dmo_517

Name	Class	Family	Strand
(GA)n	Simple_repeat	Simple_repeat	+

##################################################--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CTGCAACGATTGCTATCAACAGCTGCAGCGCAAGTCGGACGCGACGCCAGGTAAGCCAACTGCATCAGATCGATAAACAGTCGAAGCAGAAATCAGCCAAGGAGTGAAATGAATGTGCGAGAACTGAAAGAATAGACAAATAGACAGGGAGAGAGAGAGAGAGGGAGAGATAAAGGAAGTGCTATGAATAGTAGTATATTTATGGGAGAGCAAGTACGTATACATATAGAGAGAGAGAGAGAGAGGGAGAG ************************************************.....((..((...((...(((((.....)))))..(((...((.((((..............)).))))...)))............................))...))..))..........((.(((((((.....))))))).)).************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V110 male body	M046 female body	V049 head	V056 head
...............................................................ATCAGATCGATGAACGGTCGA.......................................................................................................................................................................	21	2	1	1.00	1	1	0	0	0
....................AGCTGCAGCGCAAGTCGGACGC.................................................................................................................................................................................................................	22	0	1	1.00	1	1	0	0	0
.........................CAGCGCAAGTCAGACGTG................................................................................................................................................................................................................	18	2	4	0.25	1	0	0	1	0
..............................................................................................................................................GACAGGGAGAGAGAGAGAGA.........................................................................................	20	0	20	0.15	3	3	0	0	0
.............................................................................................................................................AGACAGGGAGAGAGAGAGAGA.........................................................................................	21	0	20	0.10	2	1	1	0	0
.........................................................................................................................................................................ATAAGGGAACTGCTAAGAAT..............................................................	20	3	13	0.08	1	0	1	0	0
........................................................................CTTAACAGTCGACGCAGAAA...............................................................................................................................................................	20	3	13	0.08	1	0	1	0	0
.........................................................................................................................................................................................................ATTGGAGGGCAAGTATGTAT..............................	20	3	14	0.07	1	0	1	0	0
....................................................................................................................................................GAGAGAGAGAGAGAGGGAGA...................................................................................	20	0	20	0.05	1	0	0	0	1

GACGTTGCTAACGATAGTTGTCGACGTCGCGTTCAGCCTGCGCTGCGGTCCATTCGGTTGACGTAGTCTAGCTATTTGTCAGCTTCGTCTTTAGTCGGTTCCTCACTTTACTTACACGCTCTTGACTTTCTTATCTGTTTATCTGTCCCTCTCTCTCTCTCTCCCTCTCTATTTCCTTCACGATACTTATCATCATATAAATACCCTCTCGTTCATGCATATGTATATCTCTCTCTCTCTCTCTCCCTCTC ************************************************.....((..((...((...(((((.....)))))..(((...((.((((..............)).))))...)))............................))...))..))..........((.(((((((.....))))))).)).************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V110 male body
.....................................................TGGCTTGACGAAGTCTAGCTA.................................................................................................................................................................................	21	3	5	0.20	1	1

Re-alignment of all predicted orthologs

Species	Coordinate	ID	Alignment
droMoj3	scaffold_6328:3378534-3378784 +	dmo_517	CTGCAACGATTGCTATCAACAGCTGCAGCGCAAGTCGGACGCGACGCCAGGTAAGCCAACTGCATCAGATCGATAAACAGTCGAAGCAGAAATCAGCCAAGGAGTGAAATGAATGTGCGAGAACTGAAAGAATAGA-----------CAA-----------------------------------------------------------------------------------------------------------------------ATAGACA-GGGAGA------GAGAGAGAGAGGGAGAGAT----------------------------------------------------------------AAAGGAA------------GTG------------------CTAT--------------------------------G-AATAGTAGTATATTTATGGG---------AGAGCAAGTACGTATACATATAGAGAGAGAGAGAGAGAGGGAGAG
droVir3	scaffold_12970:9560333-9560525 +		ATTAGATAGATGTGAG-----------------------------------------------AG----------------TAGAGAGATAGCGA-------------------------------GG----------------------------------------------------------------GAGA--------------------------------------------------------------------------GAGAGA-------GAGAGAGAGAGAAAGATAGAGAGAG----------------------------------AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA----GAGAGAGAGAGAGAGAGAGAGGGAGA-------------------------------------------T------AGAG-----AGGGAGAGAGAAAAAGAAAGATATAGAGACGGAGAGAGAGAGAGAGAGAGATAG
droGri2	scaffold_14906:3910452-3910602 +		GCACGAA--TT------------------------------------------------------------------------------------------------------------------GGGCGAAGAGCGAGCGAACCCCCAA-------------------------------------------------------------------------------AGAAATAACTGAATGTGGTGCGCC----------------ACAGAGA-GG----------GAGAGACAGAT------------------------------------------AGAGAGAGAGA--------GACAGTATAATAGCGAGAGA-----------------------------------------------------------------------------------------------------GACAGTTTGTGTGTATGCAGATAGAGAGAGAGAGAGAGAGAG
droWil2	scf2_1100000004513:3439998-3440173 +		GATCACT-------------------------------------------------------------------A---------------------------------------------------GG----------------------------------------------------------------CAACCAGAGTAGAGACCTAAAAGCTAATTGTCTCCAAAAAATTGAC-----------CACAACAGAAAAATATCCAAATAGATAAGG----------GATAGAAAAATATAGAGAC----------------------------------------------------------------A------------AAT---------------------------------------------TGTATGTAGACAGAAATGCATTA------------------------TAACCATTCTGCATACATATAGAGGGAGTGAGAGAGAGAGAGAG
dp5	XR_group6:6231360-6231502 -		ATTGATA-AAATCCA------------------------------------------------------------------------------------------------------------------------------------CCAACATACGGTGGAGGGAGAGGGGGGGACAGGGCAGAAAGTGGGCGGCTGGAGTAGAAGG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTTGGCGATTCAGCGAGGGGATA--------------------------------------ATCGAGTACATATGTACATGGAGAGAGAGAGGGAGAGGGAGAG
droPer2	scaffold_3:6652060-6652235 +		GAGAAAGAGTAGAAG-----------------------------------GCC---------------------A---------------------------------------------------GG----------------------------------------------------------------CAGCGGCAGTGGA------------------------------------------------------------------------------------------------------------GAGAGAAACAGGAATGCAATTGCAGAGGCAGAGACACAGAGACACAGAGAGAGCGAGACAGAGGGAGC----GATCGTGTGCGTGTGTGTGTGTGCGT-------------------------------------------A------AGAG-----TG-----------GGCTAGCGTATGCACACAGAGAGAGAGAGAGAGAGGGAGAG
droAna3	scaffold_8722:6987-7175 -		CAGAGAG-ACAGAGAG----------------------------------------------------------------ACAGAGAGACAGAGAGACAGAGAGACAGAGGCAGAGAC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAGACAGAGAGACAGAGAGACAGAGAGACAGAGAGACA----GAGAGACAGAGAGACAGAGAGACAGAGAGAC--------------------------------A-GAGAGTCAGAGAGACAGAGA---------GACAGAGAGACAGAGAGACAGAGAGACAGAGAGACAGAGAGACAG
droKik1	scf7180000302398:480764-480932 -		AAAAAACGAAATCGAA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATCGAAAAAGAAAA------GAAATGAGAGAAAAATAAGAAAGAA--------------------------------------------------ATCA-AACAAACA------------------CCAAAACCACAAAAGCGTAACTAAACAAAAAACTACGTAAGGATCGAATACGTAAGG----------AGAAAGAGAGAGTAAACGTAAGGAGAGAGAGAGAGAGAGAGAGAG
droFic1	scf7180000453549:48732-48843 -		GAAGACA----------------------------------------------------------------------------------------------------------------------GGGAGAAGAGAA-----------GA-----------------------------------------------------------------------------------------------------------------------AGAGAGA-GAGATAGAGATAGAGAGAGAGAG------AGAAAGGG----------------------------AGAGATA------------------------------------TAG---------------------------------------------------------------------------------------------ATAGAGTAGAGAGAAAGAGGGAGAAAGAGATGGAGAGAGAGAG
droBia1	scf7180000302113:3335837-3335852 -		GTGCGACAACTGCTAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droTak1	scf7180000410579:201063-201077 +		GTGCGACAACTGCTA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droEug1	scf7180000407075:42298-42435 -		ATAGAAAGATAGACA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAG------------------------------------------AGATAGAGAGA--------GAGAGCGAGATAGAGAAAGCGGCA-AGCGTGTG------------------TTATGGGTATTCGGGTGTGAGTGTGTGTATGTGTGAGTGCGTGA-----------------------------------TGTATGTGTAATTGAATGGAAAGAGACAAAGAA
dm3	chr3R:23055551-23055566 -		GTGTGACAATTGCTAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droSim2	3r:22497335-22497349 -		GTGCGACAATTGCTA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droSec2	scaffold_0:3460921-3461021 -		TGCTG-CAACA------------------------------------------------------------------------------------------------------------------GAGCGAAGAGAG----GCCCCCCAA-----------------------------------------------------------------------------------------------------------------------ACAGACA-------GAGATAGAGAGAAAGAGGGAAAGAG----------------------------------AGAG------------------------------------------------------------------------------------------------------------------------------------------------AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGCGAG
droYak3	X:11203799-11203883 +		AGACAGA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAGACAGAAAGACAGAGAGAC----------------------------------AGACAGACAGA--------CA---------------------------------------------------------------------------------------------------------------------GGGCAAATTCACACAGACAGAGAGAGAGAGAGAGAGAGAGAGAG
droEre2	scaffold_4770:17744377-17744429 +		GTACATG-TGTGTGAT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGATACATAAAGAGAGAGAGAGAGAGAGAGAGAG

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droMoj3

CTGCAACGATTGCTATCAACAGCTGCAGCGCAAGTCGGACGCGACGCCAGGTAAGCCAACTGCATCAGATCGATAAACAGTCGAAGCAGAAATCAGCCAAGGAGTGAAATGAATGTGCGAGAACTGAAAGAATAGA-----------CAA-----------------------------------------------------------------------------------------------------------------------ATAGACA-GGGAGA------GAGAGAGAGAGGGAGAGAT----------------------------------------------------------------AAAGGAA------------GTG------------------CTAT--------------------------------G-AATAGTAGTATATTTATGGG---------AGAGCAAGTACGTATACATATAGAGAGAGAGAGAGAGAGGGAGAG	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
....................AGCTGCAGCGCAAGTCGGACGC..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	22	1	1.00	1	0	0	0	0	0	1
................................................................................................................................................................................................................................................................................GACA-GGGAGA------GAGAGAGAGA.................................................................................................................................................................................................................................	20	20	0.15	3	0	0	0	0	0	3
...............................................................................................................................................................................................................................................................................AGACA-GGGAGA------GAGAGAGAGA.................................................................................................................................................................................................................................	21	20	0.10	2	1	0	0	0	0	1
.......................................................................................................................................................................................................................................................................................GAGA------GAGAGAGAGAGGGAGA...........................................................................................................................................................................................................................	20	20	0.05	1	0	0	0	1	0	0

droVir3

ATTAGATAGATGTGAG-----------------------------------------------AG----------------TAGAGAGATAGCGA-------------------------------GG----------------------------------------------------------------GAGA--------------------------------------------------------------------------GAGAGA-------GAGAGAGAGAGAAAGATAGAGAGAG----------------------------------AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA----GAGAGAGAGAGAGAGAGAGAGGGAGA-------------------------------------------T------AGAG-----AGGGAGAGAGAAAAAGAAAGATATAGAGACGGAGAGAGAGAGAGAGAGAGATAG	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
..................................................................................................................................................................................................................................................................................................................................................................................AGAGAGAGAGA----GAGAGAGAGA.................................................................................................................................	21	20	0.45	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9
.................................................................................................................................................................................................................................................................................................GAGAGAAAGATAGAGAGAG----------------------------------AGAGA.................................................................................................................................................................................	24	8	0.13	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	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
............................................................................................................................................................................................................................................................................................................................................................................................A----GAGAGAGAGAGAGAGAGAGAGGGA...................................................................................................................	25	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	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
.................................................................................................................................................................................................................................................................................................................................................................................................GAGAGAGAGAGAGAGAGAGAGGGA...................................................................................................................	24	20	0.05	1	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
...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GAGACGGAGAGAGAGAGA...........	18	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
........................................................................................................................................................................................................................................................................................................................................................AGAGAGAGAGAGAGAGAG..................................................................................................................................................................	18	20	0.05	1	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
..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ACGGAGAGAGAGAGAGAGA.......	19	20	0.05	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
..............................................................................................................................................................................................................................................................................GAGAGA-------GAGAGAGAGAGAAAGA.................................................................................................................................................................................................................................	22	20	0.05	1	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
...............................................................................................................................................................................................................................................................................................................................................................................GAGAGAGAGAGAGA----GAGA.......................................................................................................................................	18	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	0	0	0	0	0	0	0	0	0	0	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
...............................................................................................................................G----------------------------------------------------------------GAGA--------------------------------------------------------------------------GAGAGA-------GAGAGAGA.........................................................................................................................................................................................................................................	19	20	0.05	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
.......................................................................................................................................................................................................................................................................................................................................................GAGAGAGAGAGAGAGAGAGAGAGAGA...........................................................................................................................................................	26	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	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
..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ACGGAGAGAGAGAGAGAG........	18	20	0.05	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
..........................................................................................................................................................................................................................................................................................................ATAGAGAGAG----------------------------------AGAGAGAGAGAGA.........................................................................................................................................................................	23	20	0.05	1	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
.........................................................................................................................................................................................................................................................................................................GATAGAGAGAG----------------------------------AGAGAGA...............................................................................................................................................................................	18	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	0	0	0	0	0	0	0	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

droGri2

GCACGAA--TT------------------------------------------------------------------------------------------------------------------GGGCGAAGAGCGAGCGAACCCCCAA-------------------------------------------------------------------------------AGAAATAACTGAATGTGGTGCGCC----------------ACAGAGA-GG----------GAGAGACAGAT------------------------------------------AGAGAGAGAGA--------GACAGTATAATAGCGAGAGA-----------------------------------------------------------------------------------------------------GACAGTTTGTGTGTATGCAGATAGAGAGAGAGAGAGAGAGAG	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

droWil2

GATCACT-------------------------------------------------------------------A---------------------------------------------------GG----------------------------------------------------------------CAACCAGAGTAGAGACCTAAAAGCTAATTGTCTCCAAAAAATTGAC-----------CACAACAGAAAAATATCCAAATAGATAAGG----------GATAGAAAAATATAGAGAC----------------------------------------------------------------A------------AAT---------------------------------------------TGTATGTAGACAGAAATGCATTA------------------------TAACCATTCTGCATACATATAGAGGGAGTGAGAGAGAGAGAGAG	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
No Reads

dp5

ATTGATA-AAATCCA------------------------------------------------------------------------------------------------------------------------------------CCAACATACGGTGGAGGGAGAGGGGGGGACAGGGCAGAAAGTGGGCGGCTGGAGTAGAAGG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTTGGCGATTCAGCGAGGGGATA--------------------------------------ATCGAGTACATATGTACATGGAGAGAGAGAGGGAGAGGGAGAG	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
........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AGAGAGAGGGAGAGGGAGAG	20	20	0.05	1	0	1	0	0	0	0	0	0	0	0

droPer2

GAGAAAGAGTAGAAG-----------------------------------GCC---------------------A---------------------------------------------------GG----------------------------------------------------------------CAGCGGCAGTGGA------------------------------------------------------------------------------------------------------------GAGAGAAACAGGAATGCAATTGCAGAGGCAGAGACACAGAGACACAGAGAGAGCGAGACAGAGGGAGC----GATCGTGTGCGTGTGTGTGTGTGCGT-------------------------------------------A------AGAG-----TG-----------GGCTAGCGTATGCACACAGAGAGAGAGAGAGAGAGGGAGAG	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
.......................................................................................................................................................................................................................................................................................................................................................................................................GTGCGTGTGTGTGTGTGCG..................................................................................................................	19	20	0.05	1	0	0	0	0	0	1

droAna3

CAGAGAG-ACAGAGAG----------------------------------------------------------------ACAGAGAGACAGAGAGACAGAGAGACAGAGGCAGAGAC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAGACAGAGAGACAGAGAGACAGAGAGACAGAGAGACA----GAGAGACAGAGAGACAGAGAGACAGAGAGAC--------------------------------A-GAGAGTCAGAGAGACAGAGA---------GACAGAGAGACAGAGAGACAGAGAGACAGAGAGACAGAGAGACAG	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
No Reads

droKik1

AAAAAACGAAATCGAA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATCGAAAAAGAAAA------GAAATGAGAGAAAAATAAGAAAGAA--------------------------------------------------ATCA-AACAAACA------------------CCAAAACCACAAAAGCGTAACTAAACAAAAAACTACGTAAGGATCGAATACGTAAGG----------AGAAAGAGAGAGTAAACGTAAGGAGAGAGAGAGAGAGAGAGAGAG	Size	Hit Count	Total Norm	Total
No Reads

droFic1

GAAGACA----------------------------------------------------------------------------------------------------------------------GGGAGAAGAGAA-----------GA-----------------------------------------------------------------------------------------------------------------------AGAGAGA-GAGATAGAGATAGAGAGAGAGAG------AGAAAGGG----------------------------AGAGATA------------------------------------TAG---------------------------------------------------------------------------------------------ATAGAGTAGAGAGAAAGAGGGAGAAAGAGATGGAGAGAGAGAG	Size	Hit Count	Total Norm	Total
No Reads

droBia1

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

droTak1

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

droEug1

ATAGAAAGATAGACA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAG------------------------------------------AGATAGAGAGA--------GAGAGCGAGATAGAGAAAGCGGCA-AGCGTGTG------------------TTATGGGTATTCGGGTGTGAGTGTGTGTATGTGTGAGTGCGTGA-----------------------------------TGTATGTGTAATTGAATGGAAAGAGACAAAGAA	Size	Hit Count	Total Norm	Total
No Reads

dm3

GTGTGACAATTGCTAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

Total

GSM154618
Ovary

GSM154620
Ovary

GSM154621
Ovary

GSM154622
Ovary

GSM180328
Head

GSM180329
Mixed-body

GSM180330
Embryo

GSM180331
Embryo

GSM180332
Embryo

GSM180333
Embryo

GSM180334
Larvae

GSM180335
Disc

GSM180336
Pupae

GSM180337
S2

GSM231091
Ovary

GSM239041
Head

GSM239050
Head

GSM239051
S2

GSM239052
S2

GSM246084
Head

GSM266765
S2

GSM280082
Ovary

GSM280083
Ovary

GSM280084
Ovary

GSM280085
Testis

GSM280086
Ovary

GSM280087
S2-NP

GSM280088
S2-NP

GSM312995
Head

GSM313160
Head

GSM313161
Head

GSM313162
Head

GSM313163
Head

GSM313164
Head

GSM313165
Head

GSM343287
Embryo

GSM379050
Ovary

GSM379051
Ovary

GSM379052
Ovary

GSM379053
Ovary

GSM379054
Ovary

GSM379055
Ovary

GSM379056
Ovary

GSM379057
Ovary

GSM379058
Ovary

GSM379059
Ovary

GSM379060
Ovary

GSM379061
Ovary

GSM379062
Ovary

GSM379063
Ovary

GSM379064
Ovary

GSM379065
Ovary

GSM379066
Ovary

GSM379067
Ovary

GSM424739
S2

GSM424740
S2

GSM424741
S2

GSM467729
Female-body

GSM467730
Female-body

GSM467731
Female-body

M002
CS

M003
Male-body

M004
Male-body

M005
ML-DmD32

M006
ML-DmD32

M029
OSC

M030
OSC

M031
OSC

M032
S2-R+

M033
S2-R+

M034
S2-R+

M035
S2-R+

M036
S2-R+

M037
S2-R+

M038
S2-R+

M039
S2-R+

M048
S2-R+

OSS2
OSS

OSS6
OSS

OSS7
OSS

OSS8
OSS

S1
Head

S10
Embryo

S11
Embryo

S12
Embryo

S13
Embryo

S14
Embryo

S15
S2-GMR

S16
Kc

S17
Larvae

S18
Larvae

S19
Pupae

S2
Head

S20
Pupae

S21
Disc

S22
Head

S23
Female-body

S24
Male-body

S25
Larvae

S26
Larvae

S27
Pupae

S28
Pupae

S29
Head

S3
Male-body

S30
S2-GMR

S31
S2

S32
S2

S33
Kc

S34
Kc

S35
Kc

S4
Female-body

S5
Disc

S6
Embryo

S7
Embryo

S8
S2

S9
Embryo

SRR001337
Head

SRR001338
Head

SRR001339
Head

SRR001340
Head

SRR001341
Head

SRR001342
Head

SRR001343
Head

SRR001344
Head

SRR001345
Head

SRR001346
Head

SRR001347
Head

SRR001348
Head

SRR001349
Head

SRR001664
Head

SRR010951
Ovary

SRR010952
Ovary

SRR010953
Ovary

SRR010954
Ovary

SRR010955
Ovary

SRR010956
Ovary

SRR010957
Ovary

SRR010958
Ovary

SRR010959
Ovary

SRR010960
Ovary

SRR014268
Embryo

SRR014269
Embryo

SRR014270
Embryo

SRR014271
Embryo

SRR014272
Embryo

SRR014273
Ovary

SRR014274
Ovary

SRR014275
Ovary

SRR014276
Ovary

SRR014277
Ovary

SRR014278
Ovary

SRR014279
Ovary

SRR014280
Ovary

SRR014281
Ovary

SRR014282
Ovary

SRR023197
S2

SRR023399
S2

SRR023400
S2

SRR023402
S2

SRR023407
S2

SRR029028
S2

SRR029029
S2

SRR029030
S2

SRR029031
S2

SRR029032
S2

SRR029033
S2

SRR029608
Head

SRR029633
Head

SRR030145
gb3

SRR031692
Head

SRR031693
Head

SRR031694
Head

SRR031696
Head

SRR031697
Head

SRR031698
Head

SRR031699
Head

SRR031700
Head

SRR031701
Head

SRR031702
Head

SRR031703
Head

SRR031704
Head

SRR032092
S2

SRR032093
S2

SRR032094
S2

SRR032095
S2-NP

SRR032096
S2-NP

SRR032152
Head

SRR060643
Testis

SRR060644
Ovary

SRR060645
Testis

SRR060646
Ovary

SRR060647
Ovary

SRR060648
Ovary

SRR060649
Ovary

SRR060650
Testis

SRR060651
Ovary

SRR060652
Testis

SRR060653
Ovary

SRR065151
Ovary

SRR065152
Ovary

SRR065153
Ovary

SRR065154
Ovary

SRR065155
Ovary

SRR065800
Ovary

SRR065801
Ovary

SRR065802
Ovary

SRR065803
Ovary

SRR065804
Ovary

SRR065805
Ovary

SRR065806
Ovary

SRR065807
Ovary

SRR097865
S2-NP

SRR097866
S2-NP

SRR097867
S2-NP

SRR298536
Ovary

SRR298537
Ovary

SRR298711
Ovary

SRR298712
Ovary

SRR317110
Ovary

SRR317111
Ovary

SRR317112
Ovary

SRR317113
Ovary

SRR317114
Ovary

SRR317115
Ovary

SRR317116
Ovary

SRR317117
Ovary

SRR341115
S2

SRR341116
S2

SRR341117
S2

SRR341118
S2

SRR351332
Mixed-body

SRR351333
Mixed-body

T004
OSC

T005
CME-L1

V001
Embryo

V002
Embryo

V003
S2

V006
Female-body

V007
Head

V008
S2

V009
CME-L1

V010
ML-DmD20-C5

V011
Sg4

V012
Male-body

V013
Head

V014
DTT

V015
DreRFHV

V018
Kc167

V019
GM2

V020
S2-R+

V021
ML-DmD21

V022
ML-DmD32

V023
Head

V024
Kc167

V025
S2-R+

V026
1182-2H

V027
ML-DmD21

V028
CME-W1-Cl.8+

V029
ML-DmD9

V030
ML-DmD8

V031
GM2

V032
S1

V033
CME-W1-Cl.8+

V034
ML-DmD16-C3

V035
ML-DmD32

V036
ML-DmD20-C5

V037
S2

V038
S2

V063
Ovary

V0632
Ovary

V064
Ovary

V0642
Ovary

V065
Ovary

V0652
Ovary

V066
Ovary

V0662
Ovary

V067
S2-NP

V073
mbn2

V074
S3

V075
ML-DmBG1-C1

V076
ML-DmBG3-C2

V077
Head

V078
Head

V079
Head

V080
Head

V081
Embryo

V082
Embryo

V083
Male-body

V084
Female-body

V085
CME-W2

V086
Female-body

V088
Ovary

V0882
Ovary

V089
Ovary

V0892
Ovary

V090
Male-body

V091
fGS/OSS

V092
Male-body

V093
Male-body

V094
S2-R+

V095
S2-R+

V096
Ovary

V097
Ovary

V098
Ovary

V125
ML-DmD9

V126
CME-L1

V127
G2

V128
S3

V129
ML-DmBG1-C1

V130
ML-DmBG3-C2

V131
ML-DmD16-C3

V132
ML-DmD32

V133
Sg4

V134
ML-DmD8

V135
CME-W2

V136
Male-body

V137
Head

V138
Male-body

V139
Female-body

V140
Female-body

V141
Female-body

V142
Female-body

V144
OSC

V145
S2

V146
S1

V147
1182-2H

V148
mbn2

GSM1528798
follicle cells

No Reads

droSim2

GTGCGACAATTGCTA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

Total

M023
Head

M024
Male-body

M025
Embryo

M053
Female-body

O001
Testis

O002
Head

SRR553485
Ovary

SRR553486
Ovary

SRR553487
Ovary

SRR553488
Ovary

SRR618934
Ovary

V044
Embryo

SRR902008
Ovary

SRR902009
Testis

SRR1275487
Male larvae

SRR1275485
Male prepupae

SRR1275483
Male prepupae

No Reads

droSec2

TGCTG-CAACA------------------------------------------------------------------------------------------------------------------GAGCGAAGAGAG----GCCCCCCAA-----------------------------------------------------------------------------------------------------------------------ACAGACA-------GAGATAGAGAGAAAGAGGGAAAGAG----------------------------------AGAG------------------------------------------------------------------------------------------------------------------------------------------------AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGCGAG	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GAGAGAGAGAGAGAGAGAGAGAGAGA.......	26	20	0.05	1	0	1	0	0
.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GAGAGAGAGAGAGAGAGAGAGAGAGA.....	26	20	0.05	1	0	1	0	0
..................................................................................................................................................................................................................................................................................................................AG----------------------------------AGAG------------------------------------------------------------------------------------------------------------------------------------------------AGAGAGAGAGAGAGA...................	21	20	0.05	1	0	0	1	0
..............................................................................................................................................................................................................................................................................................................AAAGAG----------------------------------AGAG------------------------------------------------------------------------------------------------------------------------------------------------AGAGAGAGAG........................	20	20	0.05	1	0	1	0	0

droYak3

AGACAGA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAGACAGAAAGACAGAGAGAC----------------------------------AGACAGACAGA--------CA---------------------------------------------------------------------------------------------------------------------GGGCAAATTCACACAGACAGAGAGAGAGAGAGAGAGAGAGAGAG	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
.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GAGAGAGAGAGAGAGAGA.....	18	20	0.15	3	0	0	0	0	0	0	3	0	0	0	0
...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GACAGAGAGAGAGAGAGA...........	18	20	0.05	1	0	0	0	0	0	0	1	0	0	0	0
...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GACAGAGAGAGAGAGAGAGA.........	20	20	0.05	1	0	0	0	0	0	0	1	0	0	0	0

droEre2

GTACATG-TGTGTGAT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGATACATAAAGAGAGAGAGAGAGAGAGAGAGAG	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

dmo_517

scaffold_6328:3378584-3378734 +

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

-14.2	-14.2	-14.1