dsi_20479

Name	Class	Family	Strand
Gypsy8-I_Dpse-int	LTR	Gypsy	+
TART_DV	LINE	Jockey	+
AT_rich	Low_complexity	Low_complexity	+

GAGCAATTGTTGCTGGCGCGTCGCAGCCGCAGCAGCAACATCAACCAAAGGTAAGACCAGTGATGAGAAAGGTAACATTTAGTTCAATCTGTATCTTTTTCCAAAAGTAATTCCTAAGTATCAAAAAACATAATTTTAAAATTTATTTAAGTCAATTTGCTTCTTAAATCACTATTAAGGATATTGTGAAAGTATGCTGGCCAAATGTTGTATCTATTTGTAGAGCCTTTAAATTGTTCCAAAATTATAA ************************************************........((((((((((((((((.....(((......)))))))))))))...((((((....((((((.......................)))))).......)))))).....))))))....((.(((((.....))))).))..************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M024 male body	SRR553488 RT_0-2 hours eggs	SRR618934 dsim w501 ovaries	SRR553485 Chicharo_3 day-old ovaries
................................................................................................................................................................................AAGGATATTGTGAAAGTATGCTGGCC................................................	26	0	1	1.00	1	1	0	0	0
.............................................................................................................................TGACATAATTTTGAAATTTATTTA.....................................................................................................	24	3	5	0.20	1	0	1	0	0
......................................................GACTAGTGATGAGAATG...................................................................................................................................................................................	17	2	11	0.09	1	0	0	1	0
.............................................................................................................................................................................ATTAAGAATATTGTGA.............................................................	16	1	14	0.07	1	0	0	0	1

CTCGTTAACAACGACCGCGCAGCGTCGGCGTCGTCGTTGTAGTTGGTTTCCATTCTGGTCACTACTCTTTCCATTGTAAATCAAGTTAGACATAGAAAAAGGTTTTCATTAAGGATTCATAGTTTTTTGTATTAAAATTTTAAATAAATTCAGTTAAACGAAGAATTTAGTGATAATTCCTATAACACTTTCATACGACCGGTTTACAACATAGATAAACATCTCGGAAATTTAACAAGGTTTTAATATT ************************************************........((((((((((((((((.....(((......)))))))))))))...((((((....((((((.......................)))))).......)))))).....))))))....((.(((((.....))))).))..************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	SRR553486 Makindu_3 day-old ovaries	SRR618934 dsim w501 ovaries	O002 Head	SRR553487 NRT_0-2 hours eggs	SRR553485 Chicharo_3 day-old ovaries	SRR553488 RT_0-2 hours eggs	SRR902009 testis
..................................CGTTGTAGTTGGTTTCCATTCTGGT...............................................................................................................................................................................................	25	0	1	2.00	2	2	0	0	0	0	0	0
.......................................TAGATGGTTTCCATTC...................................................................................................................................................................................................	16	1	1	1.00	1	0	1	0	0	0	0	0
......................................................................................................................................................................TTAGTGATAATTCCTATA..................................................................	18	0	1	1.00	1	0	0	1	0	0	0	0
......................................................................CCAGTGTAAATCAAGTGAG.................................................................................................................................................................	19	2	2	0.50	1	0	0	0	1	0	0	0
..................................................................................................................................................AATTCAGTTAAGCGAAAAGTTTA.................................................................................	23	3	7	0.14	1	0	0	0	0	1	0	0
...................................................................................................AGGTTTTCGTTAAGGA.......................................................................................................................................	16	1	8	0.13	1	0	0	0	0	0	1	0
.....................................................................................TTAGACGTACAAAAAGGTT..................................................................................................................................................	19	2	13	0.08	1	0	0	0	1	0	0	0
.......................................................................................................................................................................................AACAGTTTCATACGA....................................................	15	1	13	0.08	1	1	0	0	0	0	0	0
.........................CGGCGTCGTTGTTGTAGTTCG............................................................................................................................................................................................................	21	2	18	0.06	1	0	1	0	0	0	0	0
...............................................................................................AAAAAGGGTTTCGTTGAGGA.......................................................................................................................................	20	3	20	0.05	1	0	0	0	0	0	0	1

Re-alignment of all predicted orthologs

Species	Coordinate	ID	Alignment
droSim2	2r:14662411-14662660 +	dsi_20479	GAGCAATTGT----------TGCTGGCGCGTCGCAGCCGCAGCAGCAA---------CATCAACC---AAAGGTAAGACCAGTGATGAGAAA---------GGTAACATTTAGTTCAATCTGTATCTTTTTCCAAA--------------------------------------------------------------------AGTAA---------------------------------------------------------------------------------------------------------------------------------------------------TTCCTAAG------------------------TA---TCAAAAA-----------ACATAATTTTAAAATTTATTTAAGTCAATTTGC--------------------TTC--------TT-----AA------ATCACTATTAAGGATATTGTGAAAGTATGCTGGCCAA------------------------------------------------------------ATGTTGTATCTATTTGTAG---AGC-CTTTAAA----------------------------TTGTTC-CAAAA--------------TTA----------------T-----------------------------AA
droSec2	scaffold_1:11471807-11472047 +		GAGCAATTAT----------TGCTGGCGCGTCGCAGCCGCAGCAGCAA---------CATCAACC---AAAGGTAAGACCAGTGATGAGAAA---------GGTAACATTTAGTTTAATCTGTATCTTTTTCCAAA--------------------------------------------------------------------AGTAA---------------------------------------------------------------------------------------------------------------------------------------------------TGCCTAAG------------------------TA---TTAAAAA-----------ACATAATTTTAAAATTTAGTTAAGTCAATTTGC--------------------TTC--------TG-----AGAC--ATATCGCTCTTAAGGATGTTTTG-------------AAA------------------------------------------------------------ATGTTGTATCTATTTGTAG---AGC-CTTTGAA----------------------------TTGTTC-CAAAA--------------ATA----------------T-----------------------------TA
dm3	chr2R:13978121-13978360 +		GAGCAATTGT----------TGCTGGAGCGTCGCAGCCGCAGCAGCAA---------CATCAACC---AAAGGTAAGACCAGTGATGAGAAA---------GGTAACATTTACTTCAATCTGTATATTTTGCAACA--------------------------------------------------------------------AGTAA---------------------------------------------------------------------------------------------------------------------------------------------------TTCCAAAG------------------------TA---TTAAAACCAATTCAAAGACCAAAATTTGAAAATTTAGTTAATTCAATTTGC--------------------AT-------------------------------------ATACTGTGAAAGTAAGCTTGCCAA------------------------------------------------------------AT---GTATCTATTTGTAG---AGC-CTTTAAA----------------------------TTGTTT-CAAAA--------------ATA----------------T-----------------------------TA
droEre2	scaffold_4845:8200348-8200543 +		GAGCCCTTGT----------TGCTGGCGCGTCGCAGCCGCAGCAGCAA---------CATCAACC---AAAGGTAAGACCAGTGATGGAAGA---------GGTAACATTTACTTTTACCTATATTT-TAGCCAAA--------------------------------------------------------------------AGTAA---------------------------------------------------------------------------------------------------------------------------------------------------TGCCCGAG------------------------TG---TCAAAAATTTCCCAAATTT--------------------TCTTTCATATGC--------------------------------------------------------------------ATACATGCTAACGAA------------------------------------------------------------ATGTT------------------GC-CCTTTTC----------------------------TTATTT-TAAAA--------------ACC----------------T-----------------------------GG
droYak3	2R:15204962-15205138 -		GAGCAATTGT----------TGCTCGCGCGTCGCAGTCGCAGCAGCAA---------CATGAACC---AAAGGTAAGACCCGTGATGGAAAA---------GGTAACACTTAATTGTACTTGTATTT-TAGCCAAA--------------------------------------------------------------------AGTAA---------------------------------------------------------------------------------------------------------------------------------------------------TGACCAAC------------------------CT---T-----------------------------------------------------------------------------------------------------------------------------CTTTCCAA------------------------------------------------------------ATGTTGTATCTGTATGTAAAGAAGC-TATTATC----------------------------TTATTT-CAAAA--------------ACA----------------T-----------------------------TT
droEug1	scf7180000409672:1114272-1114487 -		GAGCAATTGT----------TGCTGGCACGTCGCAGCCGCAGCAGCAG---------CATCAACC---AAAGGTAAGACCAGTGATGTGAAA---------GGTAAATTTTTGTTTTACTAATATATAATGGAAAA--------------------------------------------------------------------AG-G-----------------------------------------------------------------------------------TT--AACT---AACTA--CAGGT-------------------------------------ACAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------ATGCTTAAGATAAGTTGCTAAATCTACAAACTTAA-AAACTATAATTATAAAGAAGA--------------------------------------A------GTAAGGGTTACCTTGAA-------------TGG----TAAAA--------------ATC----------------A-----------------------------GA
droBia1	scf7180000302428:5896024-5896175 +		CAGCAATCTC---------------------CGCAACACCATCAGCAACAGCAT---TGGTCGCC---CCAAGTG---------AGTGGAAA----------ATAAAAACTCATA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATTTTGTTGTTTATAAAAGT----------ATTCCTATGAACATT------------------------------------------------TTTAAAATTAATTTTAG-----------------------------------------------------------------------------------------------------------------------------------------------------------------TTGTTGATTG---TTT-CATTAAA----------------------------TTTCCA-C-------------------------------------A-----------------------------AA
droTak1	scf7180000415795:336470-336667 +		GAGCAATTGT----------TGCTGGCACGTCGCAGCCGCAGCAGCAA---------CATCAACC---AAAGGTAAGATTAGTGATGGGAAA---------GGTAACAGTTTTTTCTTTTAT------------------------------------------------------------------------------------------------------------------------------------------AA-----------------TAAAATTAAAATTT--ACCT---AACTAAATTAGT-------------------------------------ACTA-----------------------------------ATTTGA--------------------------------------------TA----------------------------------------------------------------------------GCTAATTTA------------------------------------------------------------TTGTT-------------T---ATT-CATTTAG----------------------------TTATTT-TAAATAACTTTTAAAAAAATTC----------AAA-TGAAA---------------------------AT
droEle1	scf7180000490728:497766-498019 +		GTTGGCCTGCCACAATCTCGA--------TTTGCA---GCAGCAACAG---------CACCAGGT---AATGT-----CCCACTTAGAGAAATTAT-----ATTAACAATTTATAATATGTTTACCACATTTCTTA--------------------------------------------------------------------ACTAA---------------------------------------------------------------------------------------------------------------------------------------------------TTTAAAAG------------------------CAACTTTAAAAT----------ACTGGGCTATAAAAACTTATTTAATTTAATATCC--------------------ATT--------TTTTTATATACCAAAATTGGTCTCAA-AATTTGTTT-------------AAA------------------------------------------------------------ATTTTATATCAATAGAAAA---AAC-TATAAGA------------TAGTA-----------TAGCCT-CAGGG--------------TTA----------------T-----------------------------AA
droRho1	scf7180000779949:126889-127168 -		GAGCAATTGT----------TGCTGGCACGTCGCAGTCGCAGCAGCAA---------CATCAACC---AAAGGTAAGA-CAGTGATGAGAAA---------GGTAACATTTTGCTTTACTTATATTTGTAGAAAAAAAATAATCAAATAGTGCAACTGTGTATGGCATCTTATTTATTTTTTTTATACATTTACTTCCAGTTTAAAT---CAAAGCGTTATATTTTTAACTATAGTGTTCTTAACTAGAAATTTCTATCAGAAAAAAATATT--TATTT-------------------------------------------------T----------AAACCTT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAAGA--------------------------------------A-------------------------TTTAAAGT---TCGGTT-CAA-G--------------TCA----------------G-----------------------------TA
droFic1	scf7180000453948:1456771-1457003 -		GAGCAATTGT----------TGCTGGCTCGTCGCAGTCGCAGCAGCAA---------CATCAACC---AAAGGTT-----AGTGATGGGAAA---------GGTAACATTTTCATTGACTTAAATATTTAGG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T-------------------------------------ATTAATTCCTAAGAA-------ATTCTCCCTCAGCGT-T---CTGTAA------TATATTA--------------------TTTTTTGTTTGCTTATAATGAAGTTAATTAAACAATAATAAGT-----------------T-A-----------------AA----------------------------GCCAAT-----------------------------------TAGTT---TTAATATACG-----------------------------ACGAGTA-----------TTCCCC-TCATA--------------TTT----------------T-----------------------------AA
droKik1	scf7180000302385:782379-782616 +		GAGCAATTCC----------TGCTGGCACGTCGCAGCCGCAGCAGCAG---------CTACAGTCGAAGAAGGTAAGACCAGGGATGGGAAG---------TGTATAAATTAATTAAAAATTTATTATTAGTAGAA--------------------------------------------------------------------ATATA---------------------------------------------------------------------------------------------------------------------------------------------------TTTTTAAA------------------------TA---TAAGATAAAATTCAAATAT--------------------A-------------------------------TAATAATAAAT-----------------A-T-----------------AT----------------------------GTATATAAATATAT------T---TTGAGATTTTAAGAGTACCTAC---AGTACCTACCTCTAG---GTA-------------------------CCCCTAGC---TCTCCT-CATCA--------------CTG----------------C-----------------------------CA
droAna3	scaffold_13266:10218186-10218419 -		GACCAATTGC----------TTCTTACTCGTCGAAGTCGCAACAGCAA---------CATTAGCC---AAAGGTAAGTGG--TTTTAAGATAGTATCTAAAGATAGAAATTATTT-------------------------------------------------------------------------------------------------AATAA---------------AAAT-ATGTTG-----GGAAATATTTATGAAGAACTTAAAAGTTT-----------------------------AAAGCAGA------------------------------------TC-CA---------ATT-TTTTATTTTTTATTTAATAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCTGCACTGT---ACCC-----------TGCACTC------CTTTTTGTTTTCCAT-CCCAA-A--------------CCCCAAAAAGTGGAAACTGA-----------------------------AA
droBip1	scf7180000396428:637391-637589 -		GACCAATTGC----------AACTTACTCGACGAAGCCGCAACAGCAA---------CATTAATC---AAAGGTTGGT-------------A---------GAAAACAATTATTT-------------------------------------------------------------------------------------------------TATTA---------------ACAAATTTTTG-----ATAAATCGTTATGGAGCACTTACCAGTTTTT-------------------------------------------------T----------AAATATTCAAGTC----------TCATTATTTTTATTATTATACAATAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCTGCACTTT---ATC-------------------------CTTTTGGTTTGCCATCC-CCAAA--------------CCC----------------T-----------------------------AA
dp5	2:12636830-12637023 -		CTGTAATTGC----------AACTGCAACA--GCAGCGGCCACAACAA---------CAACAGCT---CCAGATAGCTGCAGCAGCAAGAAC----------ATA-------TTACAATATATATTT-----------------------------------------------TATTTTTTTAATTTAATTATTTAA------AGTAA----------------------------ACAAAG-----AGAAACAAAAATGCAAGCGATAAT--TATTT-------------------------------------------------T----------AAACGTT-------------------------------------------------------------------------------------TAAGTAACTTTAA--------------------ATT--------AT-----AA------ATTAAAGCT-----------------------------------------------------------------------------AA-------------------------------------------------------------------------------------------------AA----------------A-----------------------------TA
droPer2	scaffold_144:67502-67609 +		CAGCGACTTC----------A-----------GCGGCAGCAGTAACAA---------CAACAGCAGAAGCAGAATTCATCAGCTA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A---GTCT-----------CATATTT------CAAATTGTTTTTAAG-CCTAA-T--------------TAAGTAAAAGTAAAAAA--A-----------------------------AA
droWil2	scf2_1100000004909:8723182-8723328 +		CAGCAATTGC----------AACGAC--AGCAGCAGCTATATCAGCAA---------CAGCAACA---GCAGGAG-------------GA-G---------CATAACGGTGACTTTCAATCAAATG------------------------------------------------------TG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G-----------------AA----------------------------ACAAAT-----------------------------------TATAT---GGAGCAGACC-----------------------------TCGAGTGGACATAGT---TCGAAT-CAAAA--------------TTC----------------T-------------------AATTTAAATCAA
droVir3	scaffold_13047:11148806-11148990 +		TTAACGCCGGCGAACACTACA--------ACTACAACAACAGCAACAA---------CACCAGC----AACAACAACAACAACAACGGGAGC---------GGCTGAACTCAATTCAATA----------------------------------------------------------------------------------------A----------------------------------------------------------------------TGGAGAAGAA--CTTAATTTAAAATCTA--TAGAAACAAAACGAAAAGTTTTTTTTCAATAAAATT----------ACTAATCGCAACAAT------------------------------------------------AATAAAAATAAT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AT----------------T-----------------------------AA
droMoj3	scaffold_6473:10293240-10293396 +		CAGCAAGCAG----------CAGCAACACGTCAAA-CAACAGCAGCAG------CAACAGCAACA---G-CAGCAAAAACAACAACAATAAA---------GGTGTAAG-TATTT-------------------------------------------------------------------------------------------------CACT---------------ATACTATTCTTA-----ACGAATCG-----------------------------------------------------------------------------------------------------------CA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G-CAAAA--------------TGCC---------AAA-GTAACATGCTCATGTCAAAGTTCATGTTAGTTGA
droGri2	scaffold_14830:41166-41336 -		CAGCAACAGC----------A-----------GCAACAGCAGCAGCAA---------CTGCTGCA---GCAGACAAAATCAGCGACAGGAGG---------AG-GACATCAGGCATCATCAGCGGCATCCAGCTCA--------------------------------------------------------------------GGTAATCCAAATG---------------ATAGATTTAA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAGAAAATACTTAAGTCAGTTT-----------------------------------------------------------------------A----------------------------GCAATTTAAGAAAT------T---TTGAAGAATTGA-------------------------------------------------------------------------------------------------AA----------------G-----------------------------TA

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droSim2

GAGCAATTGT----------TGCTGGCGCGTCGCAGCCGCAGCAGCAA---------CATCAACC---AAAGGTAAGACCAGTGATGAGAAA---------GGTAACATTTAGTTCAATCTGTATCTTTTTCCAAA--------------------------------------------------------------------AGTAA---------------------------------------------------------------------------------------------------------------------------------------------------TTCCTAAG------------------------TA---TCAAAAA-----------ACATAATTTTAAAATTTATTTAAGTCAATTTGC--------------------TTC--------TT-----AA------ATCACTATTAAGGATATTGTGAAAGTATGCTGGCCAA------------------------------------------------------------ATGTTGTATCTATTTGTAG---AGC-CTTTAAA----------------------------TTGTTC-CAAAA--------------TTA----------------T-----------------------------AA	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
...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AAGGATATTGTGAAAGTATGCTGGCC........................................................................................................................................................................................................	26	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droSec2

GAGCAATTAT----------TGCTGGCGCGTCGCAGCCGCAGCAGCAA---------CATCAACC---AAAGGTAAGACCAGTGATGAGAAA---------GGTAACATTTAGTTTAATCTGTATCTTTTTCCAAA--------------------------------------------------------------------AGTAA---------------------------------------------------------------------------------------------------------------------------------------------------TGCCTAAG------------------------TA---TTAAAAA-----------ACATAATTTTAAAATTTAGTTAAGTCAATTTGC--------------------TTC--------TG-----AGAC--ATATCGCTCTTAAGGATGTTTTG-------------AAA------------------------------------------------------------ATGTTGTATCTATTTGTAG---AGC-CTTTGAA----------------------------TTGTTC-CAAAA--------------ATA----------------T-----------------------------TA	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
No Reads

dm3

GAGCAATTGT----------TGCTGGAGCGTCGCAGCCGCAGCAGCAA---------CATCAACC---AAAGGTAAGACCAGTGATGAGAAA---------GGTAACATTTACTTCAATCTGTATATTTTGCAACA--------------------------------------------------------------------AGTAA---------------------------------------------------------------------------------------------------------------------------------------------------TTCCAAAG------------------------TA---TTAAAACCAATTCAAAGACCAAAATTTGAAAATTTAGTTAATTCAATTTGC--------------------AT-------------------------------------ATACTGTGAAAGTAAGCTTGCCAA------------------------------------------------------------AT---GTATCTATTTGTAG---AGC-CTTTAAA----------------------------TTGTTT-CAAAA--------------ATA----------------T-----------------------------TA	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
.....................GCTGGAGCGTCGCAGCCGCA............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	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	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
.......................................CAGCAGCAA---------CATCAACC---A................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	3	0.33	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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

droEre2

GAGCCCTTGT----------TGCTGGCGCGTCGCAGCCGCAGCAGCAA---------CATCAACC---AAAGGTAAGACCAGTGATGGAAGA---------GGTAACATTTACTTTTACCTATATTT-TAGCCAAA--------------------------------------------------------------------AGTAA---------------------------------------------------------------------------------------------------------------------------------------------------TGCCCGAG------------------------TG---TCAAAAATTTCCCAAATTT--------------------TCTTTCATATGC--------------------------------------------------------------------ATACATGCTAACGAA------------------------------------------------------------ATGTT------------------GC-CCTTTTC----------------------------TTATTT-TAAAA--------------ACC----------------T-----------------------------GG	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
No Reads

droYak3

GAGCAATTGT----------TGCTCGCGCGTCGCAGTCGCAGCAGCAA---------CATGAACC---AAAGGTAAGACCCGTGATGGAAAA---------GGTAACACTTAATTGTACTTGTATTT-TAGCCAAA--------------------------------------------------------------------AGTAA---------------------------------------------------------------------------------------------------------------------------------------------------TGACCAAC------------------------CT---T-----------------------------------------------------------------------------------------------------------------------------CTTTCCAA------------------------------------------------------------ATGTTGTATCTGTATGTAAAGAAGC-TATTATC----------------------------TTATTT-CAAAA--------------ACA----------------T-----------------------------TT

Size

Hit Count

Total Norm

Total

M026
Head

M043
Female-body

M056
Embryo

V046
Embryo

V052
Head

V058
Head

V120
Male-body

SRR1275488
Male larvae

SRR1275486
Male prepupae

SRR1275484
Male prepupae

GSM1528802
follicle cells

No Reads

droEug1

GAGCAATTGT----------TGCTGGCACGTCGCAGCCGCAGCAGCAG---------CATCAACC---AAAGGTAAGACCAGTGATGTGAAA---------GGTAAATTTTTGTTTTACTAATATATAATGGAAAA--------------------------------------------------------------------AG-G-----------------------------------------------------------------------------------TT--AACT---AACTA--CAGGT-------------------------------------ACAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------ATGCTTAAGATAAGTTGCTAAATCTACAAACTTAA-AAACTATAATTATAAAGAAGA--------------------------------------A------GTAAGGGTTACCTTGAA-------------TGG----TAAAA--------------ATC----------------A-----------------------------GA	Size	Hit Count	Total Norm	Total
No Reads

droBia1

CAGCAATCTC---------------------CGCAACACCATCAGCAACAGCAT---TGGTCGCC---CCAAGTG---------AGTGGAAA----------ATAAAAACTCATA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATTTTGTTGTTTATAAAAGT----------ATTCCTATGAACATT------------------------------------------------TTTAAAATTAATTTTAG-----------------------------------------------------------------------------------------------------------------------------------------------------------------TTGTTGATTG---TTT-CATTAAA----------------------------TTTCCA-C-------------------------------------A-----------------------------AA	Size	Hit Count	Total Norm	Total
No Reads

droTak1

GAGCAATTGT----------TGCTGGCACGTCGCAGCCGCAGCAGCAA---------CATCAACC---AAAGGTAAGATTAGTGATGGGAAA---------GGTAACAGTTTTTTCTTTTAT------------------------------------------------------------------------------------------------------------------------------------------AA-----------------TAAAATTAAAATTT--ACCT---AACTAAATTAGT-------------------------------------ACTA-----------------------------------ATTTGA--------------------------------------------TA----------------------------------------------------------------------------GCTAATTTA------------------------------------------------------------TTGTT-------------T---ATT-CATTTAG----------------------------TTATTT-TAAATAACTTTTAAAAAAATTC----------AAA-TGAAA---------------------------AT	Size	Hit Count	Total Norm	Total
No Reads

droEle1

GTTGGCCTGCCACAATCTCGA--------TTTGCA---GCAGCAACAG---------CACCAGGT---AATGT-----CCCACTTAGAGAAATTAT-----ATTAACAATTTATAATATGTTTACCACATTTCTTA--------------------------------------------------------------------ACTAA---------------------------------------------------------------------------------------------------------------------------------------------------TTTAAAAG------------------------CAACTTTAAAAT----------ACTGGGCTATAAAAACTTATTTAATTTAATATCC--------------------ATT--------TTTTTATATACCAAAATTGGTCTCAA-AATTTGTTT-------------AAA------------------------------------------------------------ATTTTATATCAATAGAAAA---AAC-TATAAGA------------TAGTA-----------TAGCCT-CAGGG--------------TTA----------------T-----------------------------AA	Size	Hit Count	Total Norm	Total
No Reads

droRho1

GAGCAATTGT----------TGCTGGCACGTCGCAGTCGCAGCAGCAA---------CATCAACC---AAAGGTAAGA-CAGTGATGAGAAA---------GGTAACATTTTGCTTTACTTATATTTGTAGAAAAAAAATAATCAAATAGTGCAACTGTGTATGGCATCTTATTTATTTTTTTTATACATTTACTTCCAGTTTAAAT---CAAAGCGTTATATTTTTAACTATAGTGTTCTTAACTAGAAATTTCTATCAGAAAAAAATATT--TATTT-------------------------------------------------T----------AAACCTT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAAGA--------------------------------------A-------------------------TTTAAAGT---TCGGTT-CAA-G--------------TCA----------------G-----------------------------TA	Size	Hit Count	Total Norm	Total
No Reads

droFic1

GAGCAATTGT----------TGCTGGCTCGTCGCAGTCGCAGCAGCAA---------CATCAACC---AAAGGTT-----AGTGATGGGAAA---------GGTAACATTTTCATTGACTTAAATATTTAGG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T-------------------------------------ATTAATTCCTAAGAA-------ATTCTCCCTCAGCGT-T---CTGTAA------TATATTA--------------------TTTTTTGTTTGCTTATAATGAAGTTAATTAAACAATAATAAGT-----------------T-A-----------------AA----------------------------GCCAAT-----------------------------------TAGTT---TTAATATACG-----------------------------ACGAGTA-----------TTCCCC-TCATA--------------TTT----------------T-----------------------------AA	Size	Hit Count	Total Norm	Total
No Reads

droKik1

GAGCAATTCC----------TGCTGGCACGTCGCAGCCGCAGCAGCAG---------CTACAGTCGAAGAAGGTAAGACCAGGGATGGGAAG---------TGTATAAATTAATTAAAAATTTATTATTAGTAGAA--------------------------------------------------------------------ATATA---------------------------------------------------------------------------------------------------------------------------------------------------TTTTTAAA------------------------TA---TAAGATAAAATTCAAATAT--------------------A-------------------------------TAATAATAAAT-----------------A-T-----------------AT----------------------------GTATATAAATATAT------T---TTGAGATTTTAAGAGTACCTAC---AGTACCTACCTCTAG---GTA-------------------------CCCCTAGC---TCTCCT-CATCA--------------CTG----------------C-----------------------------CA	Size	Hit Count	Total Norm	Total
No Reads

droAna3

GACCAATTGC----------TTCTTACTCGTCGAAGTCGCAACAGCAA---------CATTAGCC---AAAGGTAAGTGG--TTTTAAGATAGTATCTAAAGATAGAAATTATTT-------------------------------------------------------------------------------------------------AATAA---------------AAAT-ATGTTG-----GGAAATATTTATGAAGAACTTAAAAGTTT-----------------------------AAAGCAGA------------------------------------TC-CA---------ATT-TTTTATTTTTTATTTAATAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCTGCACTGT---ACCC-----------TGCACTC------CTTTTTGTTTTCCAT-CCCAA-A--------------CCCCAAAAAGTGGAAACTGA-----------------------------AA	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
No Reads

droBip1

GACCAATTGC----------AACTTACTCGACGAAGCCGCAACAGCAA---------CATTAATC---AAAGGTTGGT-------------A---------GAAAACAATTATTT-------------------------------------------------------------------------------------------------TATTA---------------ACAAATTTTTG-----ATAAATCGTTATGGAGCACTTACCAGTTTTT-------------------------------------------------T----------AAATATTCAAGTC----------TCATTATTTTTATTATTATACAATAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCTGCACTTT---ATC-------------------------CTTTTGGTTTGCCATCC-CCAAA--------------CCC----------------T-----------------------------AA	Size	Hit Count	Total Norm	Total
No Reads

dp5

CTGTAATTGC----------AACTGCAACA--GCAGCGGCCACAACAA---------CAACAGCT---CCAGATAGCTGCAGCAGCAAGAAC----------ATA-------TTACAATATATATTT-----------------------------------------------TATTTTTTTAATTTAATTATTTAA------AGTAA----------------------------ACAAAG-----AGAAACAAAAATGCAAGCGATAAT--TATTT-------------------------------------------------T----------AAACGTT-------------------------------------------------------------------------------------TAAGTAACTTTAA--------------------ATT--------AT-----AA------ATTAAAGCT-----------------------------------------------------------------------------AA-------------------------------------------------------------------------------------------------AA----------------A-----------------------------TA	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--GCAGCGGCCACAAC.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	1	2.00	2	0	1	1	0	0	0	0	0	0	0
.........................................ACAACAA---------CAACAGCT---CCAGATAGC........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	24	1	2.00	2	0	2	0	0	0	0	0	0	0	0
.....................................GGCCACAACAA---------CAACAGCT---CCA..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	22	1	2.00	2	0	2	0	0	0	0	0	0	0	0
.............................................................................................................................................................................................................GTAA----------------------------ACAAAG-----AGAAACAAAA...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0	0	0	0	0
..............................................AA---------CAACAGCT---CCAGATAGCTGCAGCA.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	26	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.........................CAACA--GCAGCGGCCACAAC.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	1	0	1	0	0	0	0	0	0	0	0
...............................................................CT---CCAGATAGCTGCAGCAGCA..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	1	0	0	0	0	0	0	0	0
................................................................T---CCAGATAGCTGCAGCAGCAAGAAC----------...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	0	0	0	1	0	0	0	0	0
................................................................................................................................................................................................................................................................AAATGCAAGCGATAAT--TATTT-------------------------------------------------T----------..................................................................................................................................................................................................................................................................................................................................................................................................	22	1	1.00	1	0	1	0	0	0	0	0	0	0	0
................................................................................................................................................................................................................................................AAG-----AGAAACAAAAATGCAAGCGATAAT--T..................................................................................................................................................................................................................................................................................................................................................................................................................................................................	28	1	1.00	1	0	0	0	0	1	0	0	0	0	0
...................................GCGGCCACAACAA---------CAACAGCT---.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	1	0	0	0	0	0	0	0
.............................................................................................................................................................................................................................................ACAAAG-----AGAAACAAAAATGCAAGCGAT........................................................................................................................................................................................................................................................................................................................................................................................................................................................................	27	1	1.00	1	0	1	0	0	0	0	0	0	0	0
....................................................................CCAGATAGCTGCAGCAGCAAGAAC----------AT.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	26	1	1.00	1	0	1	0	0	0	0	0	0	0	0
..........................................CAACAA---------CAACAGCT---CCAGATAGC........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0	0	0	0	0
............................................................................................................................................................................................................................................................ACAAAAATGCAAGCGATA.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	1	0	0	0	0	1	0	0	0	0	0
.............................................................................................................................................................................................ATTATTTAA------AGTAA----------------------------ACAAAG-----AGA..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	1	0	0	0	0	0	0	0
....AATTGC----------AACTGCAACA--GCAGCGGCC............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	1	0	0	0	0	0	0	0	0
..............................................................GCT---CCAGATAGCTGCAGCAGCAAGAAC----------A..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	28	1	1.00	1	0	1	0	0	0	0	0	0	0	0
........................................................................................................................................................................................................................................................AGAAACAAAAATGCAAGCGA.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0	0	0	0	0
...............................................................................................................................................................................................................AA----------------------------ACAAAG-----AGAAACAAAAATGCAAGC...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................	26	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.............................................................................................................................................................................................................GTAA----------------------------ACAAAG-----AGAAACAAAAATGCAAGC...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................	28	1	1.00	1	0	0	1	0	0	0	0	0	0	0
.....................ACTGCAACA--GCAGCGGCCA...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	1	0	1	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................................G-----AGAAACAAAAATGCAAGCGATA.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0	0	0	0	0
...............................................................CT---CCAGATAGCTGCAGCAGC...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	0	1	0	0	0	0	0	0	0
...............................................................CT---CCAGATAGCTGCAGCAGCAAG............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	1	0	0	0	0	0
.............................................................................................................................................................................................................GTAA----------------------------ACAAAG-----AGAAACAAAAATGC...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................	24	1	1.00	1	0	1	0	0	0	0	0	0	0	0
...........................................AACAA---------CAACAGCT---CCAGATAGCTGCAGC..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	28	1	1.00	1	0	1	0	0	0	0	0	0	0	0
..GTAATTGC----------AACTGCAACA--GC...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0	0	0	0	0
........GC----------AACTGCAACA--GCAGCGGC.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	2	0.50	1	0	1	0	0	0	0	0	0	0	0
.....ATTGC----------AACTGCAACA--GCAGC................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	2	0.50	1	0	1	0	0	0	0	0	0	0	0

droPer2

CAGCGACTTC----------A-----------GCGGCAGCAGTAACAA---------CAACAGCAGAAGCAGAATTCATCAGCTA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A---GTCT-----------CATATTT------CAAATTGTTTTTAAG-CCTAA-T--------------TAAGTAAAAGTAAAAAA--A-----------------------------AA	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTT------CAAATTGTTTTTAAG-CCT.....................................................................	21	20	0.05	1	0	1	0	0	0	0
...........................................................................TCATCAGCTA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A---GTCT-----------CATATTT------CAAATA..................................................................................	28	20	0.05	1	0	1	0	0	0	0
.....................................AGCAGTAACAA---------CAACAGCAGAAGCAG.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	26	20	0.05	1	0	1	0	0	0	0
.....................................AGCAGTAACAA---------CAACAGCAGAA.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	22	20	0.05	1	0	1	0	0	0	0

droWil2

CAGCAATTGC----------AACGAC--AGCAGCAGCTATATCAGCAA---------CAGCAACA---GCAGGAG-------------GA-G---------CATAACGGTGACTTTCAATCAAATG------------------------------------------------------TG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G-----------------AA----------------------------ACAAAT-----------------------------------TATAT---GGAGCAGACC-----------------------------TCGAGTGGACATAGT---TCGAAT-CAAAA--------------TTC----------------T-------------------AATTTAAATCAA	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
...........................................AGCAA---------CAGCAACA---GCAGG............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	20	0.05	1	0	0	0	1	0

droVir3

TTAACGCCGGCGAACACTACA--------ACTACAACAACAGCAACAA---------CACCAGC----AACAACAACAACAACAACGGGAGC---------GGCTGAACTCAATTCAATA----------------------------------------------------------------------------------------A----------------------------------------------------------------------TGGAGAAGAA--CTTAATTTAAAATCTA--TAGAAACAAAACGAAAAGTTTTTTTTCAATAAAATT----------ACTAATCGCAACAAT------------------------------------------------AATAAAAATAAT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AT----------------T-----------------------------AA	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
..........................................................................AACAACAACAACGGGAGC---------GG..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	1	2.00	2	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	1	0
.................................................................................ACAACGGGAGC---------GGCTGAACTC......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	2.00	2	1	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
.......................................................................................................................A----------------------------------------------------------------------------------------A----------------------------------------------------------------------TGGAGAAGAA--CTTAATT...........................................................................................................................................................................................................................................................................................................................................................................................................................................	19	1	2.00	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...........................................................................................................ACTCAATTCAATA----------------------------------------------------------------------------------------A----------------------------------------------------------------------TGGAGAAGAA--..................................................................................................................................................................................................................................................................................................................................................................................................................................................	24	1	2.00	2	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..AACGCCGGCGAACACTACA--------A.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	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	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
.........................................................................CAACAACAACAACGGGAGC---------GG..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
................................................................................................................ATTCAATA----------------------------------------------------------------------------------------A----------------------------------------------------------------------TGGAGAAGAA--CT................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
......................................................................................GGGAGC---------GGCTGAACTCAATTCAATA----------------------------------------------------------------------------------------.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..AACGCCGGCGAACACTACA--------ACTA....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.........................................................................................................GAACTCAATTCAATA----------------------------------------------------------------------------------------A----------------------------------------------------------------------TGGAGAAG......................................................................................................................................................................................................................................................................................................................................................................................................................................................	24	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	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
.....................................................................................................................................................................................................................................................................................................................TAGAAACAAAACGAAAAGTTTTTT........................................................................................................................................................................................................................................................................................................................................................................................................	24	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	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
.......................................................................................................................A----------------------------------------------------------------------------------------A----------------------------------------------------------------------TGGAGAAGAA--CTTAATTTAA........................................................................................................................................................................................................................................................................................................................................................................................................................................	22	1	1.00	1	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
..........................................................................................................AACTCAATTCAATA----------------------------------------------------------------------------------------A----------------------------------------------------------------------TGGAGA........................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	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
.....................................................................................................................ATA----------------------------------------------------------------------------------------A----------------------------------------------------------------------TGGAGAAGAA--CTTAATTTAAA.......................................................................................................................................................................................................................................................................................................................................................................................................................................	25	1	1.00	1	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
.................................................................................................................................................................................................................................................................................................................TA--TAGAAACAAAACGAAAAGT.............................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
......................................ACAGCAACAA---------CACCAGC----AACAACA..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	24	2	0.50	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
........................................................................ACAACAACAACAACGGGAGC---------................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	5	0.40	2	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.........................................................................CAACAACAACAACGGGAGC---------................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	5	0.40	2	0	0	1	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
.......................................................................AACAACAACAACAACGGGAGC---------................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	5	0.40	2	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...............................................................C----AACAACAACAACAACAACGGGAGC---------................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	25	3	0.33	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...................................ACAACAGCAACAA---------CACCAGC----AA...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	22	4	0.25	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	1	0

droMoj3

CAGCAAGCAG----------CAGCAACACGTCAAA-CAACAGCAGCAG------CAACAGCAACA---G-CAGCAAAAACAACAACAATAAA---------GGTGTAAG-TATTT-------------------------------------------------------------------------------------------------CACT---------------ATACTATTCTTA-----ACGAATCG-----------------------------------------------------------------------------------------------------------CA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G-CAAAA--------------TGCC---------AAA-GTAACATGCTCATGTCAAAGTTCATGTTAGTTGA	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
.....................................AACAGCAGCAG------CAACAGCAACA---.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	22	20	0.70	14	0	4	0	0	10	0
............................................GCAG------CAACAGCAACA---G-CAGCA..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	20	0.10	2	2	0	0	0	0	0
.....................................AACAGCAGCAG------CAACAGCAAC.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	20	0.05	1	0	1	0	0	0	0
...........................................AGCAG------CAACAGCAACA---G-CA.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	20	0.05	1	1	0	0	0	0	0

droGri2

CAGCAACAGC----------A-----------GCAACAGCAGCAGCAA---------CTGCTGCA---GCAGACAAAATCAGCGACAGGAGG---------AG-GACATCAGGCATCATCAGCGGCATCCAGCTCA--------------------------------------------------------------------GGTAATCCAAATG---------------ATAGATTTAA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAGAAAATACTTAAGTCAGTTT-----------------------------------------------------------------------A----------------------------GCAATTTAAGAAAT------T---TTGAAGAATTGA-------------------------------------------------------------------------------------------------AA----------------G-----------------------------TA	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

dsi_20479

2r:14662461-14662610 +

Candidate

Unknown

Predicted structure

Flybase annnotation

Repeatable elements

Sense Strand Reads

Anti-sense strand reads

Re-alignment of all predicted orthologs

Re-alignment of all predicted orthologs with sRNA reads