dvi_1100

##################################################--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CTCATTATGCGCTAAGAGATTTTTTGGCACTATCGGAATCGTCCAAGCTTGTAAGTAGTTTACCTAATCTACATATTGAAGAAGTTTGCCTTGATTGTTTACTAACTGGTGACTGAATAACCGACCTACAGGGTTATATAGGCTGAGAACCTTAAATTTGTACAGCGGGTTTTTGATCGAAACTAATCACGAAAACGAAGTTTTGGATAATTTGAATTGCATGTTAGGGGAAACGGTTGTCTGGCTACACA ************************************************((...((((((((((....((((.(((.(((..((((((((.......(((((....)))))....((((((.........))))))..))))...))))))).))).))))....)))).........))))))...))...........************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	SRR060663 160_0-2h_embryos_total	SRR060678 9x140_testes_total	M047 female body	SRR060666 160_males_carcasses_total	V053 head	M027 male body	V047 embryo	SRR060668 160x9_males_carcasses_total	SRR060679 140x9_testes_total	V116 male body	M061 embryo
......ATGCGCTAAGAGATTTTTT..................................................................................................................................................................................................................................	19	0	1	2.00	2	2	0	0	0	0	0	0	0	0	0	0
.................GATTTTTTGGCACTATCGGA......................................................................................................................................................................................................................	20	0	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0
.....TATGCGCTAAGAGATTTTTTGGCAC.............................................................................................................................................................................................................................	25	0	1	1.00	1	0	0	0	1	0	0	0	0	0	0	0
.....................TTTTGGCACTATCGGAATCGTCCAAG............................................................................................................................................................................................................	26	0	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
........................TGGCACTATCGGAATCGTCCAAGCTT.........................................................................................................................................................................................................	26	0	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
.................................................................................................................................................................................................................................AGGGGAATCGGTTCTGTGGCT.....	21	3	2	0.50	1	0	0	0	0	1	0	0	0	0	0	0
.........................................................................................................................................................................TTTGTGATCGACACTAAT................................................................	18	2	5	0.20	1	0	0	0	0	1	0	0	0	0	0	0
....................................................................................................................................GTCATATAGGGTGAGAATC....................................................................................................	19	3	12	0.17	2	0	0	0	0	0	0	0	0	1	1	0
............................................................................TGAAGAAGCTCGCCTTGA.............................................................................................................................................................	18	2	7	0.14	1	0	0	0	0	0	1	0	0	0	0	0
.............................................................................................................................CTAGAGGGTGAGATAGGCT...........................................................................................................	19	3	11	0.09	1	0	0	0	0	0	0	1	0	0	0	0
.......................................CGACCAAGCTGGTAAGAAG.................................................................................................................................................................................................	19	3	12	0.08	1	0	0	0	0	0	0	0	1	0	0	0
..............................................................................................................................................................................GAACGAAACAAATCCCGAAA.........................................................	20	3	18	0.06	1	0	0	0	0	0	0	0	0	0	0	1

GAGTAATACGCGATTCTCTAAAAAACCGTGATAGCCTTAGCAGGTTCGAACATTCATCAAATGGATTAGATGTATAACTTCTTCAAACGGAACTAACAAATGATTGACCACTGACTTATTGGCTGGATGTCCCAATATATCCGACTCTTGGAATTTAAACATGTCGCCCAAAAACTAGCTTTGATTAGTGCTTTTGCTTCAAAACCTATTAAACTTAACGTACAATCCCCTTTGCCAACAGACCGATGTGT ************************************************((...((((((((((....((((.(((.(((..((((((((.......(((((....)))))....((((((.........))))))..))))...))))))).))).))))....)))).........))))))...))...........************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	SRR060666 160_males_carcasses_total	SRR060672 9x160_females_carcasses_total	SRR060687 9_0-2h_embryos_total	SRR1106725 embryo_14-16h	SRR1106729 mixed whole adult body	SRR060661 160x9_0-2h_embryos_total
.................................................................................................................................................................................................TGGCTTCAAAACCTATTATG......................................	20	3	7	0.29	2	1	1	0	0	0	0
......................................................................TGAATAACATCTTCAAACAG.................................................................................................................................................................	20	3	11	0.09	1	0	0	1	0	0	0
............................................................................................................................................................................................TGCTAGTGCTCCAAAACCTA...........................................	20	3	12	0.08	1	0	0	0	0	1	0
.....................................................................................................................................................GGAATTTAAAAAAGTCGC....................................................................................	18	2	12	0.08	1	0	0	0	1	0	0
....................AGAAACCGTGATAGCCGTCG...................................................................................................................................................................................................................	20	3	20	0.05	1	0	0	0	0	0	1

Re-alignment of all predicted orthologs

Species	Coordinate	ID	Alignment
droVir3	scaffold_12723:84845-85095 +	dvi_1100	CTCATTATGCGCTAAGAGATTTTTTGGCACTATCGGAATCGTCCAAGCTTGTAAGTAGT-----------TTACCTAATCTACATATTGAAGAAGTTTGCCTTGATTGTTTACTAACTGGTGACTGAATAACCGACCTACAGGGTTATATAGGCTGAGAACCTTAAATTTGTACAGCGGGTTTTTGATCGAAACTAATCACGAAAACGAAGTTTTGGATAATTTGAATTGCATGTTAGGGGAAACGGTTGTCTGGCTACACA
droMoj3	scaffold_6500:32088760-32088819 +		CTCACTTTGCATTAAAGGAATTTTTGGCATTATCAAAATCGAGCGATATTGTAAGTGTT-----------T-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	scaffold_15126:1649572-1649631 +		CACATTATGCTTTGAGGGAATTTTTGACATTATCAGAATCGTCTAAACTTGTAAGTTAT-----------T-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil2	scf2_1100000004967:1154129-1154199 -		CACACAAGGCTTTGCGAGAGTTTTTGGTGATGTCTCAATCTTTAGAACTGGTTAGTGAAAATAATTTATCT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
dp5	Unknown_group_792:3786-3860 +		CTCACAACGCTTTAAAAGAATTTTTAACTATATCCGAAACCCTAAAACTAGTAAGTTGT-----------AATCTTAATTAAGATA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer2	scaffold_1:1151775-1151849 +		CTCACAACGCTTTAAAAGAATTTTTAGCTATATCCGAAACCCTAAAACTAGTAAGTTGT-----------AATCTTAATTAAGATA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droAna3	scaffold_12916:14169261-14169317 +		CACATAATGCTTTAAAAGAATTTTTAATTATATCAAAAACACTCAAACTAGTAAGTA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droBip1	scf7180000396572:2791755-2791814 -		CACATAATGCTTTAAAAGAATTTTTAAATATATCAAAAACTCACAAACTAGTAAGTATT-----------T-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droRho1	scf7180000776565:8753-8809 -		CACAAATAGCTTTGAAAGAATTTTTAAATATATCAAAAAATCTCAAACTAGTAAGTA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droBia1	scf7180000302422:8243917-8243973 +		CACAAATAGCTTTGCAAGAATTTTTAAATATATCAAAAAATTTGAATCTAGTAAGTA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droYak3	2L:13014747-13014803 +		CACAAATAGCTTTGAATGAATTTTTAAATATATCCAAAAATCTTAGACCAGTAAGTA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droVir3

CTCATTATGCGCTAAGAGATTTTTTGGCACTATCGGAATCGTCCAAGCTTGTAAGTAGT-----------TTACCTAATCTACATATTGAAGAAGTTTGCCTTGATTGTTTACTAACTGGTGACTGAATAACCGACCTACAGGGTTATATAGGCTGAGAACCTTAAATTTGTACAGCGGGTTTTTGATCGAAACTAATCACGAAAACGAAGTTTTGGATAATTTGAATTGCATGTTAGGGGAAACGGTTGTCTGGCTACACA	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
......ATGCGCTAAGAGATTTTTT.............................................................................................................................................................................................................................................	19	1	2.00	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.................GATTTTTTGGCACTATCGGA.................................................................................................................................................................................................................................	20	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
.....TATGCGCTAAGAGATTTTTTGGCAC........................................................................................................................................................................................................................................	25	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.....................TTTTGGCACTATCGGAATCGTCCAAG.......................................................................................................................................................................................................................	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
........................TGGCACTATCGGAATCGTCCAAGCTT....................................................................................................................................................................................................................	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

droMoj3

CTCACTTTGCATTAAAGGAATTTTTGGCATTATCAAAATCGAGCGATATTGTAAGTGTT-----------T-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
..........ATTAAAGGAATTTTTGGCATTATC....................................................................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	1

droGri2

CACATTATGCTTTGAGGGAATTTTTGACATTATCAGAATCGTCTAAACTTGTAAGTTAT-----------T-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

droWil2

CACACAAGGCTTTGCGAGAGTTTTTGGTGATGTCTCAATCTTTAGAACTGGTTAGTGAAAATAATTTATCT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
...............................GTCTCAATCTTTAGAACTGGA..................................................................................................................................................................................................................	21	1	1.00	1	1	0	0	0	0
...................................CAATCTTTAGAACTGGTTAGT..............................................................................................................................................................................................................	21	1	1.00	1	1	0	0	0	0
............TGCGAGAGTTTTTGGTGATGTC....................................................................................................................................................................................................................................	22	1	1.00	1	0	0	1	0	0

dp5

CTCACAACGCTTTAAAAGAATTTTTAACTATATCCGAAACCCTAAAACTAGTAAGTTGT-----------AATCTTAATTAAGATA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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

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

droAna3

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

droBip1

CACATAATGCTTTAAAAGAATTTTTAAATATATCAAAAACTCACAAACTAGTAAGTATT-----------T-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droRho1

CACAAATAGCTTTGAAAGAATTTTTAAATATATCAAAAAATCTCAAACTAGTAAGTA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droBia1

CACAAATAGCTTTGCAAGAATTTTTAAATATATCAAAAAATTTGAATCTAGTAAGTA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droYak3

CACAAATAGCTTTGAATGAATTTTTAAATATATCCAAAAATCTTAGACCAGTAAGTA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	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
...........................ATATATCCAAAAATCTTAGACCA....................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0

dvi_1100

scaffold_12723:84895-85045 +

Candidate

Unknown

Predicted structure

Flybase annnotation

Sense Strand Reads

Anti-sense strand reads

Re-alignment of all predicted orthologs

Re-alignment of all predicted orthologs with sRNA reads