dsi_28249

AGATAATAATTTAAGCAATATGCCAAAGAAACTGAATAACGCGGTAACGGGTAAGTGCACTTAAATACTTTAACTAATATTAATTAAGCGCAGCACACACAGACGAAGCGAAAAAGTTAATAATATTACACAGCAGTGTTGCCAATACATTAATCGAATTTACGCAAAAATGTGCTAGTAATATTTAGCCTAAACGACTAAACAAACAGTATGTTAACTATATTCTTACTTTGAAAATTCTATATATTAA ************************************************.....(((.(((((...................))))).)))..............((((.....(((((..(((((((..((((...((((.....................)))).....)))).)))))))))))).....)).)).************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	SRR553486 Makindu_3 day-old ovaries	SRR618934 dsim w501 ovaries	O002 Head	SRR553485 Chicharo_3 day-old ovaries	SRR553488 RT_0-2 hours eggs
.....................GCCAAAGAAACTGAATAACGCGGT.............................................................................................................................................................................................................	24	0	1	2.00	2	0	1	0	1	0
......TAATTTAAGCAATATGCCAAAGAAACTGAA......................................................................................................................................................................................................................	30	0	1	1.00	1	1	0	0	0	0
..............................ACTGAATAACGCGGTAAC..........................................................................................................................................................................................................	18	0	1	1.00	1	0	0	1	0	0
...........TAAGCAATATGCCAAAGAAACTGAA......................................................................................................................................................................................................................	25	0	1	1.00	1	0	0	0	0	1
....................TGCCAAAGAAACTGAATAACGCGGT.............................................................................................................................................................................................................	25	0	1	1.00	1	1	0	0	0	0
........................................................................................................................................................................................TTAGCCTGAACGACGAAA................................................	18	2	9	0.11	1	0	1	0	0	0
..........................................GGTAACGGGGAAGTTC................................................................................................................................................................................................	16	2	20	0.05	1	0	1	0	0	0

TCTATTATTAAATTCGTTATACGGTTTCTTTGACTTATTGCGCCATTGCCCATTCACGTGAATTTATGAAATTGATTATAATTAATTCGCGTCGTGTGTGTCTGCTTCGCTTTTTCAATTATTATAATGTGTCGTCACAACGGTTATGTAATTAGCTTAAATGCGTTTTTACACGATCATTATAAATCGGATTTGCTGATTTGTTTGTCATACAATTGATATAAGAATGAAACTTTTAAGATATATAATT ************************************************.....(((.(((((...................))))).)))..............((((.....(((((..(((((((..((((...((((.....................)))).....)))).)))))))))))).....)).)).************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	SRR618934 dsim w501 ovaries	SRR553487 NRT_0-2 hours eggs
..............................................................................................................................................................................................ATTTGCTGATTTGTTTA...........................................	17	1	4	0.25	1	1	0
..................................................................TGAACTTGAGTATAATT.......................................................................................................................................................................	17	2	20	0.05	1	0	1
.........................................................................................................................................................................................ATAGGATTGGCTGATCTG...............................................	18	3	20	0.05	1	0	1

Species	Coordinate	ID	Alignment
droSim2	x:12440822-12441071 -	dsi_28249	AGATAATAATT-TAA------GCAAT-ATGCCAAAGAAACTG------------AATAACGCGGTAACGGGTAAGT------GCA---------------------------------CTTAAATACTTTAACTAA-------------------------------------------TATTAATTA----------------------------------AGCGCA--------------------------------------------------------------------GCACACACAG--ACGAAGCGAA--------------AAAGTTAATA---------ATATTACACAGCAGTGTTGCCAATACATTAATCGAATTTAC-GCAAAAA---------------------------------------------------------------------------------TGTGCTAGTA--------------------------------------------------------ATATTTAGCCTAAACGACTAAACAAACA---GTATGT---T---------------AAC----------------------TATATTCTTACTTT-----------GAAAATTCTAT----------------------------------------------ATAT---TAA
droSec2	scaffold_21:843152-843401 -		AGATAATAATT-TAA------GCAAT-ATGCCAAAGAAACTG------------AATAACGCGGTAACGGGTAAGT------GCA---------------------------------CTTAAATACTTTAACTAA-------------------------------------------TATCAATTA----------------------------------AGCGCA--------------------------------------------------------------------GCACACACAG--ACGAAGCGAA--------------AAAGTTAATA---------ATATTACACAGCAGTGTTGCCAATACATTAATCGAATTTAC-GCAAAAA---------------------------------------------------------------------------------TGTGCTAGTA--------------------------------------------------------ATATTTAGCCTAAATGACTAAACAAACA---GTATGT---C---------------AAC----------------------TATATTCTTACTTT-----------GAAAATTCAAT----------------------------------------------ATAT---TAA
dm3	chrX:13097575-13097792 -		AGATAATAATT-TAA------GCAAT-ATGCCAAAGAAACTG------------AATAACATGGTAACGGGTAAGT------GCA---------------------------------TTTAAATA-TTTAAATAA-------------------------------------------TATCAATTA----------------------------------AGCACA--------------------------------------------------------------------GCACA---------GAAGCGAA---------C----CAACTTAATA---------ATATTTAACAGCAGTGTTGCCAATTCATTAATCGAATTTAC-CAAAAAA----------------------------------------------------------------------AA-------AATGTGCG-------------------------------------------------------------------------------------ACA---GTATGT---T---------------AAC----------------------TATATTCTTACGTT-----------AAAAATTCCAT----------------------------------------------ATGT---TAA
droEre2	scaffold_4690:13778119-13778395 +		AGAGAATAATT-TAA------GCAAT-ATGCCAAAGAAACTC------------AATAACGCGATAACGGGTAAGT------GCC---------------------------------ATTAATTACGTTTAATAC-------------------------------------------TTGTAATA-----------------ACAAAT------GAACACAGCACA--------------------------------------------------------------------GCACACACAG--ACGAAGCGAA--------------CAACTTAATA---------ATATT-AACAGCAGTGTTGCCAATTCATTAATCGAATTTAC-CAAAAAAAAAAAAACAAAAAAACC----AAATAGCAAAGGAAT---------------------------------------------------------------------------------------------------------------------GGCTTAAATGACTGAACAAAGA---GTGTCT---T--------------AAAC----------------------TATATTCTTATGTG-----------CAAAATTCATT----------------------------------------------GTAT---TAA
droYak3	X:7368240-7368584 -		AGAGAATAATT-TAA------ACAAT-ATGCCAAAGAAACTG------------AATAACGCGATAACGGGTAAGT------GCA---------------------------------ATTAATCTCCTCAAAAAA-------------------------------------------AATAAATGAAGATATATTATCAAAAAAAAATAAAAATAA-A-GAACACA--------------------------------------------------------------------GCACACACAGACGAGAAGCGGA--------------GAACTTAATA---------ATATT-AACAGCAGTGTTGCCAATTCATTAATCGAATTTAC-ACAAAAA---------------------------------------------------------------------------------TTTACCAGAA----AGTGGCAGTCACTTTATAAATGTGTATTAAACTAGAAACTATAAACTATATAAATTGGAAAA-CT-CCATT----TATTATAAAT-GTGTATTAAACTAGAAGCTATAAAC----------------------TATAT---AAATTG-----------GAAAACTCCAT----------------------------------------------TTAT---TA-
droEug1	scf7180000409110:1557276-1557539 -		AGAGAATAATT-TAA------ATAAT-ATGCCAAAGAAACTG------------AATAATACGATAACGGGTAAGT------GTG---------------------------------AGTAATTAAT------------------------------------------------------------------------------GTTT------TAGA-TTCGAAAAT-----A------------------------------------------------------------ACATAGCAGA--AC-ATAGCACGGGAGAGGGGAGAAGTACTAAATA---------ATATT-AACAGCAGTGTTGCCAATTTTAGG---TTTTATGACCCAAACT---------------------GGTCAGA---GAAATGTCTTAAATA-----------------------AAT-------------ATGAAA-----------------ATATGTAACTGAAAGA-----------------------------------CATGTTT----AAAAATTGAT-TTC----------------------------------------AAATT-----CTT------------------------------------------------------------------TTAAACTATAT---CAA
droBia1	scf7180000302421:1623049-1623272 -		GGAGAACAACC-TGA------ACAAC-ATGCCAAAGAAAGTG------------AACAACGCAATCACGGGTAAGT------TCT------------A-----------------GCACCTAAATG------------------------------------------------------------------------------ACCTGC------GAAA-CTCTACA--------------------------------------------------------------------GCACAC-----------GAGAG--------------AAAGTGAAAAGTATTG---TTGCGTAACAGCAGTGTTGCCAATTCTCTGAGCGAAACTAT-CTCAAAC---------------------------------------------A-----------------------AAG-------------ACAGTC--------------------------------------------------------AGAAGTAGCCTGAATAA----------------------------------------AG----------------------GATAATTGTATTGT-----------CTAAAGACTGT----------------------------------------------ATCT---CGA
droTak1	scf7180000414113:16438-16665 -		AGAGAATAATT-TAA------ACAAT-ATGCCAAAGAAACTG------------AATAACGCAATAACGGGTAAGT------GCA---------------------------------ATTAAATC--------AA-------------------------------------------AAATAAT------------------------------AA-A-ATTCACA----------------------------------------------------------------------ACACACAG--GCGAAGCAAA--------------AAACG-AATT-----ATATAT-TTAAAGAGCAGTGCTGCCAATTTTTTAATCGAAAATTG-GTCGAAT---------------------------------------------A-----------------------AAA-------------CTAGTT--------------------------------------------------------AT-----------------------------------------------------AAAGTTTATTTTTTAGATTTTTAAA-----TACTTTTGTT-----------ATAAAAACTGT----------------------------------------------A-AT---TAA
droEle1	scf7180000491043:54674-55020 +		AGAGAATAATT-TAA------ACAAT-ATGCCAAAGAAACTG------------AATAACACGATAACGGGTAAGT------GCA---------------------------------AGTAATTAAGTTAAAC----------------------------------------------------------------------------------AAAA-TTCCACAACA-CACACACACGCACACCCCCTTTCACACACACACACACACCCCAACTCTCACACACATAGACATAACACGCACAG--GCGTACAGAG--------------AATTTGATTC---------AT-TTGTTTAGCAGTGTTGCCAATTGTTTAATTAAACTTAA-ATCTCAT---------------------------------------------T-----------------------ACG-------------AAAAATATAAAAAGCTTGTTAATATATGTATATGTATGAG--------------------TAAAATCGAAATCCTATGATT----AATATTTAAT-ATG----------------------------------------TTATG------TTACTTATAAAAAAAGAAGA--AAATTAT----------------------------------------------AATT---TAA
droRho1	scf7180000779333:870023-870184 -		AGAGAATAATT-TAA------ACAAT-ATGCCAAAGAAACTG------------AATAACACGATAACGGGTAAGT------GTA---------------------------------ATTTAATA------------------------------------------------------------------------------AAAAAT------AAAA-TTCCACAAC-----ACACACGCACACTCCCACTTACACACACACACACAT---------------------------ACACAAAT--GCGTAGAGAA--------------AAACT-GATA---------ACATTGTTCAGCA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droFic1	scf7180000454050:1059418-1059742 -		AGAGAATAATT-TAA------ACAAT-ATGCCAAAGAAATTA------------AACAACACGATAACGGGTAAGT------GCT---------------------------------TTTAATTTTAATAAAT----------------------------------------------------------------------------------AA-G-AAACACAAAACCTAACACACGCACAC-CCAACTCACACATACACGCACAC---------------------------ACACACA-------AGCGAA--------------AAATTGATCA---------ACTTTATTCAGCAGTGTTGCCAATTCTTAAAAGAAATGCAT-CCCAAAT-----------------TATTCGTCAGAAATGG-ATGCGTTAAATGTTATATTACAATGTAATTTAATACGCACGAAAAAATGTGAAATTA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAATTTGATAAATTAGTGAACTGAACTGTTTTAAAAAATTTTAA---ATATAGACAA
droKik1	scf7180000302610:1228621-1228891 -		ATATAATATTA-AAAAAACCAGA----AA-GAAAATGCAACAAAAGAAAACCACGATAAAACAATA-----TAATAGTGAATGTTTAATGATAATTCAAGATCAAAAGGACAACAACAAATATA-CATCCAGCTGAAACAAAATGAAATCTATATACATTATACAGTTTTTTTTATAATTTATAATA-----------------ACAAAC------AAA----------------------------------------------------------------------------------------------------------------------CGGC----------------------------------------ATCAAAATTTG-TTTATAA---------------------------------------------------------------------------------TTTACAAGTG--------------------------------------------------------AAATTTGGCTTAAACAAATGAAAAACAATT-GAAACT---T---------------GGT----------------------TATATT----------------------------TT----------------------------------------------ATAA---TAG
droAna3	scaffold_13117:2413767-2413823 -		AGAGAATAATT-TAA------GCAAC-ATGCCAAAGAAACTA------------AATAACACAATAACTGGTAAGT------G-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droBip1	scf7180000396696:708818-708900 +		AGAGAATAATT-TAA------GCAAC-ATGCCAAAGAAACTA------------AACAACCCAGTAACTGGTGAGT------ATT-----------------------------------TAAAAAA-------------------------------------------------------------------------------TAAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAT------------------------AAT----------------------------------------------AATT---AAG
dp5	XL_group1a:2070733-2070852 -		AACAAC-ACCA-ATA------G--CT-GCATCAACAACTCCA------------AATGAAGCAATAACTTCCAC--------------------------TT--CACGGATAACTACACCAAAA-ATTCCAGCTAGACCAACA-------------------------------------------TC----------------------------------AAAGCC----------------------------------------------------------------------AAACACAG--TTGCAGCAAA--------------GGA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer2	scaffold_22:79466-79501 -		AGAGAATAGTTTTAA------ACAAT-ATGCCAAAGAAATTG------------A-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil2	scf2_1100000004909:7773783-7773861 +		AAATGT-GCTT-GTG------AAATG-GTGTCTAAAACTTAA------------AACAAACAAATAATT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATT----------------------TATATATATATATA-----------GAAA----TAT----------------------------------------------ATAT---ATA
droVir3	scaffold_13047:11636466-11636574 -		AGCAGC-AGCA-GCA------GCATG-ATGAGAAAATAATTT------------AATAAT-------------------------------------------------------------AATTACTGAAAACAA-------------------------------------------AAAGAATTA----------------------------------TGT-AA--------------------------------------------------------------------GCATAAACAT--TTAAAGCGAG--------------AAAGCTACCA---------ACAA--CACAGCA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6359:4047269-4047400 +		CAATAACAACT-A--------GCAATAGTGGCAGATGCAACA------------GCAACAACAACTACAAGTAGCT------GCA---------------------------------TTAACA-GCTATCAGCAA-------------------------------------------CAATAACCA----------------------------------GAAGCA--------------------------------------------------------------------ACATATACAT--ACAACAGCAA--------------CAAA-TAGCA---------ACAATA-GCAGCAG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	scaffold_14853:1440399-1440495 -		ATCGATG-ACG-ATG------A--CG-ATAACGAAAACGATA------------ATCATCATAAGAACGAA---------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTAAGCACAG-TTAAG-CACAAATCCATTGACTA---------------------------AATATTA-------AG-------------------------------------------CGCATCA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droSim2

AGATAATAATT-TAA------GCAAT-ATGCCAAAGAAACTG------------AATAACGCGGTAACGGGTAAGT------GCA---------------------------------CTTAAATACTTTAACTAA-------------------------------------------TATTAATTA----------------------------------AGCGCA--------------------------------------------------------------------GCACACACAG--ACGAAGCGAA--------------AAAGTTAATA---------ATATTACACAGCAGTGTTGCCAATACATTAATCGAATTTAC-GCAAAAA---------------------------------------------------------------------------------TGTGCTAGTA--------------------------------------------------------ATATTTAGCCTAAACGACTAAACAAACA---GTATGT---T---------------AAC----------------------TATATTCTTACTTT-----------GAAAATTCTAT----------------------------------------------ATAT---TAA	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
.............................GCCAAAGAAACTG------------AATAACGCGGT...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	24	1	2.00	2	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0
......TAATT-TAA------GCAAT-ATGCCAAAGAAACTG------------AA........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	30	1	1.00	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
......................................ACTG------------AATAACGCGGTAAC............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
............TAA------GCAAT-ATGCCAAAGAAACTG------------AA........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
............................TGCCAAAGAAACTG------------AATAACGCGGT...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0

droSec2

AGATAATAATT-TAA------GCAAT-ATGCCAAAGAAACTG------------AATAACGCGGTAACGGGTAAGT------GCA---------------------------------CTTAAATACTTTAACTAA-------------------------------------------TATCAATTA----------------------------------AGCGCA--------------------------------------------------------------------GCACACACAG--ACGAAGCGAA--------------AAAGTTAATA---------ATATTACACAGCAGTGTTGCCAATACATTAATCGAATTTAC-GCAAAAA---------------------------------------------------------------------------------TGTGCTAGTA--------------------------------------------------------ATATTTAGCCTAAATGACTAAACAAACA---GTATGT---C---------------AAC----------------------TATATTCTTACTTT-----------GAAAATTCAAT----------------------------------------------ATAT---TAA	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
........................................TG------------AATAACGCGGTAACGG..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	1	0	0	1	0

dm3

AGATAATAATT-TAA------GCAAT-ATGCCAAAGAAACTG------------AATAACATGGTAACGGGTAAGT------GCA---------------------------------TTTAAATA-TTTAAATAA-------------------------------------------TATCAATTA----------------------------------AGCACA--------------------------------------------------------------------GCACA---------GAAGCGAA---------C----CAACTTAATA---------ATATTTAACAGCAGTGTTGCCAATTCATTAATCGAATTTAC-CAAAAAA----------------------------------------------------------------------AA-------AATGTGCG-------------------------------------------------------------------------------------ACA---GTATGT---T---------------AAC----------------------TATATTCTTACGTT-----------AAAAATTCCAT----------------------------------------------ATGT---TAA	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
........................................TG------------AATAACATGGTAACGG..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	1	3.00	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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........................AT-ATGCCAAAGAAACTG------------AATA......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
........................................TG------------AATAACATGGTAACGGGTAAGT------GCA---------------------------------..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	27	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	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
...................................................................................................................................................................................................................................................................................................................................................ATA---------ATATTTAACAGCAGG..................................................................................................................................................................................................................................................................................................................................................................	18	2	0.50	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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

droEre2

AGAGAATAATT-TAA------GCAAT-ATGCCAAAGAAACTC------------AATAACGCGATAACGGGTAAGT------GCC---------------------------------ATTAATTACGTTTAATAC-------------------------------------------TTGTAATA-----------------ACAAAT------GAACACAGCACA--------------------------------------------------------------------GCACACACAG--ACGAAGCGAA--------------CAACTTAATA---------ATATT-AACAGCAGTGTTGCCAATTCATTAATCGAATTTAC-CAAAAAAAAAAAAACAAAAAAACC----AAATAGCAAAGGAAT---------------------------------------------------------------------------------------------------------------------GGCTTAAATGACTGAACAAAGA---GTGTCT---T--------------AAAC----------------------TATATTCTTATGTG-----------CAAAATTCATT----------------------------------------------GTAT---TAA	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
...........................................................................................................................................................................................................................................................................................................................................................................................................AAAAAAAAAAAACAAAAAAA.................................................................................................................................................................................................................................................................................................................	20	20	0.05	1	1	0	0	0	0	0	0

droYak3

AGAGAATAATT-TAA------ACAAT-ATGCCAAAGAAACTG------------AATAACGCGATAACGGGTAAGT------GCA---------------------------------ATTAATCTCCTCAAAAAA-------------------------------------------AATAAATGAAGATATATTATCAAAAAAAAATAAAAATAA-A-GAACACA--------------------------------------------------------------------GCACACACAGACGAGAAGCGGA--------------GAACTTAATA---------ATATT-AACAGCAGTGTTGCCAATTCATTAATCGAATTTAC-ACAAAAA---------------------------------------------------------------------------------TTTACCAGAA----AGTGGCAGTCACTTTATAAATGTGTATTAAACTAGAAACTATAAACTATATAAATTGGAAAA-CT-CCATT----TATTATAAAT-GTGTATTAAACTAGAAGCTATAAAC----------------------TATAT---AAATTG-----------GAAAACTCCAT----------------------------------------------TTAT---TA-	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
.................................AAGAAACTG------------AATAACGCGATAACGG..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	25	1	2.00	2	2	0	0	0	0	0	0	0	0	0	0

droEug1

AGAGAATAATT-TAA------ATAAT-ATGCCAAAGAAACTG------------AATAATACGATAACGGGTAAGT------GTG---------------------------------AGTAATTAAT------------------------------------------------------------------------------GTTT------TAGA-TTCGAAAAT-----A------------------------------------------------------------ACATAGCAGA--AC-ATAGCACGGGAGAGGGGAGAAGTACTAAATA---------ATATT-AACAGCAGTGTTGCCAATTTTAGG---TTTTATGACCCAAACT---------------------GGTCAGA---GAAATGTCTTAAATA-----------------------AAT-------------ATGAAA-----------------ATATGTAACTGAAAGA-----------------------------------CATGTTT----AAAAATTGAT-TTC----------------------------------------AAATT-----CTT------------------------------------------------------------------TTAAACTATAT---CAA	Size	Hit Count	Total Norm	Total
No Reads

droBia1

GGAGAACAACC-TGA------ACAAC-ATGCCAAAGAAAGTG------------AACAACGCAATCACGGGTAAGT------TCT------------A-----------------GCACCTAAATG------------------------------------------------------------------------------ACCTGC------GAAA-CTCTACA--------------------------------------------------------------------GCACAC-----------GAGAG--------------AAAGTGAAAAGTATTG---TTGCGTAACAGCAGTGTTGCCAATTCTCTGAGCGAAACTAT-CTCAAAC---------------------------------------------A-----------------------AAG-------------ACAGTC--------------------------------------------------------AGAAGTAGCCTGAATAA----------------------------------------AG----------------------GATAATTGTATTGT-----------CTAAAGACTGT----------------------------------------------ATCT---CGA	Size	Hit Count	Total Norm	Total
No Reads

droTak1

AGAGAATAATT-TAA------ACAAT-ATGCCAAAGAAACTG------------AATAACGCAATAACGGGTAAGT------GCA---------------------------------ATTAAATC--------AA-------------------------------------------AAATAAT------------------------------AA-A-ATTCACA----------------------------------------------------------------------ACACACAG--GCGAAGCAAA--------------AAACG-AATT-----ATATAT-TTAAAGAGCAGTGCTGCCAATTTTTTAATCGAAAATTG-GTCGAAT---------------------------------------------A-----------------------AAA-------------CTAGTT--------------------------------------------------------AT-----------------------------------------------------AAAGTTTATTTTTTAGATTTTTAAA-----TACTTTTGTT-----------ATAAAAACTGT----------------------------------------------A-AT---TAA	Size	Hit Count	Total Norm	Total
No Reads

droEle1

AGAGAATAATT-TAA------ACAAT-ATGCCAAAGAAACTG------------AATAACACGATAACGGGTAAGT------GCA---------------------------------AGTAATTAAGTTAAAC----------------------------------------------------------------------------------AAAA-TTCCACAACA-CACACACACGCACACCCCCTTTCACACACACACACACACCCCAACTCTCACACACATAGACATAACACGCACAG--GCGTACAGAG--------------AATTTGATTC---------AT-TTGTTTAGCAGTGTTGCCAATTGTTTAATTAAACTTAA-ATCTCAT---------------------------------------------T-----------------------ACG-------------AAAAATATAAAAAGCTTGTTAATATATGTATATGTATGAG--------------------TAAAATCGAAATCCTATGATT----AATATTTAAT-ATG----------------------------------------TTATG------TTACTTATAAAAAAAGAAGA--AAATTAT----------------------------------------------AATT---TAA	Size	Hit Count	Total Norm	Total
No Reads

droRho1

AGAGAATAATT-TAA------ACAAT-ATGCCAAAGAAACTG------------AATAACACGATAACGGGTAAGT------GTA---------------------------------ATTTAATA------------------------------------------------------------------------------AAAAAT------AAAA-TTCCACAAC-----ACACACGCACACTCCCACTTACACACACACACACAT---------------------------ACACAAAT--GCGTAGAGAA--------------AAACT-GATA---------ACATTGTTCAGCA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droFic1

AGAGAATAATT-TAA------ACAAT-ATGCCAAAGAAATTA------------AACAACACGATAACGGGTAAGT------GCT---------------------------------TTTAATTTTAATAAAT----------------------------------------------------------------------------------AA-G-AAACACAAAACCTAACACACGCACAC-CCAACTCACACATACACGCACAC---------------------------ACACACA-------AGCGAA--------------AAATTGATCA---------ACTTTATTCAGCAGTGTTGCCAATTCTTAAAAGAAATGCAT-CCCAAAT-----------------TATTCGTCAGAAATGG-ATGCGTTAAATGTTATATTACAATGTAATTTAATACGCACGAAAAAATGTGAAATTA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAATTTGATAAATTAGTGAACTGAACTGTTTTAAAAAATTTTAA---ATATAGACAA	Size	Hit Count	Total Norm	Total
No Reads

droKik1

ATATAATATTA-AAAAAACCAGA----AA-GAAAATGCAACAAAAGAAAACCACGATAAAACAATA-----TAATAGTGAATGTTTAATGATAATTCAAGATCAAAAGGACAACAACAAATATA-CATCCAGCTGAAACAAAATGAAATCTATATACATTATACAGTTTTTTTTATAATTTATAATA-----------------ACAAAC------AAA----------------------------------------------------------------------------------------------------------------------CGGC----------------------------------------ATCAAAATTTG-TTTATAA---------------------------------------------------------------------------------TTTACAAGTG--------------------------------------------------------AAATTTGGCTTAAACAAATGAAAAACAATT-GAAACT---T---------------GGT----------------------TATATT----------------------------TT----------------------------------------------ATAA---TAG	Size	Hit Count	Total Norm	Total
No Reads

droAna3

AGAGAATAATT-TAA------GCAAC-ATGCCAAAGAAACTA------------AATAACACAATAACTGGTAAGT------G-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
No Reads

droBip1

AGAGAATAATT-TAA------GCAAC-ATGCCAAAGAAACTA------------AACAACCCAGTAACTGGTGAGT------ATT-----------------------------------TAAAAAA-------------------------------------------------------------------------------TAAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAT------------------------AAT----------------------------------------------AATT---AAG	Size	Hit Count	Total Norm	Total
No Reads

dp5

AACAAC-ACCA-ATA------G--CT-GCATCAACAACTCCA------------AATGAAGCAATAACTTCCAC--------------------------TT--CACGGATAACTACACCAAAA-ATTCCAGCTAGACCAACA-------------------------------------------TC----------------------------------AAAGCC----------------------------------------------------------------------AAACACAG--TTGCAGCAAA--------------GGA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

Total

M022
Male-body

M040
Female-body

M059
Embryo

M062
Head

V043
Embryo

V051
Head

V112
Male-body

SRR902010
Ovary

SRR902011
Testis

SRR902012
CNS imaginal disc

No Reads

droPer2

AGAGAATAGTTTTAA------ACAAT-ATGCCAAAGAAATTG------------A-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
No Reads

droWil2

AAATGT-GCTT-GTG------AAATG-GTGTCTAAAACTTAA------------AACAAACAAATAATT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATT----------------------TATATATATATATA-----------GAAA----TAT----------------------------------------------ATAT---ATA	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
.AATGT-GCTT-GTG------AAATG-G....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	1	0	0	0	0	1

droVir3

AGCAGC-AGCA-GCA------GCATG-ATGAGAAAATAATTT------------AATAAT-------------------------------------------------------------AATTACTGAAAACAA-------------------------------------------AAAGAATTA----------------------------------TGT-AA--------------------------------------------------------------------GCATAAACAT--TTAAAGCGAG--------------AAAGCTACCA---------ACAA--CACAGCA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	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
............GCA------GCATG-ATGAGAAAAT...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	1	2.00	2	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	1	0	0
............................................................................................................................................................................................................................................................................................................AAACAT--TTAAAGCGAG--------------AAAGC...............................................................................................................................................................................................................................................................................................................................................................................................	21	1	2.00	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
.................................................................................................................................................................................................................................................................................................................T--TTAAAGCGAG--------------AAAGCTACCA---------.................................................................................................................................................................................................................................................................................................................................................................................	21	1	2.00	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
............................................................................................................................TACTGAAAACAA-------------------------------------------AAAGAAT......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	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
.......................................................................................................................................A-------------------------------------------AAAGAATTA----------------------------------TGT-AA--------------------------------------------------------------------GCATAA..................................................................................................................................................................................................................................................................................................................................................................................................................................	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
...AGC-AGCA-GCA------GCATG-ATGAGA...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
...........................................................................................................................................................................................A----------------------------------TGT-AA--------------------------------------------------------------------GCATAAACAT--TTAAAGCGAG--------------....................................................................................................................................................................................................................................................................................................................................................................................................	26	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
..................................................................................................................................................................................................................................AA--------------------------------------------------------------------GCATAAACAT--TTAAAGC.....................................................................................................................................................................................................................................................................................................................................................................................................................	19	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
AGCAGC-AGCA-GCA------GCATG-AT...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	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
.......AGCA-GCA------GCATG-ATGAGAAAAT...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	22	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
................................................................................................................................GAAAACAA-------------------------------------------AAAGAATTA----------------------------------TGT-AA--------------------------------------------------------------------........................................................................................................................................................................................................................................................................................................................................................................................................................................	22	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
..........................................................AT-------------------------------------------------------------AATTACTGAAAACAA-------------------------------------------AA...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	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
........GCA-GCA------GCATG-ATGAGAAAA............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	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
.................................................................................................................................................................................................................................................................................................................T--TTAAAGCGAG--------------AAAGCTACCA---------ACA..............................................................................................................................................................................................................................................................................................................................................................................	24	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
............GCA------GCATG-ATGAGAAAATAAT........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	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	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
..............A------GCATG-ATGAGAAAATAA.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
......................................................................................................................................................................................................................................................................................................................AAAGCGAG--------------AAAGCTACCA---------ACAA--CA.........................................................................................................................................................................................................................................................................................................................................................................	24	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
AGCAGC-AGCA-GCA------GCATG-ATGAGAAAAT...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	28	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	1	0	0	0
........GCA-GCA------GCATG-ATGAGAA..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	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	1	0	0	0
.............................................................................................................................................................................................................................................................................................................................................AAGCTACCA---------ACAA--CACAGC.....................................................................................................................................................................................................................................................................................................................................................................	19	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
......................................................................................................................................................................................................................................................................................................................AAAGCGAG--------------AAAGCTACCA---------ACAA--CACA.......................................................................................................................................................................................................................................................................................................................................................................	26	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
.......................................................................................................................................................................................................................................................................................................................AAGCGAG--------------AAAGCTACCA---------ACAA--CA.........................................................................................................................................................................................................................................................................................................................................................................	23	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
...............................................................................................................................................................................................................................GT-AA--------------------------------------------------------------------GCATAAACAT--TTAAAGCGA...................................................................................................................................................................................................................................................................................................................................................................................................................	23	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
............................................................................................................................TACTGAAAACAA-------------------------------------------AAAGAATT.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	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
...AGC-AGCA-GCA------GCATG-ATGAGAAAAT...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	25	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	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
....................................................................................................................................ACAA-------------------------------------------AAAGAATTA----------------------------------TGT-AA--------------------------------------------------------------------GCAT....................................................................................................................................................................................................................................................................................................................................................................................................................................	22	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
.GCAGC-AGCA-GCA------GCATG-ATGAGAAAATA..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	28	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
....................................................................................................................................................................................................................................................................................................................TTAAAGCGAG--------------AAAGCTACCA---------AC...............................................................................................................................................................................................................................................................................................................................................................................	22	1	1.00	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.GCAGC-AGCA-GCA------GCATG-ATGAGAA..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	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	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
...................................................................................................................................................................................AAAGAATTA----------------------------------TGT-AA--------------------------------------------------------------------GCAT....................................................................................................................................................................................................................................................................................................................................................................................................................................	18	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	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
..........................................................................................................................ATTACTGAAAACAA-------------------------------------------AAAGAAT......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	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
..........A-GCA------GCATG-ATGAGAAAAT...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	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	1	0	0	0
.......AGCA-GCA------GCATG-ATGAGAA..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	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
.....C-AGCA-GCA------GCATG-ATGAGAAAAT...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
..........................................................................................................................................................................................................................................................................................................................CGAG--------------AAAGCTACCA---------ACAA--CACAGC.....................................................................................................................................................................................................................................................................................................................................................................	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	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
.........................................................................................................................AATTACTGAAAACAA-------------------------------------------AAAGAAT......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	22	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
...................................................................................................................................AACAA-------------------------------------------AAAGAATTA----------------------------------TGT-AA--------------------------------------------------------------------GCAT....................................................................................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................................A--------------------------------------------------------------------GCATAAACAT--TTAAAGC.....................................................................................................................................................................................................................................................................................................................................................................................................................	18	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
............................................................................................................................................................................................................................................................................................................................................AAAGCTACCA---------ACAA--CACAGC.....................................................................................................................................................................................................................................................................................................................................................................	20	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
................................................................................................................................................................................................................................................................................................................AT--TTAAAGCGAG--------------AAAGCTACC...........................................................................................................................................................................................................................................................................................................................................................................................	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
....................................................................................................................................................................................AAGAATTA----------------------------------TGT-AA--------------------------------------------------------------------GCATAA..................................................................................................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	1	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
.GCAGC-AGCA-GCA------GCATG-AT...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	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

droMoj3

CAATAACAACT-A--------GCAATAGTGGCAGATGCAACA------------GCAACAACAACTACAAGTAGCT------GCA---------------------------------TTAACA-GCTATCAGCAA-------------------------------------------CAATAACCA----------------------------------GAAGCA--------------------------------------------------------------------ACATATACAT--ACAACAGCAA--------------CAAA-TAGCA---------ACAATA-GCAGCAG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
No Reads

droGri2

ATCGATG-ACG-ATG------A--CG-ATAACGAAAACGATA------------ATCATCATAAGAACGAA---------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTAAGCACAG-TTAAG-CACAAATCCATTGACTA---------------------------AATATTA-------AG-------------------------------------------CGCATCA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

dsi_28249

x:12440872-12441021 -

Candidate

Unknown

Predicted structure

Flybase annnotation

Sense Strand Reads

Anti-sense strand reads

Re-alignment of all predicted orthologs

Re-alignment of all predicted orthologs with sRNA reads