dvi_4149

Name	Class	Family	Strand
AT_rich	Low_complexity	Low_complexity	+

Name

Class

Family

Strand

AT_rich

Low_complexity

##################################################--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- GCGGGGCGCCATGAAGAAGAAGCGCAAGAGATGTGTTGATGTGTATAACGGTATAACAGTTAAGCGCAGGAAATGCATCAAGGAATGGGCAGAATTAGCTAAATGTAATCAAAGCAATGAAAGAAATCAGCAAAAGACTCCAACTAAACAGGAAATTGGATATGATGCTGATGATGAATATTAATAAATCCTTTAATACTCTTTAAATTATTATAAAAAAATTGTTTTGTTGATGCATGAAATAAAAATGT *******************************************************************....(((.(((.....))))))......(((...((....)).)))............(((((......(((((............))))).....)))))*******************************************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	SRR060678 9x140_testes_total	SRR060679 140x9_testes_total	SRR060680 9xArg_testes_total	SRR060655 9x160_testes_total	SRR060670 9_testes_total	V047 embryo	SRR060666 160_males_carcasses_total
.....................................................................GAAATGCATCAAGGAATGGGCAGAA.............................................................................................................................................................	25	0	1	2.00	2	0	0	2	0	0	0	0
.............................GATGTGTTGATGTGTATAACGGTA......................................................................................................................................................................................................	24	0	1	1.00	1	1	0	0	0	0	0	0
....................AGCGCAAGAGATGTGTTGATGTGTA..............................................................................................................................................................................................................	25	0	1	1.00	1	1	0	0	0	0	0	0
..............................................AACGGTATAACAGTTAAG...........................................................................................................................................................................................	18	0	1	1.00	1	0	1	0	0	0	0	0
......................................................................................................................................................GGAAATTGGATATGATGCTG.................................................................................	20	0	1	1.00	1	0	0	0	1	0	0	0
.............................................................................................................................ATCAGCAAAAGACTCCAACT..........................................................................................................	20	0	1	1.00	1	0	1	0	0	0	0	0
......................................................................AAATGCATCAAGGAATGGGCA................................................................................................................................................................	21	0	1	1.00	1	0	0	0	0	1	0	0
.............AAGGGGGAGCGCAAGAGATGT.........................................................................................................................................................................................................................	21	3	2	0.50	1	0	0	0	0	0	1	0
............GAAGAAGAAGCGCAAGAG.............................................................................................................................................................................................................................	18	0	20	0.10	2	2	0	0	0	0	0	0
.................................................................................................................................................................ATGAAGCTGATGACGAAT........................................................................	18	2	20	0.05	1	0	0	0	0	0	0	1

##################################################---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
GCGGGGCGCCATGAAGAAGAAGCGCAAGAGATGTGTTGATGTGTATAACGGTATAACAGTTAAGCGCAGGAAATGCATCAAGGAATGGGCAGAATTAGCTAAATGTAATCAAAGCAATGAAAGAAATCAGCAAAAGACTCCAACTAAACAGGAAATTGGATATGATGCTGATGATGAATATTAATAAATCCTTTAATACTCTTTAAATTATTATAAAAAAATTGTTTTGTTGATGCATGAAATAAAAATGT
*********************************************************************....(((.(((.....))))))......(((...((....)).)))............(((((......(((((............))))).....)))))*********************************************************************************

Read size

# Mismatch

Hit Count

Total Norm

Total

SRR060678
9x140_testes_total

SRR060679
140x9_testes_total

SRR060680
9xArg_testes_total

SRR060655
9x160_testes_total

SRR060670
9_testes_total

V047
embryo

SRR060666
160_males_carcasses_total

.....................................................................GAAATGCATCAAGGAATGGGCAGAA.............................................................................................................................................................

2.00

.............................GATGTGTTGATGTGTATAACGGTA......................................................................................................................................................................................................

1.00

....................AGCGCAAGAGATGTGTTGATGTGTA..............................................................................................................................................................................................................

1.00

..............................................AACGGTATAACAGTTAAG...........................................................................................................................................................................................

1.00

......................................................................................................................................................GGAAATTGGATATGATGCTG.................................................................................

1.00

.............................................................................................................................ATCAGCAAAAGACTCCAACT..........................................................................................................

1.00

......................................................................AAATGCATCAAGGAATGGGCA................................................................................................................................................................

1.00

.............AAGGGGGAGCGCAAGAGATGT.........................................................................................................................................................................................................................

0.50

............GAAGAAGAAGCGCAAGAG.............................................................................................................................................................................................................................

0.10

.................................................................................................................................................................ATGAAGCTGATGACGAAT........................................................................

0.05

CGCCCCGCGGTACTTCTTCTTCGCGTTCTCTACACAACTACACATATTGCCATATTGTCAATTCGCGTCCTTTACGTAGTTCCTTACCCGTCTTAATCGATTTACATTAGTTTCGTTACTTTCTTTAGTCGTTTTCTGAGGTTGATTTGTCCTTTAACCTATACTACGACTACTACTTATAATTATTTAGGAAATTATGAGAAATTTAATAATATTTTTTTAACAAAACAACTACGTACTTTATTTTTACA *******************************************************************************....(((.(((.....))))))......(((...((....)).)))............(((((......(((((............))))).....)))))*******************************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	SRR060678 9x140_testes_total	V047 embryo	M061 embryo	SRR060687 9_0-2h_embryos_total	V116 male body
.............................................................................................................................................................CCTATACAACGACGACTAGTTATA......................................................................	24	3	2	0.50	1	1	0	0	0	0
..............................................................................................AATTGATCTACATCAGTTTCGT.......................................................................................................................................	22	3	3	0.33	1	0	1	0	0	0
.................................................................CGTCCTTTCTGTATTTCCTTA.....................................................................................................................................................................	21	3	5	0.20	1	0	0	1	0	0
..............................................................................................AATTGATATACATAAGTTTCGT.......................................................................................................................................	22	3	9	0.11	1	0	1	0	0	0
..........................................................CAATTCGGGTCCTTAAAGTA.............................................................................................................................................................................	20	3	20	0.05	1	0	0	0	0	1
...............................................................................................................................................................TATACAACGACGACTAGTTATA......................................................................	22	3	20	0.05	1	0	0	0	1	0

CGCCCCGCGGTACTTCTTCTTCGCGTTCTCTACACAACTACACATATTGCCATATTGTCAATTCGCGTCCTTTACGTAGTTCCTTACCCGTCTTAATCGATTTACATTAGTTTCGTTACTTTCTTTAGTCGTTTTCTGAGGTTGATTTGTCCTTTAACCTATACTACGACTACTACTTATAATTATTTAGGAAATTATGAGAAATTTAATAATATTTTTTTAACAAAACAACTACGTACTTTATTTTTACA
*********************************************************************************....(((.(((.....))))))......(((...((....)).)))............(((((......(((((............))))).....)))))*********************************************************************

Read size

# Mismatch

Hit Count

Total Norm

Total

SRR060678
9x140_testes_total

V047
embryo

M061
embryo

SRR060687
9_0-2h_embryos_total

V116
male body

.............................................................................................................................................................CCTATACAACGACGACTAGTTATA......................................................................

0.50

..............................................................................................AATTGATCTACATCAGTTTCGT.......................................................................................................................................

0.33

.................................................................CGTCCTTTCTGTATTTCCTTA.....................................................................................................................................................................

0.20

..............................................................................................AATTGATATACATAAGTTTCGT.......................................................................................................................................

0.11

..........................................................CAATTCGGGTCCTTAAAGTA.............................................................................................................................................................................

0.05

...............................................................................................................................................................TATACAACGACGACTAGTTATA......................................................................

0.05

Species	Coordinate	ID	Alignment
droVir3	scaffold_12855:6064122-6064372 -	dvi_4149	GCGGGGCGCCATGAAGAAGAAGCGCAAGAGATGTGTTGATGTGTATAACGGTATAACAGTTAAGCGCAGGAAATGCATCAAGGAATGGGCAGAATTAGCTAAATGTAATCAAAGCAATGAAAGAAATCAGCAAAAGACTCCAACTAAACAGGAAATTGGATATGATGCTGATGATGAATATTAATAAAT---CCTTTAATACTCTTTAAATTATTATAAAAAAATTGTTTTGTTGATGCATGAAATAAAAATGT
droMoj3	scaffold_6540:6383467-6383622 -		ACGAGGCCTTATGAAGAAGAAGCGCAAGCGACGTGTCGATTTGTACACTGAGCGATCAGTCAAGCGCAGAAAGTTCTTTAAGGAGTGGCCCGGAACACCCAAAGTGC----------TGAG--------TC------------CTAGGCAGGAATTGGGCTACGAGGCTGACGATGAAAATTAATA--------------------------------------------------------------------
droGri2	scaffold_14906:8001563-8001783 +		GCT----------AAGAAGAATCGTAAGAGAAGCATAAGCGTATGCATCGAGATATCAGCCAAACGTAGAAAGTGTGCTACGGAGTTGGAAGAAATTCCGGAATTTA----------CTCA--------TTCAAGTAATCTAATTAGAATGGATATAGGCTATGAAGCTGACGATGAACAATAATGAAAGTAGTTTTAATATTCCTA-----ATTAAAATCTAGCATTTTTATTGAATATACAAATGGACATGT

Species

Coordinate

Alignment

droVir3

scaffold_12855:6064122-6064372 -

dvi_4149

GCGGGGCGCCATGAAGAAGAAGCGCAAGAGATGTGTTGATGTGTATAACGGTATAACAGTTAAGCGCAGGAAATGCATCAAGGAATGGGCAGAATTAGCTAAATGTAATCAAAGCAATGAAAGAAATCAGCAAAAGACTCCAACTAAACAGGAAATTGGATATGATGCTGATGATGAATATTAATAAAT---CCTTTAATACTCTTTAAATTATTATAAAAAAATTGTTTTGTTGATGCATGAAATAAAAATGT

droMoj3

scaffold_6540:6383467-6383622 -

ACGAGGCCTTATGAAGAAGAAGCGCAAGCGACGTGTCGATTTGTACACTGAGCGATCAGTCAAGCGCAGAAAGTTCTTTAAGGAGTGGCCCGGAACACCCAAAGTGC----------TGAG--------TC------------CTAGGCAGGAATTGGGCTACGAGGCTGACGATGAAAATTAATA--------------------------------------------------------------------

droGri2

scaffold_14906:8001563-8001783 +

GCT----------AAGAAGAATCGTAAGAGAAGCATAAGCGTATGCATCGAGATATCAGCCAAACGTAGAAAGTGTGCTACGGAGTTGGAAGAAATTCCGGAATTTA----------CTCA--------TTCAAGTAATCTAATTAGAATGGATATAGGCTATGAAGCTGACGATGAACAATAATGAAAGTAGTTTTAATATTCCTA-----ATTAAAATCTAGCATTTTTATTGAATATACAAATGGACATGT

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droVir3

GCGGGGCGCCATGAAGAAGAAGCGCAAGAGATGTGTTGATGTGTATAACGGTATAACAGTTAAGCGCAGGAAATGCATCAAGGAATGGGCAGAATTAGCTAAATGTAATCAAAGCAATGAAAGAAATCAGCAAAAGACTCCAACTAAACAGGAAATTGGATATGATGCTGATGATGAATATTAATAAAT---CCTTTAATACTCTTTAAATTATTATAAAAAAATTGTTTTGTTGATGCATGAAATAAAAATGT	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
.....................................................................GAAATGCATCAAGGAATGGGCAGAA................................................................................................................................................................	25	1	2.00	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
.............................GATGTGTTGATGTGTATAACGGTA.........................................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
....................AGCGCAAGAGATGTGTTGATGTGTA.................................................................................................................................................................................................................	25	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
..............................................AACGGTATAACAGTTAAG..............................................................................................................................................................................................	18	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	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
......................................................................................................................................................GGAAATTGGATATGATGCTG....................................................................................	20	1	1.00	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.............................................................................................................................ATCAGCAAAAGACTCCAACT.............................................................................................................	20	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	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
......................................................................AAATGCATCAAGGAATGGGCA...................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
............GAAGAAGAAGCGCAAGAG................................................................................................................................................................................................................................	18	20	0.10	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droMoj3

ACGAGGCCTTATGAAGAAGAAGCGCAAGCGACGTGTCGATTTGTACACTGAGCGATCAGTCAAGCGCAGAAAGTTCTTTAAGGAGTGGCCCGGAACACCCAAAGTGC----------TGAG--------TC------------CTAGGCAGGAATTGGGCTACGAGGCTGACGATGAAAATTAATA--------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
No Reads

droGri2

GCT----------AAGAAGAATCGTAAGAGAAGCATAAGCGTATGCATCGAGATATCAGCCAAACGTAGAAAGTGTGCTACGGAGTTGGAAGAAATTCCGGAATTTA----------CTCA--------TTCAAGTAATCTAATTAGAATGGATATAGGCTATGAAGCTGACGATGAACAATAATGAAAGTAGTTTTAATATTCCTA-----ATTAAAATCTAGCATTTTTATTGAATATACAAATGGACATGT	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

dvi_4149

scaffold_12855:6064172-6064322 -

Candidate

Unknown

Predicted structure

Flybase annnotation

Repeatable elements

Sense Strand Reads

Anti-sense strand reads

Re-alignment of all predicted orthologs

Re-alignment of all predicted orthologs with sRNA reads

-10.6	-10.4	-10.3