dwi_99

CTCTATCTCTCTCTCATAACCATTAACATATTTCAATGTACATAAAGAGTATTTTACATATGTGGATTGTATTTAATTTTGAAATCTAAAACAATCCTTATATGTACTTTGTTTTATGTGTGTGCTTGTCTGCTGTGTATGTGTTTATGTATATTCAATTTGA *********************************..(((((((.((((((...((((((((.(((((((.((((...........))))))))))).))))))))...))))))...)))))))...*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M020 head	V118 embryo	V119 head	M045 female body
..................................................ATTTTACATATGTGGATTGTATT..........................................................................................	23	0	1	46.00	46	42	4	0	0
..................................................ATTTTACATATGTGGATTGTA............................................................................................	21	0	1	9.00	9	4	4	1	0
..................................................ATTTTACATATGTGGATTGTAT...........................................................................................	22	0	1	4.00	4	3	0	0	1
..................................................ATTTTACATATGTGGATTGT.............................................................................................	20	0	1	3.00	3	3	0	0	0
..................................................ATTTTACATATGTGGATTGTATC..........................................................................................	23	1	1	1.00	1	1	0	0	0
..................................................ATTTTACATATCTGGATTGT.............................................................................................	20	1	1	1.00	1	1	0	0	0
....................................................ATTACATATGTGGATTGTATT..........................................................................................	21	1	1	1.00	1	1	0	0	0
.........................................................................................CACAATCCTTATATGTACTTTGT...................................................	23	1	1	1.00	1	0	0	1	0

GAGATAGAGAGAGAGTATTGGTAATTGTATAAAGTTACATGTATTTCTCATAAAATGTATACACCTAACATAAATTAAAACTTTAGATTTTGTTAGGAATATACATGAAACAAAATACACACACGAACAGACGACACATACACAAATACATATAAGTTAAACT *********************************..(((((((.((((((...((((((((.(((((((.((((...........))))))))))).))))))))...))))))...)))))))...*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V118 embryo
..............................................................................................................................GCAGACGACACATACATAA..................	19	2	6	0.17	1	1

Re-alignment of all predicted orthologs

Species	Coordinate	ID	Type	Alignment
droWil2	scf2_1100000004909:7982484-7982646 +	dwi_99	candidate	CTCTATCTCTCTCTCATA------ACCATTA----------------------ACATATTTCAATGTACATAAAGAGTATTTTACATATGT-GGATTGTATTTA----ATTTTGAAA-TCTAAA-ACAATCCTTA---------------TATGTACTTTGTTTTATGTG---T------GTGCTTGT----CT-GCTGTG------TATGTGTTTATGTATA------------TTCAATTTGA
droVir3	scaffold_12963:18528853-18528979 -			CAGAATAAATATATTA--------------------------------------------------------------------GGTATATTAAATTATATTTGGCACGTTTTGCAAATTGATAAACAA-TAAAT--------ATG-ATGT------------GTGTATGTTT---GTGT------GT----TT-GTTGTGT--GTGTGTGTGTGAAGGCGCG------------TTTAATTTGA
droMoj3	scaffold_6473:14055463-14055626 -			CTCTCTCTCTCTCTCTCT------CACTCACACACACTCTCTCTCTCTC-------CCTCTCGTTTTGTATTACGCTGATGTCTCGTAATT-GGAATATTTTTT----A-----------------------------------------CTTTTTTTTTTTTATATATT---TTTATTT------AC----GTTT-G------TTGTTGTTGTTGTTGCAATTTATTGCACATTTTTAA--TTT
droGri2	scaffold_14830:4346039-4346199 -			CCTTATGCCTGTGCCTTCGTTTCATTTGCTTGACTTTATTTTTTT-ATTTTCTACACTTTTA----------------------AATACGTGTAATTA----------ATTTTGGATATGTATG-TTTGTTGCTA---------------TGGATGTATTTATGTATGTA---T------GTATGTATGT--A-TG-----------TATGTATGTATGTATG------------TATGTTGTGA
dp5	XR_group3a:570762-570776 +			CTCTATCTCTCTCTC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer2	scaffold_35:9223-9296 -			CTCCGTCGCCCCCTCAAG------GCCAATG----------------------ATTAATGCTTATATCCCATGGTCGTGTTCTACACATGT-AAAA-------------------------------------------------------------------------------------------------------------------------TGTATT------------T---------
droAna3	scaffold_13117:3454524-3454575 +			TG----------------------------------------------------------------------------------------------------------------------------------------------------T------------GTGGGTGGGT---GGGT------GC----GT-A-CGCGTATGTGTGTG------TGTGTC------------TTCAATTTGA
droRho1	scf7180000778944:3047-3104 +			TA----------------------------------------------------------------------------------------------------------------------------------------------------TGTCTATCTTGATATGTATT---TGTATGT------GT----TTTG-T------GTGTGTGTGTTTATGCAAC------------TTC-------
droSec2	scaffold_4:421419-421482 -			ATCTCTA-----------------------------------------------------------------------------------------------------------------------------------------------TATGTATATGCATGTATGTA---T------GTACATATATGCTTCG-----------CATATACATATGTATG------------TACA------
droEre2	scaffold_4690:12998998-12999124 -			CTCGCCCTCTTTGTCTCA------CCCATCCGCATATTCTCTTTT-CGCCTTTG-----------------------TCTTTTTCGTGCGC----------------------------------------GTTGTCTGCACTTTGTCTGT------------GTGCGTGCGT---GCGT------GT----CTCGCTGTGGTTGTGTGTG------TGTGTA------------AGCA-----A

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droWil2

CTCTATCTCTCTCTCATA------ACCATTA----------------------ACATATTTCAATGTACATAAAGAGTATTTTACATATGT-GGATTGTATTTA----ATTTTGAAA-TCTAAA-ACAATCCTTA---------------TATGTACTTTGTTTTATGTG---T------GTGCTTGT----CT-GCTGTG------TATGTGTTTATGTATA------------TTCAATTTGA	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
..............................................................................ATTTTACATATGT-GGATTGTATT...............................................................................................................................................	23	1	46.00	46	42	0	0	4	0
..............................................................................ATTTTACATATGT-GGATTGTA.................................................................................................................................................	21	1	9.00	9	4	0	0	4	1
..............................................................................ATTTTACATATGT-GGATTGTAT................................................................................................................................................	22	1	4.00	4	3	1	0	0	0
..............................................................................ATTTTACATATGT-GGATTGT..................................................................................................................................................	20	1	3.00	3	3	0	0	0	0
..............................................................................ATTTTACATATGT-GGATTGTATC...............................................................................................................................................	23	1	1.00	1	1	0	0	0	0

droVir3

CAGAATAAATATATTA--------------------------------------------------------------------GGTATATTAAATTATATTTGGCACGTTTTGCAAATTGATAAACAA-TAAAT--------ATG-ATGT------------GTGTATGTTT---GTGT------GT----TT-GTTGTGT--GTGTGTGTGTGAAGGCGCG------------TTTAATTTGA	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	SRR2096013 Ovary_Strain_9_oxidized	SRR2096014 Ovary_Strain_160_oxidized	SRR2096026 embryo_0-2h from 14 day old Strain 9 mothers	SRR2096038 embryo_0-2h from 14 day old Strain 9 mothers	SRR2096050 embryo_0-2h from 14 day old Strain 160 mothers	SRR2096055 Ovary_Min_43	SRR2096056 Ovary_Min_46	SRR2096057 Ovary_Min_50	SRR2096058 Ovary_Min_98	SRR2096059 Ovary_Min_164	SRR2096060 Ovary_Min_193	SRR2096061 embryo_0-2h from 14 day old Strain 160 mothers	SRR2096072 embryo_0-2h from 15to16 day old dysgenic mothers	SRR2096079 embryo_0-2h from 15to16 day old dysgenic mothers	SRR2096080 embryo_0-2h from 15to16 day old nondysgenic mothers	SRR2096081 embryo_0-2h from 15to16 day old nondysgenic mothers
............................................................................................................................................................................T---GTGT------GT----TT-GTTGTGT--GTGTG....................................	21	6	0.17	1	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.................................................................................................................................................................................TGT------GT----TT-GTTGTGT--GTGTGTG..................................	21	9	0.11	1	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................................................................................................................................................................T---GTGT------GT----TT-GTTGTGT--GT.......................................	18	13	0.08	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	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
.................................................................................................................................................................................................T-GTTGTGT--GTGTGTGTGTG..............................	19	20	0.05	1	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................................TGTGT--GTGTGTGTGTGAAGG..........................	20	20	0.05	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droMoj3

CTCTCTCTCTCTCTCTCT------CACTCACACACACTCTCTCTCTCTC-------CCTCTCGTTTTGTATTACGCTGATGTCTCGTAATT-GGAATATTTTTT----A-----------------------------------------CTTTTTTTTTTTTATATATT---TTTATTT------AC----GTTT-G------TTGTTGTTGTTGTTGCAATTTATTGCACATTTTTAA--TTT	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
.........................................................................CGCTGATGTCTCGTAATT-.........................................................................................................................................................	18	1	1.00	1	0	0	0	1	0	0

droGri2

CCTTATGCCTGTGCCTTCGTTTCATTTGCTTGACTTTATTTTTTT-ATTTTCTACACTTTTA----------------------AATACGTGTAATTA----------ATTTTGGATATGTATG-TTTGTTGCTA---------------TGGATGTATTTATGTATGTA---T------GTATGTATGT--A-TG-----------TATGTATGTATGTATG------------TATGTTGTGA	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

dp5

CTCTATCTCTCTCTC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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

CTCCGTCGCCCCCTCAAG------GCCAATG----------------------ATTAATGCTTATATCCCATGGTCGTGTTCTACACATGT-AAAA-------------------------------------------------------------------------------------------------------------------------TGTATT------------T---------	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
No Reads

droAna3

TG----------------------------------------------------------------------------------------------------------------------------------------------------T------------GTGGGTGGGT---GGGT------GC----GT-A-CGCGTATGTGTGTG------TGTGTC------------TTCAATTTGA	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
...................................................................................................................................................................GTGGGTGGGT---GGGT------GC----GT-A-................................................	19	1	2.00	2	0	0	0	0	0	2
......................................................................................................................................................T------------GTGGGTGGGT---GGGT------GC----GT-..................................................	19	1	1.00	1	0	0	0	0	0	1
TG----------------------------------------------------------------------------------------------------------------------------------------------------T------------GTGGGTGGGT---GGGT------GC----G....................................................	20	1	1.00	1	0	0	0	0	0	1
TG----------------------------------------------------------------------------------------------------------------------------------------------------T------------GTGGGTGGGT---GGGT------G..........................................................	18	19	0.11	2	0	0	0	0	0	2

droRho1

TA----------------------------------------------------------------------------------------------------------------------------------------------------TGTCTATCTTGATATGTATT---TGTATGT------GT----TTTG-T------GTGTGTGTGTTTATGCAAC------------TTC-------	Size	Hit Count	Total Norm	Total
No Reads

droSec2

ATCTCTA-----------------------------------------------------------------------------------------------------------------------------------------------TATGTATATGCATGTATGTA---T------GTACATATATGCTTCG-----------CATATACATATGTATG------------TACA------	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
No Reads

droEre2

CTCGCCCTCTTTGTCTCA------CCCATCCGCATATTCTCTTTT-CGCCTTTG-----------------------TCTTTTTCGTGCGC----------------------------------------GTTGTCTGCACTTTGTCTGT------------GTGCGTGCGT---GCGT------GT----CTCGCTGTGGTTGTGTGTG------TGTGTA------------AGCA-----A	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

dwi_99

scf2_1100000004909:7982534-7982596 +

candidate

Canonical miRNA

intron

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

-21.7	-21.5	-21.3