dvi_13474

Name	Class	Family	Strand
(T)n	Simple_repeat	Simple_repeat	+

Name

Class

Family

Strand

(T)n

Simple_repeat

--------------------------------------############--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ATCTTTACCCAGTAATCTCATTAAAAAAAAAAACGAATATGTATCCATACGTAAGTAGAACTTTCTTAAACTTGATCTTTTTGCACCAGCATTTTCGGCAATAGATGCACTTATATATTTTTTTTTTTTTTTTTTTTTTTTTGGTATCACAATTTTCATTTAAATAGTTGTCGAATGTACGCTTCTTAGATACATGTCGCTCGTTTTTTTTTTTTTGTCTTTTCTTTTCATAAAATACAAACCATTTTTTT **********************************************************.....................(((....))).........*****************************************************************************************************************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	GSM1528803 follicle cells	SRR060667 160_females_carcasses_total	SRR060677 Argx9_ovaries_total	SRR060669 160x9_females_carcasses_total	SRR060689 160x9_testes_total
..................................................................................GCACCAGCATTTTCGGCA.......................................................................................................................................................	18	0	1	1.00	1	0	1	0	0	0
............................................................CTTTCTTAAACTTGAT...............................................................................................................................................................................	16	0	1	1.00	1	1	0	0	0	0
.....................................................................................................................................................................................................................TTTGTCTATTCTTTTTATAAA.................	21	2	6	0.17	1	0	0	1	0	0
.........................................................................................................................................................................GTCGCACGTACGGTTCTTA...............................................................	19	3	12	0.08	1	0	0	0	1	0
............................................................................................................................................................................................................TTGTTTTTTTTTGTCTTTTC...........................	20	1	15	0.07	1	0	0	0	0	1
.....................TAAAAAAAAAATTGAATATGTA................................................................................................................................................................................................................	22	2	15	0.07	1	0	0	1	0	0

--------------------------------------############---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
ATCTTTACCCAGTAATCTCATTAAAAAAAAAAACGAATATGTATCCATACGTAAGTAGAACTTTCTTAAACTTGATCTTTTTGCACCAGCATTTTCGGCAATAGATGCACTTATATATTTTTTTTTTTTTTTTTTTTTTTTTGGTATCACAATTTTCATTTAAATAGTTGTCGAATGTACGCTTCTTAGATACATGTCGCTCGTTTTTTTTTTTTTGTCTTTTCTTTTCATAAAATACAAACCATTTTTTT
************************************************************.....................(((....))).........*******************************************************************************************************************************************************

Read size

# Mismatch

Hit Count

Total Norm

Total

GSM1528803
follicle cells

SRR060667
160_females_carcasses_total

SRR060677
Argx9_ovaries_total

SRR060669
160x9_females_carcasses_total

SRR060689
160x9_testes_total

..................................................................................GCACCAGCATTTTCGGCA.......................................................................................................................................................

1.00

............................................................CTTTCTTAAACTTGAT...............................................................................................................................................................................

1.00

.....................................................................................................................................................................................................................TTTGTCTATTCTTTTTATAAA.................

0.17

.........................................................................................................................................................................GTCGCACGTACGGTTCTTA...............................................................

0.08

0.07

.....................TAAAAAAAAAATTGAATATGTA................................................................................................................................................................................................................

0.07

TAGAAATGGGTCATTAGAGTAATTTTTTTTTTTGCTTATACATAGGTATGCATTCATCTTGAAAGAATTTGAACTAGAAAAACGTGGTCGTAAAAGCCGTTATCTACGTGAATATATAAAAAAAAAAAAAAAAAAAAAAAAACCATAGTGTTAAAAGTAAATTTATCAACAGCTTACATGCGAAGAATCTATGTACAGCGAGCAAAAAAAAAAAAACAGAAAAGAAAAGTATTTTATGTTTGGTAAAAAAA *****************************************************************************************************************************************************.....................(((....))).........**********************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	SRR060682 9x140_0-2h_embryos_total	SRR060684 140x9_0-2h_embryos_total	SRR060674 9x140_ovaries_total	SRR060686 Argx9_0-2h_embryos_total	SRR060685 9xArg_0-2h_embryos_total	SRR060687 9_0-2h_embryos_total	SRR060672 9x160_females_carcasses_total	M047 female body	SRR060665 9_females_carcasses_total	M061 embryo	SRR060679 140x9_testes_total
....................................................................................................................................AAAAAAAAAACCATTGTGTTAAAAA..............................................................................................	25	2	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
...............AAAGTAATTTTTTTTTTTGCTCATACGT................................................................................................................................................................................................................	28	3	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0
.................................................................................ACGTGGGCGTCAAAGCCATTA.....................................................................................................................................................	21	3	2	0.50	1	1	0	0	0	0	0	0	0	0	0	0
...................................................................................................................................AAAAAAAAAAACCATAGGGTTGACA...............................................................................................	25	3	4	0.50	2	2	0	0	0	0	0	0	0	0	0	0
......TGGGCCATTAGGGTAATTT..................................................................................................................................................................................................................................	19	2	2	0.50	1	0	1	0	0	0	0	0	0	0	0	0
.................................................................................................................................AAAAAAAAAAAAACCATAGGGTTGA.................................................................................................	25	2	2	0.50	1	0	0	0	0	0	1	0	0	0	0	0
.....................................................................................................................................AAAAAAAAACCATAGGGTTGA.................................................................................................	21	2	5	0.40	2	1	0	0	1	0	0	0	0	0	0	0
......TGGGCCATTAGGGTAATT...................................................................................................................................................................................................................................	18	2	3	0.33	1	0	0	0	0	1	0	0	0	0	0	0
..................................................................................................................................AAAAAAAAAAAACCATAGGGTTG..................................................................................................	23	2	7	0.29	2	0	0	0	2	0	0	0	0	0	0	0
......................................................................................................................................AAAAAAAACCATAGGGTTGA.................................................................................................	20	2	7	0.29	2	0	0	0	0	2	0	0	0	0	0	0
......TGGGCCATTAGGGTAATTTTA................................................................................................................................................................................................................................	21	3	4	0.25	1	1	0	0	0	0	0	0	0	0	0	0
...................................................................................................................................AAAACATAAAACCATAGAGTTAA.................................................................................................	23	3	4	0.25	1	1	0	0	0	0	0	0	0	0	0	0
....................................................................................................................................AAAAAAAAAACCATAGGGTTGA.................................................................................................	22	2	4	0.25	1	0	0	0	1	0	0	0	0	0	0	0
.................................................................................ACGTGGGCGTCAAAGCCAT.......................................................................................................................................................	19	3	9	0.22	2	1	0	0	1	0	0	0	0	0	0	0
....................................................................................................................................AAAAAAAAAACCATAGGGTTGACA...............................................................................................	24	3	6	0.17	1	0	0	0	0	1	0	0	0	0	0	0
............................................................................................................................................................................................................AAAAAAAAAAGCCCGAAAAGAAAAGT.....................	26	3	7	0.14	1	0	0	0	0	0	0	1	0	0	0	0
........................................................................................................................................AAAAAACCATAGGGTTGA.................................................................................................	18	2	17	0.12	2	0	0	1	0	1	0	0	0	0	0	0
............................................................................................................................AAAAAAAAAAAAAAAAAACCATA........................................................................................................	23	0	20	0.10	2	0	0	0	0	0	0	0	2	0	0	0
......................................................................................................................................AAAAAAAACCATAGGGTTGACA...............................................................................................	22	3	13	0.08	1	0	1	0	0	0	0	0	0	0	0	0
..........................................................................................................................AAAAAAAAAAAAAAAAAAAACCATA........................................................................................................	25	0	15	0.07	1	0	0	0	0	0	0	0	0	1	0	0
..........................................................................................................................AAAAAAAAAAAAAAAAAAAACCA..........................................................................................................	23	0	20	0.05	1	0	0	0	0	0	0	1	0	0	0	0
.....................................................................TGAAAGAGAAAAACGTGG....................................................................................................................................................................	18	2	20	0.05	1	0	0	0	0	0	0	0	0	0	0	1
.............................................................................................................................................................................................TATGTCCAGCGAGTAAAAG...........................................	19	3	20	0.05	1	0	0	0	0	0	0	0	0	0	1	0
.....................................................................................................................................................................TCATCACCATACATGCGA....................................................................	18	3	20	0.05	1	0	0	0	0	0	0	0	1	0	0	0

TAGAAATGGGTCATTAGAGTAATTTTTTTTTTTGCTTATACATAGGTATGCATTCATCTTGAAAGAATTTGAACTAGAAAAACGTGGTCGTAAAAGCCGTTATCTACGTGAATATATAAAAAAAAAAAAAAAAAAAAAAAAACCATAGTGTTAAAAGTAAATTTATCAACAGCTTACATGCGAAGAATCTATGTACAGCGAGCAAAAAAAAAAAAACAGAAAAGAAAAGTATTTTATGTTTGGTAAAAAAA
*******************************************************************************************************************************************************.....................(((....))).........************************************************************

Read size

# Mismatch

Hit Count

Total Norm

Total

SRR060682
9x140_0-2h_embryos_total

SRR060684
140x9_0-2h_embryos_total

SRR060674
9x140_ovaries_total

SRR060686
Argx9_0-2h_embryos_total

SRR060685
9xArg_0-2h_embryos_total

SRR060687
9_0-2h_embryos_total

SRR060672
9x160_females_carcasses_total

M047
female body

SRR060665
9_females_carcasses_total

M061
embryo

SRR060679
140x9_testes_total

....................................................................................................................................AAAAAAAAAACCATTGTGTTAAAAA..............................................................................................

1.00

...............AAAGTAATTTTTTTTTTTGCTCATACGT................................................................................................................................................................................................................

1.00

.................................................................................ACGTGGGCGTCAAAGCCATTA.....................................................................................................................................................

0.50

...................................................................................................................................AAAAAAAAAAACCATAGGGTTGACA...............................................................................................

0.50

......TGGGCCATTAGGGTAATTT..................................................................................................................................................................................................................................

0.50

.................................................................................................................................AAAAAAAAAAAAACCATAGGGTTGA.................................................................................................

0.50

.....................................................................................................................................AAAAAAAAACCATAGGGTTGA.................................................................................................

0.40

......TGGGCCATTAGGGTAATT...................................................................................................................................................................................................................................

0.33

..................................................................................................................................AAAAAAAAAAAACCATAGGGTTG..................................................................................................

0.29

......................................................................................................................................AAAAAAAACCATAGGGTTGA.................................................................................................

0.29

......TGGGCCATTAGGGTAATTTTA................................................................................................................................................................................................................................

0.25

...................................................................................................................................AAAACATAAAACCATAGAGTTAA.................................................................................................

0.25

....................................................................................................................................AAAAAAAAAACCATAGGGTTGA.................................................................................................

0.25

.................................................................................ACGTGGGCGTCAAAGCCAT.......................................................................................................................................................

0.22

....................................................................................................................................AAAAAAAAAACCATAGGGTTGACA...............................................................................................

0.17

0.14

........................................................................................................................................AAAAAACCATAGGGTTGA.................................................................................................

0.12

............................................................................................................................AAAAAAAAAAAAAAAAAACCATA........................................................................................................

0.10

......................................................................................................................................AAAAAAAACCATAGGGTTGACA...............................................................................................

0.08

..........................................................................................................................AAAAAAAAAAAAAAAAAAAACCATA........................................................................................................

0.07

..........................................................................................................................AAAAAAAAAAAAAAAAAAAACCA..........................................................................................................

0.05

.....................................................................TGAAAGAGAAAAACGTGG....................................................................................................................................................................

0.05

.............................................................................................................................................................................................TATGTCCAGCGAGTAAAAG...........................................

0.05

.....................................................................................................................................................................TCATCACCATACATGCGA....................................................................

0.05

Re-alignment of all predicted orthologs

Species	Coordinate	ID	Alignment
droVir3	scaffold_12970:7567420-7567670 +	dvi_13474	ATCTTTACCCAGTAATCTCATTAAAAA-AAAA----AACGAATATGTATCCATACGTAAGTAGAACTTTCTTAAACTTGATCTTTTTGCACCAGCATTTTCGGCAATAGATGCACTTATATATTTTTTTTTTTTTTTTTTTTTTTTTGGTATCACAATTTTCATTTAAATAGTTGTCGAATGTACGCTTCTTAGATACATGTCGCTCGTTTTTTTTTTTTTGTCTTTTCTTTTCATAAAATACAAACCATTTTTTT
droMoj3	scaffold_6482:2153877-2153945 -		ATTCTTACAGAGTAATCTCATTAAAAACATACAAATAACCATCATGTATCCATATGTAAGTAGCCTTTT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	scaffold_15203:7044746-7044812 -		ATCCTAACCCAGTAATCTCATTTATAAAACAAAACTA--CAACATGTATCCATACGTAAGTAAAACATT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer2	scaffold_48:237294-237320 -		TTTTT----------------------------------------------------------------------------------------------------------------------------GTGTTTTTTTTTTTTTTTGGTA---------------------------------------------------------------------------------------------------------
droRho1	scf7180000777354:2265-2305 +		TTCTATATAT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCATTTTTATAAAATGAAAATCGCATTTTT

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droVir3

ATCTTTACCCAGTAATCTCATTAAAAA-AAAA----AACGAATATGTATCCATACGTAAGTAGAACTTTCTTAAACTTGATCTTTTTGCACCAGCATTTTCGGCAATAGATGCACTTATATATTTTTTTTTTTTTTTTTTTTTTTTTGGTATCACAATTTTCATTTAAATAGTTGTCGAATGTACGCTTCTTAGATACATGTCGCTCGTTTTTTTTTTTTTGTCTTTTCTTTTCATAAAATACAAACCATTTTTTT	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
.......................................................................................GCACCAGCATTTTCGGCA.......................................................................................................................................................	18	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
.................................................................CTTTCTTAAACTTGAT...............................................................................................................................................................................	16	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	1

droMoj3

ATTCTTACAGAGTAATCTCATTAAAAACATACAAATAACCATCATGTATCCATATGTAAGTAGCCTTTT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
No Reads

droGri2

ATCCTAACCCAGTAATCTCATTTATAAAACAAAACTA--CAACATGTATCCATACGTAAGTAAAACATT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

droPer2

TTTTT----------------------------------------------------------------------------------------------------------------------------GTGTTTTTTTTTTTTTTTGGTA---------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
No Reads

droRho1

TTCTATATAT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCATTTTTATAAAATGAAAATCGCATTTTT	Size	Hit Count	Total Norm	Total
No Reads

dvi_13474

scaffold_12970:7567470-7567620 +

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

-1.4	-1.0	-1.0