTATACACACACACACACGTAAGAGGCTGGGGTATTTCATATATATATACTTGTCATAGTTGTCAGCTGAGCTATATCGGTACAGGCAGACAGAAATTCTTTTATTTTAACATAAGTTTTGAAAAAACAAAAAGT ************************************************(((.((((...(((........(((((((((((........)))))).))))).......)))((((...))))(((((((((((..................)))))))))))(((......)))...((((...)))).)))))))...************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	SRR060677 Argx9_ovaries_total	V053 head	SRR060679 140x9_testes_total	SRR060676 9xArg_ovaries_total	SRR060685 9xArg_0-2h_embryos_total	GSM1528803 follicle cells	M047 female body	SRR060658 140_ovaries_total	SRR060681 Argx9_testes_total	SRR060684 140x9_0-2h_embryos_total	SRR060662 9x160_0-2h_embryos_total	SRR060659 Argentina_testes_total	SRR060674 9x140_ovaries_total	SRR060675 140x9_ovaries_total	SRR060680 9xArg_testes_total	SRR060686 Argx9_0-2h_embryos_total	V116 male body
................................................................................................................................................TGGGTATTTCATATATATATACT....................................................................................	23	1	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...............................CAGTGTTGGTGAAGCAGGCC........................................................................................................................................................................................................	20	2	2	0.50	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.......................................................................................................................................TAAGAGGCTGGGGTATTTCATATGTAT.........................................................................................	27	1	15	0.27	4	1	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0
.........................................................................................................................................AGAGGCTGGGGTATTTCATAT.............................................................................................	21	0	20	0.15	3	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.........................................................................ACCACTAATTCTGCTTTTAA..............................................................................................................................................................	20	3	17	0.12	2	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0
.............................................CAGGCCACTCGCTTCTAAG...........................................................................................................................................................................................	19	3	9	0.11	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
..............................................................................................................................................................................................TATCGGTACAGGCAGACAGA.........................................	20	0	20	0.10	2	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0
............................................................................................................................................GGCTGGGGTATTTCATATATATATA......................................................................................	25	0	20	0.10	2	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0
........................................................................................................................................AAGAGGCTGGGGTATTTCATAT.............................................................................................	22	0	20	0.10	2	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0
..........................................................................................................................................GAGGCTGGGGTATTTCATATAT...........................................................................................	22	0	20	0.10	2	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0
.........................................................................................................................................AGAGGCTGGGGTATTTCATATATATAT.......................................................................................	27	0	20	0.10	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0
........................................................................................................................................AAGAGGCTGGGGTATTTCATATA............................................................................................	23	0	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0
...........................................................................................................................................AGGCTGGGGTATTTCATATATATAT.......................................................................................	25	0	20	0.05	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
...................................................................................................GTGCTTTCGATCCTGTCTT.....................................................................................................................................	19	3	20	0.05	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
..........................................................................................................................................GAGGCTGGGGTATTTCATATATATA........................................................................................	25	0	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1
........................................................................................................................................AAGAGGCTGGGGTATTTCATATATAT.........................................................................................	26	0	20	0.05	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
.............................................................................................................................................GCTGGGGTATTTCATATA............................................................................................	18	0	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0
..........................................................................................................................................GAGGCTGGGGTATTTCATATATATAT.......................................................................................	26	0	20	0.05	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0