dya_542

##################################################--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TCCCACCAGTCTGGAGGATAAGAACAAGCATGAGTTCGTGAAGGGGAAAAGTAAGTCGCAAACGTCCAAGGATCTATCCATCTATCCATCTTCCTCAAGCCGTCCATCTATCACAATGTGTTTATGTAGATCATCTGCTGGTGACTAGTGACTGGTGACTGGTGACTGGTATGGGCAGCCCATATATCAAAAGCCAAAGAGCCAAGTCGGCGGCCCGAATTTGGCCACCGTATCAGTTGGTCTCTGGAGTT ************************************************...((((((....(((..((((...................))))...((((((...(((((((...........(((((...)))))..)))).))).))).))))))..)))))).(((((((...)))))))................************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M026 head	V120 male body	V058 head
.........TCTGGAGGATAAGAACAAGCATGAG.........................................................................................................................................................................................................................	25	0	1	1.00	1	1	0	0
..........CTGGAGGATAAGAACAAGCATGAGT........................................................................................................................................................................................................................	25	0	1	1.00	1	1	0	0
............................................................................................................................................................................................AAAAGCCAAAGAGCCAAGTCGGC........................................	23	0	1	1.00	1	0	1	0
..............................................................................................................................................GACTAGTGACTGGTGACTGGTGAC.....................................................................................	24	0	2	0.50	1	0	1	0
...............................................................................................................................................................................................................CGGCGGCCCGGATTTGGCGGC.......................	21	3	5	0.20	1	0	0	1
........................................................................................................................................................................GTATGGGCAGGCCCGATAT................................................................	19	3	9	0.11	1	0	0	1

AGGGTGGTCAGACCTCCTATTCTTGTTCGTACTCAAGCACTTCCCCTTTTCATTCAGCGTTTGCAGGTTCCTAGATAGGTAGATAGGTAGAAGGAGTTCGGCAGGTAGATAGTGTTACACAAATACATCTAGTAGACGACCACTGATCACTGACCACTGACCACTGACCATACCCGTCGGGTATATAGTTTTCGGTTTCTCGGTTCAGCCGCCGGGCTTAAACCGGTGGCATAGTCAACCAGAGACCTCAA ************************************************...((((((....(((..((((...................))))...((((((...(((((((...........(((((...)))))..)))).))).))).))))))..)))))).(((((((...)))))))................************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V058 head
.....................................................................................GGCGGGAGGAGTTCGGCAGG..................................................................................................................................................	20	3	4	0.25	1	1
................GTATTCTTGTTCGGACT..........................................................................................................................................................................................................................	17	2	20	0.05	1	1

Re-alignment of all predicted orthologs

Species	Coordinate	ID	Alignment
droYak3	2R:11741106-11741356 -	dya_542	TCCCACCAGT------CTGGAGGATAAGAACAAG---CATGAGTTCGTGAAGGGGAAAAGTAAGTCGCAAACGTC----------------------------------CAAGGATCTA------TC-------------CAT-CTATCCATCTTCCTCAAGC---------------------------CGTC---CATCTATCACAA----TG--TGTTTATGTAGATCATCTGCTGGTGACTAGTGACTGGTG-----ACTGGTGACTGGTATGGGCAGCCCATATATCAAAA-----------------GCCAAAGAGC--CAAGTCGGC-------------GGC-CC-GAATTT----GGCCA-CCG--------TATC------A-GTTGGTCT--------------------------------CTGGAGTT
droEre2	scaffold_4845:11580365-11580569 +		TCCCACCAGT------CTGGAGGATAAGAACAAG---CACGAGTTCGTGAAGGGGAAAAGTAAGTCCG---CC-----------------------------------GCAAGGATCT----------------------------ATCCATCTTCCTCAAGC---------------------------CGCC---CATCTATCACAA----TG--TGTTTATGTAGATCATCTGCC--T-------G------------ACT---------GCCTGGCTGCCCATATATCAA-----------------------AAGAGC--CAAGTCGGC-----------------CC-GAATTT----GGCCA-CCG--------TATC------A-GTTGGTCT--------------------------------CTAGAGTT
droSec2	scaffold_9:763233-763440 +		TCCCACCAGT------CTGGAGGATAAGAACAAG---AACGAGTTCGTCAAGGGGAAAAGTAAGTGCA---GC-----------------------------------GCAAGGATCT----------------------------ATCCATCTTCCTCAAGC---------------------------CGCCCATCATCTATCAAAA----TG--TGTTTATGTAGATCATCTGGT--T-------G------------ACT---------GCCTGGCTGGCCATATATCAA-----------------------AAGAGC--CAGGTCGGC-----------------CC-GAATGT----GGCCA-CCG--------TATC------A-GTTGGTCT--------------------------------CCAGAGTT
droSim2	2r:17990076-17990283 +	dsi_9732	TCCCACCAGT------CTGGAGGATAAGAACAAG---AACGAGTTCGTCAAGGGGAAAAGTAAGTGCA---GC-----------------------------------GCAAGGATCT----------------------------ATCCATCTTCCTCAAGC---------------------------CGCCCATCATCTATCAAAA----TG--TGTTTATGTAGATCATCTGGC--T-------G------------ACT---------GCCTGGCTGCCCATATATCAA-----------------------AAGAGC--CAGGTCGGC-----------------CC-GAATTT----GGCCA-CCG--------TATC------A-GTTGGTCT--------------------------------CCAGAGTT
dm3	chr2R:17435347-17435554 +		TCCCACCAGT------CTGGAGGATAAGAACAAG---AACGAGTTCGTCAAGGGGAAAAGTAAGTGCA---CC-----------------------------------GCAAGGATCT----------------------------ATCCATCTTCCTCAAGC---------------------------CGCCCATCATCTATCAAAA----TG--TGTTTATGTAGATCATCTGGC--T-------G------------ACT---------GACTGGCTGCCCATATATCAA-----------------------AAGAGC--CAAGTCGTC-----------------CC-GAATTT----GGCCA-CCG--------TATC------A-GTTGGTCT--------------------------------CTAGAGTT
droEug1	scf7180000409474:491582-491797 -		TCCCACCAGT------ATCGAGGAGAAGTCAAAG---AACGAATTCGTCAAGGGAAAAAGTAAGTCCA---AC-----------------------------------GCCAGGATCT----------------------------ATCCGTCTTCTTCAAGT---------------------------CGCC---CATCTATCACAA----TG--TGTTTATGTAGATCATCTCCC--T-------GCCTGCCGGCCCAACT---------GCCTGCCTGCCCATATATCAA-----------------------AA-GGC--CAACTCAAC-----------------CC-GAATAT----GCCCA-CCA--------TATC------A-GTTGAGCT--------------------------------CTGGAGTT
droBia1	scf7180000302143:940925-941133 -		TCCCACCATT------CTGGAGGATCAGAGCAAG---AACGAGTTCGTCAAGGGGAAAAGTAAGTCGCCCGCC-----------------------------------GCCGGGATCT----------------------------ATCCATCTTCTTCAAAA----------CTG--------------CG--CCCCATCTATCACAA----TG--TGTTTGGTTAGATCATCTGC--------------------------------------CTGCCCGCCCATATATCATCC-----------------G-AAAAAAGC--CAAGTCAAC-----------------CC-ATATAT----GGCCA-CAG--------TATC------A-GTTTAACT--------------------------------CTAGAGTT
droTak1	scf7180000415722:376093-376310 +		TCCCACCGGT------CTGGAGGATCAGAATAAG---AACGAGTTCGTCAAGGGGAAAAGTAAGTCGT-----------------------------------------CCAGGATCTA------G------------------CCATCCATCTTCTTCAAGT-A-----GTGCCA-----------G--TGCC---CATCTATCACAA----TG--TGTTTATGTAGATCATCTGT--------------------------------------CTGCCCGCCCATATATCATCC-----------------ACGAAAAAGC--CAACTCAAC-----------------CC-GAATATTTCGGGCCC-CCG--------TATC------A-GTTTAACT-CT-----------------------------GTAGAGTT
droEle1	scf7180000491201:1678270-1678491 -		TCCCACCAGT------CTGGAGGATCAGAAGCCC---AACGAGTTTGTCAAGGGAAAAAGTAAGTTGTCCACC-----------------------------------GCCAGGATCTA------GC------CAGC---CAT-CCATCCGTCTTCGTTACAC---------------------------AGCC---CATCTATCACAA----TG--TGTTTGTGTAGATCATCCGC-------------------------CT---------GCTTGGCTGCCCATATATCAA-----------------------AAAAGC--CAAGTCGGC-----------------CC-AAATAT----GACCA-CCG--------AATCGGTATCA-CTTGGGCT--------------------------------CTTGAGTT
droRho1	scf7180000780066:411229-411431 +		TCCCACCAGT------CTGGAGGATCAGAGGCCC---AACGAGTTCGTCAAGGGGAAAAGTAAGTCCA---TG-----------------------------------GCCAGGATCTA------G------------------CCATCCGTCTTCGTCACTG---------------------------TGCC---CATCTATCACAA----TG--TGTTTATGTAGATCATCT------------------------------------------GCCCGTCCATATATCAA-----------------------AAAAGC--CAAGTCGGC-----------------CC-AAATAT----GGCCA-CCG--------TTTCATTATCA-GTTGGGCT--------------------------------CTTGAGTT
droFic1	scf7180000453201:117939-118161 -		TCCCACCAGT------CTGGAGGACAAGAAGCCC---AACGAGTTTGTCAAGGGAAAAAGTAAGTGCACCAC--C----------------------------------GAAGGATCTACTGTATTC-------------CAT-CCATCCGTCTTCTTCAAAGAAAAG-----AGG-----------G--GACC---CATCTATCACAA----TC--TGTTTATGTAGATCATCTGC--------------------------------------CTGCCTGCCCATATATCATC----------------------AAGAGC--CAAGTCGGC-----------------CC-AAATAT----GGCCA-CCG--------TATC------A-CCTGAAGT--------------------------------CTTGATTT
droKik1	scf7180000302411:721873-722119 +		TGCTGCGGGT------CAGGAGGA---GCCCAAG---AGCGAGTTTGTCAAGGGAAAAAGTAAGTTCACA-TT-AGAAGGAT-ATACATAT----CTCTAG----------AGTATCTG------TC-------------TGG-CCATCCATCTTCGTCAGCC-ACTGAGGTGCTG--------------CC--CCCCATCTATCACAA----TC--TGTTTATGTAGATT---TGC----------------------------------------GCCTGCCCATATATCAAA----------------------AAAAGCATCAAGACGTC-----------------CCTAAATAG----GGTGT-CTG--------TATT----------TGGTTT---------------TTGGGGTT-TTTGAGT-TTTCAGTT
droAna3	scaffold_13266:5259831-5260122 +	dan_1801	TGCCAAGCCC------CTCGACGAGCAGAAGTCC---AACAAATTTGTAAATGGAAAAAGTAAGTCCACAGG--------ATCATCCATATATATGTATATACTCTCCG----------------------ACCATATCT---ACCATCCATCTTCGTAAAGG---------------------------CAC--CCCATCCATCACAA----TG--TGTTTATGTAGATT--------------------------------------------TTGGCTGCCCATATATCAAAATAAGTGAGAACAAAAATAAGAAAAAGC--CAAGACATCCAACAAGCCAGCCAGCCAG-CCATTG----AGCCAACCATC----CATATC------A-GCTTGGTT-CTGTT--------TTTGGGGTT-TTCGGTTTTTGGAGTT
droBip1	scf7180000395751:1051217-1051458 +		TGCCAAGCCC------CTCGAGGAACAGAAGTCC---AACGAGTTTGTGAAAGGAAAAAGTAAGTCCACAGG--------ATCATCCATATATA----------CTCC-----------------------ACCATATCT---CCCATCCATCTTCGTCAAGA---------------------------CAC--CCCATCCATCACAA----TG--TGTTTATGTAGATT--------------------------------------------TCGGCTGCCCATATATCAAAATAA-TGAGAAAAAAACTAAGAAAAAGC--CAAGACAGC-----------------CA-GC---C----AGCCA----GCCAGCCATATC------A-GCTTGGTT-CTGT---------------------------TTGGGGTT
dp5	3:15716023-15716249 +		GGCCAACAGC------ATGGAGGACCAGAAGTCG---AACGAGTTCGTTAAGGGCAAAAGTAAGTCAC---CG-----------------------------------GCCAGGC--CA------GGCCAGGCCAGATCT---GGATCCCCCGCTCGATATGA------------------------GAACC--CTCGATCTATCACAA----TGCATATTTATGTAGATT---TGC--------------------------------------GTCCGTGCTCATATATCAT-----------------------T--AGC--GAAGACGGC-----------------CC-GAATAT----GGCCA-CCATGCAAACATATC------A-TCGG-AGTAGTGA---------------------------GTGTGGTT
droPer2	scaffold_4:3335399-3335610 -		GGCCAACAGC------ATGGAGGACCAGAAGTCG---AACGAGTTCGTTAAGGGCAAAAGTAAGTCAC---CG-----------------------------------GC-CAGATCT-------------------------GGAACCCCCGCTCGATATGA------------------------GAACC--CTCGATCTATCACAA----TGCATATTTATGTAGATT---TGC--------------------------------------GTCCGTGCTCATATATCAT-----------------------T--AGC--GAAGACGGC-----------------CC-GAATAT----GGCCA-CCATGCAAACATATC------A-TCGG-AGTAGTGA---------------------------GTGTGGTT
droWil2	scf2_1100000004382:1357042-1357294 +		TTCCAATGGC------CGCGAGGATCATCCCAAGCACACGGAATTCGTGAAGGGCAAAAGTAAGTCTTAG--------------------------------------TC---AATCTA------TC-------------CAT-CTATCTGTCTTCGTCAAGA----------GTTCTTCTCTTTGGGGCCTC--CAAATCCATCACATTCTATGTGTATTTATGTAGATT---------------------------------------------TGCGTGCCCATATATCAA-----------------------AA---T--CAA---GAC-----------------CC-AAATAT----GGCCG-CCA--------TATCAGTAGTAGTCGT-AGTAGTAGAGAAAAACCCATGGGCATATCTATGC-TTTACTTT
droVir3	scaffold_12875:17762086-17762152 -		GGCCAACGGTGGCGTTGTCGGTGATCACAACAAG---GACACGTTTCCCAAAGGCAAAAGTAAGTGTCAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_4170:1777-1827 -		C------------------GGCGACAACAACAAG---GACACATTCCCCAAGGGCAAAAGTAAGTGCCAAAC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	scaffold_15245:13925337-13925388 +		-------------------GGCGATAACAACAAG---GATACGTTCCCCAAAGGCAAAAGTAAGTGGCAA------------------------------------------TCAT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droYak3

TCCCACCAGT------CTGGAGGATAAGAACAAG---CATGAGTTCGTGAAGGGGAAAAGTAAGTCGCAAACGTC----------------------------------CAAGGATCTA------TC-------------CAT-CTATCCATCTTCCTCAAGC---------------------------CGTC---CATCTATCACAA----TG--TGTTTATGTAGATCATCTGCTGGTGACTAGTGACTGGTG-----ACTGGTGACTGGTATGGGCAGCCCATATATCAAAA-----------------GCCAAAGAGC--CAAGTCGGC-------------GGC-CC-GAATTT----GGCCA-CCG--------TATC------A-GTTGGTCT--------------------------------CTGGAGTT	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
.........T------CTGGAGGATAAGAACAAG---CATGAG..............................................................................................................................................................................................................................................................................................................................................................................................................	25	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0
................CTGGAGGATAAGAACAAG---CATGAGT.............................................................................................................................................................................................................................................................................................................................................................................................................	25	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................................................................................AAAA-----------------GCCAAAGAGC--CAAGTCGGC-------------..............................................................................................	23	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
.................................................................................................................................................................................................................................................GACTAGTGACTGGTG-----ACTGGTGAC...........................................................................................................................................................................	24	2	0.50	1	0	0	0	0	0	0	1	0	0	0	0

droEre2

TCCCACCAGT------CTGGAGGATAAGAACAAG---CACGAGTTCGTGAAGGGGAAAAGTAAGTCCG---CC-----------------------------------GCAAGGATCT----------------------------ATCCATCTTCCTCAAGC---------------------------CGCC---CATCTATCACAA----TG--TGTTTATGTAGATCATCTGCC--T-------G------------ACT---------GCCTGGCTGCCCATATATCAA-----------------------AAGAGC--CAAGTCGGC-----------------CC-GAATTT----GGCCA-CCG--------TATC------A-GTTGGTCT--------------------------------CTAGAGTT	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

droSec2

TCCCACCAGT------CTGGAGGATAAGAACAAG---AACGAGTTCGTCAAGGGGAAAAGTAAGTGCA---GC-----------------------------------GCAAGGATCT----------------------------ATCCATCTTCCTCAAGC---------------------------CGCCCATCATCTATCAAAA----TG--TGTTTATGTAGATCATCTGGT--T-------G------------ACT---------GCCTGGCTGGCCATATATCAA-----------------------AAGAGC--CAGGTCGGC-----------------CC-GAATGT----GGCCA-CCG--------TATC------A-GTTGGTCT--------------------------------CCAGAGTT	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
..............................................................................................................................................................................................................................................................................................................................................................................................ATC------A-GTTGGTCT--------------------------------CCAGAG..	18	1	1.00	1	0	0	0	1

droSim2

TCCCACCAGT------CTGGAGGATAAGAACAAG---AACGAGTTCGTCAAGGGGAAAAGTAAGTGCA---GC-----------------------------------GCAAGGATCT----------------------------ATCCATCTTCCTCAAGC---------------------------CGCCCATCATCTATCAAAA----TG--TGTTTATGTAGATCATCTGGC--T-------G------------ACT---------GCCTGGCTGCCCATATATCAA-----------------------AAGAGC--CAGGTCGGC-----------------CC-GAATTT----GGCCA-CCG--------TATC------A-GTTGGTCT--------------------------------CCAGAGTT	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
...................GAGGATAAGAACAAG---AACGAG..............................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................AGATCATCTGGC--T-------G------------ACT---------GC......................................................................................................................................................................	19	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...............................................................................................................................................................................................................AA----TG--TGTTTATGTAGATC..................................................................................................................................................................................................................	18	1	1.00	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
................................................................................................................................................................................................................................GTAGATCATCTGGC--T-------G------------ACT---------GCCT....................................................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

dm3

TCCCACCAGT------CTGGAGGATAAGAACAAG---AACGAGTTCGTCAAGGGGAAAAGTAAGTGCA---CC-----------------------------------GCAAGGATCT----------------------------ATCCATCTTCCTCAAGC---------------------------CGCCCATCATCTATCAAAA----TG--TGTTTATGTAGATCATCTGGC--T-------G------------ACT---------GACTGGCTGCCCATATATCAA-----------------------AAGAGC--CAAGTCGTC-----------------CC-GAATTT----GGCCA-CCG--------TATC------A-GTTGGTCT--------------------------------CTAGAGTT	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
...................................................................A---CC-----------------------------------GCAAGGATCT----------------------------ATCCATCT...............................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
......................................................................................................................................................................................................................G--TGTTTATGTAGATCATCTGG............................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.............................................................................................................................................................TCAAGC---------------------------CGCCCATCATCTATCAAAA----TG--TG..............................................................................................................................................................................................................................	29	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	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

droEug1

TCCCACCAGT------ATCGAGGAGAAGTCAAAG---AACGAATTCGTCAAGGGAAAAAGTAAGTCCA---AC-----------------------------------GCCAGGATCT----------------------------ATCCGTCTTCTTCAAGT---------------------------CGCC---CATCTATCACAA----TG--TGTTTATGTAGATCATCTCCC--T-------GCCTGCCGGCCCAACT---------GCCTGCCTGCCCATATATCAA-----------------------AA-GGC--CAACTCAAC-----------------CC-GAATAT----GCCCA-CCA--------TATC------A-GTTGAGCT--------------------------------CTGGAGTT	Size	Hit Count	Total Norm	Total
No Reads

droBia1

TCCCACCATT------CTGGAGGATCAGAGCAAG---AACGAGTTCGTCAAGGGGAAAAGTAAGTCGCCCGCC-----------------------------------GCCGGGATCT----------------------------ATCCATCTTCTTCAAAA----------CTG--------------CG--CCCCATCTATCACAA----TG--TGTTTGGTTAGATCATCTGC--------------------------------------CTGCCCGCCCATATATCATCC-----------------G-AAAAAAGC--CAAGTCAAC-----------------CC-ATATAT----GGCCA-CAG--------TATC------A-GTTTAACT--------------------------------CTAGAGTT	Size	Hit Count	Total Norm	Total
No Reads

droTak1

TCCCACCGGT------CTGGAGGATCAGAATAAG---AACGAGTTCGTCAAGGGGAAAAGTAAGTCGT-----------------------------------------CCAGGATCTA------G------------------CCATCCATCTTCTTCAAGT-A-----GTGCCA-----------G--TGCC---CATCTATCACAA----TG--TGTTTATGTAGATCATCTGT--------------------------------------CTGCCCGCCCATATATCATCC-----------------ACGAAAAAGC--CAACTCAAC-----------------CC-GAATATTTCGGGCCC-CCG--------TATC------A-GTTTAACT-CT-----------------------------GTAGAGTT	Size	Hit Count	Total Norm	Total
No Reads

droEle1

TCCCACCAGT------CTGGAGGATCAGAAGCCC---AACGAGTTTGTCAAGGGAAAAAGTAAGTTGTCCACC-----------------------------------GCCAGGATCTA------GC------CAGC---CAT-CCATCCGTCTTCGTTACAC---------------------------AGCC---CATCTATCACAA----TG--TGTTTGTGTAGATCATCCGC-------------------------CT---------GCTTGGCTGCCCATATATCAA-----------------------AAAAGC--CAAGTCGGC-----------------CC-AAATAT----GACCA-CCG--------AATCGGTATCA-CTTGGGCT--------------------------------CTTGAGTT	Size	Hit Count	Total Norm	Total
No Reads

droRho1

TCCCACCAGT------CTGGAGGATCAGAGGCCC---AACGAGTTCGTCAAGGGGAAAAGTAAGTCCA---TG-----------------------------------GCCAGGATCTA------G------------------CCATCCGTCTTCGTCACTG---------------------------TGCC---CATCTATCACAA----TG--TGTTTATGTAGATCATCT------------------------------------------GCCCGTCCATATATCAA-----------------------AAAAGC--CAAGTCGGC-----------------CC-AAATAT----GGCCA-CCG--------TTTCATTATCA-GTTGGGCT--------------------------------CTTGAGTT	Size	Hit Count	Total Norm	Total
No Reads

droFic1

TCCCACCAGT------CTGGAGGACAAGAAGCCC---AACGAGTTTGTCAAGGGAAAAAGTAAGTGCACCAC--C----------------------------------GAAGGATCTACTGTATTC-------------CAT-CCATCCGTCTTCTTCAAAGAAAAG-----AGG-----------G--GACC---CATCTATCACAA----TC--TGTTTATGTAGATCATCTGC--------------------------------------CTGCCTGCCCATATATCATC----------------------AAGAGC--CAAGTCGGC-----------------CC-AAATAT----GGCCA-CCG--------TATC------A-CCTGAAGT--------------------------------CTTGATTT	Size	Hit Count	Total Norm	Total
No Reads

droKik1

TGCTGCGGGT------CAGGAGGA---GCCCAAG---AGCGAGTTTGTCAAGGGAAAAAGTAAGTTCACA-TT-AGAAGGAT-ATACATAT----CTCTAG----------AGTATCTG------TC-------------TGG-CCATCCATCTTCGTCAGCC-ACTGAGGTGCTG--------------CC--CCCCATCTATCACAA----TC--TGTTTATGTAGATT---TGC----------------------------------------GCCTGCCCATATATCAAA----------------------AAAAGCATCAAGACGTC-----------------CCTAAATAG----GGTGT-CTG--------TATT----------TGGTTT---------------TTGGGGTT-TTTGAGT-TTTCAGTT	Size	Hit Count	Total Norm	Total
No Reads

droAna3

TGCCAAGCCC------CTCGACGAGCAGAAGTCC---AACAAATTTGTAAATGGAAAAAGTAAGTCCACAGG--------ATCATCCATATATATGTATATACTCTCCG----------------------ACCATATCT---ACCATCCATCTTCGTAAAGG---------------------------CAC--CCCATCCATCACAA----TG--TGTTTATGTAGATT--------------------------------------------TTGGCTGCCCATATATCAAAATAAGTGAGAACAAAAATAAGAAAAAGC--CAAGACATCCAACAAGCCAGCCAGCCAG-CCATTG----AGCCAACCATC----CATATC------A-GCTTGGTT-CTGTT--------TTTGGGGTT-TTCGGTTTTTGGAGTT	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
...............................................................................................................................................................................................................................................................................................................................................AACAAGCCAGCCAGCCAG-CC.....................................................................................	20	2	0.50	1	0	1	0	0	0	0

droBip1

TGCCAAGCCC------CTCGAGGAACAGAAGTCC---AACGAGTTTGTGAAAGGAAAAAGTAAGTCCACAGG--------ATCATCCATATATA----------CTCC-----------------------ACCATATCT---CCCATCCATCTTCGTCAAGA---------------------------CAC--CCCATCCATCACAA----TG--TGTTTATGTAGATT--------------------------------------------TCGGCTGCCCATATATCAAAATAA-TGAGAAAAAAACTAAGAAAAAGC--CAAGACAGC-----------------CA-GC---C----AGCCA----GCCAGCCATATC------A-GCTTGGTT-CTGT---------------------------TTGGGGTT	Size	Hit Count	Total Norm	Total
No Reads

dp5

GGCCAACAGC------ATGGAGGACCAGAAGTCG---AACGAGTTCGTTAAGGGCAAAAGTAAGTCAC---CG-----------------------------------GCCAGGC--CA------GGCCAGGCCAGATCT---GGATCCCCCGCTCGATATGA------------------------GAACC--CTCGATCTATCACAA----TGCATATTTATGTAGATT---TGC--------------------------------------GTCCGTGCTCATATATCAT-----------------------T--AGC--GAAGACGGC-----------------CC-GAATAT----GGCCA-CCATGCAAACATATC------A-TCGG-AGTAGTGA---------------------------GTGTGGTT	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
................ATGGAGGACCAGAAGTCG---AACGAGTTCG..........................................................................................................................................................................................................................................................................................................................................................................................................	28	1	1.00	1	0	0	0	0	0	0	0	0	0	1
.GCCAACAGC------ATGGAGGACCA..............................................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0	0	0	0	0

droPer2

GGCCAACAGC------ATGGAGGACCAGAAGTCG---AACGAGTTCGTTAAGGGCAAAAGTAAGTCAC---CG-----------------------------------GC-CAGATCT-------------------------GGAACCCCCGCTCGATATGA------------------------GAACC--CTCGATCTATCACAA----TGCATATTTATGTAGATT---TGC--------------------------------------GTCCGTGCTCATATATCAT-----------------------T--AGC--GAAGACGGC-----------------CC-GAATAT----GGCCA-CCATGCAAACATATC------A-TCGG-AGTAGTGA---------------------------GTGTGGTT	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
.......................................................AAAAGTAAGTCAC---CG-----------------------------------GC-CAGATCT-------------------------G.........................................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	1	0	0	0	0
.......................................................................................................................................................CGCTCGATATGA------------------------GAACC--CTC....................................................................................................................................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0

droWil2

TTCCAATGGC------CGCGAGGATCATCCCAAGCACACGGAATTCGTGAAGGGCAAAAGTAAGTCTTAG--------------------------------------TC---AATCTA------TC-------------CAT-CTATCTGTCTTCGTCAAGA----------GTTCTTCTCTTTGGGGCCTC--CAAATCCATCACATTCTATGTGTATTTATGTAGATT---------------------------------------------TGCGTGCCCATATATCAA-----------------------AA---T--CAA---GAC-----------------CC-AAATAT----GGCCG-CCA--------TATCAGTAGTAGTCGT-AGTAGTAGAGAAAAACCCATGGGCATATCTATGC-TTTACTTT	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
..............................CAAGCACACGGAATTCGTGAAGGGC..................................................................................................................................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	0	1	0	0

droVir3

GGCCAACGGTGGCGTTGTCGGTGATCACAACAAG---GACACGTTTCCCAAAGGCAAAAGTAAGTGTCAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	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
.............................ACAAG---GACACGTTTCCCAAA.....................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droMoj3

C------------------GGCGACAACAACAAG---GACACATTCCCCAAGGGCAAAAGTAAGTGCCAAAC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
.........................................CATTCCCCAAGGGCAAAA..............................................................................................................................................................................................................................................................................................................................................................................................	18	2	0.50	1	0	0	0	0	1	0

droGri2

-------------------GGCGATAACAACAAG---GATACGTTCCCCAAAGGCAAAAGTAAGTGGCAA------------------------------------------TCAT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

dya_542

2R:11741156-11741306 -

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

-28.7	-28.4	-28.2