dwi_249

exon [dwil_GLEANR_4297:1]; CDS [Dwil\GK21267-cds]; CDS [Dwil\GK21267-cds]; exon [dwil_GLEANR_4297:2]; intron [Dwil\GK21267-in]

Name	Class	Family	Strand
Gypsy-6_DWil-I-int	LTR	Gypsy	+

##################################################-------------------------------------------------------------------------------------------------------------################################################## GCCAAGTACACCGGATCAAGTGGGTGCTAACCAGTCGCCGACGATGTCTTGTGAGACCCCTGTAGGGCCAGACACGAACGTGCATGTTCGTGAAGGCGCACAAGCGAGCAAAACCGACGAATTGGCTTCGATTCTTTAGTAGCATCGAATTGTATACAGCACGTAAAAACCTAATGGAGCTAAAAACACGTGTTATGGAGCTGGAGGAG ****************************************************.........((((((((...((....(((.((((.(((......))).)))).)))....)).....))))))......))************************************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M045 female body	V118 embryo	V117 male body	V119 head	M020 head
.................................................................................................................................................................CGGAAAGACCTCATGGAGC.............................	19	3	20	0.20	4	1	0	2	1	0
.................................................................................................................................................................CGGAAAGACCTCATGGAGCT............................	20	3	20	0.15	3	2	0	1	0	0
..................................................................................................................................................................GTAAAGACCCCATGGAGCT............................	19	3	20	0.10	2	2	0	0	0	0
...............................................................................................................AACCGACGAATTGGCTTCGATTCT..........................................................................	24	0	20	0.10	2	2	0	0	0	0
..............................................................................................................AAACCGACGAATTGGCTTCGATTCT..........................................................................	25	0	20	0.10	2	0	2	0	0	0
....................................................................................................CAAGCCAGCAAAACGGAC...........................................................................................	18	2	17	0.06	1	0	0	0	0	1
....................................................................................................................................................................................TAAAAACACGTGTTATGGAGCTGGT....	25	1	20	0.05	1	0	1	0	0	0
...........................................................................................................................................................................TAATGGAGCTAAAAACACGTGTTATG............	26	0	20	0.05	1	1	0	0	0	0
....................................................................................................................................................ATTGTATACAGCACGTAAAAACCT.....................................	24	0	20	0.05	1	0	1	0	0	0
...................................................................................ATGTTCGTGAAGGCGCACAAGCGAGC....................................................................................................	26	0	20	0.05	1	0	0	1	0	0
.................................................................................................................................................................CGTAAAGACCCCATGGAGC.............................	19	3	20	0.05	1	0	0	0	1	0
................................................................................TGCATGTTCGTGAAGGCGCACAAGCGAGC....................................................................................................	29	0	20	0.05	1	0	1	0	0	0
.............GATCAAGTGGGTGCTAACCAGTCGC...........................................................................................................................................................................	25	0	20	0.05	1	0	1	0	0	0
...................GTGGGTGCTAACCAGTCGC...........................................................................................................................................................................	19	0	20	0.05	1	0	1	0	0	0
......................................................GACCCCTGTAGGGCCAGA.........................................................................................................................................	18	0	20	0.05	1	1	0	0	0	0
.................................................................................................................................................................CGGAAAGACCCAATGGAGC.............................	19	3	20	0.05	1	0	0	0	1	0
.................................................................................................................................................................CGTAAAGACCCCATGGAGCT............................	20	3	20	0.05	1	1	0	0	0	0
....................................................................................................................................................ATTGTATACAGCACGTAAAAACCTA....................................	25	0	20	0.05	1	0	1	0	0	0
................................................................................................................................................................ACGTAAAGACCCCATGGAGCT............................	21	3	20	0.05	1	0	0	1	0	0
......................................................GACCCCTGTAGGGCCAGACACGAACGTG...............................................................................................................................	28	0	20	0.05	1	0	1	0	0	0
................................................................................................................................................................ACGGAAAGACCTCATGGAGC.............................	20	3	20	0.05	1	1	0	0	0	0
..............................................................................................................................................................................TGGAGCTAAAAACACGTGTTATGGAGC........	27	0	20	0.05	1	0	1	0	0	0
....................................................................................................................................................................................TAAAAACACGTGTTATGGATCTGGAG...	26	1	20	0.05	1	1	0	0	0	0
..........................................................................................................................................................................CTAATGGAGCAAAATACACG...................	20	2	20	0.05	1	0	1	0	0	0
...........................................................................................................................................................ACAGCACGTAAAAACCTAATGGAGC.............................	25	0	20	0.05	1	0	1	0	0	0

CGGTTCATGTGGCCTAGTTCACCCACGATTGGTCAGCGGCTGCTACAGAACACTCTGGGGACATCCCGGTCTGTGCTTGCACGTACAAGCACTTCCGCGTGTTCGCTCGTTTTGGCTGCTTAACCGAAGCTAAGAAATCATCGTAGCTTAACATATGTCGTGCATTTTTGGATTACCTCGATTTTTGTGCACAATACCTCGACCTCCTC ************************************************************************.........((((((((...((....(((.((((.(((......))).)))).)))....)).....))))))......))****************************************************	Read size	Hit Count	Total Norm	Total	M045 female body	V118 embryo	V117 male body
....................................................................................................GTTCGCTCGTTTTGGCTGCTTAAC.....................................................................................	24	2	1.00	2	2	0	0
................................................................................................GCGTGTTCGCTCGTTTTGGCTGCTT........................................................................................	25	2	0.50	1	1	0	0
..............................................................................................................................................................CGTGCATTTTTGGATTACCTCGATTTT........................	27	20	0.35	7	1	6	0
.............................TGGTCAGCGGCTGCTACAGAACACTCT.........................................................................................................................................................	27	3	0.33	1	0	1	0
..................................................................................................................................................................................CGATTTTTGTGCACAATACCTCGACCT....	27	20	0.30	6	0	6	0
........................................................GGGGACATCCCGGTCTGTGCTTGCACGT.............................................................................................................................	28	20	0.25	5	1	2	2
..........................................................................................................................................CATCGTAGCTTAACATATGTCGTGCAT............................................	27	20	0.20	4	4	0	0
............CCTAGTTCACCCACGATTGGTCAGC............................................................................................................................................................................	25	19	0.11	2	2	0	0
..................TCACCCACGATTGGTCAGCGGCTGCT.....................................................................................................................................................................	26	20	0.10	2	2	0	0
...............................................................................................................................................................GTGCATTTTTGGATTACCTCGATTTT........................	26	20	0.10	2	0	2	0
.........................................................................................................................................................................GGATTACCTCGATTTTTGTGCACAAT..............	26	20	0.10	2	0	2	0
........................................................................................................................................................ATATGTCGTGCATTTTTGGATTACCT...............................	26	18	0.06	1	1	0	0
..........GGCCTAGTTCACCCACGATTGGTCAGCG...........................................................................................................................................................................	28	19	0.05	1	1	0	0
..........GGCCTAGTTCACCCACGATTGGTCAG.............................................................................................................................................................................	26	19	0.05	1	1	0	0
..........GGCCTAGTTCACCCACGATTGGTCAGC............................................................................................................................................................................	27	19	0.05	1	1	0	0
............CCTAGTTCACCCACGATTGGTCAGCG...........................................................................................................................................................................	26	19	0.05	1	1	0	0
...........GCCTAGTTCACCCACGATTGGTCAGCG...........................................................................................................................................................................	27	19	0.05	1	1	0	0
...........................................................................CTTGCACGTACAAGCACTTCCGCGTGT...........................................................................................................	27	20	0.05	1	1	0	0
...............AGTTCACCCACGATTGGTCAGCGGCT........................................................................................................................................................................	26	20	0.05	1	1	0	0
..........................................................GGACATCCCGGTCTGTGCTTGCACGT.............................................................................................................................	26	20	0.05	1	1	0	0
..............................................................................................................................................................CGTGCATTTTTGGATTACCTCGAT...........................	24	20	0.05	1	0	1	0
.............CTAGTTCACCCACGATTGGTCAGC............................................................................................................................................................................	24	20	0.05	1	1	0	0
................................................................CCCGGTCTGTGCTTGCACGTACAAGC.......................................................................................................................	26	20	0.05	1	1	0	0
..........GGCCTAGTTCACCCACGATTGGTCA..............................................................................................................................................................................	25	20	0.05	1	1	0	0
......ATGTGGCCTAGTTCACCCACGATTGG.................................................................................................................................................................................	26	20	0.05	1	0	1	0
...TTCATGTGGCCTAGTTCACCCACGA.....................................................................................................................................................................................	25	20	0.05	1	1	0	0
....TCATGTGGCCTAGTTCACCCACGATTGGT................................................................................................................................................................................	29	20	0.05	1	1	0	0
.............................................................................................................................................CGTAGCTTAACATATGTCGTGCATTTTT........................................	28	20	0.05	1	0	1	0
.................................................................CCGGTCTGTGCTTGCACGTACAAGCACT....................................................................................................................	28	20	0.05	1	1	0	0
...................................................................................................................................................................ATTTTTGGATTACCTCGATTTTTGT.....................	25	20	0.05	1	1	0	0
................................................................................................................................................................TGCATTTTTGGATTACCTCGATTTT........................	25	20	0.05	1	0	1	0
........................................................................................................................................................................TGGATTACCTCGATTTTTGTGCACAA...............	26	20	0.05	1	0	1	0
.................................................................................................................................................................GCATTTTTGGATTACCTCGATTT.........................	23	20	0.05	1	1	0	0

Species	Coordinate	ID	Alignment
droWil2	scf2_1100000001801:1174-1382 +	dwi_249	GCCAA-GTACACCGGATCAAGTG-----GGTGCTAACCAGTCGCCGACGATGTCT------------------------------------------------------TGTGAGACCCCTGTAGGGCCAGACACGAACGTGCATGTTCGTGAAGGCGCACAAGCGAGCAAA-------------------------ACCGACGAATTGGCTTCGATTCTTTAGTAGC-----ATCGAATTGTATACAGCACGTAAAAACCTAATGGAGCTAAAAACACGTGT---------------TATGGA-GCTGGAGGAG
droVir3	scaffold_12728:368456-368635 -		GTATG-CTGTGTTGATTGAGGAT-----GAACCTAGCCATGTGTCC--------------------TCTGCTG---ACTGGTGCGAATGTTGC------------------------------------------------------------CAATTCAGAAGCGAATGGT-------------------------TCAGATAAGTTAGCGTCCGTGATAAATGA-G-----ATCTCCCTATACACTGCTCGAAAAAATCTTGCAAAGCTGAAGGCACGTGT---------------TTTCGAACTTGAAAGTG
dp5	Unknown_group_103:27844-28044 -		GTAGA--------------------GGCGG----------CGCCAGA------------------------------------AGAATATTATGCAAATATGGAGAAGGTTCGAGAAGCATTCATGCCACGACAAGACAACGCTTGC-C--GAAATTAACCATGCGATCA--GACGAATACGAAAAGGAGTCGCGCC----------------------GTTTGCAGAAGTTGGAACAATTGTACGTTTCTCGCAAGCGCCTAGCTGATCTTAAATTA--GGC---------------TATGGA-GTTGGAA---
droPer2	scaffold_133:85798-86033 +		ACCGTAGTGCACAACACGCAGTAAAAGCGG----------CGCCAGA------------------------------------AGAATATGGTGAAAATGTGCAGAAGGCTCGAGAAGCATTCATGCCGCGACAAGACAACGCTTGTTC--GAAATTGACCATGCGATCA--GATGAATACGAAGAAGAATCGCGCC----------------------GTTTGCAGCAGTTGGAACAATTGTACGTTTCTCGCAAGCGCTTAGCTGATCTCAAATTAAGCATATTGAAAACGGAGAAAGAGGC-TATG------
droAna3	scaffold_13043:302585-302586 +		AA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droKik1	scf7180000299276:10897-11001 -		GAGC-------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGGT-------------------------CCAGGCGAAATGGCTGAAATTACGAGGCA-G-----ATGGCACTGTATGCAGCACGAAAGGACCTTGCGGAGCTAAAGGCGAAGGT---------------TGCCGC-CTTGGAAGGC
droEle1	scf7180000489655:36407-36523 +		CATGTT----------------------------------------------------------------------------------------------------------------------------------------------GATGCAAGAAC-CGATTGAGCAAA-------------------------ACATAC------GCTC-AATCAGTCAGGT-T-----GTTGAACTGTACATTGCCCGAAAGGAGCTGGCTGAACATAAATTAGTTGC---------------CGCTGA-ATTGAAAGA-
droBia1	scf7180000299044:413-472 +		A---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTGTACACGACTAGAAAGAAGCTAGCCGAACTCAAATTGAGAGT---------------AGCCGA-ATTGTAAG--
droTak1	scf7180000415857:218499-218597 -		CGAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATGGAAGAAATGGCCGAAATTCTGAACCA-G-----ATGACCCTGTACAAAGCCCGGAAAGAACTTGCCGAGTTGAAAGTGCAAGT---------------GGCCGC-TTTGGAGAG-
droEug1	scf7180000409595:29214-29304 +		CG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAATGGCTGAAATCATGAGGCA-G-----ATGACGCTATATACAGCACGAAAGGACCTCGTTGAGTTAAAGGTGAAGGT---------------TGCCGC-TTTGGAAGGC
droYak3	v2_chrUn_003:77456-77644 -		GCTGTG-AGCG-----------------------------TGGCGGAGAGCGTCGCGGGAAGCGCCGCTG-TGAGCGTGGCAGAGAGCGTCGCGGGAAGAGAGAGTGAGCAGGAGGAGC------------------------------------------------GGGTG-------------------------TCGGACGAGTTGACCGAAATTACGAAGCA-G-----ATGACGTTGTATACAGCACGAAAGGATCTCGCGGAGTTGAAAGCGAAGGT---------------TGCCGC-CTTGGAAGGC
droEre2	scaffold_4784:23185576-23185666 -		GA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGATATGGCCGAAATTACGAAGCA-G-----ATTATGCTGTATAAAGCACGAAAGGATCTCG--GAGTTCAAAGTGAAGGT---------------TGTCGC-TTTGGAAGGC

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droWil2

GCCAA-GTACACCGGATCAAGTG-----GGTGCTAACCAGTCGCCGACGATGTCT------------------------------------------------------TGTGAGACCCCTGTAGGGCCAGACACGAACGTGCATGTTCGTGAAGGCGCACAAGCGAGCAAA-------------------------ACCGACGAATTGGCTTCGATTCTTTAGTAGC-----ATCGAATTGTATACAGCACGTAAAAACCTAATGGAGCTAAAAACACGTGT---------------TATGGA-GCTGGAGGAG	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
...........................................................................................................................................................................A-------------------------ACCGACGAATTGGCTTCGATTCT...............................................................................................	24	20	0.10	2	0	2	0	0	0
..........................................................................................................................................................................AA-------------------------ACCGACGAATTGGCTTCGATTCT...............................................................................................	25	20	0.10	2	0	0	0	2	0
..............................................................................................................................................................................................................................................................................TAAAAACACGTGT---------------TATGGA-GCTGGT....	25	20	0.05	1	0	0	0	1	0
.....................................................................................................................................................................................................................................................................TAATGGAGCTAAAAACACGTGT---------------TATG.............	26	20	0.05	1	0	1	0	0	0
..............................................................................................................................................................................................................................................ATTGTATACAGCACGTAAAAACCT.....................................................	24	20	0.05	1	0	0	0	1	0
...............................................................................................................................................ATGTTCGTGAAGGCGCACAAGCGAGC..................................................................................................................................................	26	20	0.05	1	0	0	1	0	0
............................................................................................................................................TGCATGTTCGTGAAGGCGCACAAGCGAGC..................................................................................................................................................	29	20	0.05	1	0	0	0	1	0
..............GATCAAGTG-----GGTGCTAACCAGTCGC...............................................................................................................................................................................................................................................................................	25	20	0.05	1	0	0	0	1	0
....................GTG-----GGTGCTAACCAGTCGC...............................................................................................................................................................................................................................................................................	19	20	0.05	1	0	0	0	1	0
..................................................................................................................GACCCCTGTAGGGCCAGA.......................................................................................................................................................................................	18	20	0.05	1	0	1	0	0	0
..............................................................................................................................................................................................................................................ATTGTATACAGCACGTAAAAACCTA....................................................	25	20	0.05	1	0	0	0	1	0
..................................................................................................................GACCCCTGTAGGGCCAGACACGAACGTG.............................................................................................................................................................................	28	20	0.05	1	0	0	0	1	0
........................................................................................................................................................................................................................................................................TGGAGCTAAAAACACGTGT---------------TATGGA-GC........	27	20	0.05	1	0	0	0	1	0
.....................................................................................................................................................................................................................................................ACAGCACGTAAAAACCTAATGGAGC.............................................	25	20	0.05	1	0	0	0	1	0

droVir3

GTATG-CTGTGTTGATTGAGGAT-----GAACCTAGCCATGTGTCC--------------------TCTGCTG---ACTGGTGCGAATGTTGC------------------------------------------------------------CAATTCAGAAGCGAATGGT-------------------------TCAGATAAGTTAGCGTCCGTGATAAATGA-G-----ATCTCCCTATACACTGCTCGAAAAAATCTTGCAAAGCTGAAGGCACGTGT---------------TTTCGAACTTGAAAGTG	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
.............................................................................................................................................................TCAGAAGCGAATGGT-------------------------TCAGATAAGTT...........................................................................................................	26	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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

dp5

GTAGA--------------------GGCGG----------CGCCAGA------------------------------------AGAATATTATGCAAATATGGAGAAGGTTCGAGAAGCATTCATGCCACGACAAGACAACGCTTGC-C--GAAATTAACCATGCGATCA--GACGAATACGAAAAGGAGTCGCGCC----------------------GTTTGCAGAAGTTGGAACAATTGTACGTTTCTCGCAAGCGCCTAGCTGATCTTAAATTA--GGC---------------TATGGA-GTTGGAA---	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
............................................................................................................................................................TAACCATGCGATCA--GACGAATACGA....................................................................................................................................	25	1	3.00	3	0	0	0	0	0	0	0	3	0	0
..................................................................................................................................................................TGCGATCA--GACGAATACGAAAAGGAG.............................................................................................................................	26	1	3.00	3	0	0	0	0	0	0	0	3	0	0
.........................................................................................................................................................................................................................................................................TGATCTTAAATTA--GGC---------------TATGGA-GT........	24	2	3.00	6	0	6	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................AGTTGGAACAATTGTACGTTTCTC...............................................................	24	10	1.60	16	0	9	0	0	0	1	0	3	3	0
....................................................................................................................................................................................................................................AGTTGGAACAATTGTACGTTTC.................................................................	22	10	1.40	14	0	13	0	0	1	0	0	0	0	0
..................................................................................................................GAAGCATTCATGCCACGACAAGAC.................................................................................................................................................................................	24	1	1.00	1	0	1	0	0	0	0	0	0	0	0
........................................CGCCAGA------------------------------------AGAATATTATGCAAATATGG....................................................................................................................................................................................................................	27	1	1.00	1	0	1	0	0	0	0	0	0	0	0
..............................................................................................................................................................................................................................................ATTGTACGTTTCTCGCAAGCGCCT.....................................................	24	1	1.00	1	0	1	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................AGTTGGAACAATTGTACGTTTCTCGCAA...........................................................	28	10	0.50	5	0	0	0	0	0	0	0	5	0	0
.........................................................................................................................................................................................................................................................................TGATCTTAAATTA--GGC---------------TATGGA-G.........	23	2	0.50	1	0	1	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................AGTTGGAACAATTGTACGTTT..................................................................	21	10	0.40	4	0	4	0	0	0	0	0	0	0	0
...GA--------------------GGCGG----------CGCCAGA------------------------------------AGAATAT.................................................................................................................................................................................................................................	21	3	0.33	1	0	1	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................AGTTGGAACAATTGTACGTTTCTCGC.............................................................	26	10	0.30	3	0	3	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................AGTTGGAACAATTGTACGTTTCTCG..............................................................	25	10	0.30	3	0	3	0	0	0	0	0	0	0	0
..........................................................................................................................................................................................................................................AACAATTGTACGTTTCTCGCAAGC.........................................................	24	11	0.27	3	0	0	1	0	0	0	0	0	2	0
....................................................................................................................................................................................................................................AGTTGGAACAATTGTACGTTTCT................................................................	23	10	0.20	2	0	2	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................................................................GTTGGAACAATTGTACGTTTCTC...............................................................	23	10	0.20	2	0	2	0	0	0	0	0	0	0	0
..........................................................................................................................................................................................................................................AACAATTGTACGTTTCTCGCAAGCGC.......................................................	26	11	0.18	2	0	0	0	0	0	0	0	0	2	0
....................................................................................................................................................................................................................................AGTTGGAACAATTGTACGTTTG.................................................................	22	10	0.10	1	0	1	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................AGTTGGAACAATTGTACGTT...................................................................	20	10	0.10	1	0	1	0	0	0	0	0	0	0	0
......................................................................................................................................................................................................................................TTGGAACAATTGTACGTTTCT................................................................	21	10	0.10	1	0	0	0	0	0	0	0	0	1	0
......................................................................................................................................................................................................................................TTGGAACAATTGTACGTTT..................................................................	19	10	0.10	1	0	1	0	0	0	0	0	0	0	0
......................................................................................................................................................................................................................................TTGGAACAATTGTACGTTTCTC...............................................................	22	10	0.10	1	0	1	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................AGTTGGAACAATTGTACGTTTCTCGCA............................................................	27	10	0.10	1	0	1	0	0	0	0	0	0	0	0
..............................................................................................................................................................................................................................................ATTGTACGTTTCTCGCAAGC.........................................................	20	11	0.09	1	0	1	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................................................GAACAATTGTACGTTTCTCGCAAGCG........................................................	26	11	0.09	1	0	1	0	0	0	0	0	0	0	0
........................................................................................................................................................................................................................................GGAACAATTGTACGTTTCTCGCAAGCGC.......................................................	28	11	0.09	1	0	0	0	0	0	0	0	0	1	0
..........................................................................................................................................................................................................................................AACAATTGTACGTTTCTCGC.............................................................	20	11	0.09	1	0	0	0	0	0	0	0	1	0	0

droPer2

ACCGTAGTGCACAACACGCAGTAAAAGCGG----------CGCCAGA------------------------------------AGAATATGGTGAAAATGTGCAGAAGGCTCGAGAAGCATTCATGCCGCGACAAGACAACGCTTGTTC--GAAATTGACCATGCGATCA--GATGAATACGAAGAAGAATCGCGCC----------------------GTTTGCAGCAGTTGGAACAATTGTACGTTTCTCGCAAGCGCTTAGCTGATCTCAAATTAAGCATATTGAAAACGGAGAAAGAGGC-TATG------	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
...........................................CAGA------------------------------------AGAATATGGTGAAAATGTGC....................................................................................................................................................................................................................	24	12	0.50	6	0	4	0	0	0	2
...............................................................................................................................................TTGTTC--GAAATTGACCATGCGATC..................................................................................................................................................	24	17	0.47	8	0	8	0	0	0	0
...........................................CAGA------------------------------------AGAATATGGTGAAAATGTG.....................................................................................................................................................................................................................	23	12	0.33	4	0	4	0	0	0	0
...............................................................................................................................................TTGTTC--GAAATTGACCATGCGAT...................................................................................................................................................	23	17	0.29	5	0	4	0	0	0	1
...............................................................................................................................................TTGTTC--GAAATTGACCATGCGATCA--GA.............................................................................................................................................	27	17	0.24	4	0	4	0	0	0	0
...........................................CAGA------------------------------------AGAATATGGTGAAAATGTGCAG..................................................................................................................................................................................................................	26	12	0.17	2	0	2	0	0	0	0
...........................................CAGA------------------------------------AGAATATGGTGAAAATGTGCA...................................................................................................................................................................................................................	25	12	0.17	2	0	1	0	0	0	1
.......................................................................................TATGGTGAAAATGTGCAGAAGGCT............................................................................................................................................................................................................	24	7	0.14	1	0	0	0	0	0	1
.......................................................................................TATGGTGAAAATGTGCAGAAGG..............................................................................................................................................................................................................	22	8	0.13	1	0	0	0	0	0	1
...............................................................................................................................................TTGTTC--GAAATTGACCATGCGATCA--...............................................................................................................................................	25	17	0.12	2	0	2	0	0	0	0
...............................................................................................................................................TTGTTC--GAAATTGACCATGCGA....................................................................................................................................................	22	17	0.12	2	0	2	0	0	0	0
................................................................................................................................................TGTTC--GAAATTGACCATGCGAT...................................................................................................................................................	22	20	0.10	2	0	2	0	0	0	0
..................................................................................................................................................................................TACGAAGAAGAATCGCGCC----------------------GTTTGCA.........................................................................................	26	20	0.10	2	0	2	0	0	0	0
..............................................................................................................................................................................TGAATACGAAGAAGAATCGCGCC----------------------GTT.............................................................................................	26	20	0.10	2	0	1	0	0	0	1
....................................................................................................................................................................................................................................AGTTGGAACAATTGTACGTTTCTC...............................................................	24	20	0.10	2	0	1	1	0	0	0
............................................AGA------------------------------------AGAATATGGTGAAAATGTGC....................................................................................................................................................................................................................	23	12	0.08	1	0	1	0	0	0	0
...............................................................................................................................................TTGTTC--GAAATTGACCATGCG.....................................................................................................................................................	21	17	0.06	1	0	1	0	0	0	0
...............................................................................................................................................TTGTTC--GAAATTGACCATGCGATCA--G..............................................................................................................................................	26	17	0.06	1	0	1	0	0	0	0
...........................................................................................GTGAAAATGTGCAGAAGGC.............................................................................................................................................................................................................	19	19	0.05	1	0	0	1	0	0	0
.......TGCACAACACGCAGTAAAAGCGG----------C..................................................................................................................................................................................................................................................................................	24	20	0.05	1	1	0	0	0	0	0
.........................................................................................................................................................................................AAGAATCGCGCC----------------------GTTTGCA.........................................................................................	19	20	0.05	1	0	1	0	0	0	0
..............................................................................................................TCGAGAAGCATTCATGCCGCGACAAGAC.................................................................................................................................................................................	28	20	0.05	1	0	1	0	0	0	0
..............................................................................................................TCGAGAAGCATTCATGCCGCGAC......................................................................................................................................................................................	23	20	0.05	1	0	1	0	0	0	0
...............................................................................................................CGAGAAGCATTCATGCCGCGA.......................................................................................................................................................................................	21	20	0.05	1	0	1	0	0	0	0
..........................................................................................................................................................................................................................................................................GATCTCAAATTAAGCATATTGA...........................	22	20	0.05	1	0	1	0	0	0	0
.................................................................................................................................................................................................CGCC----------------------GTTTGCAGCAGTTGGAACA.............................................................................	23	20	0.05	1	0	0	0	0	0	1
....................................................................................................................................................................................CGAAGAAGAATCGCGCC----------------------GTTTGC..........................................................................................	23	20	0.05	1	0	0	0	0	0	1
..................................................................................................................................................................................TACGAAGAAGAATCGCGCC----------------------GTTTGCAGC.......................................................................................	28	20	0.05	1	0	1	0	0	0	0
..............................................................................................................TCGAGAAGCATTCATGCCGCGACA.....................................................................................................................................................................................	24	20	0.05	1	0	1	0	0	0	0
...........................................................................................................................................................................................................................GTTTGCAGCAGTTGGAACAATT..........................................................................	22	20	0.05	1	0	0	0	0	0	1
............................................................................................................................................................................................................................................................................................TTGAAAACGGAGAAAGAGGC-..........	20	20	0.05	1	0	0	0	0	0	1
...................................................................................................................................................................................................................................CAGTTGGAACAATTGTACGTTTCTC...............................................................	25	20	0.05	1	0	1	0	0	0	0
.........................................................................................................................................................................................................................................................................TGATCTCAAATTAAGCATATTG............................	22	20	0.05	1	0	1	0	0	0	0
...............................................................................................................................................................................GAATACGAAGAAGAATCGCGCC----------------------GTT.............................................................................................	25	20	0.05	1	0	1	0	0	0	0
...............................................................................................................................................................CCATGCGATCA--GATGAATACGAAGA.................................................................................................................................	25	20	0.05	1	0	1	0	0	0	0

droAna3

AA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
No Reads

droKik1

GAGC-------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGGT-------------------------CCAGGCGAAATGGCTGAAATTACGAGGCA-G-----ATGGCACTGTATGCAGCACGAAAGGACCTTGCGGAGCTAAAGGCGAAGGT---------------TGCCGC-CTTGGAAGGC	Size	Hit Count	Total Norm	Total
No Reads

droEle1

CATGTT----------------------------------------------------------------------------------------------------------------------------------------------GATGCAAGAAC-CGATTGAGCAAA-------------------------ACATAC------GCTC-AATCAGTCAGGT-T-----GTTGAACTGTACATTGCCCGAAAGGAGCTGGCTGAACATAAATTAGTTGC---------------CGCTGA-ATTGAAAGA-	Size	Hit Count	Total Norm	Total
No Reads

droBia1

A---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTGTACACGACTAGAAAGAAGCTAGCCGAACTCAAATTGAGAGT---------------AGCCGA-ATTGTAAG--	Size	Hit Count	Total Norm	Total
No Reads

droTak1

CGAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATGGAAGAAATGGCCGAAATTCTGAACCA-G-----ATGACCCTGTACAAAGCCCGGAAAGAACTTGCCGAGTTGAAAGTGCAAGT---------------GGCCGC-TTTGGAGAG-	Size	Hit Count	Total Norm	Total
No Reads

droEug1

CG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAATGGCTGAAATCATGAGGCA-G-----ATGACGCTATATACAGCACGAAAGGACCTCGTTGAGTTAAAGGTGAAGGT---------------TGCCGC-TTTGGAAGGC	Size	Hit Count	Total Norm	Total
No Reads

droYak3

GCTGTG-AGCG-----------------------------TGGCGGAGAGCGTCGCGGGAAGCGCCGCTG-TGAGCGTGGCAGAGAGCGTCGCGGGAAGAGAGAGTGAGCAGGAGGAGC------------------------------------------------GGGTG-------------------------TCGGACGAGTTGACCGAAATTACGAAGCA-G-----ATGACGTTGTATACAGCACGAAAGGATCTCGCGGAGTTGAAAGCGAAGGT---------------TGCCGC-CTTGGAAGGC	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
...................................................................................................................................................................................................................................G-----ATGACGTTGTATACAGCACGAAAGGA........................................................	27	5	2.00	10	0	0	0	0	0	0	0	0	0	0	10
..............................................................................................................................................................................................................................................................................TGAAAGCGAAGGT---------------TGCCGC-CTTGGAA...	26	8	1.25	10	0	1	0	0	0	0	0	0	0	0	9
.............................................................................................................................................................................................................................................CGTTGTATACAGCACGAAAGGATC......................................................	24	6	1.17	7	0	4	3	0	0	0	0	0	0	0	0
..........................................................................................................................................................................................................................................TGACGTTGTATACAGCACGAAAGGATCT.....................................................	28	5	1.00	5	0	0	0	0	0	0	0	0	0	0	5
...................................................................................................................................................................................................................................G-----ATGACGTTGTATACAGCACGAAAGG.........................................................	26	5	0.80	4	0	0	0	0	0	0	0	0	0	0	4
.............................................................................TGGCAGAGAGCGTCGCGGGAAGAGA.....................................................................................................................................................................................................................	25	5	0.40	2	0	0	1	0	0	0	0	0	0	0	1
.......................................................................TGAGCGTGGCAGAGAGCGTCGCGGG...........................................................................................................................................................................................................................	25	5	0.40	2	0	2	0	0	0	0	0	0	0	0	0
..............................................................................................................................................................................................................................................................................TGAAAGCGAAGGT---------------TGCCGC-CTTGG.....	24	8	0.25	2	0	1	0	1	0	0	0	0	0	0	0
....................................................................TG-TGAGCGTGGCAGAGAGCGTCGCG.............................................................................................................................................................................................................................	25	4	0.25	1	0	1	0	0	0	0	0	0	0	0	0
............................................................................GTGGCAGAGAGCGTCGCGGGA..........................................................................................................................................................................................................................	21	5	0.20	1	0	1	0	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................................................................................................TCGCGGAGTTGAAAGCGAAGGT---------------TGC..............	25	10	0.20	2	0	1	0	1	0	0	0	0	0	0	0
...........................................................................................................................................................................................................................CGAAGCA-G-----ATGACGTTGTATACAG..................................................................	24	5	0.20	1	0	1	0	0	0	0	0	0	0	0	0
............................................................................GTGGCAGAGAGCGTCGCGGGAAGAG......................................................................................................................................................................................................................	25	5	0.20	1	0	1	0	0	0	0	0	0	0	0	0
..............................................................................................................................................................................................................................................GTTGTATACAGCACGAAAGGATCTCG...................................................	26	5	0.20	1	0	1	0	0	0	0	0	0	0	0	0
............................................................................GTGGCAGAGAGCGTCGCGGGAA.........................................................................................................................................................................................................................	22	5	0.20	1	0	1	0	0	0	0	0	0	0	0	0
.............................................................................................................................................................................................................................................CGTTGTATACAGCACGAAAGGATCTCGC..................................................	28	5	0.20	1	0	1	0	0	0	0	0	0	0	0	0
.....................................................................................................................GC------------------------------------------------GGGTG-------------------------TCGGACGAGTTGACCGT.....................................................................................................	24	6	0.17	1	0	1	0	0	0	0	0	0	0	0	0
........................................TGGCGGAGAGCGTCGCGGGAAGCGCC.........................................................................................................................................................................................................................................................	26	6	0.17	1	0	1	0	0	0	0	0	0	0	0	0
.............................................................................................................................................................................................................GTTGACCGAAATTACGAAGCA-G-----ATGAC.............................................................................	27	6	0.17	1	0	0	0	0	0	0	0	0	0	0	1
.............................................................................................................................................................................................................................................CGTTGTATACAGCACGAAAGGATCTC....................................................	26	6	0.17	1	0	1	0	0	0	0	0	0	0	0	0
..............................................................................................................................................................................................................................................GTTGTATACAGCACGAAAGGATC......................................................	23	6	0.17	1	0	1	0	0	0	0	0	0	0	0	0
....................................................TCGCGGGAAGCGCCGCTG-TGAGC...............................................................................................................................................................................................................................................	23	6	0.17	1	0	1	0	0	0	0	0	0	0	0	0
.............................................................................................................................................................................................................................................CGTTGTATACAGCACGAAAGGATA......................................................	24	6	0.17	1	0	0	0	0	0	0	1	0	0	0	0
.............................................................................................................................................................................................................................................CGTTGTATACAGCACGAAAGGA........................................................	22	6	0.17	1	0	0	0	0	0	0	1	0	0	0	0
.............................................................................................................................................................................................................................................CGTTGTATACAGCACGAAAGGAT.......................................................	23	6	0.17	1	0	1	0	0	0	0	0	0	0	0	0
.............................................................................................................................................................................................................................................CGTTGTATACAGCACGAAAGGATCT.....................................................	25	6	0.17	1	0	0	1	0	0	0	0	0	0	0	0
............................................................................................................................................................................................................AGTTGACCGAAATTACGAAGCA-G-----A.................................................................................	24	7	0.14	1	0	0	0	0	0	0	1	0	0	0	0
.....................................................................................................AGAGTGAGCAGGAGGAGC------------------------------------------------GG..................................................................................................................................................	20	7	0.14	1	0	1	0	0	0	0	0	0	0	0	0
..................................................................................................GAGAGAGTGAGCAGGAGGAGC------------------------------------------------G...................................................................................................................................................	22	7	0.14	1	0	1	0	0	0	0	0	0	0	0	0
.............................................................................................................................................................................................................................................................................TTGAAAGCGAAGGT---------------TGCCGC-CTTGGAA...	27	8	0.13	1	0	1	0	0	0	0	0	0	0	0	0
..............................................................................................................................................................................................................................................................................TGAAAGCGAAGGT---------------TGCCGC-CTTGGAAG..	27	8	0.13	1	0	1	0	0	0	0	0	0	0	0	0
............................................................................................................................................................................................................................................................................GTTGAAAGCGAAGGT---------------TGCCGC-CT........	23	8	0.13	1	0	0	1	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................................................................................GGAGTTGAAAGCGAAGGT---------------TGCCT............	23	10	0.10	1	0	1	0	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................................................................................................TCGCGGAGTTGAAAGCGAAGGT---------------TGCC.............	26	10	0.10	1	0	1	0	0	0	0	0	0	0	0	0
......................................................................................................................................................................................................................................................................CGCGGAGTTGAAAGCGAAGGT---------------TGCC.............	25	10	0.10	1	0	0	1	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................................................................................GGAGTTGAAAGCGAAGGT---------------TGCCGC-..........	24	10	0.10	1	0	1	0	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................................................................................................GCGGAGTTGAAAGCGAAGGT---------------T................	21	10	0.10	1	0	0	1	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................................................................................GGAGTTGAAAGCGAAGGT---------------TGCCGC-C.........	25	10	0.10	1	0	1	0	0	0	0	0	0	0	0	0

droEre2

GA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGATATGGCCGAAATTACGAAGCA-G-----ATTATGCTGTATAAAGCACGAAAGGATCTCG--GAGTTCAAAGTGAAGGT---------------TGTCGC-TTTGGAAGGC	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
No Reads

-20.5	-20.3	-20.2	-20.0

dwi_249

scf2_1100000001801:1224-1332 +

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