dpe_565

Name	Class	Family	Strand
TART_B1	LINE	Jockey	-

##################################################--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- GAGCGGGACCAGGCGGCAGCCTACAATGGAATTTGACCACAAATCATTTGGTGAGTTATCATGAGAATACGTCTTTGATCCTATTACGATGTCAGCTATATCTTTAATCATTTAACTTGATGTCTTTGTCTCCAGCACAATCAGCACACACTCCACCAGCAGCAGCAACAGCAGTTGCAACAGCACCAGCAGCAACATGCCCCGTCCATGCATCAGTATGATAACGGNNNNNNNNNNNNNNNNNNNNNNNN ************************************************((((....))))((((..(((((.((((....((((.(((((.....)))))..))))...))))...))))).....))))..........................(((((.((....)).)))))..........(((......))).************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V057 head	M042 female body
.............................................................................................................TTTTAACTTGAAGACTTTGTC.........................................................................................................................	21	3	9	0.11	1	1	0
..........................................................................................................................................................ACCAGCAGCAGCAACAGCAG.............................................................................	20	0	20	0.05	1	0	1

CTCGCCCTGGTCCGCCGTCGGATGTTACCTTAAACTGGTGTTTAGTAAACCACTCAATAGTACTCTTATGCAGAAACTAGGATAATGCTACAGTCGATATAGAAATTAGTAAATTGAACTACAGAAACAGAGGTCGTGTTAGTCGTGTGTGAGGTGGTCGTCGTCGTTGTCGTCAACGTTGTCGTGGTCGTCGTTGTACGGGGCAGGTACGTAGTCATACTATTGCCNNNNNNNNNNNNNNNNNNNNNNNN ************************************************((((....))))((((..(((((.((((....((((.(((((.....)))))..))))...))))...))))).....))))..........................(((((.((....)).)))))..........(((......))).************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M042 female body	V057 head
................................................................................................................................AGAGGTCGTGTTAGACGCGT.......................................................................................................	20	2	3	0.33	1	1	0
...................................................................................................................................GGGCGTGTTAGTCGTGCG......................................................................................................	18	2	3	0.33	1	1	0
....................................................................................................................AACTACAGAAAAGGAGGTC....................................................................................................................	19	2	8	0.25	2	1	1
..................................................................................................................TTAACTACAGAAAAGGAGGTC....................................................................................................................	21	3	20	0.25	5	5	0
........................................................................................................................................................................GTCCTCAACGCTGTGGTGGT...............................................................	20	3	20	0.05	1	1	0
..........................................................................................................................................................................CGTCAACGTGGTCGAGGTCG.............................................................	20	2	20	0.05	1	0	1

Species	Coordinate	ID	Alignment
droPer2	scaffold_1:5019184-5019434 -	dpe_565	GAGCGGGACCAGGCGG----CAGCCT------ACAATGGAATTTGACCA----------------------CAAA----TCATTTGGTGAGTTATC-A---------TG-----AGAATACGTCTTTGAT-------CCTAT---------------------T---ACG------------------------------------------------------------------------------ATGTC-----------------------------------AGCTAT------ATCTTTAATCA---------------------------------------------------------------------------TTTA---ACTTGATG----TCTTTGT---------------------------------CTCCAGCACAATCAGCACACACTCC---------------------------ACCAGCAGCAGCAACAGCAGTTGCAACAGCA---------CCAGCAGCAACATGCCCCGTCCATGCA-------------------------TCAGT-------------ATGATAACGGNNNNNNNNNNNNNNNNNNNNNNNN
dp5	4_group3:3539270-3539496 -		GAGCGGGACCAGGCGG----CAGCCT------TCAATGGAATTTGACCA----------------------CAAA----TCATTTGGTGAGTTATC-A---------TG-----AGAATACGTCTTTGAT-------CCTAT---------------------T---ACG------------------------------------------------------------------------------ATGTC-----------------------------------AGCTAT------ATCTTTAATCA---------------------------------------------------------------------------TTTA---ACTTGATG----TTTTTGT---------------------------------CTCCAGCACAATCAGCACACACTCC---------------------------ACCAGCAGCAGCAACAGCAGTTGCAACAGCA---------CCAGCAGCAACATGCCCCGTCCATGCA-------------------------TCAGT-------------ATGATAACGG------------------------
droWil2	scf2_1100000004949:1596626-1596833 -		GC--AGGTGCTGCTAA----TAATTT------GCAATGGAATTTAACCA----------------------CAAA----TCATTTGGTAAGACTT------------TGACTTAAACA--------------------------------------------TTTCAAT-------------TG-----------------------------A----AA-----------C-------------------------------------------------------------------TAA---------TTCTTCTAATGCTCAAATACCT------------------------------------------------------------------------TGTTTAC---------------------------------CCACAGCAAACTCAACAAAATCTGC---------------------------AGCAGCAGCAAC---AGCAACAGCTACAACA---------GCAGCAGCAACATCCCACGCCCATGCA-------------------------GCAAT-------------ACGACAGCAG------------------------
droVir3	scaffold_13246:547262-547451 +		GC--GGGCGCGGCCAG----CAATCT------GCAATGGAATCTGACCA----------------------CGAA----TCACTTGGTAGGTTCGCAA----------------G----------------------CCTGA---------------------A---ATA-------------------------------------AACTCAACTTCAT-----------TCAATAA-------------------------------------------------------------TAA---------TTT-------------------------------------------------------------------------------------------TTATACT---------------------------------TTGCAGCAAAATCAGCATACTCTGC---------------------------AGCAGCATCAGCAGCAACAATT---------------------GCAGCAGCATATTACGCCCATGCATCA----------------------GCAGT-------------ACGACAAC--------------------------
droMoj3	scaffold_6473:14043749-14043979 -		CCGCTGGCCAT-GCAG----CAGCTC------AAGATGGAAACGCTGCCACAGCTGCAGCAGCAGCTGCAACAGC----TGACGTCGCAGGTGCAT-----------------------GCGGCACGTGG-------CATGG---------------------TG--CCG------------------------------------------------------------------------------CCGCC-----------------------------------AACTGT------GTCAGCATCCA---------------------------------------------------------------------------ATGC---GCAGCTGA----TCAGCTT---------------------------------CTCCACCAGCAGCAGCAACAGCAGCAGC------------------AGCAACAACA---------ACAACAACAGCAGCAGCA---------GCAGCAGCAACA-GCAGCGCCCAAGCT-------------------------TCAGT-------------A---------------------------------
droGri2	scaffold_15252:4695086-4695298 -		CAGCAGCAGCA-GCAG----CAGCCACAATTGCCAGTAGGACA-----A-------CAGCAGCAGCAATATCAGCTCACTCCTCAGCTAGGCTTGCCA---------------------------------------------------------------------CT-------------GC-----------------------------C----CT-----------C-------------------------------------------------------------------AAACTTTAATAA---------TTTACAATCGACT---------------------------------------------------------------G----C---TTTTCCA---------------------------------CTGCAGCAGCAGCAACATCAACAGCAAC------------------AGCAATATCCCCAACAGC------AGCAGC---AACA---------GCAACAGCAACAT-------CAGTTCATCAACAATGCA--------------CCA-------------------------------------------------
droAna3	scaffold_12916:3438266-3438454 +		GTCCTGGGGCTGGCAG----CAATCC------GCAGTGGAATCTGACCT----------------------CAAA----TCATCTGGTAGGTGGC-------------------------------A-------------------------TAGCCAG--------------------------------------------------GTCC------------------TTGTCGG--------------------------------------------------------GCATT------------------------C---------------------------------------------------------------------------------------------------------TAACTCACAGAATCAATTGCAGCACAACCAGCACACGCTCC---------------------------ACCAGCAACAGC------AGTTGC---AACA---------GCAGCAGCAACATGTCCCGCCAATGCA-------------------------TCAGT-------------ATGATAACAG------------------------
droBip1	scf7180000396737:1332407-1332609 -		GTGCTGGGGCAGGCGG----CAATCT------GCAGTGGAATCTGCCCA----------------------CAAA----TCATCTGGTAGGTGGAGGA----------------AG------------------------------------------C--------------------------------------------------TACCAGAATAG-----------TAGTCAG--------------------------------------------------------ACATT------------------------CTA-----------------------------------------------------ACCTG---------------CA----CATTCGT---------------------------------TTCCAGCATAACCAGCACACGCTCC---------------------------AGCAGCAGCAGCAGCAGCAATTGCAACAGCA---------GCAGCAGCAACATGTCCCGCCCATGCA-------------------------TCAGT-------------ATGATAATAG------------------------
droKik1	scf7180000302472:745618-745820 -		GTCCCGGCACTGGCAG----CAATCT------GCAATGGAACCTAAGCA----------------------CAAA----TCATCTGGTGGGTTAAGCA----------------AATATCC---------------------------------------------------------------------------------------------CAGAAA-----------TTATCAA----------------------------------------------------------------------------ACAAATATCCTAA---------------------------------------------------AACTTGTATCAAATT---------------CATT---------------------------------TTGCAGCATAATCAGCACACGCTCC---------------------------AGCAGCAGCAGC------AACTGCAACAGCA---------GCAGCAGCAACATGTCCCGCCCATGCA-------------------------TCAGT-------------ATGATAA---------------------------
droFic1	scf7180000453882:156909-157096 -		GAACAGCAACATTAAG----CAGGCA------TCGGTGAAGCTGATCGA----------------------AGGA----TACTCGGATC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAAGGATACGCGCAATCACAAGAAGGTCTATCATAAAAAGGCCAAGAAGCG----ATCT---GGCCCCAA----TCACAAG-------------------CGC-----------CACTTGCAACAGCAGCAAG------------------------------------------------TGCAGTTGCAGCAGCA---------GCAACAGCAACATCTGCAGTCATTGC------------------------------------------------------------------------------
droEle1	scf7180000491046:127001-127228 -		TAGCAAC----GGCAG----CAATCT------GCAGTGGAACCTAACTG----------------------CAAA----TCATCTGGTGGGTTTGCAA----------------AGAGTATTCTTAAAAT-------TCTATC--------------------T---TC----------------------------------------------------------------AAAAACGGCAAAATATTATT--------TA-------AAAACTTCTCTA------------------------AAATA---------------------------------------------------------------------------TATA---TTTTTATT----ATTTTCA---------------------------------TTACAGCAAAATCAGCTGGCGCTGC---------------------------AACAGCAGCAGC------AA---CTACAGCA---------ACACCAGCAACATGCCCCGCCCATGCA-------------------------TCAAT-------------ACAACAAC--------------------------
droRho1	scf7180000780006:14909-15169 -		GTCCTGGCAACGGCAG----CAATCT------GCAGTGGAATTTGACAA----------------------CAAA----TCACCTGGTGGGTTTACCA----------------ACAGTATTTGATAAATAAATCTGTCTATCTGGTAAAAATAACCAGTTATTTTAAT-------------TA-----------------------------A----AATTTAACCAAAAATGGAGAGTAGAAATTTTCTAAAACATATTTGCATT------------------------------------------------------------------------------------------------------------------------------------------TACCTGA---------------------------------CTACAGCAAAATCAGCTGACGCTGC---------------------------AACAGCAGCAGC------AA---CTACAGCA---------ACACCAGCAACATGCCCCGCCCATGCA-------------------------TCAAT-------------ATAACA----------------------------
droBia1	scf7180000302188:210810-210988 -		AGGCAGCATC-AGCAA----CAACCG------CCAGTGGCATTGT---------------------------------------------------------------------------------------------------------------------------TGTTGAGAACTATTTTAACGAATATGAGCGTCAGGAAATCATTTATC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATCATCC-----------CACAAGCAACAGTAGCAAAAGTAGC---------------------------AACAATAGCAGCAGCAGCAACAGCAACAGCA---------ACT----------------------CGGCAGCAACACGCCAACTTCCCCGCAGCAAT-----------------------------------------------
droTak1	scf7180000415079:151165-151362 +		GGGGAGGACCTGGCAG----CAATCT------GCAGTGGAACCTGACCC----------------------CAAA----TCATATGGTAAGTTTATCA----------------GGAATATT------------------------------------------------------------------------------------------AATTATAT-----------TTAAAAAGTAGAAAATAATGAAAATAAAAATGTATT------------------------------------------------------------------------------------------------------------------------------------------TATTAAA---------------------------------TTACAGCACAATCAGCAAACGCTTC---------------------------ATCAGCAGCAA------------------CT---------ACAGCAGCAAAATGCCCCGCCCATGCA-------------------------TCAGT-------------ACGACAA---------------------------
droEug1	scf7180000409016:61318-61498 -		GAAC-------GGCAG----CAATCT------GCAGTGGAACCTGACCA----------------------CAAA----TCATCTGGTGAGTGAACTT----------------ATTATT--------------------------------------------------------------TT-----------------------------A----TT-----------T-------------------------------------------------------------------TAT---------TTATTTTATTTACTAAATATTT---------------------------------------------------------------A----A---TATTTAA---------------------------------TTGTAGCACAATCAGCATACGCTCC---------------------------ATCAGCAGCAA---------------CAGCT---------ACAGCAACAACATGCCCCGCCCATGCA-------------------------TCAGT-------------ACGACAA---------------------------
dm3	chrX:21204429-21204662 -		GAGCCAGATCTACCAG----CAGATT------CCGGCGCACTTGGCGCC-----------------------GC-------AACTGGCGGCCAATGGC----------------------------AA------------------------------T--------------------------------------------------CCCCACTCCAT-----------TTATCAGCCGCTAGTTGCTGTT-----------------------------------AGCCAG------GGCTCCATATA-----------------------------------------------------------------------TGTATCCA---ATATGGCGACAA--TGCGTCGCCAGAACAGTCAGGGCGGCCCACAGATACCGG---------------------CGCACC------------------AGCATCC------------ACCCAGCTTGCATCAGCA---------ACAGCAGCAACCACCGCCCCCCTCGCA-------------------------GCAGC-------------A---------------------------------
droSim2	x:19937316-19937549 -		GAGCCAGATCTACCAG----CAGATT------CCGGCGCATTTGGCGCC----------------------CCAA--------CTGGCGGCGAATGGC----------------------------AA------------------------------T--------------------------------------------------CCCCACTCCAT-----------TTATCAGCCGCTAGTTGCTGTT-----------------------------------AGCCAG------GGCTCCATATA-----------------------------------------------------------------------TGTATCCA---ATTTGGCCACAA--TGCGTCGCCAGAACAGCCAGGGCGGCCCACAGATACCGG---------------------CGCACC------------------AGCATCC------------ACCCAGCTTGCATCAGCA---------ACAGCAGCAACCCCCGCCCCCCTCGCA-------------------------GCAGC-------------A---------------------------------
droSec2	scaffold_6:1124516-1124708 -		AACC-GCACCA-AGAG----CCAGCAGAACTTCCAGCACACTCTTCGTA----------------------TGCA----GCAGATGATGGCTC-----------------------------------------------------------------C--------------------------------------------------CTCCATGCCCA-----------ACATCAG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAAT---------------------------------ATGTACCAT---------------CACCAGCAGCAACAACAGCAACAGCTGCCCCTGCAGCAA---------------CAGCA---------GCAGCAGCAACAGCAACCT-CTGATGAGCA----------------------GCAGTCAGAGCATGCAGAATGTTAAC-G------------------------
droYak3	3R:27587687-27587901 +		GCGCATCCAAC-GCGCCGAGTACTCT------TCAAC----TTGGA-------------------------TAAA----TTGCCTTATGATTTATTGAATGCACCGCAGCCGCAGCCG--------------------------------------------CATCCAC-------------TG-----------------------------G----AG-----------C-------------------------------------------------------------------CAA---------TTTTATCGAA----------------------------------------------------------GCA----CTCA---GGTCCGAG----TCACTAC---------------------------------CACCAGCAACATCAGAAGCAGCAGC---------------------------ATCAGCAGCAGCAACAGCAGCAGCAGCAGCA---------TCTGCAGCAACACGAACCGCAACAGCA-------------------------ACAGC-------------A---------------------------------
droEre2	scaffold_4845:6813776-6814006 +		CC--TGGCAACGGCAA----CAATCT------GCACTGGAACCTGACCA----------------------CAAA----TCATCTGGTGGGTAAAGCA----------------AGAAGCCTACTTTGAA-------A-TA-C--------------------T---TC---------------------------------------------------------------------------------GAAATTAAATATGCATATATCGAACTTCTTACGGCAATGGCTTT------TTT-T--------------TAACCCAA---------------------------------------------------AACCC--------TT---------------CATC---------------------------------TTACAGCACAACCAGCATACGCTTC---------------------------ACCAGCAGCAGC------AA---CTTCAGCAGCAGCAGCAGCAGCAGC---------------AGCA-------------------------GCAGT-------------ACGACAAC--------------------------

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droPer2

GAGCGGGACCAGGCGG----CAGCCT------ACAATGGAATTTGACCA----------------------CAAA----TCATTTGGTGAGTTATC-A---------TG-----AGAATACGTCTTTGAT-------CCTAT---------------------T---ACG------------------------------------------------------------------------------ATGTC-----------------------------------AGCTAT------ATCTTTAATCA---------------------------------------------------------------------------TTTA---ACTTGATG----TCTTTGT---------------------------------CTCCAGCACAATCAGCACACACTCC---------------------------ACCAGCAGCAGCAACAGCAGTTGCAACAGCA---------CCAGCAGCAACATGCCCCGTCCATGCA-------------------------TCAGT-------------ATGATAACGGNNNNNNNNNNNNNNNNNNNNNNNN	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ACCAGCAGCAGCAACAGCAG............................................................................................................................	20	20	0.05	1	0	1	0	0	0	0

dp5

GAGCGGGACCAGGCGG----CAGCCT------TCAATGGAATTTGACCA----------------------CAAA----TCATTTGGTGAGTTATC-A---------TG-----AGAATACGTCTTTGAT-------CCTAT---------------------T---ACG------------------------------------------------------------------------------ATGTC-----------------------------------AGCTAT------ATCTTTAATCA---------------------------------------------------------------------------TTTA---ACTTGATG----TTTTTGT---------------------------------CTCCAGCACAATCAGCACACACTCC---------------------------ACCAGCAGCAGCAACAGCAGTTGCAACAGCA---------CCAGCAGCAACATGCCCCGTCCATGCA-------------------------TCAGT-------------ATGATAACGG------------------------	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
........................................................................................................................................................................................................................................................................................................................................................................................................................................................................TCAGCACACACTCC---------------------------ACCAGCAGCAG.....................................................................................................................................	25	1	2.00	2	0	0	0	0	0	0	0	0	2	0
...CGGGACCAGGCGG----CAGCCT------TCAATG...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	1	0	0	0	0	0	0	0	0

droWil2

GC--AGGTGCTGCTAA----TAATTT------GCAATGGAATTTAACCA----------------------CAAA----TCATTTGGTAAGACTT------------TGACTTAAACA--------------------------------------------TTTCAAT-------------TG-----------------------------A----AA-----------C-------------------------------------------------------------------TAA---------TTCTTCTAATGCTCAAATACCT------------------------------------------------------------------------TGTTTAC---------------------------------CCACAGCAAACTCAACAAAATCTGC---------------------------AGCAGCAGCAAC---AGCAACAGCTACAACA---------GCAGCAGCAACATCCCACGCCCATGCA-------------------------GCAAT-------------ACGACAGCAG------------------------	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................AACTCAACAAAATCTGC---------------------------AGCAGC..........................................................................................................................................	23	1	1.00	1	1	0	0	0	0
....................................................................................................................................................................................................................................................................................................................................................................................................................................................................AAACTCAACAAAATCTGC---------------------------AGCAGC..........................................................................................................................................	24	1	1.00	1	0	0	0	1	0
....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GC---------------------------AGCAGCAGCAAC---AGCAACAGC........................................................................................................................	23	20	0.05	1	0	0	0	1	0
.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................C---------------------------AGCAGCAGCAAC---AGCAACAG.........................................................................................................................	21	20	0.05	1	0	0	0	0	1

droVir3

GC--GGGCGCGGCCAG----CAATCT------GCAATGGAATCTGACCA----------------------CGAA----TCACTTGGTAGGTTCGCAA----------------G----------------------CCTGA---------------------A---ATA-------------------------------------AACTCAACTTCAT-----------TCAATAA-------------------------------------------------------------TAA---------TTT-------------------------------------------------------------------------------------------TTATACT---------------------------------TTGCAGCAAAATCAGCATACTCTGC---------------------------AGCAGCATCAGCAGCAACAATT---------------------GCAGCAGCATATTACGCCCATGCATCA----------------------GCAGT-------------ACGACAAC--------------------------	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
......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................T---------------------GCAGCAGCATATTACGCCCA.................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.........................T------GCAATGGAATCTGACCA----------------------CGAA----TCACT.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	27	1	1.00	1	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
.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTACGCCCATGCATCA----------------------GCAGT-------------..................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ATATTACGCCCATGCATCA----------------------GC..................................................	21	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ATCAGCAGCAACAATT---------------------GCAGCAGC.............................................................................................	24	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CATCAGCAGCAACAATT---------------------GCAGCAGC.............................................................................................	25	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................C---------------------------AGCAGCATCAGCAGCAACAATT---------------------GCAGC................................................................................................	28	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AGCAGCATCAGCAGCAAC..............................................................................................................................	18	20	0.05	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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

CCGCTGGCCAT-GCAG----CAGCTC------AAGATGGAAACGCTGCCACAGCTGCAGCAGCAGCTGCAACAGC----TGACGTCGCAGGTGCAT-----------------------GCGGCACGTGG-------CATGG---------------------TG--CCG------------------------------------------------------------------------------CCGCC-----------------------------------AACTGT------GTCAGCATCCA---------------------------------------------------------------------------ATGC---GCAGCTGA----TCAGCTT---------------------------------CTCCACCAGCAGCAGCAACAGCAGCAGC------------------AGCAACAACA---------ACAACAACAGCAGCAGCA---------GCAGCAGCAACA-GCAGCGCCCAAGCT-------------------------TCAGT-------------A---------------------------------	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
...........................................................................................................................................TGG---------------------TG--CCG------------------------------------------------------------------------------CCGCC-----------------------------------AACTGT------GTCAGC...............................................................................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	0	0	0	1	0
.......................................................................................................................GCGGCACGTGG-------CATGG---------------------TG--..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	1	1	0	0	0	0	0
...............G----CAGCTC------AAGATGGAAACGCT...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	1	0	0	0	0	0
...............G----CAGCTC------AAGATGGAAACGC....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	1	0	0	0	0	0
.........................................................................................................................GGCACGTGG-------CATGG---------------------TG--CCG------------------------------------------------------------------------------CCGC.....................................................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	1	0	0	0	0	0
.................................................................CTGCAACAGC----TGACGTCGCAGGT.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	1	0	0	0	0	0
...........................................................................................................................................................................................................................................................................................................................................................................................................................T---------------------------------CTCCACCAGCAGCAGCAACA................................................................................................................................................................................	21	1	1.00	1	0	1	0	0	0	0
..........................................................................................GTGCAT-----------------------GCGGCACGTGG-------CATGG---------------------TG--CC........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	26	1	1.00	1	1	0	0	0	0	0
...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................A---------GCAGCAGCAACA-GCAGCGCCCAAGCC-------------------------....................................................	27	1	1.00	1	0	0	0	0	1	0
......................GCTC------AAGATGGAAACGCTGCC................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	1	0
................................AAGATGGAAACGCTGCCACAG............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	1	0	0	0	0
...................................................................GCAACAGC----TGACGTCGCA........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	1	1	0	0	0	0	0
.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GCAGCAGCAACA-GCAGCGCCC..................................................................................	21	2	0.50	1	0	0	0	0	1	0
..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CAACAGCAGCAGCA---------GCAGCAGCAAC.............................................................................................	25	20	0.05	1	1	0	0	0	0	0
.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................GCAGCAGCAACAGCAGCAGC------------------AGC...................................................................................................................................................	23	20	0.05	1	0	0	0	0	1	0
.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................CAGCAACAGCAGCAGC------------------AGCA..................................................................................................................................................	20	20	0.05	1	0	1	0	0	0	0
.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................AACAGCAGCAGC------------------AGCAACAACA---------AC.................................................................................................................................	24	20	0.05	1	1	0	0	0	0	0
...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CAACAACAGCAGCAGCA---------GCAGCAG.................................................................................................	24	20	0.05	1	1	0	0	0	0	0
................................................................................................................................................................................................................................................................................................................................................................................................................................................................CACCAGCAGCAGCAACAGCAGC...........................................................................................................................................................................	22	20	0.05	1	0	0	1	0	0	0
...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ACAACA---------ACAACAACAGCAGCAGCA---------GCAGC...................................................................................................	29	20	0.05	1	0	0	0	0	1	0
.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ACAACAGCAGCAGCA---------GCAGCA..................................................................................................	21	20	0.05	1	0	0	0	0	1	0

droGri2

CAGCAGCAGCA-GCAG----CAGCCACAATTGCCAGTAGGACA-----A-------CAGCAGCAGCAATATCAGCTCACTCCTCAGCTAGGCTTGCCA---------------------------------------------------------------------CT-------------GC-----------------------------C----CT-----------C-------------------------------------------------------------------AAACTTTAATAA---------TTTACAATCGACT---------------------------------------------------------------G----C---TTTTCCA---------------------------------CTGCAGCAGCAGCAACATCAACAGCAAC------------------AGCAATATCCCCAACAGC------AGCAGC---AACA---------GCAACAGCAACAT-------CAGTTCATCAACAATGCA--------------CCA-------------------------------------------------	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

droAna3

GTCCTGGGGCTGGCAG----CAATCC------GCAGTGGAATCTGACCT----------------------CAAA----TCATCTGGTAGGTGGC-------------------------------A-------------------------TAGCCAG--------------------------------------------------GTCC------------------TTGTCGG--------------------------------------------------------GCATT------------------------C---------------------------------------------------------------------------------------------------------TAACTCACAGAATCAATTGCAGCACAACCAGCACACGCTCC---------------------------ACCAGCAACAGC------AGTTGC---AACA---------GCAGCAGCAACATGTCCCGCCAATGCA-------------------------TCAGT-------------ATGATAACAG------------------------	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GC---AACA---------GCAGCAGCAACATGTC........................................................................................	22	1	1.00	1	0	0	1	0	0	0
........................................ATCTGACCT----------------------CAAA----TCATCTGCA.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	22	1	1.00	1	1	0	0	0	0	0
.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GCAACAGC------AGTTGC---AACA---------GCAGCAGCAAC.............................................................................................	29	1	1.00	1	0	1	0	0	0	0
.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GC---AACA---------GCAGCAGCAACATGT.........................................................................................	21	2	0.50	1	0	1	0	0	0	0

droBip1

GTGCTGGGGCAGGCGG----CAATCT------GCAGTGGAATCTGCCCA----------------------CAAA----TCATCTGGTAGGTGGAGGA----------------AG------------------------------------------C--------------------------------------------------TACCAGAATAG-----------TAGTCAG--------------------------------------------------------ACATT------------------------CTA-----------------------------------------------------ACCTG---------------CA----CATTCGT---------------------------------TTCCAGCATAACCAGCACACGCTCC---------------------------AGCAGCAGCAGCAGCAGCAATTGCAACAGCA---------GCAGCAGCAACATGTCCCGCCCATGCA-------------------------TCAGT-------------ATGATAATAG------------------------	Size	Hit Count	Total Norm	Total
No Reads

droKik1

GTCCCGGCACTGGCAG----CAATCT------GCAATGGAACCTAAGCA----------------------CAAA----TCATCTGGTGGGTTAAGCA----------------AATATCC---------------------------------------------------------------------------------------------CAGAAA-----------TTATCAA----------------------------------------------------------------------------ACAAATATCCTAA---------------------------------------------------AACTTGTATCAAATT---------------CATT---------------------------------TTGCAGCATAATCAGCACACGCTCC---------------------------AGCAGCAGCAGC------AACTGCAACAGCA---------GCAGCAGCAACATGTCCCGCCCATGCA-------------------------TCAGT-------------ATGATAA---------------------------	Size	Hit Count	Total Norm	Total
No Reads

droFic1

GAACAGCAACATTAAG----CAGGCA------TCGGTGAAGCTGATCGA----------------------AGGA----TACTCGGATC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAAGGATACGCGCAATCACAAGAAGGTCTATCATAAAAAGGCCAAGAAGCG----ATCT---GGCCCCAA----TCACAAG-------------------CGC-----------CACTTGCAACAGCAGCAAG------------------------------------------------TGCAGTTGCAGCAGCA---------GCAACAGCAACATCTGCAGTCATTGC------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droEle1

TAGCAAC----GGCAG----CAATCT------GCAGTGGAACCTAACTG----------------------CAAA----TCATCTGGTGGGTTTGCAA----------------AGAGTATTCTTAAAAT-------TCTATC--------------------T---TC----------------------------------------------------------------AAAAACGGCAAAATATTATT--------TA-------AAAACTTCTCTA------------------------AAATA---------------------------------------------------------------------------TATA---TTTTTATT----ATTTTCA---------------------------------TTACAGCAAAATCAGCTGGCGCTGC---------------------------AACAGCAGCAGC------AA---CTACAGCA---------ACACCAGCAACATGCCCCGCCCATGCA-------------------------TCAAT-------------ACAACAAC--------------------------	Size	Hit Count	Total Norm	Total
No Reads

droRho1

GTCCTGGCAACGGCAG----CAATCT------GCAGTGGAATTTGACAA----------------------CAAA----TCACCTGGTGGGTTTACCA----------------ACAGTATTTGATAAATAAATCTGTCTATCTGGTAAAAATAACCAGTTATTTTAAT-------------TA-----------------------------A----AATTTAACCAAAAATGGAGAGTAGAAATTTTCTAAAACATATTTGCATT------------------------------------------------------------------------------------------------------------------------------------------TACCTGA---------------------------------CTACAGCAAAATCAGCTGACGCTGC---------------------------AACAGCAGCAGC------AA---CTACAGCA---------ACACCAGCAACATGCCCCGCCCATGCA-------------------------TCAAT-------------ATAACA----------------------------	Size	Hit Count	Total Norm	Total
No Reads

droBia1

AGGCAGCATC-AGCAA----CAACCG------CCAGTGGCATTGT---------------------------------------------------------------------------------------------------------------------------TGTTGAGAACTATTTTAACGAATATGAGCGTCAGGAAATCATTTATC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATCATCC-----------CACAAGCAACAGTAGCAAAAGTAGC---------------------------AACAATAGCAGCAGCAGCAACAGCAACAGCA---------ACT----------------------CGGCAGCAACACGCCAACTTCCCCGCAGCAAT-----------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droTak1

GGGGAGGACCTGGCAG----CAATCT------GCAGTGGAACCTGACCC----------------------CAAA----TCATATGGTAAGTTTATCA----------------GGAATATT------------------------------------------------------------------------------------------AATTATAT-----------TTAAAAAGTAGAAAATAATGAAAATAAAAATGTATT------------------------------------------------------------------------------------------------------------------------------------------TATTAAA---------------------------------TTACAGCACAATCAGCAAACGCTTC---------------------------ATCAGCAGCAA------------------CT---------ACAGCAGCAAAATGCCCCGCCCATGCA-------------------------TCAGT-------------ACGACAA---------------------------	Size	Hit Count	Total Norm	Total
No Reads

droEug1

GAAC-------GGCAG----CAATCT------GCAGTGGAACCTGACCA----------------------CAAA----TCATCTGGTGAGTGAACTT----------------ATTATT--------------------------------------------------------------TT-----------------------------A----TT-----------T-------------------------------------------------------------------TAT---------TTATTTTATTTACTAAATATTT---------------------------------------------------------------A----A---TATTTAA---------------------------------TTGTAGCACAATCAGCATACGCTCC---------------------------ATCAGCAGCAA---------------CAGCT---------ACAGCAACAACATGCCCCGCCCATGCA-------------------------TCAGT-------------ACGACAA---------------------------	Size	Hit Count	Total Norm	Total
No Reads

dm3

GAGCCAGATCTACCAG----CAGATT------CCGGCGCACTTGGCGCC-----------------------GC-------AACTGGCGGCCAATGGC----------------------------AA------------------------------T--------------------------------------------------CCCCACTCCAT-----------TTATCAGCCGCTAGTTGCTGTT-----------------------------------AGCCAG------GGCTCCATATA-----------------------------------------------------------------------TGTATCCA---ATATGGCGACAA--TGCGTCGCCAGAACAGTCAGGGCGGCCCACAGATACCGG---------------------CGCACC------------------AGCATCC------------ACCCAGCTTGCATCAGCA---------ACAGCAGCAACCACCGCCCCCCTCGCA-------------------------GCAGC-------------A---------------------------------	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
...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GCAACCACCGCCCCCCTCGCA-------------------------GCAGC-------------A---------------------------------	27	1	2.00	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................................................................................................................................................................................................................................................T-----------------------------------AGCCAG------GGCTCCATATA-----------------------------------------------------------------------TGTA...............................................................................................................................................................................................................................................................	22	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................................................................................................................................................................................................CAA--TGCGTCGCCAGAACAGTCAGGGC...................................................................................................................................................................................................................	26	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TGCATCAGCA---------ACAGCAGCAACCAC..........................................................................................	24	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.........CTACCAG----CAGATT------CCGGCGCAA........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	22	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................................................................................................................................................................................................................................CACAGATACCGG---------------------CGCACC------------------AGCATC................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..............................................................................................................................................................................................................................................................................................................................................................................................TGTATCCA---ATATGGCGACAA--TGCG......................................................................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
............................................................................................................................................................................................................................................................................................................................................................................................................................................GCGGCCCACAGATACCGG---------------------C.............................................................................................................................................................................	19	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TCAGCA---------ACAGCAGCAACCACC.........................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droSim2

GAGCCAGATCTACCAG----CAGATT------CCGGCGCATTTGGCGCC----------------------CCAA--------CTGGCGGCGAATGGC----------------------------AA------------------------------T--------------------------------------------------CCCCACTCCAT-----------TTATCAGCCGCTAGTTGCTGTT-----------------------------------AGCCAG------GGCTCCATATA-----------------------------------------------------------------------TGTATCCA---ATTTGGCCACAA--TGCGTCGCCAGAACAGCCAGGGCGGCCCACAGATACCGG---------------------CGCACC------------------AGCATCC------------ACCCAGCTTGCATCAGCA---------ACAGCAGCAACCCCCGCCCCCCTCGCA-------------------------GCAGC-------------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
..........................................................................................................................................................................................................................................................................................................................................................................................................................GTCGCCAGAACAGCCAGGGC...................................................................................................................................................................................................................	20	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droSec2

AACC-GCACCA-AGAG----CCAGCAGAACTTCCAGCACACTCTTCGTA----------------------TGCA----GCAGATGATGGCTC-----------------------------------------------------------------C--------------------------------------------------CTCCATGCCCA-----------ACATCAG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAAT---------------------------------ATGTACCAT---------------CACCAGCAGCAACAACAGCAACAGCTGCCCCTGCAGCAA---------------CAGCA---------GCAGCAGCAACAGCAACCT-CTGATGAGCA----------------------GCAGTCAGAGCATGCAGAATGTTAAC-G------------------------	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CAGCAACCT-CTGATGAGC...........................................................................	18	1	1.00	1	0	0	1	0
...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AGCA----------------------GCAGTCAGAGCATG......................................	18	1	1.00	1	0	0	1	0
........................................CTCTTCGTA----------------------TGCA----GCAGATGAT.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	22	1	1.00	1	1	0	0	0
............................ACTTCCAGCACACTCTTCGT.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	1	0	0	0
........................................CTCTTCGTA----------------------TGCA----GCAGATGA..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	1	0	0
.......ACCA-AGAG----CCAGCAGAACTTCCAGC............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	1	0	0
................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CAACAGCAACCT-CTGATGAGCA----------------------GC..................................................	24	1	1.00	1	0	0	1	0
AACC-GCACCA-AGAG----CCAGC........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	1	0	0	0	1
...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................A---------GCAGCAGCAACAGCAACC......................................................................................	19	6	0.17	1	0	0	0	1
......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CAGCAA---------------CAGCA---------GCAGCAGCAACAGCA.........................................................................................	26	18	0.06	1	0	0	1	0
........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GCAA---------------CAGCA---------GCAGCAGCAA..............................................................................................	19	20	0.05	1	0	0	1	0

droYak3

GCGCATCCAAC-GCGCCGAGTACTCT------TCAAC----TTGGA-------------------------TAAA----TTGCCTTATGATTTATTGAATGCACCGCAGCCGCAGCCG--------------------------------------------CATCCAC-------------TG-----------------------------G----AG-----------C-------------------------------------------------------------------CAA---------TTTTATCGAA----------------------------------------------------------GCA----CTCA---GGTCCGAG----TCACTAC---------------------------------CACCAGCAACATCAGAAGCAGCAGC---------------------------ATCAGCAGCAGCAACAGCAGCAGCAGCAGCA---------TCTGCAGCAACACGAACCGCAACAGCA-------------------------ACAGC-------------A---------------------------------	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
..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................AGAAGCAGCAGC---------------------------ATCAGCAGCA......................................................................................................................................	22	4	0.25	1	0	0	0	0	0	0	1	0	0	0	0
...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AGCAGCAGCAGCA---------TCTGCAGCA...............................................................................................	22	5	0.20	1	0	1	0	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AGC---------------------------ATCAGCAGCAGCAACAGCAGCAG.........................................................................................................................	26	5	0.20	1	0	1	0	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AGCAGCAACAGCAGCAGCAGCAGC..................................................................................................................	24	20	0.05	1	0	0	0	1	0	0	0	0	0	0	0
..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AGCAACAGCAGCAGCAGCAGC..................................................................................................................	21	20	0.05	1	0	0	0	1	0	0	0	0	0	0	0

droEre2

CC--TGGCAACGGCAA----CAATCT------GCACTGGAACCTGACCA----------------------CAAA----TCATCTGGTGGGTAAAGCA----------------AGAAGCCTACTTTGAA-------A-TA-C--------------------T---TC---------------------------------------------------------------------------------GAAATTAAATATGCATATATCGAACTTCTTACGGCAATGGCTTT------TTT-T--------------TAACCCAA---------------------------------------------------AACCC--------TT---------------CATC---------------------------------TTACAGCACAACCAGCATACGCTTC---------------------------ACCAGCAGCAGC------AA---CTTCAGCAGCAGCAGCAGCAGCAGC---------------AGCA-------------------------GCAGT-------------ACGACAAC--------------------------	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
......................................................................................................................................................................................................................................................................................................................................................................................................................................................................AACCAGCATACGCTTC---------------------------ACCAGC..........................................................................................................................................	22	1	1.00	1	0	1	0	0	0	0	0
....TGGCAACGGCAA----CAATCT------GCACTGGAAC.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	28	1	1.00	1	1	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AA---CTTCAGCAGCAGCAGCAGCA.....................................................................................................	22	2	0.50	1	0	0	0	0	1	0	0
....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AGCAGCAGC------AA---CTTCAGCAGCA..............................................................................................................	22	5	0.20	1	0	0	0	0	0	1	0
........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GCAGC------AA---CTTCAGCAGCAGC............................................................................................................	20	8	0.13	1	1	0	0	0	0	0	0
........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CTTCAGCAGCAGCAGCAGC......................................................................................................	19	16	0.13	2	0	0	1	0	0	1	0

dpe_565

scaffold_1:5019234-5019384 -

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

-20.7	-20.7	-20.7