dan_192

TAAATTAAAACGTTCCGTACACACACACACGTCGAGAGCAAGGAGATGACCTGCCCCACAAGCTGGCACCTGCCCTCCTGTGGGTGGGTTGGTTGGTGGTTGGGTGGGTTAGCAGTTGCACTGCACCACTCGTACGTATATAGGAGTAACAATTAATTTT *********************************..((((.....((((((((((.((..((((((((((((((......))))))))..)))))).)).))))))))))....))))......*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V106 head	V055 head	V105 male body	V039 embryo	M058 embryo	M044 female body
...........................................................................................GTTGGTGGTTGGGTGGGT...................................................	18	0	1	77.00	77	76	0	1	0	0	0
...........................................................................................GTTGGTGGTTGGGTGGGTC..................................................	19	1	2	2.50	5	5	0	0	0	0	0
...........................................................................................GTGGGTGGTTGGGTGGGTTA.................................................	20	1	5	2.20	11	10	0	1	0	0	0
...........................................................................................GTTGGTGGTTGGGTGGGTAA.................................................	20	1	1	1.00	1	1	0	0	0	0	0
...........................................................................................GTGGGTGGTTGGGTGGGTT..................................................	19	1	18	0.94	17	13	0	4	0	0	0
...........................................................................................GTGGGTGGTTGGGTGGGTTAG................................................	21	1	2	0.50	1	1	0	0	0	0	0
...........................................................................................GTTTGTGGTTGGGTGGGTT..................................................	19	1	2	0.50	1	1	0	0	0	0	0
................................................................................TGGGGGGGTTGGTTGGGGGTT...........................................................	21	2	2	0.50	1	0	1	0	0	0	0
...........................................................................................GTTGGTGGTTGGGTGGGTCA.................................................	20	1	2	0.50	1	1	0	0	0	0	0
...........................................................................................GTTGGTGGTTGGGTGGGTAAA................................................	21	2	6	0.50	3	3	0	0	0	0	0
...........GTTCCGTACACACAAGCA...................................................................................................................................	18	2	2	0.50	1	0	0	0	1	0	0
...........................................................................................GTTGGCGGTTGGGTGGGT...................................................	18	1	3	0.33	1	1	0	0	0	0	0
.................................GAAAGCAACGAGATGACC.............................................................................................................	18	2	3	0.33	1	0	1	0	0	0	0
........................GCACGCATCGAGAGCAAGGA....................................................................................................................	20	3	4	0.25	1	0	0	0	0	1	0
...........................................................................................GTTGGTGGTTGGGGGGGT...................................................	18	1	4	0.25	1	1	0	0	0	0	0
................................................ACTTGAACCACAAGCTGGCAC...........................................................................................	21	3	5	0.20	1	0	0	0	0	0	1
.................................................................................................GGGTGGCGGGGTTAGCAGTTG..........................................	21	3	5	0.20	1	0	1	0	0	0	0
...........................................................................................GTTGGTGGTTGTGTGGGT...................................................	18	1	5	0.20	1	1	0	0	0	0	0
............................................................................................TTGGTGGTTGGGTGGGTC..................................................	18	1	5	0.20	1	1	0	0	0	0	0
...........................................................................................GTCGGTGGTTGGGTGGGT...................................................	18	1	11	0.18	2	2	0	0	0	0	0
...........................................................................................GTTGGTGGCTGGGTGGGT...................................................	18	1	11	0.18	2	2	0	0	0	0	0
........................................................................................................TAGGTTAGCAGTGGCAGTGC....................................	20	3	6	0.17	1	0	0	0	0	0	1
.......................................................................................GTGGGTTGGTGGTTGGGT.......................................................	18	1	20	0.15	3	3	0	0	0	0	0
...........................................................................................GTGGGTGGTTGGGAGGGTTA.................................................	20	2	9	0.11	1	1	0	0	0	0	0
................................................................................TGGGGGGGTGGGCTGGTGGTTG..........................................................	22	3	9	0.11	1	0	1	0	0	0	0
...........................................................................................GTTGGTGGTTGGGTGGGTCT.................................................	20	2	9	0.11	1	1	0	0	0	0	0
...........GTTCAGTACACACACGCA...................................................................................................................................	18	2	20	0.10	2	0	2	0	0	0	0
...........................................................................................GTAGGTGGTTGGGTGGGT...................................................	18	1	11	0.09	1	1	0	0	0	0	0
...........................................................................................GTTGGTGGTTGAGTGGGT...................................................	18	1	11	0.09	1	1	0	0	0	0	0
...........................................................................................GTTGGTGGTTGGGTTGGT...................................................	18	1	12	0.08	1	1	0	0	0	0	0
...........GTTCAGTACACACACATAC..................................................................................................................................	19	2	13	0.08	1	0	1	0	0	0	0
.................................AAAAGCAAGGAGATGACC.............................................................................................................	18	2	13	0.08	1	0	0	0	0	1	0
...........................................................................................TTTGGTGGTTGGGTGGGT...................................................	18	1	15	0.07	1	1	0	0	0	0	0
.......................................................................................GTTGGTAGTTGGTTGGGTG......................................................	19	2	16	0.06	1	0	1	0	0	0	0
.......................................................................................GTGGGTTGGTGGTTGGGTGG.....................................................	20	1	16	0.06	1	1	0	0	0	0	0
...........................................................................................GTTGGTGGTTGGGTGTGTC..................................................	19	2	19	0.05	1	1	0	0	0	0	0
...........GTTCAGTACACACAGACA...................................................................................................................................	18	2	20	0.05	1	0	1	0	0	0	0
........................................................................................TTGGTGGGTGGTTGGGTGG.....................................................	19	1	20	0.05	1	1	0	0	0	0	0
...........GTTCAGTACACACACAGA...................................................................................................................................	18	2	20	0.05	1	0	0	0	1	0	0
...........GTTCAGTACACACACGCCC..................................................................................................................................	19	3	20	0.05	1	0	0	0	1	0	0
...................................................................................GTGGGTGGGTTGGTGGTT...........................................................	18	1	20	0.05	1	1	0	0	0	0	0
............................................GATTACCTGCCCCACAGAC.................................................................................................	19	3	20	0.05	1	0	0	0	0	1	0
...........GTTCCGTACACACAGGCT...................................................................................................................................	18	3	20	0.05	1	0	1	0	0	0	0

ATTTAATTTTGCAAGGCATGTGTGTGTGTGCAGCTCTCGTTCCTCTACTGGACGGGGTGTTCGACCGTGGACGGGAGGACACCCACCCAACCAACCACCAACCCACCCAATCGTCAACGTGACGTGGTGAGCATGCATATATCCTCATTGTTAATTAAAA *********************************..((((.....((((((((((.((..((((((((((((((......))))))))..)))))).)).))))))))))....))))......*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V055 head	V105 male body	M058 embryo	V039 embryo
......................................................................................................................GTGACGTAGTGATCATGCATC.....................	21	3	1	1.00	1	1	0	0	0
..........................................CTCTAATGGAATGGGTGTTC..................................................................................................	20	3	8	0.13	1	0	1	0	0
.......................................TTCTTCTATTGGAAGGGGTGT....................................................................................................	21	3	8	0.13	1	1	0	0	0
...........................................................................................CAACCACAAACCCACCCAAA.................................................	20	2	8	0.13	1	0	0	0	1
.........................................CCTCTAATGGGAGGGGTGTT...................................................................................................	20	3	8	0.13	1	1	0	0	0
...........................................TCTAAGGGAAGGGGTGTTC..................................................................................................	19	3	20	0.10	2	0	2	0	0
...........................................TCTACGGGGAGGGGTGTTC..................................................................................................	19	3	14	0.07	1	1	0	0	0
............................................................................................AACCACCAACCCACACTA..................................................	18	2	18	0.06	1	0	0	1	0
.................................................................................ACCACCCAACAAACCACCAA...........................................................	20	2	20	0.05	1	0	0	1	0
...........................................................................................CAAGAACCAACCCACGCAA..................................................	19	3	20	0.05	1	0	0	1	0

Re-alignment of all predicted orthologs

Species	Coordinate	ID	Alignment
droAna3	scaffold_12916:5728454-5728613 +	dan_192	TAAATTAAAACGTTCCGTA---CACACACACACGT---------CGAGAGCAA----------------------------------------------------------------------GGAGATG---AC-----C-----TGC---------------------CC---CACAAGC---------TGGCACCTGCCCTC--CTG----TGGGTGGGTTGGTTG-------GTGG--TTGG------------GTGGGTTAGCAGTT--------GCA-------C----TGCACCAC--TCGTACGTATATAGGAG-----TAACAATTAATTTT
droBip1	scf7180000396568:1114751-1114910 -		TAAATTAAAACGTTCCGTA---CACA------CGACCAGT----GC-----AA----------------------------------------------------------------------GGAGA-----------GATGACCTGC---------------------CC---CACAAGCACCACCCAATGG-------CGCCACCTGACCCAGGATAGGTGGGTGGTTGGTTGGTTG-G--------------------GTTAGCAGTT---------GG-------C----TGTACTAC--ACG---GTCTATGGGAG-----TAACAATTAATTTT
droKik1	scf7180000302270:936569-936636 -		TAAATTAAAATGTCG----GC------------------------------------------------------------------------------------------------------------------TGCACC-----TGCATG-------CCGCGTGGGG------------------------------------------------------------------------------------------------------------------------------GGTTTT------------ATGTTGAAG-----TAACAATTAATTTT
droFic1	scf7180000453924:1652726-1652868 +		TAAATTAAAATGTTG----GG-----------------------GTGGAGCAA----------------------------------------------------------------------GGCGAAGGTGGGTCCACC-----TGCAAT-------CCGGGTGGTGCAACTG---ATTC------GGT--------GGTT----------------TGGCTGGC-----------TG-GCTTTT--CCGATGTAAGTGTGCGG--------------GTA-------A----TGTGTC------------ACACAGAAG-----TTGCAATTTATTTT
droEle1	scf7180000490728:391406-391546 +		TAAATTAAAATGTCT----GT-----------------------GCAGAGGAA----------------------------------------------------------------------GCCAAAG---GA-CCACC-----TGCAAT-------CCGGATGGTACAACAT---TTTT------GGT--------GGTT----------------TGGTTGGC----------TGG-GCTTT-TCTGGATGTAAGCGTGCGG--------------GTG-------A----TGTGTC------------ATATAGAAG-----TTACAATTAATTTT
droRho1	scf7180000779523:385451-385592 +		TAAATTAAAATGTACA---GAGT---------------------GCAGAGG-A----------------------------------------------------------------------GGCGAAG---CA-CCACC-----TGCAAT-------CCGGGTGGTGCAACTT---TTTC------GGT--------GGTTTT---------------GGTTGGC----------AGG-GCTTTG--TGGACGTAAGTGTGCGG--------------GTA-------A----TGT-TC------------ATATAGAAG-----TTACAATTAATTTT
droBia1	scf7180000302261:2038918-2039034 +		TAAATTAAAATGTCG----GC-----------------------ACAG-GCAA----------------------------------------------------------------------GGCGCAG---GCCCCACC-----TGCAAT-------CCGGATGGGGCAACTG---TTTC------GGT--------TGTC----------------TGGTTGAC------------------------------------TGC--------------GTA-------A----TGTGTC------------ATATAGAAG-----TTACAATTAATTTT
droTak1	scf7180000415709:197318-197435 -		TAAATTAAAATGTCG----GC-----------------------TCAGAGAAA----------------------------------------------------------------------GGCGCAG---GTCCCACC-----TGCAAT-------CCGGATGGTGTAACTG---TTTC------GCT--------TGTT----------------CGGTTGAC------------------------------------TGG--------------CTG-------A----TGTGTC------------ATACAGAAG-----TTACAATTAATTTT
droEug1	scf7180000409554:2415214-2415325 -		TAAATTAAAATGTCG----GT-----------------------GCAGAGGAA----------------------------------------------------------------------GGCGCAG---GACGCACC-----TGCATT-------CCCGATGGT----------------------------------C----------------TGGTGGGCTGAGT---GAGA--GCTTT------------ATGTG---------------------------------CTGTC------------ATATGAAAG-----TTACAATTAATTTT
dm3	chr2L:3672004-3672136 +		TAAATTAAAATGTCG----GC-----------------------ACACAGCAA----------------------------------------------------------------------GGCGAAG---GACCCACC-----TGCAAT-------CCGGATGGTGCAACTG---ATTC------GGC--------GGTTTG---------------GGCTG-----------ATGG-GCCTTG--T--------GTGTGTGG--------------ATA-------A----TGTGTC------------ATATAGAAG-----TTACAATTAATTTT
droSim2	2l:3525225-3525355 +		TAAATTAAAATGTCG----GC-----------------------ACACAGCAA----------------------------------------------------------------------GGCGAAG---GACCCACC-----TGCAAT-------CCGGATGGTGCAACTG---ATTC------GGC--------GGTTTG---------------GGCTG-----------ATGG-GCCTT------------GTGTGTGG--------------ATA-------A----TGTGTC------------ATATAGAAG-----TTACAATTAATTTT
droSec2	scaffold_5:1767625-1767755 +		TAAATTAAAATGTCG----GC-----------------------ACACAGCAA----------------------------------------------------------------------GGCGGCG---AACCCACC-----TGTAAT-------CCGGATGGTGCAACTG---ATTC------GGC--------GGTTTG---------------GGCTG-----------ATGG-GCCTT------------GTGTGTGG--------------ATA-------A----TGTGTC------------ATATAGAAG-----TTACAATTAATTTT
droYak3	2L:3665317-3665456 +		TAAATTAAAATGTCG----GCGC---------------------ACACAGCAA----------------------------------------------------------------------GGCGAAG---GACGCACC-----TGCAAT-------CCGGATGGTGCAACTG---TTTC------GGT-------TGAT-------------------GTTG-----------ATGG-GCCTTGTGTG--TGTGTGTGTGTGG--------------ATA-------A----TGTGTC------------ATATAGAAG-----TTACAATTAATTTT
droEre2	scaffold_4929:3708525-3708644 +		TAAATTAAAATGTCG----GC-----------------------ACACAGCAA----------------------------------------------------------------------GGCGCAG---GACCCACC-----TGCAAT-------CCGGATGGTGCAACTG---TTT---------------------------------------GGTTG-----------ATGG-GCCT-------------GTGTGCGG--------------ATA-------A----TGTGTC------------ATATAGAAG-----TTACAATTAATTTT
dp5	4_group3:5059666-5059886 -		TAAATTAAAATGTCACCGA---CAGA------GGAA-GATAGAGATAGAGGAAAATGGAAAAGCAAAATGCTAACCAAAAAGGAGAAAGAGGAAAGCAGAATGCCATCGAAAAAGAGGAAAATGGGGAAT---GCCCCACC-----TGCAGT-------CGAGGTGGTGCACCAG---TGGC------TTA-------TGGTCTG---------------GTCTG-----------G----CC-TGGTCTGG------TTTTTTGG--------------GTG-------G----CTTTTG------------GGGCGAAGC-----TTACAATTAATTTT
droPer2	scaffold_1:6551453-6551497 -		TAAATTAAAATGTCACCGA---CAGA------GGCATGATAGAGATAGAGGA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA----
droWil2	scf2_1100000004521:9468396-9468414 +		TAAATTAAAATGTTG-----T-----------------------ACA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	scaffold_12963:15069366-15069414 +		GGCCATCAGCTG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TA-------A----TGTGTC------------ACATAGTTGTATGCACACAATTAATTTT
droMoj3	scaffold_6500:18036500-18036643 +		TAAATTAAAACGGCG------------------------------CAAGGAAA------------------------------------------------------------------------CGGCA---ACAAAATT-----TGT----------------GCTGCAATGA---AATC------AT-----------------------------TGCTAGCC-----------TGGAG-TTATATAA------ATATATGA----GTATATGTAGATATGTATATATGTTTATGTCATCTAG------TGGC-----TATGCATACAATTAATTTT
droGri2	scaffold_15126:4324482-4324628 -		TAAATTAAAATGGCG------------------------------CAA-GGAA-----------------------------------------------------------------------GCGGCA---AACAAATT-----TGTTGTATTCATTTTGCA--------TGG---ATTC---------------------------------------GTTGGCTGGCG----GTTGGTG-CTATATA--TATATATATATAT----------ATACATATATATGTA----TGT-TT------------GTACAGAAGTATGCACACAATTAATTTT

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droAna3

TAAATTAAAACGTTCCGTA---CACACACACACGT---------CGAGAGCAA----------------------------------------------------------------------GGAGATG---AC-----C-----TGC---------------------CC---CACAAGC---------TGGCACCTGCCCTC--CTG----TGGGTGGGTTGGTTG-------GTGG--TTGG------------GTGGGTTAGCAGTT--------GCA-------C----TGCACCAC--TCGTACGTATATAGGAG-----TAACAATTAATTTT	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
.................................................................................................................................................................................................................................GTTG-------GTGG--TTGG------------GTGGGT.............................................................................	18	1	77.00	77	0	0	0	0	1	76
.................................................................................................................................................................................................................................GTTG-------GTGG--TTGG------------GTGGGTC............................................................................	19	2	2.50	5	0	0	0	0	0	5
..................................................................................................................................................................................................................................TTG-------GTGG--TTGG------------GTGGGTC............................................................................	18	5	0.20	1	0	0	0	0	0	1
.................................................................................................................................................................................................................................GTTG-------GTGG--TTGG------------GTGGGTCT...........................................................................	20	9	0.11	1	0	0	0	0	0	1

droBip1

TAAATTAAAACGTTCCGTA---CACA------CGACCAGT----GC-----AA----------------------------------------------------------------------GGAGA-----------GATGACCTGC---------------------CC---CACAAGCACCACCCAATGG-------CGCCACCTGACCCAGGATAGGTGGGTGGTTGGTTGGTTG-G--------------------GTTAGCAGTT---------GG-------C----TGTACTAC--ACG---GTCTATGGGAG-----TAACAATTAATTTT	Size	Hit Count	Total Norm	Total
No Reads

droKik1

TAAATTAAAATGTCG----GC------------------------------------------------------------------------------------------------------------------TGCACC-----TGCATG-------CCGCGTGGGG------------------------------------------------------------------------------------------------------------------------------GGTTTT------------ATGTTGAAG-----TAACAATTAATTTT	Size	Hit Count	Total Norm	Total
No Reads

droFic1

TAAATTAAAATGTTG----GG-----------------------GTGGAGCAA----------------------------------------------------------------------GGCGAAGGTGGGTCCACC-----TGCAAT-------CCGGGTGGTGCAACTG---ATTC------GGT--------GGTT----------------TGGCTGGC-----------TG-GCTTTT--CCGATGTAAGTGTGCGG--------------GTA-------A----TGTGTC------------ACACAGAAG-----TTGCAATTTATTTT	Size	Hit Count	Total Norm	Total
No Reads

droEle1

TAAATTAAAATGTCT----GT-----------------------GCAGAGGAA----------------------------------------------------------------------GCCAAAG---GA-CCACC-----TGCAAT-------CCGGATGGTACAACAT---TTTT------GGT--------GGTT----------------TGGTTGGC----------TGG-GCTTT-TCTGGATGTAAGCGTGCGG--------------GTG-------A----TGTGTC------------ATATAGAAG-----TTACAATTAATTTT	Size	Hit Count	Total Norm	Total
No Reads

droRho1

TAAATTAAAATGTACA---GAGT---------------------GCAGAGG-A----------------------------------------------------------------------GGCGAAG---CA-CCACC-----TGCAAT-------CCGGGTGGTGCAACTT---TTTC------GGT--------GGTTTT---------------GGTTGGC----------AGG-GCTTTG--TGGACGTAAGTGTGCGG--------------GTA-------A----TGT-TC------------ATATAGAAG-----TTACAATTAATTTT	Size	Hit Count	Total Norm	Total
No Reads

droBia1

TAAATTAAAATGTCG----GC-----------------------ACAG-GCAA----------------------------------------------------------------------GGCGCAG---GCCCCACC-----TGCAAT-------CCGGATGGGGCAACTG---TTTC------GGT--------TGTC----------------TGGTTGAC------------------------------------TGC--------------GTA-------A----TGTGTC------------ATATAGAAG-----TTACAATTAATTTT	Size	Hit Count	Total Norm	Total
No Reads

droTak1

TAAATTAAAATGTCG----GC-----------------------TCAGAGAAA----------------------------------------------------------------------GGCGCAG---GTCCCACC-----TGCAAT-------CCGGATGGTGTAACTG---TTTC------GCT--------TGTT----------------CGGTTGAC------------------------------------TGG--------------CTG-------A----TGTGTC------------ATACAGAAG-----TTACAATTAATTTT	Size	Hit Count	Total Norm	Total
No Reads

droEug1

TAAATTAAAATGTCG----GT-----------------------GCAGAGGAA----------------------------------------------------------------------GGCGCAG---GACGCACC-----TGCATT-------CCCGATGGT----------------------------------C----------------TGGTGGGCTGAGT---GAGA--GCTTT------------ATGTG---------------------------------CTGTC------------ATATGAAAG-----TTACAATTAATTTT	Size	Hit Count	Total Norm	Total
No Reads

dm3

TAAATTAAAATGTCG----GC-----------------------ACACAGCAA----------------------------------------------------------------------GGCGAAG---GACCCACC-----TGCAAT-------CCGGATGGTGCAACTG---ATTC------GGC--------GGTTTG---------------GGCTG-----------ATGG-GCCTTG--T--------GTGTGTGG--------------ATA-------A----TGTGTC------------ATATAGAAG-----TTACAATTAATTTT	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
.........................................................................................................................................................................................................TTTG---------------GGCTG-----------ATGG-GCCTTG--T--------GT.................................................................................	22	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
..........................................................................................................................................................................................................TTG---------------GGCTG-----------ATGG-GCCTTG--T--------GTGT...............................................................................	23	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
................................................................................................................................................................................................................................G-----------ATGG-GCCTTG--T--------GTGTGGC............................................................................	19	3	0.33	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droSim2

TAAATTAAAATGTCG----GC-----------------------ACACAGCAA----------------------------------------------------------------------GGCGAAG---GACCCACC-----TGCAAT-------CCGGATGGTGCAACTG---ATTC------GGC--------GGTTTG---------------GGCTG-----------ATGG-GCCTT------------GTGTGTGG--------------ATA-------A----TGTGTC------------ATATAGAAG-----TTACAATTAATTTT

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

TAAATTAAAATGTCG----GC-----------------------ACACAGCAA----------------------------------------------------------------------GGCGGCG---AACCCACC-----TGTAAT-------CCGGATGGTGCAACTG---ATTC------GGC--------GGTTTG---------------GGCTG-----------ATGG-GCCTT------------GTGTGTGG--------------ATA-------A----TGTGTC------------ATATAGAAG-----TTACAATTAATTTT	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
No Reads

droYak3

TAAATTAAAATGTCG----GCGC---------------------ACACAGCAA----------------------------------------------------------------------GGCGAAG---GACGCACC-----TGCAAT-------CCGGATGGTGCAACTG---TTTC------GGT-------TGAT-------------------GTTG-----------ATGG-GCCTTGTGTG--TGTGTGTGTGTGG--------------ATA-------A----TGTGTC------------ATATAGAAG-----TTACAATTAATTTT

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

No Reads

droEre2

TAAATTAAAATGTCG----GC-----------------------ACACAGCAA----------------------------------------------------------------------GGCGCAG---GACCCACC-----TGCAAT-------CCGGATGGTGCAACTG---TTT---------------------------------------GGTTG-----------ATGG-GCCT-------------GTGTGCGG--------------ATA-------A----TGTGTC------------ATATAGAAG-----TTACAATTAATTTT	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

dp5

TAAATTAAAATGTCACCGA---CAGA------GGAA-GATAGAGATAGAGGAAAATGGAAAAGCAAAATGCTAACCAAAAAGGAGAAAGAGGAAAGCAGAATGCCATCGAAAAAGAGGAAAATGGGGAAT---GCCCCACC-----TGCAGT-------CGAGGTGGTGCACCAG---TGGC------TTA-------TGGTCTG---------------GTCTG-----------G----CC-TGGTCTGG------TTTTTTGG--------------GTG-------G----CTTTTG------------GGGCGAAGC-----TTACAATTAATTTT

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

TAAATTAAAATGTCACCGA---CAGA------GGCATGATAGAGATAGAGGA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA----	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
No Reads

droWil2

TAAATTAAAATGTTG-----T-----------------------ACA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
No Reads

droVir3

GGCCATCAGCTG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TA-------A----TGTGTC------------ACATAGTTGTATGCACACAATTAATTTT

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

No Reads

droMoj3

TAAATTAAAACGGCG------------------------------CAAGGAAA------------------------------------------------------------------------CGGCA---ACAAAATT-----TGT----------------GCTGCAATGA---AATC------AT-----------------------------TGCTAGCC-----------TGGAG-TTATATAA------ATATATGA----GTATATGTAGATATGTATATATGTTTATGTCATCTAG------TGGC-----TATGCATACAATTAATTTT	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
No Reads

droGri2

TAAATTAAAATGGCG------------------------------CAA-GGAA-----------------------------------------------------------------------GCGGCA---AACAAATT-----TGTTGTATTCATTTTGCA--------TGG---ATTC---------------------------------------GTTGGCTGGCG----GTTGGTG-CTATATA--TATATATATATAT----------ATACATATATATGTA----TGT-TT------------GTACAGAAGTATGCACACAATTAATTTT	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

dan_192

scaffold_12916:5728504-5728563 +

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

-40.5	-39.6