dsi_22599

CACAGCAGCAGTAGCAGCGGCAACAACTGATACCGCAGCAACAACCACTGGTGAGTGCCCCTTGGAGGATGGAAAATTTTCCATACTTAACTCAATTGATCTGAAGTGAACTGGGGAAAAGAGACTATAAATATATATGACAGCTAGTTGTGAGCCAAAAAACTAAGTGGTTGTATGTTTACATGCAATAATTTATGAGTAGCAATCTATTTTTATTATGCTGTTTTTCATAAAATATTAAAACGATGCG ************************************************.(((((......((((((((.....))))))))......))))).....(((..((....))..)))..........((((((((((...((..(((((...........)))))..))..))))))))))((((........))))...************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	SRR553485 Chicharo_3 day-old ovaries	SRR553486 Makindu_3 day-old ovaries	M023 head	SRR553487 NRT_0-2 hours eggs	SRR553488 RT_0-2 hours eggs	SRR618934 dsim w501 ovaries
..........GTAGCAGCAGCAACAACTGAAACCGC......................................................................................................................................................................................................................	26	2	1	1.00	1	1	0	0	0	0	0
..CAGCAGCAGTAGCAGCGGCA....................................................................................................................................................................................................................................	20	0	5	0.20	1	0	0	1	0	0	0
...................................................................................................................................................TTTTGAGCCAAAAAACTGAGA..................................................................................	21	3	9	0.11	1	0	1	0	0	0	0
..............................................................TGGTGGATGGAAAATTCTGCA.......................................................................................................................................................................	21	3	12	0.08	1	0	1	0	0	0	0
.............................................................................................................................................AGCTAGTTGTGGGGTAAAA..........................................................................................	19	3	20	0.05	1	0	0	0	0	1	0
..............................................................................................................CTGACGAAAAGAGACT............................................................................................................................	16	2	20	0.05	1	0	1	0	0	0	0
.......................................................................................................................................................................CGGTAGTATGTTTACA...................................................................	16	2	20	0.05	1	0	0	0	1	0	0
...................................................................GATGGAAAATTTTCAA.......................................................................................................................................................................	16	1	20	0.05	1	0	0	0	0	0	1

GTGTCGTCGTCATCGTCGCCGTTGTTGACTATGGCGTCGTTGTTGGTGACCACTCACGGGGAACCTCCTACCTTTTAAAAGGTATGAATTGAGTTAACTAGACTTCACTTGACCCCTTTTCTCTGATATTTATATATACTGTCGATCAACACTCGGTTTTTTGATTCACCAACATACAAATGTACGTTATTAAATACTCATCGTTAGATAAAAATAATACGACAAAAAGTATTTTATAATTTTGCTACGC ************************************************.(((((......((((((((.....))))))))......))))).....(((..((....))..)))..........((((((((((...((..(((((...........)))))..))..))))))))))((((........))))...************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M023 head	M024 male body	SRR618934 dsim w501 ovaries	SRR553488 RT_0-2 hours eggs
.............................................................................GAAGGTATGAATTGAGTTGGC........................................................................................................................................................	21	3	3	0.33	1	1	0	0	0
................................................................................................................................................................................CAAATGTAGGTTATTGAA........................................................	18	2	14	0.14	2	0	2	0	0
.....................................................TCACGGGGAATGTCCT.....................................................................................................................................................................................	16	2	20	0.05	1	0	0	0	1
................................................................................................................................................................TGGATTCGCCAACATA..........................................................................	16	2	20	0.05	1	0	0	1	0
....................................................................................................................................................ACAATCGATTTTTTGATT....................................................................................	18	2	20	0.05	1	0	0	1	0

Species	Coordinate	ID	Alignment
droSim2	3r:23529338-23529587 -	dsi_22599	CACAGCAGCAGTAGCAGCGGCAAC------------A------AC---TGATA---CCGCAGC---AACAACC---ACTGGTGAGTG-------------CCCCTTGG-AGGATG---------------------------------------GAAAATT--------TTCCATACT--TAACT------------------CAATTGATCTGA------AGTGAACTG---------------------GGGA--A-----AAGAG-----------------------------------ACT-------ATAAATATATATGACAGCTAGTTGTGAGCCAAAAAACTAAGTGGTTGTATG--TTTACAT------G----------------CAATAATT------TAT----------------------------------------GAGTAGCAATCTA----TTTTTA--------------------------TTATGCTGT-TTTTC----------ATAAAATATTAA------AA-----------------------CGATGCG
droSec2	scaffold_22:755063-755308 -		CGCAGCAGCAGTAGCAGCAGCAAC------------A------AC---TGAAA---CCGCAAC---AACAACC---ACTGGTGAGTG-------------CCCCTTCG-AGGATG---------------------------------------GAAAATT--------TTCCATACT--TAACT------------------CAATTAATCTGA------AGTGAACTG---------------------GGGA--A-----AAGAG-----------------------------------ACT-------ATAAATATG----ACAGCTAATTGTGAGCCAAAAAACTAAGTGGTTGTATG--TTTACAT------G----------------CAATAATT------TAT----------------------------------------GAGTAGCAATCTA----TTTTTA--------------------------TTATGCTGT-TTTTC----------ATAAAATATTAA------AA-----------------------CGATGCG
dm3	chr3R:24151037-24151260 -		CGCAGCAGCAGTACCAGCAGCAAC------------A------AC---TGAAA---CCGCAAC---AACAACC---ACTGGTGAGTG-------------CCCCTTGG-AGGATG---------------------------------------GAAAATT--------TTCTATACT--TAACT------------------CAATTGATCTGA------AGTGAACTG---------------------GGGA--A-----AGTAA-----------------------------------ACT-------ATAAATATA----A---C-------------------TAAGTGGTTGTATG--TTTACAT------G----------------CAAAAATT------TAT----------------------------------------GAATAGCAATCTA----TTTTTA--------------------------TTATGCTGT-TTTTC----------ATCAAACATTAT------CA-----------------------CAATGCG
droEre2	scaffold_4820:3896102-3896338 +		AGCAGCAGAAGTAGCAGCAGCAAC------------A------AC---TGAAA---CCGCAACAACAACAACA---ACTGGTGAGTG-------------CTCCTTGG-A----G---------------------------------------GAAAACT--------TTGCGTACT--TAACT------------------CAATTGATCTCA------AGTGAACTG---------------------GGGA--A-----ACGAC-----------------------------------ACT-------ATAGATATT----ACTACCAGTTGTGAGTCAAAAAATTAAGTGCTTGTA-----------------G----------------TAATAGTT------TAT----------------------------------------GAAAAGCAATCTA----TTTTTA--------------------------TTATGCTGAATTTTC----------ATAAAATACTAA------CA-----------------------TGATGCG
droYak3	3R:22351657-22351897 +		CACAGCAGCAGCAGCGGCAGTAGCAGCAGCAGCAACA------AC---TGAAA---CCGCAAC---AACAACA---ACTGGTGAGTG-------------CCCCATGG-AGAATG---------------------------------------GAAAACT--------TTCCGTACT--TAACT------------------TAATTGATCTCA------AGTGAACT------------------------------------------------------------------------------------ATAAATATA----ACTGCTAGTTGTGAGCCAAAAAATTAAGTGGT---ATG--TTTACAT------T----------------CAATAATT------TAT----------------------------------------GA-AAGCAATCTA----TTTTTA--------------------------TTATGCTATATTTTC----------ATAAAATATGTA------CA-----------------------TCTTGCG
droEug1	scf7180000409787:1447976-1448263 +		AGCACCTCCACCAGCAGCTCCAAC------------A------AC---TGAAA---CAGCAACCACAACAACA---ACTGGTGAGTG-------------CC--GTGG-ATGAAA---------------------------------------GGAAATT--------TTCCATACA--AAACT------------------CAATTAATCTTA------AGTGAAGTA---------------------GGAA--A-----GA-AG-----------------------------------ACTAAAAGCCATAAATATA----G---CTAGA-------------------TAGTTATAGT--TATTAATAATATAGTTATTAATTTGAGTATTCACAAATATCACTTAAAAT-------------------------------------CT-AAGCATATAT----TTTTTA--------------------------TTACACAAAATGTTCTTAAAATTCCATAGTATGTTAATGGA--AAGACTGCCAAA-AA----------ACTTGTA
droBia1	scf7180000302075:2653013-2653302 +		CGCAGCGGCAACATCAGCGGCAGC------------A---ACAAC---CGAAC---CAGCAGC---AACAACA---ATTGGTGAGTG-------------CCC-GTGG-TTGATG---------------------------------------GAAAATT--------TTCCATACA--CAACT------------------CAATTAATCTCA------AGTAAACTA---------------------GGGA--A-----AA-AGACCTACAC--AAA----------------------ACC-------AGAAATATA----A---CTAGCTCTCAGTCAAAAAGTATAGTGAATGTGG----------------G----------------CCATAAAT------T-T----------------------------------------GGATATCAATATA----TTTGTC------------GGCGGTATTATTTAT------AGATGTTTTTGAATTTGCGTAACATATTGGTAAA--GGGGCTGC-AAA-AAACATATATTATTTTTTG
droTak1	scf7180000415383:357394-357673 +		CGCAACACCAACAACATCGGCAGC------------AGCAGCAAC---TGAAA---CAGCAAC---AACAACA---ACTGGTGAGTG-------------CCC-ATGG-ATGATG---------------------------------------GAAAATT--------TTCCATACA--AAACT------------------CAATTAATCTCA------AGTGAACTA---------------------GGAA--A-----AA-AA-----------------------------------ACT-------ATAAATATT----A---CTACCTCTCAGTCAAAAATTTTATTGGTCTTAGG--T---------------------------AGCCATAAATATCCGTTATTATAT------------------------------------AGAACTAATCTATATAT----T-----------CAGTAGTAGTG-TTAT------AGATGTTCTTTTAATTTTATAAATTTTTAATAGAAACAT--------------------GATTTTGTG
droEle1	scf7180000491280:3827293-3827485 +		AGCAGCAGCAGCAGCAGCAACAAC------------A------AC---TGAAA---CAGCAAC---AACAACA---ACTGGTGAGTG-------------CC--ATGG-ATGATG---------------------------------------GAAAATT--------TTCCATACACAAAACT------------------CAATTGATCGCA------AGTGAACTA---------------------GGAA--A-----AAAAGAC--ACAAACA-A----------------------ACA-------ATA----------AAATCTAGATCTCAGTCCAAAACTGTATT---------CTATAATTT------G----------------CAATAA--------------------------------------------------------ACAGACTA----T----------------------------------------------------------------------------------------------------------
droRho1	scf7180000779538:73366-73632 +		AACATCAGCAGCAGCAGCAGCAAC------------A------AC---TGAAA---CAGCAAC---AACAACA---ACTGGTGAGTG-------------CC--GTGG-ATGATG---------------------------------------GAAAATT--------TTCCAAATATAAAACT------------------CAATTAATCTCA------AGTGAACTA---------------------GAAA--A-----AAAAGAC--ACAA-------------------------------------CTAAATATA----A---CTAGACCCCAGTCAACAATTTTATTGGTCCAATTCCATCATTT------T----------------CAATGG---------------------ACAGACTATAAATAACTAGCTACTACTTTAGG------ATATATATAT----T-----------T---AA------------TATTAT-TTATC----------ATTTGTTTTAAA------TT-----------------------TTATATA
droFic1	scf7180000453581:468890-469156 +		GGCAGCAGCAACAACCAC------------------------------TGAAG---CAGCAACAACAACAACA---ACTGGTAAGTG-------------CC--ATGC-ATGATG---------------------------------------GAAAATT--------TTCCATACA-AAAACT------------------CAATTAATCTCA------AGTGAAATA---------------------GTCAAAA-----AAAAGAT--ACGAATT-G----------------------ACG-------ATAAATATA----G---ATAGCTCTCGGTCAACAAATTTATTGGATGTT-G--TT----T------T----------------CAATTATT------TATTGCATAGTGCTCAG---T----------------------TA-AATCATTCTA----TTTTTAAAATGGATATCT---AG------------TGTTGT-TATTC----------ATT-----TTG---GAAATAGGA----------------------TTCAG
droKik1	scf7180000301810:202224-202366 -		A-CAGCAGCAAAAACCGAAGCAAC------------A------AA---AGAAG---CCGCTGC---AGCCTGAGACAATCGAGAAGG-------------CGCCGGAG-AGCATA---------------------------------------AACAAGT---------------------ACG------------------AGATGAAATTTT------C-TGAAGTG---------------------GTAA--AGGGGCAAGAA-----------------------------------AAG-----------------------------------------ACC-------------------------------------------------------------------------------------------------------------------A----C-------------------------------------------------------------------------------TTCCGAAATG----------AATATGA
droAna3	scaffold_13266:10713888-10714029 +		AACAGCAGCAATTACAGCAACAAC------------A------GTTATTGCAA---CAGCAAC---AGCAACA---GC-----AGCG-------------CCC-TGGCAACGAGGAG-------------------------------------GAGGACT---------ACCTGACC-----------------------------GATTCCGA------TGTTGACGA---------------------GGAC--G-----AAGAG-----------------------------------CCA-------CTGGACATG---------------TGGGCCTG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CA-----------------------ACTTGTG
droBip1	scf7180000395839:161149-161358 -		AGCAACATCAGCAACACCAGCAGG------------C------C-----CAGA---CCATGTT---AGC-----------CGGACAGCTGCAGAGCAGTGTTC-ATG------TG---------------------------------------GTGAGTT--------TTT-GTTT---TAAAT------------------TTTTTAATCTTA--------TAGTTTA---------------------GGGA--C-----TA-TG-----------------------------------ACTAACTAA-------------GAGA------ATTAAATCA-AAAGTTAGTTGATAATATT--TTCATAT--------------------------TTATT------TAT----------------------------------------AAATA-AACCCTA----CTTTTA--------------------------A----GTAC-TTTTA----------GTAAGAAA---------------------------------------TTA
dp5	2:12636874-12637040 -		AACAACAACAACAACAACTGTAATTGCAACTGCAACA------GC---AGCGG---CCACAAC---AACAACA---GCTCCAGATAGCTG----------CAGC------AGCAA---------------------------------------GAACATATTACAATATAT-A------------T-TTTATTTTTTTAATTTAATT-ATTTAA------AGTAAACAA---------------------AGAG--A-----AACAA-----------------------------------A-----------------------------------------AATGC-AAGC------------------------------------------GATA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTATTT
droPer2	scaffold_27:1032040-1032151 +		AACGACAGCAACGACAACAGCAAC------------A------GC---AA------CAGAAGA---AATGGTA---AATGA-AAGTG-------------CCC--TCA-A---------------------------------------------AAGGTT--------TTCTAAATTTGTGACT------------------CG---------A------AGTGCGC---------------------------------------------------------------------------------------------------------------GACCAGCAACT-GA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAAGAG
droWil2	scf2_1100000004822:2706561-2706776 +		TACAGCCACAGCAACTACACAGAAATC---------AACAACAGC---CAACACAAATTCAAC---TTCCACA---ACAGGTCAGTA-------------ACA--AG-----ATG---------------------------------------AACA-TT----------T-ATAG---TAAATTA-TATAAG---------CAATGGATCTAATGATTGTGAGAACTAAGGGAAATACCACCATAGGGT---------------TCTCC-TCATAT-GA----------------------ACC-------CCAGAAGTG----G---ACAACTCTAAGGATTTAAATGAA----------T--TTTAAAT------G----------------CATGAA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTT
droVir3	scaffold_13049:19213981-19214205 -		CACAGTAGCAATAGTAGCAGTAGC------------T------AT---CTAAC---GAGCAGT---CGCTCCA---ACTCGTAAGGC-------------CC--TTGG--GGTTA---------------------------------------GTCTATA--------TAGTACACT--CAACA------------------AAATTGCCTTAT------CCAAAATTTAGTAAA--ATC----------GTCA--A-----AA-AA-ATTACAA--AATTCCTTATATTTACGAGAGGTTTTTTAATGAA-----------------------------------AAATATGACCTTATAAG--TTTAAAG------G----------------AAATATTT------TCT----------------------------------------ATAT-ATAGTCTT----TT---------------------------------------------------------------------------------------------------TTTTTT
droMoj3	scaffold_6496:9992863-9993022 -		AGCAGCAACAGCAGCAGCAGCAGC------------A------AC---AGCAG---CCCCAGC---AGCAGCA---ATT--TCAACG-------------CCAATTGC-AGCCTC---------------------------------------CAAGACT--------TCGCGTGAG--TGCCA------------------AAGCAGAGTTAG------ACTGCTATA---------------------G--------------AG-----------------------------------TCT-------ATAGAC---TGTGGTAGTTATCTATTAGCCAGCATGC-AAGT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATTG
droGri2	scaffold_15203:746590-746770 -		AATTGCAGTAATCGCAAAAGCAGC------------A------TC---AGCAG---CAACAAA---GACAAAA---ACAAAGAGATG-------------CAAACGAA-TGGAGGAGGCAAAAGCAATTGGAAGGTAAGTAATTATTGTACGAATAG-CTAATAAAATACAT-G------------CACACATTGTTGC------------------------------------------------------------------------------------------------------------------------------------AAGCTAATTGTC---------AGTGATTGTACA--ATGATGT------G----------------CAATAATT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droSim2

CACAGCAGCAGTAGCAGCGGCAAC------------A------AC---TGATA---CCGCAGC---AACAACC---ACTGGTGAGTG-------------CCCCTTGG-AGGATG---------------------------------------GAAAATT--------TTCCATACT--TAACT------------------CAATTGATCTGA------AGTGAACTG---------------------GGGA--A-----AAGAG-----------------------------------ACT-------ATAAATATATATGACAGCTAGTTGTGAGCCAAAAAACTAAGTGGTTGTATG--TTTACAT------G----------------CAATAATT------TAT----------------------------------------GAGTAGCAATCTA----TTTTTA--------------------------TTATGCTGT-TTTTC----------ATAAAATATTAA------AA-----------------------CGATGCG	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
..CAGCAGCAGTAGCAGCGGCA...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	5	0.20	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droSec2

CGCAGCAGCAGTAGCAGCAGCAAC------------A------AC---TGAAA---CCGCAAC---AACAACC---ACTGGTGAGTG-------------CCCCTTCG-AGGATG---------------------------------------GAAAATT--------TTCCATACT--TAACT------------------CAATTAATCTGA------AGTGAACTG---------------------GGGA--A-----AAGAG-----------------------------------ACT-------ATAAATATG----ACAGCTAATTGTGAGCCAAAAAACTAAGTGGTTGTATG--TTTACAT------G----------------CAATAATT------TAT----------------------------------------GAGTAGCAATCTA----TTTTTA--------------------------TTATGCTGT-TTTTC----------ATAAAATATTAA------AA-----------------------CGATGCG	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
......AGCAGTAGCAGCAGCAAC------------A------AC---TGA..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	24	1	1.00	1	0	0	1	0
..........GTAGCAGCAGCAAC------------A------AC---TG...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	1	0	0	1	0

dm3

CGCAGCAGCAGTACCAGCAGCAAC------------A------AC---TGAAA---CCGCAAC---AACAACC---ACTGGTGAGTG-------------CCCCTTGG-AGGATG---------------------------------------GAAAATT--------TTCTATACT--TAACT------------------CAATTGATCTGA------AGTGAACTG---------------------GGGA--A-----AGTAA-----------------------------------ACT-------ATAAATATA----A---C-------------------TAAGTGGTTGTATG--TTTACAT------G----------------CAAAAATT------TAT----------------------------------------GAATAGCAATCTA----TTTTTA--------------------------TTATGCTGT-TTTTC----------ATCAAACATTAT------CA-----------------------CAATGCG	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
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................GCAGCAAC------------A------AC---TGAAA---CCGC.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
......................AC------------A------AC---TGAAA---CCGCAAC---AACAAC.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	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	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
....................................................A---CCGCAAC---AACAACC---ACTC.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	2	0.50	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	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

droEre2

AGCAGCAGAAGTAGCAGCAGCAAC------------A------AC---TGAAA---CCGCAACAACAACAACA---ACTGGTGAGTG-------------CTCCTTGG-A----G---------------------------------------GAAAACT--------TTGCGTACT--TAACT------------------CAATTGATCTCA------AGTGAACTG---------------------GGGA--A-----ACGAC-----------------------------------ACT-------ATAGATATT----ACTACCAGTTGTGAGTCAAAAAATTAAGTGCTTGTA-----------------G----------------TAATAGTT------TAT----------------------------------------GAAAAGCAATCTA----TTTTTA--------------------------TTATGCTGAATTTTC----------ATAAAATACTAA------CA-----------------------TGATGCG	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
....GCAGAAGTAGCAGCAGCAAC------------A------......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	1	0	0
...............AGCAGCAAC------------A------AC---TGAAA---CCGCAAC..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	24	1	1.00	1	0	1	0	0	0	0	0
....GCAGAAGTAGCAGCAGCAAC------------A------AC---TGA..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	26	1	1.00	1	0	0	0	0	1	0	0
....GCAGAAGTAGCAGCAGCAAC------------.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	0	0	0	1	0	0
AGCAGCAGAAGTAGCAGC...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	5	0.20	1	0	1	0	0	0	0	0

droYak3

CACAGCAGCAGCAGCGGCAGTAGCAGCAGCAGCAACA------AC---TGAAA---CCGCAAC---AACAACA---ACTGGTGAGTG-------------CCCCATGG-AGAATG---------------------------------------GAAAACT--------TTCCGTACT--TAACT------------------TAATTGATCTCA------AGTGAACT------------------------------------------------------------------------------------ATAAATATA----ACTGCTAGTTGTGAGCCAAAAAATTAAGTGGT---ATG--TTTACAT------T----------------CAATAATT------TAT----------------------------------------GA-AAGCAATCTA----TTTTTA--------------------------TTATGCTATATTTTC----------ATAAAATATGTA------CA-----------------------TCTTGCG	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
.......GCAGCAGCGGCAGTAGCAGCA.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	2.00	2	0	0	0	0	0	0	2	0	0	0	0
..........................................................................................................GG-AGAATG---------------------------------------GAAAACT--------TTC.....................................................................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0
......AGCAGCAGCGGCAGTAGCAGC......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0
.............GCGGCAGTAGCAGCAGCAGCAACA------......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	24	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
..........................CAGCAGCAACA------AC---TGAAA---CCGCAAC---...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1
.....CAGCAGCAGCGGCAGTAGCAGCA.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
.................................AACA------AC---TGAAA---CCGCAAC---AACAACA---ACTG.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	29	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0
.........................GCAGCAGCAACA------AC---TGAAA---CC.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0
.....................................................................AACA---ACTGGTGAGTG-------------CCCCATGG-A...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	24	1	1.00	1	0	0	0	1	0	0	0	0	0	0	0
........CAGCAGCGGCAGTAGCAGCA.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................GCAGCAACA------AC---TGAAA---CCGCAAC---...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0
............................GCAGCAACA------AC---TGAAA---CCGCAAC---AA.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
.................................................GAAA---CCGCAAC---AACAACA---ACTGT................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
.......GCAGCAGCGGCAGTAGCAGCAGCAGC................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	26	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0
............................GCAGCAACA------AC---TGAAA---CCGC.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
...........CAGCGGCAGTAGCAGCAGCAG.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
..........GCAGCGGCAGTAGCAGCAGCAGC................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0
...AGCAGCAGCAGCGGCAGTAGC.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	5	0.40	2	0	1	0	0	0	0	1	0	0	0	0
..CAGCAGCAGCAGCGGCAGTAGCA........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	23	3	0.33	1	0	0	0	0	0	0	1	0	0	0	0

droEug1

AGCACCTCCACCAGCAGCTCCAAC------------A------AC---TGAAA---CAGCAACCACAACAACA---ACTGGTGAGTG-------------CC--GTGG-ATGAAA---------------------------------------GGAAATT--------TTCCATACA--AAACT------------------CAATTAATCTTA------AGTGAAGTA---------------------GGAA--A-----GA-AG-----------------------------------ACTAAAAGCCATAAATATA----G---CTAGA-------------------TAGTTATAGT--TATTAATAATATAGTTATTAATTTGAGTATTCACAAATATCACTTAAAAT-------------------------------------CT-AAGCATATAT----TTTTTA--------------------------TTACACAAAATGTTCTTAAAATTCCATAGTATGTTAATGGA--AAGACTGCCAAA-AA----------ACTTGTA	Size	Hit Count	Total Norm	Total
No Reads

droBia1

CGCAGCGGCAACATCAGCGGCAGC------------A---ACAAC---CGAAC---CAGCAGC---AACAACA---ATTGGTGAGTG-------------CCC-GTGG-TTGATG---------------------------------------GAAAATT--------TTCCATACA--CAACT------------------CAATTAATCTCA------AGTAAACTA---------------------GGGA--A-----AA-AGACCTACAC--AAA----------------------ACC-------AGAAATATA----A---CTAGCTCTCAGTCAAAAAGTATAGTGAATGTGG----------------G----------------CCATAAAT------T-T----------------------------------------GGATATCAATATA----TTTGTC------------GGCGGTATTATTTAT------AGATGTTTTTGAATTTGCGTAACATATTGGTAAA--GGGGCTGC-AAA-AAACATATATTATTTTTTG	Size	Hit Count	Total Norm	Total
No Reads

droTak1

CGCAACACCAACAACATCGGCAGC------------AGCAGCAAC---TGAAA---CAGCAAC---AACAACA---ACTGGTGAGTG-------------CCC-ATGG-ATGATG---------------------------------------GAAAATT--------TTCCATACA--AAACT------------------CAATTAATCTCA------AGTGAACTA---------------------GGAA--A-----AA-AA-----------------------------------ACT-------ATAAATATT----A---CTACCTCTCAGTCAAAAATTTTATTGGTCTTAGG--T---------------------------AGCCATAAATATCCGTTATTATAT------------------------------------AGAACTAATCTATATAT----T-----------CAGTAGTAGTG-TTAT------AGATGTTCTTTTAATTTTATAAATTTTTAATAGAAACAT--------------------GATTTTGTG	Size	Hit Count	Total Norm	Total
No Reads

droEle1

AGCAGCAGCAGCAGCAGCAACAAC------------A------AC---TGAAA---CAGCAAC---AACAACA---ACTGGTGAGTG-------------CC--ATGG-ATGATG---------------------------------------GAAAATT--------TTCCATACACAAAACT------------------CAATTGATCGCA------AGTGAACTA---------------------GGAA--A-----AAAAGAC--ACAAACA-A----------------------ACA-------ATA----------AAATCTAGATCTCAGTCCAAAACTGTATT---------CTATAATTT------G----------------CAATAA--------------------------------------------------------ACAGACTA----T----------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droRho1

AACATCAGCAGCAGCAGCAGCAAC------------A------AC---TGAAA---CAGCAAC---AACAACA---ACTGGTGAGTG-------------CC--GTGG-ATGATG---------------------------------------GAAAATT--------TTCCAAATATAAAACT------------------CAATTAATCTCA------AGTGAACTA---------------------GAAA--A-----AAAAGAC--ACAA-------------------------------------CTAAATATA----A---CTAGACCCCAGTCAACAATTTTATTGGTCCAATTCCATCATTT------T----------------CAATGG---------------------ACAGACTATAAATAACTAGCTACTACTTTAGG------ATATATATAT----T-----------T---AA------------TATTAT-TTATC----------ATTTGTTTTAAA------TT-----------------------TTATATA	Size	Hit Count	Total Norm	Total
No Reads

droFic1

GGCAGCAGCAACAACCAC------------------------------TGAAG---CAGCAACAACAACAACA---ACTGGTAAGTG-------------CC--ATGC-ATGATG---------------------------------------GAAAATT--------TTCCATACA-AAAACT------------------CAATTAATCTCA------AGTGAAATA---------------------GTCAAAA-----AAAAGAT--ACGAATT-G----------------------ACG-------ATAAATATA----G---ATAGCTCTCGGTCAACAAATTTATTGGATGTT-G--TT----T------T----------------CAATTATT------TATTGCATAGTGCTCAG---T----------------------TA-AATCATTCTA----TTTTTAAAATGGATATCT---AG------------TGTTGT-TATTC----------ATT-----TTG---GAAATAGGA----------------------TTCAG	Size	Hit Count	Total Norm	Total
No Reads

droKik1

A-CAGCAGCAAAAACCGAAGCAAC------------A------AA---AGAAG---CCGCTGC---AGCCTGAGACAATCGAGAAGG-------------CGCCGGAG-AGCATA---------------------------------------AACAAGT---------------------ACG------------------AGATGAAATTTT------C-TGAAGTG---------------------GTAA--AGGGGCAAGAA-----------------------------------AAG-----------------------------------------ACC-------------------------------------------------------------------------------------------------------------------A----C-------------------------------------------------------------------------------TTCCGAAATG----------AATATGA	Size	Hit Count	Total Norm	Total
No Reads

droAna3

AACAGCAGCAATTACAGCAACAAC------------A------GTTATTGCAA---CAGCAAC---AGCAACA---GC-----AGCG-------------CCC-TGGCAACGAGGAG-------------------------------------GAGGACT---------ACCTGACC-----------------------------GATTCCGA------TGTTGACGA---------------------GGAC--G-----AAGAG-----------------------------------CCA-------CTGGACATG---------------TGGGCCTG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CA-----------------------ACTTGTG	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
...............................................................................................................................................................CT---------ACCTGACC-----------------------------GATTCCGA------TGT.................................................................................................................................................................................................................................................................................................................................................................	21	1	2.00	2	0	0	1	0	0	1
.................................................................................................................................................................................................................................GACGA---------------------GGAC--G-----AAGAG-----------------------------------CCA-------CTGGACA.................................................................................................................................................................................................................................................................	25	1	1.00	1	1	0	0	0	0	0
....................................................................................................................................................................................................................CGA------TGTTGACGA---------------------GGAC--G-----AAGAG-----------------------------------C.................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	1
...............................................................................................................................................................CT---------ACCTGACC-----------------------------GATTCCGA------TGTTG...............................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	1	0	0	0	0	0
...................................................................................................................................................................................................................................CGA---------------------GGAC--G-----AAGAG-----------------------------------CCA-------CTGGACA.................................................................................................................................................................................................................................................................	23	1	1.00	1	1	0	0	0	0	0
......................................................................................G-------------CCC-TGGCAACGAGGAG-------------------------------------GAG....................................................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	0	0	0	1	0
..........................................................................................................................................................................ACCTGACC-----------------------------GATTCCGA------TGTT................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0
.................................................................................................................................................................................................................................GACGA---------------------GGAC--G-----AAGAG-----------------------------------CCA-------CTGGAC..................................................................................................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	1	0
..............................................................................................................................................................................GACC-----------------------------GATTCCGA------TGTTGACGA---------------------GGAC--................................................................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	1	0	0	0	0
.................................................................................................................................................................................................................................................................G-----AAGAG-----------------------------------CCA-------CTGGACATG---------------TGGGCCC.........................................................................................................................................................................................................................................	25	1	1.00	1	0	1	0	0	0	0
.........................................................................................................GGCAACGAGGAG-------------------------------------GAGGACT---------ACC....................................................................................................................................................................................................................................................................................................................................................................................................................	22	1	1.00	1	0	0	0	0	0	1
...............................................................................................................................................................CT---------ACCTGACC-----------------------------GATTCCGA------TGTT................................................................................................................................................................................................................................................................................................................................................................	22	1	1.00	1	0	0	0	0	0	1
...................................................................................................................................................................................................................................CGA---------------------GGAC--G-----AAGAG-----------------------------------CCA-------CTGGAC..................................................................................................................................................................................................................................................................	22	1	1.00	1	0	1	0	0	0	0
............................................................AAC---AGCAACA---GC-----AGCG-------------CCC-.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	1	0	0	0	0	0	1
.............................................................................................................ACGAGGAG-------------------------------------GAGGACT---------ACCT...................................................................................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	1	0	0	0	0	0	1
................................................................................................................................................................................................................................TGACGA---------------------GGAC--G-----AAGAG-----------------------------------CCA-------CT......................................................................................................................................................................................................................................................................	21	1	1.00	1	1	0	0	0	0	0
..............................................................................................................................................................ACT---------ACCTGACC-----------------------------GATTCCGA------TGTTG...............................................................................................................................................................................................................................................................................................................................................................	24	1	1.00	1	1	0	0	0	0	0
........................................................................A---GC-----AGCG-------------CCC-TGGCAACGAGGAG-------------------------------------G......................................................................................................................................................................................................................................................................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	1
..........................................................GCAAC---AGCAACA---GC-----AGCG-------------CCC-TG.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0
...........................................................................................................CAACGAGGAG-------------------------------------GAGGACT---------ACCT...................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	1	0
.........................................................AGCAAC---AGCAACA---GC-----AGCG-------------CC...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	2	0.50	1	0	1	0	0	0	0
.................................................GCAA---CAGCAAC---AGCAACA---GC-----AGC...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	23	20	0.10	2	0	2	0	0	0	0

droBip1

AGCAACATCAGCAACACCAGCAGG------------C------C-----CAGA---CCATGTT---AGC-----------CGGACAGCTGCAGAGCAGTGTTC-ATG------TG---------------------------------------GTGAGTT--------TTT-GTTT---TAAAT------------------TTTTTAATCTTA--------TAGTTTA---------------------GGGA--C-----TA-TG-----------------------------------ACTAACTAA-------------GAGA------ATTAAATCA-AAAGTTAGTTGATAATATT--TTCATAT--------------------------TTATT------TAT----------------------------------------AAATA-AACCCTA----CTTTTA--------------------------A----GTAC-TTTTA----------GTAAGAAA---------------------------------------TTA	Size	Hit Count	Total Norm	Total
No Reads

dp5

AACAACAACAACAACAACTGTAATTGCAACTGCAACA------GC---AGCGG---CCACAAC---AACAACA---GCTCCAGATAGCTG----------CAGC------AGCAA---------------------------------------GAACATATTACAATATAT-A------------T-TTTATTTTTTTAATTTAATT-ATTTAA------AGTAAACAA---------------------AGAG--A-----AACAA-----------------------------------A-----------------------------------------AATGC-AAGC------------------------------------------GATA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTATTT	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
...............................GCAACA------GC---AGCGG---CCACAAC---...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	1	2.00	2	0	1	1	0	0	0	0	0	0	0
..........................................................ACAAC---AACAACA---GCTCCAGATAGC.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	24	1	2.00	2	0	2	0	0	0	0	0	0	0	0
...................................................GG---CCACAAC---AACAACA---GCTCCA...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	22	1	2.00	2	0	2	0	0	0	0	0	0	0	0
..............................................................................................................................................................................................................................GTAAACAA---------------------AGAG--A-----AACAA-----------------------------------A-----------------------------------------A.......................................................................................................................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0	0	0	0	0
AACAACAACAACAACAACTGTAAT.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	24	1	1.00	1	0	0	1	0	0	0	0	0	0	0
.............................................................................CTCCAGATAGCTG----------CAGC------AGCA...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	1	0	0	0	0	0	0	0	0
..............................................................................TCCAGATAGCTG----------CAGC------AGCAA---------------------------------------GAAC...................................................................................................................................................................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	0	0	0	1	0	0	0	0	0
.....................................................................................................................................................................................................................................A---------------------AGAG--A-----AACAA-----------------------------------A-----------------------------------------AATGC-AAGC------------------------------------------GATA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATT....	28	1	1.00	1	0	0	0	0	1	0	0	0	0	0
........CAACAACAACTGTAATTGCAACT..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0	0	0	0	0
....ACAACAACAACAACTGTAATTGCAACC..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	27	1	1.00	1	0	0	1	0	0	0	0	0	0	0
....ACAACAACAACAACTGTAATTGCAACT..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	27	1	1.00	1	0	1	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................ACAA---------------------AGAG--A-----AACAA-----------------------------------A-----------------------------------------AATGC-AAGC------------------------------------------GAT.................................................................................................................................................................................	27	1	1.00	1	0	1	0	0	0	0	0	0	0	0
..CAACAACAACAACAACTGTAATT........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	1	0	0	0	0	0	0	0
...............................................................................CCAGATAGCTG----------CAGC------AGCAA---------------------------------------GAACAT.................................................................................................................................................................................................................................................................................................................................................................................................................................	26	1	1.00	1	0	1	0	0	0	0	0	0	0	0
........................................................................................................................................................................................................................................................................ACAA-----------------------------------A-----------------------------------------AATGC-AAGC------------------------------------------GATA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------.......	18	1	1.00	1	0	0	0	0	1	0	0	0	0	0
.............................................................................................................................................................................................................ATT-ATTTAA------AGTAAACAA---------------------AGAG--A-----..........................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	1	0	0	0	0	0	0	0
...AACAACAACAACAACTGTAATTGCA.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.............................................................................................................................................................................................................................................................AG--A-----AACAA-----------------------------------A-----------------------------------------AATGC-AAGC------------------------------------------GA..................................................................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0	0	0	0	0
..............................................................................................................................................................................................................................GTAAACAA---------------------AGAG--A-----AACAA-----------------------------------A-----------------------------------------AATGC-..................................................................................................................................................................................................................................	24	1	1.00	1	0	1	0	0	0	0	0	0	0	0
............................................................AAC---AACAACA---GCTCCAGATAGCTG----------CAGC------...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	28	1	1.00	1	0	1	0	0	0	0	0	0	0	0
..................................................................AACAACA---GCTCCAGATAGCTG----------CAGC------A..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	26	1	1.00	1	0	1	0	0	0	0	0	0	0	0
................................CAACA------GC---AGCGG---CCACAAC---...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	1	0	1	0	0	0	0	0	0	0	0
AACAACAACAACAACAACTGTA...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	22	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.................................................GCGG---CCACAAC---AACAACA---GCT..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	1	0	0	0	0	0	0	0
.ACAACAACAACAACAACTGTA...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	1	0	0	0	0	0	0	0	0
...........................................................CAAC---AACAACA---GCTCCAGATAGC.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0	0	0	0	0
....ACAACAACAACAACTGTAATTGC......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	1	0	0	0	0	0	0	0
.....................AATTGCAACTGCAACA------GC---AGCGG---CC.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	1	0	0	0	0	0	0	0	0
............................................................................GCTCCAGATAGCTG----------CAGC------AGCAA---------------------------------------GAACA..................................................................................................................................................................................................................................................................................................................................................................................................................................	28	1	1.00	1	0	1	0	0	0	0	0	0	0	0
................................................................................................................................................................................................................................AAACAA---------------------AGAG--A-----AACAA-----------------------------------A-----------------------------------------AATGC-AAGC------------------------------------------....................................................................................................................................................................................	26	1	1.00	1	0	1	0	0	0	0	0	0	0	0
..............................................................................................................................................................................................................................GTAAACAA---------------------AGAG--A-----AACAA-----------------------------------A-----------------------------------------AATGC-AAGC------------------------------------------....................................................................................................................................................................................	28	1	1.00	1	0	0	1	0	0	0	0	0	0	0
............................ACTGCAACA------GC---AGCGG---CCA......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.......ACAACAACAACTGTAATTGCAACT..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	24	1	1.00	1	0	1	0	0	0	0	0	0	0	0
............................................................................................................................................................................................................................................................GAG--A-----AACAA-----------------------------------A-----------------------------------------AATGC-AAGC------------------------------------------GATA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------.......	23	1	1.00	1	0	1	0	0	0	0	0	0	0	0
....ACAACAACAACAACTGTAATTGCAAC...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	26	1	1.00	1	0	0	1	0	0	0	0	0	0	0
.............................................................................CTCCAGATAGCTG----------CAGC------AGC................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	0	1	0	0	0	0	0	0	0
.............................................................................CTCCAGATAGCTG----------CAGC------AGCAA---------------------------------------G......................................................................................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	1	0	0	0	0	0
...................GTAATTGCAACTGCAACA------GC---.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.........................GCAACTGCAACA------GC---AGCGG---C........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	2	0.50	1	0	1	0	0	0	0	0	0	0	0
......................ATTGCAACTGCAACA------GC---AGC..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	2	0.50	1	0	1	0	0	0	0	0	0	0	0
AACAACAACAACAACAACTGT............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	4	0.25	1	0	1	0	0	0	0	0	0	0	0
AACAACAACAACAACAACTG.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	20	0.05	1	0	1	0	0	0	0	0	0	0	0

droPer2

AACGACAGCAACGACAACAGCAAC------------A------GC---AA------CAGAAGA---AATGGTA---AATGA-AAGTG-------------CCC--TCA-A---------------------------------------------AAGGTT--------TTCTAAATTTGTGACT------------------CG---------A------AGTGCGC---------------------------------------------------------------------------------------------------------------GACCAGCAACT-GA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAAGAG	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
No Reads

droWil2

TACAGCCACAGCAACTACACAGAAATC---------AACAACAGC---CAACACAAATTCAAC---TTCCACA---ACAGGTCAGTA-------------ACA--AG-----ATG---------------------------------------AACA-TT----------T-ATAG---TAAATTA-TATAAG---------CAATGGATCTAATGATTGTGAGAACTAAGGGAAATACCACCATAGGGT---------------TCTCC-TCATAT-GA----------------------ACC-------CCAGAAGTG----G---ACAACTCTAAGGATTTAAATGAA----------T--TTTAAAT------G----------------CATGAA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTT	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
No Reads

droVir3

CACAGTAGCAATAGTAGCAGTAGC------------T------AT---CTAAC---GAGCAGT---CGCTCCA---ACTCGTAAGGC-------------CC--TTGG--GGTTA---------------------------------------GTCTATA--------TAGTACACT--CAACA------------------AAATTGCCTTAT------CCAAAATTTAGTAAA--ATC----------GTCA--A-----AA-AA-ATTACAA--AATTCCTTATATTTACGAGAGGTTTTTTAATGAA-----------------------------------AAATATGACCTTATAAG--TTTAAAG------G----------------AAATATTT------TCT----------------------------------------ATAT-ATAGTCTT----TT---------------------------------------------------------------------------------------------------TTTTTT

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

AGCAGCAACAGCAGCAGCAGCAGC------------A------AC---AGCAG---CCCCAGC---AGCAGCA---ATT--TCAACG-------------CCAATTGC-AGCCTC---------------------------------------CAAGACT--------TCGCGTGAG--TGCCA------------------AAGCAGAGTTAG------ACTGCTATA---------------------G--------------AG-----------------------------------TCT-------ATAGAC---TGTGGTAGTTATCTATTAGCCAGCATGC-AAGT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATTG	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
...AGCAACAGCAGCAGCAGCAGC------------A------AC---AGC..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	27	20	0.05	1	1	0	0	0	0	0

droGri2

AATTGCAGTAATCGCAAAAGCAGC------------A------TC---AGCAG---CAACAAA---GACAAAA---ACAAAGAGATG-------------CAAACGAA-TGGAGGAGGCAAAAGCAATTGGAAGGTAAGTAATTATTGTACGAATAG-CTAATAAAATACAT-G------------CACACATTGTTGC------------------------------------------------------------------------------------------------------------------------------------AAGCTAATTGTC---------AGTGATTGTACA--ATGATGT------G----------------CAATAATT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

dsi_22599

3r:23529388-23529537 -

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