dwi_953

Name	Class	Family	Strand
(CA)n	Simple_repeat	Simple_repeat	+

-------------------------------------------#######--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- GTGTGTTTAAACTTAAACAAAAAAAAAAAAAAAATCAAACACAATGAGCAGTAAGTTTTCGGCAAAAAAGTGAAGATGAAAAAGAAGAAGAAGAAAACTCAGTGTGTGTGTGTGTGTGTATCACTGTGTGTGTGAGCCTGTAAGCATTATGCATGCAAGTCCTGCCGAAAGCGTTTTTCCATCGTTATTTTTTTGCTAACCGAAATTGCATATATCATTTAAAATAATCGTCAAAAAAATATGAAAAACGG ************************************************....(((...(((((((((((((.((((.....((((((..........((((((((((((((((.....((((.......))))........))).))))))))))....))).........)))))))))).)))))))))))))))).************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V118 embryo	V119 head	V117 male body
....................................................................AGTGAAGCTGAAAAATAAGA...................................................................................................................................................................	20	2	4	0.25	1	1	0	0
................................................................................................ACTCAGTGTGTGTGTGTG.........................................................................................................................................	18	0	15	0.07	1	0	1	0
.................................................................................................CTCAGTGTGTGTGTGTGT........................................................................................................................................	18	0	20	0.05	1	0	0	1

CACACAAATTTGAATTTGTTTTTTTTTTTTTTTTAGTTTGTGTTACTCGTCATTCAAAAGCCGTTTTTTCACTTCTACTTTTTCTTCTTCTTCTTTTGAGTCACACACACACACACACATAGTGACACACACACTCGGACATTCGTAATACGTACGTTCAGGACGGCTTTCGCAAAAAGGTAGCAATAAAAAAACGATTGGCTTTAACGTATATAGTAAATTTTATTAGCAGTTTTTTTATACTTTTTGCC ************************************************....(((...(((((((((((((.((((.....((((((..........((((((((((((((((.....((((.......))))........))).))))))))))....))).........)))))))))).)))))))))))))))).************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M045 female body	M020 head
..............................................................................................................................................................................................ACAACGATTGGATTGAACGTAT.......................................	22	3	2	0.50	1	1	0
...................................................................................................GTCACACACACACACACACAT...................................................................................................................................	21	0	20	0.05	1	0	1

Re-alignment of all predicted orthologs

Species	Coordinate	ID	Alignment
droWil2	scf2_1100000004514:136767-137017 -	dwi_953	GTGTGTTTAA----------------------------------------ACTT----AAACAA---AAAAAAAAAAAAAATCAAACACAATGAGCAGTAAGTTTTCGG-------------------------------------------------------------------------------------------CA--------AAAAA-----GTG-----------------A----AGATGAAAA----AGAAGA-AGAAGA--------------AAACTCAGTGTGTGTGTGTGT--GTGTATCACTGT--GTGTGTGAGCCTGTAAGCATTATGCATG-------------------CAAGTCCT-GCCGA----AA-GC---------GTTTTTCCATCGTT-------------------------------------------------------------------ATTTTTTTGCTAACCGAAATTGCATATATCA---TTTAAAATA-------ATCGTCAAAAAAATATGAAAAAC---GG-
droVir3	scaffold_12875:14245213-14245548 +	dvi_6836	GTGTTTTT-----------GCAGTGTT-------------TAC---AGTAG-TTAACTAACAAAAAGAAAAAAAAAAAAACAAAAACAAAATGAGCAGTAAGTTTTT-CCAGC-----------------------------A------ACA----------------------------------ACAGCAGTTGCCGCCAAAGAAGCGG-CAAAAGAAGTGACCACAGATAAA---AAA----ATATAAAAA----AAAATA-TAA--------------ATGAAAATCTGTGCGTGTGTGTGTGTGTGT--------------G--------------TTATGCATGGCTACTGCCTAT-CATATCCAA---GT--------TGAGAG-AGTCGCTGGGCCTTCCCT----------TTGCGATTGCGACTGCGAATGCGACTGCGACTGCGAGTGCAGCAGCTCTTCTCTGTTTCT----T---TT---------TATCGCAATTAAT-------------AAAAGCC-----------------GCAAAT---AAA
droMoj3	scaffold_6496:9700317-9700645 +		GTGTGCTAAAAAAATATATACA-TATTTAACAAAATAATATAC---AATAG--------------TTAAACAAAATAAATCAAATACAAAATGAGCAGTAAGTTTTTACCAAC-----------------------------A------ACA----------------------------------AGAGCGTTCGCCACCA-----------AA--GAAGTGAACACAGATAAA---------------------------AA-AAAAAAAGTTAAATCCAAAGAGAGTCTGTGTGTGTGCGTGT----------GTAT--GT--GTGTA----------CTATGCATGGCTACTGCCTATCCATATCCAC---GT--------TGAGAGGCGCTGCTGGGCCTTCCCT----------TTGCAATTGTGTTTGCAATTGCGACTGCGACTG---------CAGCTCTTCTCCGTTTCT----T---TT---------TATCGCAATTAAT-------------AAATGCC-----------------GCAAGC---AA-
droGri2	scaffold_15245:14224220-14224518 +		GAGTTTTTC----------GCAGTGTA-------------TATTCAACTATTTTAACTAACACACA-AAACAAAAAATTTCAAAATCAAAATGAGCAGTAAGTTTAT-CCAAC-----------------------------A------ACA----------------------------------ACAG---ACG---CCA--------AAAAAATGAAGTTATCACAGATAAAAAAAAAATAAAA-------AAT----------------ATAAAATCAATGAGAATCTGTGTGAGTGTGTGT----------GTGTGAGTGTGTGTGCGTC------TTATGCATGTCTGCTG---------GTCCAC---GTTATTGAGTTGAG-G--------------------------------------------------------CGACTG---------CAGCTCTTCTCTT--TCTTTCTTTCTTT---------AATCGCAATTAATA---TTTAAAA--AAAAGCC-----------------GCAAAT---AA-
dp5	3:3558081-3558255 +		GTGTGCTTTA----------------------------------------ATTT----AACGAATTTAAACAAAAAGAAAACCTAACAAAATGAGCCGTAAGTTTCAAAATGCACTACTCCCCCGCAACCGTTGATTCGGACGCAGAGTGCA----------------------------------GCAG---CCA---CCA--------GCAAA-------------------A---GGC----AAATGCGAA----TAAAGA-AAAGAA--------------AAAGTGTGTGTGTGTGTGTGT----------------------TTA-----------TAT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer2	scaffold_2:3746803-3746988 +		GTGTGCTTTA----------------------------------------ATTT----AACGAATTTAAACAAAAAGAAAACCTAACAAAATGAGCCGTAAGTTTCAAAATGCACTACTCCCCCGCAACCGTTGATTCGGACGCAGAGTGCA----------------------------------GCAG---CCA---CCA--------GCAAA-------------------A---GGC----AAATGCGAA----TAAAGA-AAAGAA--------------AAAGTGTGTGTGTGTG--TGTGTGTGT--------------GTTTA-----------TATGCATG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droBip1	scf7180000396543:384667-384788 -		AACAA--------------------------------------------------------------AAAAATAAAAAAAAAACAACTAAACGAA-----------------------------------------------------------------------------------------------------AGCA-----------AA---------------------A---AAAATAAAA-------ACTAAAAAAAAA-A--------------AGGAAACGCTGTGCATGTGTGCGT----------GTGTGTGTGTGTGTGCGTGTGATGGTTATATATG-------------------CA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droKik1	scf7180000302682:180375-180649 -		AACCCCT-----------------------------------------------------------------------------AACAAAATGAGCAGTAAGTTGGGAGGAGCACT---------------------------------GCAACTGCAATTCGCAATAAAAAAAAAAGAAATGATAA------------A-----------AG---------------------A---AAAGCGCAA-------AGCAAACGCAGA-A--------------A--AGAGTGTGTGTGCGTG--------CGTTCGAGCGT--GTGTGTGTGTGCG-------TATGCATGGCTAAAGGCTG--------CAGGCTGCAACCGAAAAAAA-GA---------GCCTGCCCCAAGTTAAAAGCTCTAATAATCCTCCCAAAAAAAACCACCCCTG---------CCCCTCT------------------------------------------CACATTTCATAACA-------CTCGC--------TTTGGGAAGG---AG-
droEle1	scf7180000491087:219945-220019 +		AAACAAAA--------------------------------------------------------------AAAAA---AAAGGAAACAAAA-----------------------------------------------------------------------------------------------ACAC---ACGCACA-----------CATA-------------------------------------------------------------------------------------------------------------------------------------AGCA-----------------TG-----------------------------------------------------------------------------------------------------------------------------------------------------------------GATATGAAATAAATATAAAAAATAATAA-
droYak3	X:7082223-7082269 +		GCGCGTGT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG--------TGTGTGAGAAT--GTGTGCGTAC-----------ATGTATGTA-----------------TT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droWil2

GTGTGTTTAA----------------------------------------ACTT----AAACAA---AAAAAAAAAAAAAATCAAACACAATGAGCAGTAAGTTTTCGG-------------------------------------------------------------------------------------------CA--------AAAAA-----GTG-----------------A----AGATGAAAA----AGAAGA-AGAAGA--------------AAACTCAGTGTGTGTGTGTGT--GTGTATCACTGT--GTGTGTGAGCCTGTAAGCATTATGCATG-------------------CAAGTCCT-GCCGA----AA-GC---------GTTTTTCCATCGTT-------------------------------------------------------------------ATTTTTTTGCTAACCGAAATTGCATATATCA---TTTAAAATA-------ATCGTCAAAAAAATATGAAAAAC---GG-	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
...............................................................................................................................................................................................................................................................................................ACTCAGTGTGTGTGTGTG................................................................................................................................................................................................................................................................	18	15	0.07	1	0	0	0	0	1
................................................................................................................................................................................................................................................................................................CTCAGTGTGTGTGTGTGT--.............................................................................................................................................................................................................................................................	18	20	0.05	1	0	0	1	0	0

droVir3

GTGTTTTT-----------GCAGTGTT-------------TAC---AGTAG-TTAACTAACAAAAAGAAAAAAAAAAAAACAAAAACAAAATGAGCAGTAAGTTTTT-CCAGC-----------------------------A------ACA----------------------------------ACAGCAGTTGCCGCCAAAGAAGCGG-CAAAAGAAGTGACCACAGATAAA---AAA----ATATAAAAA----AAAATA-TAA--------------ATGAAAATCTGTGCGTGTGTGTGTGTGTGT--------------G--------------TTATGCATGGCTACTGCCTAT-CATATCCAA---GT--------TGAGAG-AGTCGCTGGGCCTTCCCT----------TTGCGATTGCGACTGCGAATGCGACTGCGACTGCGAGTGCAGCAGCTCTTCTCTGTTTCT----T---TT---------TATCGCAATTAAT-------------AAAAGCC-----------------GCAAAT---AAA	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
.....................................................................................................................................................................................................................................................................................................................................................................................................................................TGCGATTGCGACTGCGAATGCGACTGC.................................................................................................................	27	1	2.00	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.....TTT-----------GCAGTGTT-------------TAC---AGTA...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	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
..........................................C---AGTAG-TTAACTAACAAAA................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.....TTT-----------GCAGTGTT-------------TAC---AGTAG-TTAA.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
.......T-----------GCAGTGTT-------------TAC---AGTAG-TTAACT.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.............................................................................AAACAAAAACAAAATGAGC.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	2	0.50	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
........................................................CTAACAAAAAGAAAAAAAA......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	4	0.25	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droMoj3

GTGTGCTAAAAAAATATATACA-TATTTAACAAAATAATATAC---AATAG--------------TTAAACAAAATAAATCAAATACAAAATGAGCAGTAAGTTTTTACCAAC-----------------------------A------ACA----------------------------------AGAGCGTTCGCCACCA-----------AA--GAAGTGAACACAGATAAA---------------------------AA-AAAAAAAGTTAAATCCAAAGAGAGTCTGTGTGTGTGCGTGT----------GTAT--GT--GTGTA----------CTATGCATGGCTACTGCCTATCCATATCCAC---GT--------TGAGAGGCGCTGCTGGGCCTTCCCT----------TTGCAATTGTGTTTGCAATTGCGACTGCGACTG---------CAGCTCTTCTCCGTTTCT----T---TT---------TATCGCAATTAAT-------------AAATGCC-----------------GCAAGC---AA-	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
...............................................ATAG--------------TTAAACAAAATAAAT.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	1	0	0	1	0	0	0
.........................................................................................................................................................................................................................................................................................................................................................................................................................................ATTGTGTTTGCAATTGCGA.....................................................................................................................	19	1	1.00	1	1	0	0	0	0	0

droGri2

GAGTTTTTC----------GCAGTGTA-------------TATTCAACTATTTTAACTAACACACA-AAACAAAAAATTTCAAAATCAAAATGAGCAGTAAGTTTAT-CCAAC-----------------------------A------ACA----------------------------------ACAG---ACG---CCA--------AAAAAATGAAGTTATCACAGATAAAAAAAAAATAAAA-------AAT----------------ATAAAATCAATGAGAATCTGTGTGAGTGTGTGT----------GTGTGAGTGTGTGTGCGTC------TTATGCATGTCTGCTG---------GTCCAC---GTTATTGAGTTGAG-G--------------------------------------------------------CGACTG---------CAGCTCTTCTCTT--TCTTTCTTTCTTT---------AATCGCAATTAATA---TTTAAAA--AAAAGCC-----------------GCAAAT---AA-	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

dp5

GTGTGCTTTA----------------------------------------ATTT----AACGAATTTAAACAAAAAGAAAACCTAACAAAATGAGCCGTAAGTTTCAAAATGCACTACTCCCCCGCAACCGTTGATTCGGACGCAGAGTGCA----------------------------------GCAG---CCA---CCA--------GCAAA-------------------A---GGC----AAATGCGAA----TAAAGA-AAAGAA--------------AAAGTGTGTGTGTGTGTGTGT----------------------TTA-----------TAT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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

No Reads

droPer2

GTGTGCTTTA----------------------------------------ATTT----AACGAATTTAAACAAAAAGAAAACCTAACAAAATGAGCCGTAAGTTTCAAAATGCACTACTCCCCCGCAACCGTTGATTCGGACGCAGAGTGCA----------------------------------GCAG---CCA---CCA--------GCAAA-------------------A---GGC----AAATGCGAA----TAAAGA-AAAGAA--------------AAAGTGTGTGTGTGTG--TGTGTGTGT--------------GTTTA-----------TATGCATG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
No Reads

droBip1

AACAA--------------------------------------------------------------AAAAATAAAAAAAAAACAACTAAACGAA-----------------------------------------------------------------------------------------------------AGCA-----------AA---------------------A---AAAATAAAA-------ACTAAAAAAAAA-A--------------AGGAAACGCTGTGCATGTGTGCGT----------GTGTGTGTGTGTGTGCGTGTGATGGTTATATATG-------------------CA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droKik1

AACCCCT-----------------------------------------------------------------------------AACAAAATGAGCAGTAAGTTGGGAGGAGCACT---------------------------------GCAACTGCAATTCGCAATAAAAAAAAAAGAAATGATAA------------A-----------AG---------------------A---AAAGCGCAA-------AGCAAACGCAGA-A--------------A--AGAGTGTGTGTGCGTG--------CGTTCGAGCGT--GTGTGTGTGTGCG-------TATGCATGGCTAAAGGCTG--------CAGGCTGCAACCGAAAAAAA-GA---------GCCTGCCCCAAGTTAAAAGCTCTAATAATCCTCCCAAAAAAAACCACCCCTG---------CCCCTCT------------------------------------------CACATTTCATAACA-------CTCGC--------TTTGGGAAGG---AG-	Size	Hit Count	Total Norm	Total
No Reads

droEle1

AAACAAAA--------------------------------------------------------------AAAAA---AAAGGAAACAAAA-----------------------------------------------------------------------------------------------ACAC---ACGCACA-----------CATA-------------------------------------------------------------------------------------------------------------------------------------AGCA-----------------TG-----------------------------------------------------------------------------------------------------------------------------------------------------------------GATATGAAATAAATATAAAAAATAATAA-	Size	Hit Count	Total Norm	Total
No Reads

droYak3

GCGCGTGT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG--------TGTGTGAGAAT--GTGTGCGTAC-----------ATGTATGTA-----------------TT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

Total

M026
Head

M043
Female-body

M056
Embryo

V046
Embryo

V052
Head

V058
Head

V120
Male-body

SRR1275488
Male larvae

SRR1275486
Male prepupae

SRR1275484
Male prepupae

GSM1528802
follicle cells

No Reads

dwi_953

scf2_1100000004514:136817-136967 -

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

-33.3	-33.3	-33.3