dpe_1259

exon [dper_GLEANR_9408:2]; exon [dper_GLEANR_9408:3]; CDS [Dper\GL26874-cds]; CDS [Dper\GL26874-cds]; intron [Dper\GL26874-in]

Name	Class	Family	Strand
(CAG)n	Simple_repeat	Simple_repeat	+

##################################################------------------------------------------------------------------------################################################## CCAGCTGGGGGCCACGCCCGCGGGCACAGCCACCCACCAGCAGCAGCAGCATCATCATCAGCAGCAGCAGCAGCAGCAGCATCACCACCACCAGCAGCAGCATCAGATTCAGGTGCAAGTACAGCAACAACAGCATGTAAATCTGAGCCAGAGCAACTCCAGCACCGTCACC ************************************************((...((((..........((.((.((................)).)).))..........))))...))..************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V057 head	V050 head	M021 embryo	M042 female body
..............................................................................................CAGCACCATCAGATTCAGCT..........................................................	20	2	4	0.25	1	1	0	0	0
..............................................................................................CAGCAGCGTGAGATTCAGGTC.........................................................	21	3	5	0.20	1	0	1	0	0
..............................................................................................TAGCAGCATTAGATTCAGCTG.........................................................	21	3	6	0.17	1	1	0	0	0
.................................................TATCATCGTCAGCAGCAGCAGC.....................................................................................................	22	2	20	0.15	3	0	0	3	0
.........................ACACCCACCCACCACCAGCAG..............................................................................................................................	21	2	7	0.14	1	0	1	0	0
..............................................................................................TAGCAGCATGAGATTGAGGT..........................................................	20	3	10	0.10	1	1	0	0	0
.....................................................ATCATCAGCAGCAGCAGCAGC..................................................................................................	21	0	20	0.05	1	0	0	0	1

GGTCGACCCCCGGTGCGGGCGCCCGTGTCGGTGGGTGGTCGTCGTCGTCGTAGTAGTAGTCGTCGTCGTCGTCGTCGTCGTAGTGGTGGTGGTCGTCGTCGTAGTCTAAGTCCACGTTCATGTCGTTGTTGTCGTACATTTAGACTCGGTCTCGTTGAGGTCGTGGCAGTGG ************************************************((...((((..........((.((.((................)).)).))..........))))...))..************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M042 female body	V111 male body	V057 head
...............................................................................GTAGTGATGGTGGTCGTCGT.........................................................................	20	1	9	0.11	1	1	0	0
.............................GGTGGGTGGTCGTGGTCG.............................................................................................................................	18	1	12	0.08	1	0	1	0
............................................................................................TCGTCCTCGTCGTCTAAGTCC...........................................................	21	2	13	0.08	1	1	0	0
...............................................................................ATAGTGATGGTGGTCGTCGT.........................................................................	20	2	15	0.07	1	1	0	0
........TCCGGTGCGGACGCCCATG.................................................................................................................................................	19	3	20	0.05	1	0	0	1

Species	Coordinate	ID	Alignment
droPer2	scaffold_25:771879-772050 +	dpe_1259	CCAG-C---TGG--GGGCC-------ACGCCCGCGGG-C-ACAGCCACCCACC---------------------AGCAGCAGCAGCATC---------ATCATCAGCAGCAGCAGCAGCAGCAGCATCACCACCA------------CCAGCAG--------CAGCAT------CAGATT---CAGGT---GC---------------AA---GTAC---AGCAAC---AACAGCATGTAAATC------------------------------------T-GAGCCAGAGCAACTC---CAGCACC-GTCACC
dp5	XL_group1a:6541391-6541559 -	dps_2546	CCAG-C---TGG--GGGCC-------ACGCCAGCGGG-C-ACAGCCACCCACC---------------------AGCAGCAGCAGCATC---------ATCATCAGCAGCAGCAGCAGCAG---CATCACCACCA------------CCAGCAG--------CAGCAT------CAGATT---CAGGT---GC---------------AA---GTAC---AGCAAC---AACAGCATGTAAATC------------------------------------T-CAGCCAGAGCAACTC---CAGCACC-GTCACC
droWil2	scf2_1100000003789:1833-2002 -		ACAA-C---TGCAGCAGCA--------------------------------ACAATTGCAGCAACAAC------AGCAACAGCAGCAAC---------AACAGCAGCAACAACAACAGCAGCAGCAACAGCAGCA------------TCAGC--AACA------GCAAC---AGCAG---------------------CAGCGAATGCAA---CAGC---AACAGC---AACAGCAGCAACAAT------------------------------------TGCAGCAACAACAACAA---CAGCAGC-AGCAAC
droVir3	scaffold_12928:2231181-2231347 -		GCAG-C---AGCA------------------------------GCA--TCACCAGCAGCAGCAGCAGCATCACCAGCAGCAGCACCAGC---------AGCAGCAGCTGCAGCTGCAGCAG------CATCA---------------TCACC-----------------------AG------------CAGCAACAGCAGCATCAGCACCTCCAGC---AACAGC---AGCAGCAACAGCAGC------------------------------------AGCAGCAGCAGCACCTC---CAGCAGC-AGCAGC
droMoj3	scaffold_6473:3147549-3147710 +		CCAG-C---GGA---AACAGC-----CTGACACC------GCAGCA--ACACC---------------------AACAGCATCCGCATT---------CCCATCAACAGCAGCAGCAGCAA------CAGCAGCA------------GCAGCAG--CAGCAACAGCAG------CAGCAG---CAGCA---GC---------------------------AACAGC---AGCAGCAGCAGCAGC------------------------------------AACAGCAGCAGCACCAA---CAGCATC-CGCACC
droGri2	scaffold_98:33917-34085 -		C-AT-CTGGG-----AGCGG-CGG--GCTCTGG---------------TCAGC---------------------AGCAGCAGCAGCAGCAGCAGCGTCAACATCAGCAGCAGCAGCAGCAGCAGTTAAAACAGCA------------GCAGCAT--------CAGCAG------CAGAAAAAACAGCAGCAGCAACAGCAGC---------------------------AGCAG---CAT---C------------------------------------AGCAGCAGCAGCAGCAG---CAGCAGC-GTCAAC
droAna3	scaffold_13248:2270648-2270811 -	dan_4064	GCAG-G---AGCG------------------------------ACG--GCAGCAGCAGCAGCCACAGC------AGCAACAGCAGCAGC---------AGCAACAGCAACAGCAACAGCAA---CAGCAGCAGCA------------ACAGCAG--------CAGCAA------CAG---------------------CAGCAGCAGCCA---CAGC---AGCAGC---AACAGCAGCAACGAC------------------------------------AGCAGCAGCAGCAACGT---CAGCAGC-AGCAGC
droBip1	scf7180000396543:345604-345767 +		CCAG-C---AACA---GCA-------ACC----------------------CCAACAGACCGCACACC------TGCAACAGCAACATC---------AGCAGCAGCAGCAGCAACAGCAG---CAGCAGCACCA------------CCTGCAG--------CAGCAG------CAG---------------------CAGCAGCACCAC---CACC---AGCAAC---AACAACAACAACATC------------------------------------ATGCCCAGCAGCAGCAG---CAGCAAC-ACCACC
droKik1	scf7180000302390:719856-720020 -		CCAG-C----------------------------------------------------------------------CATCAGCAACAAC---------AGCAGCAGCAACAGCAGCAGCAGCAGCAACAACAGCA------------GCAAC--AGCA------GCAGC---AGCAG------------CAACAACAGCAAC---------------------------AGCAG---CAACACGTGGCCCACGGCAAGAAGGCAGCCAGAAAGCACCTGCAACATCTACAGCAACAG---CAGCAAC-AGCAAC
droFic1	scf7180000454072:698280-698451 +		CCAG-CCACC-----GGCGT-CAT--TCATCAT-----------CA--CCACC---------------------AGCAGCAGCAACAGC---AGCACCAGCATCAGCAGTAGCAGCAGCAG------CAGCATCAGCAGCA------TCAGCAG--------TAGCAG------CAG---------------------CAGCATCAGCAA---CTCC---AACATC---AACAGCAGCAACAGC------------------------------------AGCATCAACAGCAGCAA---CAGCAGC-ATCAAC
droEle1	scf7180000491356:120867-121032 -		CCAG-CCGCC-----GGCGG-CAT--TCACCAGCAAC-A-GCAGCA--ACACC---------------------AGCAACAGCAGCAAC---------ATCAGCAACAGCAGCAACATCTG------CAGCAGCA------------GCAACAT--CA------GCAA------CAG---------------------CAGCAACACCAT------CAGCAGCAACAACAGCAG---CAA---C------------------------------------ACCATCAGCAGCAGCAG---CAACACC-ATCAGC
droRho1	scf7180000780080:429534-429694 -		C---GCCGCG-----GGCGGT-----TCGCCGGT------GATGCT--TCACC---------------------AGCAGCAGCAGCATC---------AGCAACAGCAGCAGCAGCAGCATCAGCA---------------------ACAGC--AGCAGCAACAGCAA------CACCTT---CAGCA---GCAACATCAGC---------------------------AACACCATCAACAAC------------------------------------AGCAACACCACCAGCAG---CAGCACC-ATCAGC
droBia1	scf7180000301760:5644849-5645015 +		C---GCCGCG-----GGCGGT-----TCGCCGGT------GATGCT--CCACC---------------------AGCAGCAGCAGCAGC---------AGCAGCAGCAACAGCAGCAACATCAGCAGCAGCAGCA------------GCAGC--ACCA------GCAGC---AGCAG------------------------CAGCACCTG---CAAC---AGCAGC---AACACCACCAACACC------------------------------------TTCACCAGCAATTCGGG---CAGCAGC-AGCAGC
droTak1	scf7180000415345:325208-325385 +		C-AG-CAACAGC--CGGCTA-CAACGGCGCCAGCAAC-TTGATCAT--CATCG---------------------AGCCGCAGCAGCAGC---------AGCAGCAGCAACAACAGCAACAGCAGCAGCAGCCGCC------------GCAGC--AGCA------GCAACAG-TTCAG------------CTAC---------------------CAC---AGCAAC---AGCAGCAATAACAAC------------------------------------TACTACCACAGCAATGCCAGCA--AGCAGGCAGC
droEug1	scf7180000409061:49467-49653 -		T----CCGCC-----GGCGG-CAT--ACACCAGCAGC-A-TCAGCA--ACAGC------AGCACCAGC------AGCAACAACAGCAAC---------AACATCAGCAACAACAGCATCAGCAGCAACAACACCA------------CCAGCAG--------CAGCAA------CACCAC---CAA------------CAGCAGCAACAC---CACC---AACAGC---AACAACATCTACAAC------------------------------------AGCAGCAGCAGCAACAC---CAGCAGC-AGCAGC
dm3	chrX:5647021-5647190 +		GCAG-C---AGCA-------------ACACCA-------------------GCAGCACCAGCAGCAGCAACACCAGCAGCAGCAGCACC---------AGCAACACCAGCAGCAACAGCAG------CAGCAACA------CCAACATCAGCA-----------GCAG------CAA---------------------CAGCAACACCTT---CAGC---AGCAGC---AACACCACCAGCTGC------------------------------------AGCAGCAACAGCAGCAG---CAGCAGC-ATCAAC
droSim2	x:9192700-9192854 +		C---GCCGCG-----GGCGGT-----TCGCCGGT------GATGCT--TCACC---------------------AGCAGCAGCAGCAAC---------ATCAGCAGCAACAGCAGCAGCAGCAGCATCAACAGCA------------ACAGC--AGCA------GCAAC---ATCAG------------CAGCAACAGCAGC---------------------------AGCAG---CAACAC---------------------------------------CACCAGCAACAGCAG---CAGCATC-ATCACC
droSec2	scaffold_15:411144-411298 +		C---GCCGCG-----GGCGGT-----TCGCCGGT------GATGCT--TCACC---------------------AGCAGCAGCAGCAAC---------ATCAGCAGCAACAGCAGCAGCAGCAGCATCAACAGCA------------GCAGC--AGCA------GCAAC---ATCAG------------CAGCAACAGCAGC---------------------------AGCAG---CAACAC---------------------------------------CACCAGCAACAGCAG---CAGCATC-ATCACC
droYak3	X:18247254-18247420 +		C---GCCGCG-----GGCGGT-----TCGCCGGT------GATGCT--CCACC---------------------AGCAGCAGCAGCATC---------AGCAGCAACAACAGCAGCAGCAGCAGCAGCAACATCA------------ACAGCAG--------CAGCAGCAGCAACAG---------CA---GC---------------AT---CATC---AGCAGC---AACAGCAACAACACC------------------------------------ACCAGCAACAGCAGCAG---CAGCATC-ATCATC
droEre2	scaffold_4784:8771283-8771459 +		CCAA-C---GGG--GGTGC-------AGG--ATCTGGAC-AC--CA--CCACC---------------------ATCATCATCATCACC---------ATCACAGTCATGAGCAGCAGCAGCAGCAACAGCAGCA------------GCAGC--AACA------GCAGC---AACAG---------------------CAGCAGCAGCAT------CAGAAACAACAACAGCAG---CAACAGC------------------------------CCATGCAGACTGTTCCGCACCAC---CATCACT-ATCCCC

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droPer2

CCAG-C---TGG--GGGCC-------ACGCCCGCGGG-C-ACAGCCACCCACC---------------------AGCAGCAGCAGCATC---------ATCATCAGCAGCAGCAGCAGCAGCAGCATCACCACCA------------CCAGCAG--------CAGCAT------CAGATT---CAGGT---GC---------------AA---GTAC---AGCAAC---AACAGCATGTAAATC------------------------------------T-GAGCCAGAGCAACTC---CAGCACC-GTCACC	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
..................................................................................................ATCATCAGCAGCAGCAGCAGC...................................................................................................................................................................................................	21	20	0.05	1	0	1	0	0	0	0

dp5

CCAG-C---TGG--GGGCC-------ACGCCAGCGGG-C-ACAGCCACCCACC---------------------AGCAGCAGCAGCATC---------ATCATCAGCAGCAGCAGCAGCAG---CATCACCACCA------------CCAGCAG--------CAGCAT------CAGATT---CAGGT---GC---------------AA---GTAC---AGCAAC---AACAGCATGTAAATC------------------------------------T-CAGCCAGAGCAACTC---CAGCACC-GTCACC	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
.........................................................................................................................................................G--------CAGCAT------CAGATT---CAGGT---GC---------------AA---GTA..................................................................................................	25	1	1.00	1	0	0	0	0	1	0	0	0	0	0
.............................................................................................................................ATCACCACCA------------CCAGCAG--------C.......................................................................................................................................................	18	6	0.17	1	0	1	0	0	0	0	0	0	0	0
.....................................................................................CATC---------ATCATCAGCAGCAGCAGCAG....................................................................................................................................................................................................	24	12	0.08	1	0	0	0	0	0	0	1	0	0	0
...........................................................................................................AGCAGCAGCAGCAG---CATCA.........................................................................................................................................................................................	19	20	0.05	1	0	1	0	0	0	0	0	0	0	0
........................................................................................C---------ATCATCAGCAGCAGCAGCAG....................................................................................................................................................................................................	21	20	0.05	1	0	1	0	0	0	0	0	0	0	0

droWil2

ACAA-C---TGCAGCAGCA--------------------------------ACAATTGCAGCAACAAC------AGCAACAGCAGCAAC---------AACAGCAGCAACAACAACAGCAGCAGCAACAGCAGCA------------TCAGC--AACA------GCAAC---AGCAG---------------------CAGCGAATGCAA---CAGC---AACAGC---AACAGCAGCAACAAT------------------------------------TGCAGCAACAACAACAA---CAGCAGC-AGCAAC	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
.............................................................................................................................AACAGCAGCA------------TCAGC--AACA------GC....................................................................................................................................................	21	4	0.25	1	0	0	0	1	0
.................................................................................................................................................................................................................................................AAT------------------------------------TGCAGCAACAACAACAA---CAGC..........	24	10	0.20	2	0	2	0	0	0
.............................................................................................................................................................................................................................................................................................CAACAACAACAA---CAGCAGC-A.....	20	20	0.20	4	0	0	0	4	0
..................A--------------------------------ACAATTGCAGCAACAAC------AG..............................................................................................................................................................................................................................................	20	20	0.15	3	0	3	0	0	0
......................................................................................................GCAGCAACAACAACAGCA..................................................................................................................................................................................................	18	20	0.15	3	0	0	0	3	0
.................................................................................................................................................................................................................................................AAT------------------------------------TGCAGCAACAACAACAA---CAG...........	23	10	0.10	1	0	1	0	0	0
...........................................................AGCAACAAC------AGCAACAGCAG.....................................................................................................................................................................................................................................	20	20	0.10	2	0	2	0	0	0
..............................................................................................................................................................................................................................................AACAAT------------------------------------TGCAGCAACAACAACAA---CAGC..........	27	10	0.10	1	0	1	0	0	0
..............................................................AACAAC------AGCAACAGCAGCAAC---------AA......................................................................................................................................................................................................................	23	20	0.10	2	0	2	0	0	0
........................................................TGCAGCAACAAC------AGCAACAGCAG.....................................................................................................................................................................................................................................	23	20	0.10	2	0	2	0	0	0
..................A--------------------------------ACAATTGCAGCAACAAC------AGCA............................................................................................................................................................................................................................................	22	20	0.10	2	0	0	0	2	0
.................................................................................................................................................................................................................................................AAT------------------------------------TGCAGCAACAACAACA..................	19	13	0.08	1	0	0	0	1	0
......................................................................................................................................................................................................................AGC---AACAGC---AACAGCAGCAACAAT------------------------------------T.................................	25	16	0.06	1	0	0	0	1	0
.............................................................................................................................................................................................................TGCAA---CAGC---AACAGC---AACAGCAGC............................................................................	24	17	0.06	1	0	1	0	0	0
...................................................................................................................................AGCA------------TCAGC--AACA------GCAAC---AGCAG---------------------....................................................................................................................	23	17	0.06	1	0	1	0	0	0
................................................................................................................................................................................................................................................................................................CAACAACAA---CAGCAGC-AGCAA.	21	20	0.05	1	0	1	0	0	0
.....................................................................................................................................................AGC--AACA------GCAAC---AGCAG---------------------CA..................................................................................................................	19	20	0.05	1	0	1	0	0	0
.....................................................AATTGCAGCAACAAC------AGCAACAGC.......................................................................................................................................................................................................................................	24	20	0.05	1	0	1	0	0	0
............................................................................................................ACAACAACAGCAGCAGCAACAG........................................................................................................................................................................................	22	20	0.05	1	0	0	0	1	0
............................................................................................................................................................................................................................................................................................GCAACAACAACAA---CAGCAGC-AGCA..	24	20	0.05	1	0	1	0	0	0
..............................................................................................................................................................................................................................................AACAAT------------------------------------TGCAGCAACAACAACAG---..............	23	20	0.05	1	0	1	0	0	0
..................A--------------------------------ACAATTGCAGCAACAAC------AGCAAC..........................................................................................................................................................................................................................................	24	20	0.05	1	0	1	0	0	0
.............................................................CAACAAC------AGCAACAGCAGCAAC---------........................................................................................................................................................................................................................	22	20	0.05	1	0	0	0	1	0
.....................................................................................................AGCAGCAACAACAACAGCAG.................................................................................................................................................................................................	20	20	0.05	1	0	0	0	1	0
.............................................................................................................................................................................................................................................................................................CAACAACAACAA---CAGCAGC-AGC...	22	20	0.05	1	0	1	0	0	0
.......................................................TTGCAGCAACAAC------AGCAACAGCAGC....................................................................................................................................................................................................................................	25	20	0.05	1	0	1	0	0	0
........................................................................................C---------AACAGCAGCAACAACAACAGCAGC................................................................................................................................................................................................	25	20	0.05	1	0	0	0	1	0
.....................................................................................CAAC---------AACAGCAGCAACAACAAC......................................................................................................................................................................................................	22	20	0.05	1	0	1	0	0	0
...................................................................................................ACAGCAGCAACAACAACAGCA..................................................................................................................................................................................................	21	20	0.05	1	0	0	0	0	1
..................A--------------------------------ACAATTGCAGCAACAAC------AGC.............................................................................................................................................................................................................................................	21	20	0.05	1	0	1	0	0	0
............................................................................CAACAGCAGCAAC---------AACAGC..................................................................................................................................................................................................................	19	20	0.05	1	0	0	0	1	0
........................................................TGCAGCAACAAC------AGCAACAGCA......................................................................................................................................................................................................................................	22	20	0.05	1	0	1	0	0	0
..............................................................................................................AACAACAGCAGCAGCAACAGCA......................................................................................................................................................................................	22	20	0.05	1	0	1	0	0	0
...............................................................................................................................................................................................................................AGC---AACAGCAGCAACAAT------------------------------------TG................................	20	20	0.05	1	0	1	0	0	0
..................A--------------------------------ACAATTGCAGCAACAAC------AGCAA...........................................................................................................................................................................................................................................	23	20	0.05	1	0	1	0	0	0
.................CA--------------------------------ACAATTGCAGCAACAAC------AGCAA...........................................................................................................................................................................................................................................	24	20	0.05	1	0	0	0	1	0
.......................................................TTGCAGCAACAAC------AGCAACAGCAG.....................................................................................................................................................................................................................................	24	20	0.05	1	0	0	0	1	0
................................................................................................................................................................................................................AA---CAGC---AACAGC---AACAGCAGC............................................................................	21	20	0.05	1	0	0	0	0	1
........................................................TGCAGCAACAAC------AGCAACAGCAGC....................................................................................................................................................................................................................................	24	20	0.05	1	0	1	0	0	0

droVir3

GCAG-C---AGCA------------------------------GCA--TCACCAGCAGCAGCAGCAGCATCACCAGCAGCAGCACCAGC---------AGCAGCAGCTGCAGCTGCAGCAG------CATCA---------------TCACC-----------------------AG------------CAGCAACAGCAGCATCAGCACCTCCAGC---AACAGC---AGCAGCAACAGCAGC------------------------------------AGCAGCAGCAGCACCTC---CAGCAGC-AGCAGC	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
.........................................................................................................................................................................................................CATCAGCACCTCCAGC---AACAGC---AGCA.................................................................................	26	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
....................................................................................................................................................CACC-----------------------AG------------CAGCAACAGCAGCATCAGC..........................................................................................................	25	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
................................................................................................................................ATCA---------------TCACC-----------------------AG------------CAGCAACAGCAG.................................................................................................................	23	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
....................................................................................................................AGCAG------CATCA---------------TCACC-----------------------AG------------CAGCAACAGCA..................................................................................................................	28	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
...............................................................................................................................................................................................................................................................................................GCAGCACCTC---CAGCAGC-AGCA..	21	2	0.50	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
........................................................................................................................................................................................................................................................................................AGCAGCAGCAGCACCTC---CAGCAGC-AGC...	27	2	0.50	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
.............................................................................................................................................................................................................................................................................................CAGCAGCACCTC---CAGCAGC-AG....	21	2	0.50	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
...................................................................................................................................................................................................................TCCAGC---AACAGC---AGCAGCAACAGCA........................................................................	25	2	0.50	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
.....C---AGCA------------------------------GCA--TCACCAGCAGCAGCAGC.........................................................................................................................................................................................................................................................	25	3	0.33	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
.....................................................................................................................GCAG------CATCA---------------TCACC-----------------------AG------------CAGCA........................................................................................................................	21	3	0.33	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
.................................................................................................................................................................................................................................................AGC------------------------------------AGCAGCAGCAGCACCTC---CA............	22	3	0.33	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	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
.......................................................................................................................AG------CATCA---------------TCACC-----------------------AG------------CAGC.........................................................................................................................	18	4	0.25	1	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
.................................................................................................................................................................................................................................................AGC------------------------------------AGCAGCAGCAGCACCTC---C.............	21	4	0.25	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
..........GCA------------------------------GCA--TCACCAGCAGCAGCAGCA........................................................................................................................................................................................................................................................	24	5	0.20	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	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
..........................................................CAGCAGCAGCATCACCAGCAGCAGC.......................................................................................................................................................................................................................................	25	6	0.17	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
.CAG-C---AGCA------------------------------GCA--TCACCAGCAGCAGC............................................................................................................................................................................................................................................................	25	6	0.17	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
...........CA------------------------------GCA--TCACCAGCAGCAGCAGCA........................................................................................................................................................................................................................................................	23	7	0.14	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
............A------------------------------GCA--TCACCAGCAGCAGCAGCA........................................................................................................................................................................................................................................................	22	7	0.14	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
...........CA------------------------------GCA--TCACCAGCAGCAGCAG..........................................................................................................................................................................................................................................................	21	9	0.11	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
................................................................................AGCACCAGC---------AGCAGCAGCT..............................................................................................................................................................................................................	19	10	0.10	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	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
............................................................................................................................................................................................................................AACAGC---AGCAGCAACAGCA........................................................................	19	20	0.10	2	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
......................................................................................................................................................................................................................................GCAGCAACAGCAGC------------------------------------AGCAGCAGC.........................	23	20	0.10	2	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
.....................................................AGCAGCAGCAGCAGCATCA..................................................................................................................................................................................................................................................	19	20	0.10	2	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
.........AGCA------------------------------GCA--TCACCAGCAGCA..............................................................................................................................................................................................................................................................	19	11	0.09	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..............................................................AGCAGCATCACCAGCAGCA.........................................................................................................................................................................................................................................	19	11	0.09	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.....................................................................................................AGCAGCTGCAGCTGCAGCAG------CA.........................................................................................................................................................................................	22	13	0.08	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
...................................................................................................................................A---------------TCACC-----------------------AG------------CAGCAACAGCA..................................................................................................................	19	14	0.07	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
.........................................................................CAGCAGCAGCACCAGC---------AGCAGCA.................................................................................................................................................................................................................	23	20	0.05	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
............................................................................................................................................................................................................................AACAGC---AGCAGCAACAGCAGC------------------------------------AGC...............................	24	20	0.05	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
...........................................................................................................................................................................................................................................AACAGCAGC------------------------------------AGCAGCAGCAGC......................	21	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................................CA--TCACCAGCAGCAGCAGCA........................................................................................................................................................................................................................................................	20	20	0.05	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
......................................................................................................................................................................................................................AGC---AACAGC---AGCAGCAACAGCAGC------------------------------------AGCA..............................	28	20	0.05	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
...............................................................................................................................................................................................................................AGC---AGCAGCAACAGCAGC------------------------------------AGCA..............................	22	20	0.05	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	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
.......................................................................................................................................................................................................................................CAGCAACAGCAGC------------------------------------AGCAGCAGC.........................	22	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
................................................................CAGCATCACCAGCAGCAG........................................................................................................................................................................................................................................	18	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
........................................................AGCAGCAGCAGCATCACCAGCAA...........................................................................................................................................................................................................................................	23	20	0.05	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
...........CA------------------------------GCA--TCACCAGCAGCAG.............................................................................................................................................................................................................................................................	18	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................................................................AGCAGCAACAGCAGC------------------------------------AGCAGCA...........................	22	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...............................................................................................................................................................................................................................AGC---AGCAGCAACAGCAGC------------------------------------A.................................	19	20	0.05	1	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
...............................................................................................................................................................................AG------------CAGCAACAGCAGCATCAG...........................................................................................................	20	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droMoj3

CCAG-C---GGA---AACAGC-----CTGACACC------GCAGCA--ACACC---------------------AACAGCATCCGCATT---------CCCATCAACAGCAGCAGCAGCAA------CAGCAGCA------------GCAGCAG--CAGCAACAGCAG------CAGCAG---CAGCA---GC---------------------------AACAGC---AGCAGCAGCAGCAGC------------------------------------AACAGCAGCAGCACCAA---CAGCATC-CGCACC	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
.......................................................................................................CAACAGCAGCAGCAGCAA------C..........................................................................................................................................................................................	19	20	0.10	2	0	0	0	0	2	0
......................................................................................................................................................................AG------CAGCAG---CAGCA---GC---------------------------AACAGC---.....................................................................................	21	20	0.05	1	1	0	0	0	0	0
.................................................................................................................................................................................................................................C---AGCAGCAGCAGCAGC------------------------------------AACAGCAGCAGCA.....................	29	20	0.05	1	0	0	0	0	1	0
.....................................................................................................................................................................................................................................AGCAGCAGCAGCAGC------------------------------------AACAGC............................	21	20	0.05	1	1	0	0	0	0	0
...................................................................................................................................AGCA------------GCAGCAG--CAGCAACAGCAG------CAGCA.......................................................................................................................................	28	20	0.05	1	0	0	0	0	1	0
...............................................................................................................................................................CAACAGCAG------CAGCAG---CAGC...............................................................................................................................	19	20	0.05	1	0	0	0	0	1	0
...................................................................................................................................AGCA------------GCAGCAG--CAGCAACAGC....................................................................................................................................................	21	20	0.05	1	1	0	0	0	0	0
...................................................................................................................................................................................................................................................C------------------------------------AACAGCAGCAGCACCAA---CA............	20	20	0.05	1	0	0	0	0	1	0
..............................................................................................................................................................GCAACAGCAG------CAGCAG---CAGCA---GC---------------------------A.............................................................................................	24	20	0.05	1	1	0	0	0	0	0
.....................................................................................................................GCAA------CAGCAGCA------------GCAGCAG--CAGCA.........................................................................................................................................................	24	20	0.05	1	1	0	0	0	0	0
................................................................................................................................................................................................C---------------------------AACAGC---AGCAGCAGCAGC.........................................................................	19	20	0.05	1	0	0	0	0	1	0
...............................................................................................................................................................................................GC---------------------------AACAGC---AGCAGCAGCAGCAGC------------------------------------A.................................	24	20	0.05	1	1	0	0	0	0	0
.....................................................................................................................................................................CAG------CAGCAG---CAGCA---GC---------------------------AACAGC---AGCAGCA..............................................................................	29	20	0.05	1	0	0	0	0	1	0

droGri2

C-AT-CTGGG-----AGCGG-CGG--GCTCTGG---------------TCAGC---------------------AGCAGCAGCAGCAGCAGCAGCGTCAACATCAGCAGCAGCAGCAGCAGCAGTTAAAACAGCA------------GCAGCAT--------CAGCAG------CAGAAAAAACAGCAGCAGCAACAGCAGC---------------------------AGCAG---CAT---C------------------------------------AGCAGCAGCAGCAGCAG---CAGCAGC-GTCAAC	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

droAna3

GCAG-G---AGCG------------------------------ACG--GCAGCAGCAGCAGCCACAGC------AGCAACAGCAGCAGC---------AGCAACAGCAACAGCAACAGCAA---CAGCAGCAGCA------------ACAGCAG--------CAGCAA------CAG---------------------CAGCAGCAGCCA---CAGC---AGCAGC---AACAGCAGCAACGAC------------------------------------AGCAGCAGCAGCAACGT---CAGCAGC-AGCAGC	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
.......................................................................................................................................................................A------CAG---------------------CAGCAGCAGCCA---CAGC---..............................................................................................	20	1	1.00	1	0	1	0	0	0	0
..................................................................................................................................................................CAGCAA------CAG---------------------CAGCAGCAGCCA---C....................................................................................................	22	2	0.50	1	0	1	0	0	0	0
.................................................................................................................................GCAGCA------------ACAGCAG--------CAGCAA------CAG---------------------CAGCAGC.............................................................................................................	29	6	0.17	1	0	1	0	0	0	0
........................................................................................................................................................................................................GCAGCAGCCA---CAGC---AGCAGC---.....................................................................................	20	7	0.14	1	0	1	0	0	0	0
.........................................................................................................................................................G--------CAGCAA------CAG---------------------CAGCAGCAGCC.........................................................................................................	21	16	0.13	2	0	1	1	0	0	0
...................................................GCAGCAGCAGCCACAGC------AGC.............................................................................................................................................................................................................................................	20	8	0.13	1	0	0	0	0	0	1
................................................................................................................................................................................G---------------------CAGCAGCAGCCA---CAGC---AGC...........................................................................................	20	8	0.13	1	0	0	0	0	0	1
..........................................................................AGCAACAGCAGCAGC---------AGCAACAGCA..............................................................................................................................................................................................................	25	20	0.10	2	0	1	1	0	0	0
..................................................................................................................................CAGCA------------ACAGCAG--------CAGCAA------CAG---------------------CAGCA...............................................................................................................	26	13	0.08	1	0	1	0	0	0	0
...................................................................................................................CAGCAA---CAGCAGCAGCA------------ACAGCAG--------CA......................................................................................................................................................	26	13	0.08	1	0	1	0	0	0	0
...............................................................................................................GCAACAGCAA---CAGCAGCAGCA------------ACAGC..................................................................................................................................................................	26	14	0.07	1	0	1	0	0	0	0
...........................................................................................................AACAGCAACAGCAA---CAGCAGCAGCA------------AC.....................................................................................................................................................................	27	15	0.07	1	0	0	0	0	0	1
......................................................................................................................CAA---CAGCAGCAGCA------------ACAGCAG--------CAGC....................................................................................................................................................	25	20	0.05	1	0	1	0	0	0	0
....................................................................................................CAACAGCAACAGCAACAGCAA---CAGCAGC.......................................................................................................................................................................................	28	20	0.05	1	0	1	0	0	0	0
................................................................................AGCAGCAGC---------AGCAACAGCAACAGC.........................................................................................................................................................................................................	24	20	0.05	1	0	0	0	0	0	1
.................................................................................................................................GCAGCA------------ACAGCAG--------CAGCAA------CAG---------------------CAGA................................................................................................................	26	20	0.05	1	1	0	0	0	0	0
.............................................................................................................CAGCAACAGCAA---CAGCAGCA......................................................................................................................................................................................	20	20	0.05	1	0	1	0	0	0	0
................................................................................................................CAACAGCAA---CAGCAGCAGCA------------.......................................................................................................................................................................	20	20	0.05	1	1	0	0	0	0	0
.................................................................................................................AACAGCAA---CAGCAGCAGCA------------ACAGC..................................................................................................................................................................	24	20	0.05	1	0	1	0	0	0	0
...................................................................................................................................................................AGCAA------CAG---------------------CAGCAGCAGCC.........................................................................................................	19	20	0.05	1	0	0	0	0	0	1
........................................................................................................AGCAACAGCAACAGCAA---CAGC..........................................................................................................................................................................................	21	20	0.05	1	0	0	1	0	0	0
...................................................................................................................................AGCA------------ACAGCAG--------CAGCAA------CA..........................................................................................................................................	19	20	0.05	1	0	1	0	0	0	0
......................................................................................................ACAGCAACAGCAACAGCAA---C.............................................................................................................................................................................................	20	20	0.05	1	0	1	0	0	0	0
.....................................................................................................................................CA------------ACAGCAG--------CAGCAA------CAG---------------------CAGCAGC.............................................................................................................	25	20	0.05	1	0	1	0	0	0	0
......................................................................................................................................A------------ACAGCAG--------CAGCAA------CAG---------------------CA..................................................................................................................	19	20	0.05	1	0	0	0	0	0	1
.................................................................................................................................GCAGCA------------ACAGCAG--------CAGCAA------CAG---------------------C...................................................................................................................	23	20	0.05	1	0	1	0	0	0	0

droBip1

CCAG-C---AACA---GCA-------ACC----------------------CCAACAGACCGCACACC------TGCAACAGCAACATC---------AGCAGCAGCAGCAGCAACAGCAG---CAGCAGCACCA------------CCTGCAG--------CAGCAG------CAG---------------------CAGCAGCACCAC---CACC---AGCAAC---AACAACAACAACATC------------------------------------ATGCCCAGCAGCAGCAG---CAGCAAC-ACCACC	Size	Hit Count	Total Norm	Total
No Reads

droKik1

CCAG-C----------------------------------------------------------------------CATCAGCAACAAC---------AGCAGCAGCAACAGCAGCAGCAGCAGCAACAACAGCA------------GCAAC--AGCA------GCAGC---AGCAG------------CAACAACAGCAAC---------------------------AGCAG---CAACACGTGGCCCACGGCAAGAAGGCAGCCAGAAAGCACCTGCAACATCTACAGCAACAG---CAGCAAC-AGCAAC	Size	Hit Count	Total Norm	Total
No Reads

droFic1

CCAG-CCACC-----GGCGT-CAT--TCATCAT-----------CA--CCACC---------------------AGCAGCAGCAACAGC---AGCACCAGCATCAGCAGTAGCAGCAGCAG------CAGCATCAGCAGCA------TCAGCAG--------TAGCAG------CAG---------------------CAGCATCAGCAA---CTCC---AACATC---AACAGCAGCAACAGC------------------------------------AGCATCAACAGCAGCAA---CAGCAGC-ATCAAC	Size	Hit Count	Total Norm	Total
No Reads

droEle1

CCAG-CCGCC-----GGCGG-CAT--TCACCAGCAAC-A-GCAGCA--ACACC---------------------AGCAACAGCAGCAAC---------ATCAGCAACAGCAGCAACATCTG------CAGCAGCA------------GCAACAT--CA------GCAA------CAG---------------------CAGCAACACCAT------CAGCAGCAACAACAGCAG---CAA---C------------------------------------ACCATCAGCAGCAGCAG---CAACACC-ATCAGC	Size	Hit Count	Total Norm	Total
No Reads

droRho1

C---GCCGCG-----GGCGGT-----TCGCCGGT------GATGCT--TCACC---------------------AGCAGCAGCAGCATC---------AGCAACAGCAGCAGCAGCAGCATCAGCA---------------------ACAGC--AGCAGCAACAGCAA------CACCTT---CAGCA---GCAACATCAGC---------------------------AACACCATCAACAAC------------------------------------AGCAACACCACCAGCAG---CAGCACC-ATCAGC	Size	Hit Count	Total Norm	Total
No Reads

droBia1

C---GCCGCG-----GGCGGT-----TCGCCGGT------GATGCT--CCACC---------------------AGCAGCAGCAGCAGC---------AGCAGCAGCAACAGCAGCAACATCAGCAGCAGCAGCA------------GCAGC--ACCA------GCAGC---AGCAG------------------------CAGCACCTG---CAAC---AGCAGC---AACACCACCAACACC------------------------------------TTCACCAGCAATTCGGG---CAGCAGC-AGCAGC	Size	Hit Count	Total Norm	Total
No Reads

droTak1

C-AG-CAACAGC--CGGCTA-CAACGGCGCCAGCAAC-TTGATCAT--CATCG---------------------AGCCGCAGCAGCAGC---------AGCAGCAGCAACAACAGCAACAGCAGCAGCAGCCGCC------------GCAGC--AGCA------GCAACAG-TTCAG------------CTAC---------------------CAC---AGCAAC---AGCAGCAATAACAAC------------------------------------TACTACCACAGCAATGCCAGCA--AGCAGGCAGC	Size	Hit Count	Total Norm	Total
No Reads

droEug1

T----CCGCC-----GGCGG-CAT--ACACCAGCAGC-A-TCAGCA--ACAGC------AGCACCAGC------AGCAACAACAGCAAC---------AACATCAGCAACAACAGCATCAGCAGCAACAACACCA------------CCAGCAG--------CAGCAA------CACCAC---CAA------------CAGCAGCAACAC---CACC---AACAGC---AACAACATCTACAAC------------------------------------AGCAGCAGCAGCAACAC---CAGCAGC-AGCAGC	Size	Hit Count	Total Norm	Total
No Reads

dm3

GCAG-C---AGCA-------------ACACCA-------------------GCAGCACCAGCAGCAGCAACACCAGCAGCAGCAGCACC---------AGCAACACCAGCAGCAACAGCAG------CAGCAACA------CCAACATCAGCA-----------GCAG------CAA---------------------CAGCAACACCTT---CAGC---AGCAGC---AACACCACCAGCTGC------------------------------------AGCAGCAACAGCAGCAG---CAGCAGC-ATCAAC	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
................................................................................................................................................................................................................TT---CAGC---AGCAGC---AACACCAC.............................................................................	20	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
...............................................................................................................................................AACATCAGCA-----------GCAG------CAA---------------------CAGCAA..............................................................................................................	23	3	1.33	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..............................................................................................................................................................................................................................CAGC---AACACCACCAGCTGC------------------------------------AG................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
..........................................................................AGCAGCAGCAGCACC---------AGCAACACCA..............................................................................................................................................................................................................	25	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
..............................................................................................................................................................................CAA---------------------CAGCAACACCTT---CAGC---AG............................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
............................................................................................................................................................................................................CACCTT---CAGC---AGCAGC---AACACCACCAGC.........................................................................	28	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
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.........................................................................CAGCAGCAGCAGCACC---------AG......................................................................................................................................................................................................................	18	20	0.05	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	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
.........................................................................................................................................................................................................................................................................................GCAGCAACAGCAGCAG---CAGCA.........	21	20	0.05	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	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
............................................................................................................GCAGCAACAGCAG------CAGCAACA------.............................................................................................................................................................................	21	20	0.05	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	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
.............................................................................................................CAGCAACAGCAG------CAGCAACA------.............................................................................................................................................................................	20	20	0.05	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	0	1	0	0	0	0	0
..................................................................................................................................................ATCAGCA-----------GCAG------CAA---------------------CAGCA...............................................................................................................	19	20	0.05	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	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
.............................................................................................................CAGCAACAGCAG------CAGCAA.....................................................................................................................................................................................	18	20	0.05	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

droSim2

C---GCCGCG-----GGCGGT-----TCGCCGGT------GATGCT--TCACC---------------------AGCAGCAGCAGCAAC---------ATCAGCAGCAACAGCAGCAGCAGCAGCATCAACAGCA------------ACAGC--AGCA------GCAAC---ATCAG------------CAGCAACAGCAGC---------------------------AGCAG---CAACAC---------------------------------------CACCAGCAACAGCAG---CAGCATC-ATCACC	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
.................................................................................................................................................................................................................................................AC---------------------------------------CACCAGCAACAGCAG---CA............	19	11	1.00	11	0	0	0	0	0	11	0	0	0	0	0	0	0	0	0	0	0
.....................................................................................................AGCAGCAACAGCAGCAGCAGCAGCA............................................................................................................................................................................................	25	20	0.10	2	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0
................................................................................................................................AACAGCA------------ACAGC--AGCA------GCAAC---AT............................................................................................................................................	23	10	0.10	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
.............................................................................................................................................................................TCAG------------CAGCAACAGCA..................................................................................................................	15	20	0.05	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
.................................................CACC---------------------AGCAGCAGCAGC....................................................................................................................................................................................................................................	16	20	0.05	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
...................................................................................................TCAGCAGCAACAGCA........................................................................................................................................................................................................	15	20	0.05	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
.......................................................................................................................................................................AC---ATCAG------------CAGCAACAGC...................................................................................................................	17	20	0.05	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
....................................................C---------------------AGCAGCAGCAGCAAC---------ATCAGC..................................................................................................................................................................................................................	22	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0
...................................................................................................................................AGCA------------ACAGC--AGCA------GCAAC---A.............................................................................................................................................	19	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0
.......................................................................................AC---------ATCAGCAGCAACAGC.........................................................................................................................................................................................................	17	20	0.05	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0

droSec2

C---GCCGCG-----GGCGGT-----TCGCCGGT------GATGCT--TCACC---------------------AGCAGCAGCAGCAAC---------ATCAGCAGCAACAGCAGCAGCAGCAGCATCAACAGCA------------GCAGC--AGCA------GCAAC---ATCAG------------CAGCAACAGCAGC---------------------------AGCAG---CAACAC---------------------------------------CACCAGCAACAGCAG---CAGCATC-ATCACC	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
.............................................................................................................................ATCAACAGCA------------GCAGC--AGCA------GCAAC---..............................................................................................................................................	24	4	0.25	1	0	1	0	0
...................................................................................................................CAGCAGCAGCATCAACAGCA------------GC.....................................................................................................................................................................	22	8	0.13	1	0	0	0	1
.................................................................................GCAGCAAC---------ATCAGCAGCAAC............................................................................................................................................................................................................	20	13	0.08	1	0	0	1	0
...........................................................................................................................................................GCA------GCAAC---ATCAG------------CAGCAAC......................................................................................................................	20	13	0.08	1	0	0	1	0
................................................................................................................................AACAGCA------------GCAGC--AGCA------GCA...................................................................................................................................................	19	20	0.05	1	0	0	1	0
...........................................................................................................................................................................................................................................................................................ACCAGCAACAGCAG---CAGC..........	18	20	0.05	1	0	0	1	0
................................................................................................................................AACAGCA------------GCAGC--AGCA------GCAAC---..............................................................................................................................................	21	20	0.05	1	0	0	1	0
....................................................................................................................................................................................................AGCAGC---------------------------AGCAG---CAACAC---------------------------------------CA..............................	19	20	0.05	1	0	0	1	0

droYak3

C---GCCGCG-----GGCGGT-----TCGCCGGT------GATGCT--CCACC---------------------AGCAGCAGCAGCATC---------AGCAGCAACAACAGCAGCAGCAGCAGCAGCAACATCA------------ACAGCAG--------CAGCAGCAGCAACAG---------CA---GC---------------AT---CATC---AGCAGC---AACAGCAACAACACC------------------------------------ACCAGCAACAGCAGCAG---CAGCATC-ATCATC	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
........................................................................................................................................................AG--------CAGCAGCAGCAACAG---------CA---GC---------------AT---.....................................................................................................	23	10	0.10	1	0	0	0	0	0	0	1	0	0	0	0
......................................................................................................................................A------------ACAGCAG--------CAGCAGCAGCAAC...........................................................................................................................................	21	20	0.10	2	0	2	0	0	0	0	0	0	0	0	0
............................................................................................................ACAGCAGCAGCAGCAGCAGC..........................................................................................................................................................................................	20	20	0.10	2	0	2	0	0	0	0	0	0	0	0	0
.................................................................................................................................................................................................................................................................................................AGCAGCAG---CAGCATC-ATCATC	21	11	0.09	1	0	1	0	0	0	0	0	0	0	0	0
........................................................................................................AACAACAGCAGCAGCAGCAGCAGCAACA......................................................................................................................................................................................	28	11	0.09	1	0	1	0	0	0	0	0	0	0	0	0
.........................................................................................................ACAACAGCAGCAGCAGCAGCAGCAAC.......................................................................................................................................................................................	26	13	0.08	1	0	1	0	0	0	0	0	0	0	0	0
...........................................................................................................................GCAGCAACATCA------------ACAGCAG--------CA......................................................................................................................................................	21	16	0.06	1	0	1	0	0	0	0	0	0	0	0	0
...............................................................................................................................CAACATCA------------ACAGCAG--------CAGCA...................................................................................................................................................	20	18	0.06	1	0	0	0	0	0	0	1	0	0	0	0
........................................................................................................................................................................................................................................................................................ACCAGCAACAGCAGCAG---CAGC..........	21	19	0.05	1	0	1	0	0	0	0	0	0	0	0	0
...................................................................................................GCAGCAACAACAGCAGCAGCAGCAGC.............................................................................................................................................................................................	26	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
.........................................................................................................ACAACAGCAGCAGCAGCAGCA............................................................................................................................................................................................	21	20	0.05	1	0	0	0	1	0	0	0	0	0	0	0
.......................................................................................................................................................CAG--------CAGCAGCAGCAACAG---------CA---GC---------------..........................................................................................................	22	20	0.05	1	0	0	0	1	0	0	0	0	0	0	0
........................................................................................................................................................AG--------CAGCAGCAGCAACAG---------CA---GC---------------..........................................................................................................	21	20	0.05	1	0	0	0	1	0	0	0	0	0	0	0
....................................................................................................................................................CAGCAG--------CAGCAGCAGCAACAG---------CA---GC---------------..........................................................................................................	25	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
....................................................................................................CAGCAACAACAGCAGCAGCA..................................................................................................................................................................................................	20	20	0.05	1	0	0	0	0	0	0	1	0	0	0	0
.................................................................................................................AGCAGCAGCAGCAGCAACATC....................................................................................................................................................................................	21	20	0.05	1	0	0	0	1	0	0	0	0	0	0	0
.............................................................................................................CAGCAGCAGCAGCAGCAGCAAC.......................................................................................................................................................................................	22	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
...................................................................................................................................ATCA------------ACAGCAG--------CAGCAGCAG...............................................................................................................................................	20	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
...................................................................................................................................................ACAGCAG--------CAGCAGCAGCAACA..........................................................................................................................................	21	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0

droEre2

CCAA-C---GGG--GGTGC-------AGG--ATCTGGAC-AC--CA--CCACC---------------------ATCATCATCATCACC---------ATCACAGTCATGAGCAGCAGCAGCAGCAACAGCAGCA------------GCAGC--AACA------GCAGC---AACAG---------------------CAGCAGCAGCAT------CAGAAACAACAACAGCAG---CAACAGC------------------------------CCATGCAGACTGTTCCGCACCAC---CATCACT-ATCCCC	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
.....................................................................................CACC---------ATCACAGTCATGAGCAGC......................................................................................................................................................................................................	22	1	1.00	1	0	0	1	0	0	0	0
..........................................................................................................................................................AACA------GCAGC---AACAG---------------------CAGCA...............................................................................................................	19	20	0.10	2	0	0	0	2	0	0	0
............................................................................................................................CAACAGCAGCA------------GCAGC--AACA------GC....................................................................................................................................................	22	20	0.10	2	0	1	0	1	0	0	0
......................................................................................................................................................................AGC---AACAG---------------------CAGCAGCAGCAT------CA................................................................................................	22	17	0.06	1	0	0	0	0	1	0	0
.............................................................................................................................AACAGCAGCA------------GCAGC--AACA------GCAGC---A.............................................................................................................................................	25	20	0.05	1	0	0	0	1	0	0	0
...................................................................................................................................................GCAGC--AACA------GCAGC---AACAG---------------------CAGCA...............................................................................................................	24	20	0.05	1	0	0	0	0	1	0	0
....................................................................................................................................................CAGC--AACA------GCAGC---AACAG---------------------CAGCA...............................................................................................................	23	20	0.05	1	1	0	0	0	0	0	0
......................................................................................................................CAGCAGCAACAGCAGCA------------GC.....................................................................................................................................................................	19	20	0.05	1	0	1	0	0	0	0	0
.....................................................................................................................................................AGC--AACA------GCAGC---AACAG---------------------CAGCAGCAGC..........................................................................................................	27	20	0.05	1	1	0	0	0	0	0	0
....................................................................................................................................................................GCAGC---AACAG---------------------CAGCAGCAGC..........................................................................................................	20	20	0.05	1	1	0	0	0	0	0	0
......................................................................................................................................A------------GCAGC--AACA------GCAGC---AACAG---------------------CAGCAG..............................................................................................................	26	20	0.05	1	1	0	0	0	0	0	0
................................................................................................................................AGCAGCA------------GCAGC--AACA------GCAGC---A.............................................................................................................................................	22	20	0.05	1	0	0	0	0	1	0	0
...................................................................................................................................................GCAGC--AACA------GCAGC---AACAG---------------------CAGCAGC.............................................................................................................	26	20	0.05	1	0	1	0	0	0	0	0
.......................................................................................................................................................................GC---AACAG---------------------CAGCAGCAGCAT------C.................................................................................................	20	20	0.05	1	0	0	0	0	1	0	0
...............................................................................................................GCAGCAGCAGCAGCAACAGCAGC....................................................................................................................................................................................	23	20	0.05	1	0	1	0	0	0	0	0
..............................................................................................................................ACAGCAGCA------------GCAGC--AACA------GCA...................................................................................................................................................	21	20	0.05	1	1	0	0	0	0	0	0
........................................................................................................................................................................C---AACAG---------------------CAGCAGCAGCAT------C.................................................................................................	19	20	0.05	1	0	0	0	1	0	0	0
...................................................................................................................CAGCAGCAGCAACAGCAGC....................................................................................................................................................................................	19	20	0.05	1	0	0	0	0	0	1	0

dpe_1259

scaffold_25:771929-772000 +

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

-10.4	-9.6