dan_1106

Name	Class	Family	Strand
AT_rich	Low_complexity	Low_complexity	+

##################################################--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TGGACGCAAGGGTCATTTCCCATTCACGCATGTCGAGTTCGTCGATGATTGTGATTTAATCGATAACTCTAAATTTTTTAATGTTTCATTGCATGAAGAAAGAGAATCTATGGGACAATGAATAACAACACACAACTGTATTTAATATTAAATTTAAAATGAATTAACATTAAGTGGTGAGTTCCAGTTGTTAATATATTTAAAATACTATGTAACAAAAAAAAAATGGATGTATTTTATTTGGGAGTCGA *************************************************************************************************.......................(((((((....((((.((((((((.((((.((......)).)))).))))))))...))))...)))))))..******************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V106 head	V105 male body	M058 embryo	V039 embryo	V055 head	M044 female body
........................................................................................................................................................................ATTAAGTGGTGAGTTCCAGTTGTTAAT........................................................	27	0	1	2.00	2	1	1	0	0	0	0
...................................................................................................AAGAGAATCTATGGGACAATGAATAACA............................................................................................................................	28	0	1	1.00	1	0	1	0	0	0	0
....................................GTTCGTCGATGATTGTGAT....................................................................................................................................................................................................	19	0	1	1.00	1	0	0	0	1	0	0
.........................................................................................................................................................................TTAAGTGGTGAGTTCCAGTTGTTAAT........................................................	26	0	1	1.00	1	0	0	0	1	0	0
............................................................................................................................................................................AGTGGTGAGTTCCAGTTGTTAATAT......................................................	25	0	1	1.00	1	1	0	0	0	0	0
............................................................................................ATGAAGAAAGAGAATCTATGG..........................................................................................................................................	21	0	1	1.00	1	0	0	1	0	0	0
...............................................................................AATGTTTCATTGCATGAAGAAAGAGA..................................................................................................................................................	26	0	1	1.00	1	0	1	0	0	0	0
....................................GTTCGTCGATGATTGTGATTTAAT...............................................................................................................................................................................................	24	0	1	1.00	1	1	0	0	0	0	0
.......................................................................................ATTGCATGAAGAAAGAGA..................................................................................................................................................	18	0	1	1.00	1	0	0	0	0	1	0
............................................................................................ATGAAGAAAGAGAATCTATGGGA........................................................................................................................................	23	0	1	1.00	1	0	0	1	0	0	0
..........................................CGATGATTGTGATTTAATCGATAACC.......................................................................................................................................................................................	26	1	1	1.00	1	0	0	1	0	0	0
.............................ATGTCGAGTTCGTCGATGATTGTGA.....................................................................................................................................................................................................	25	0	1	1.00	1	1	0	0	0	0	0
.......................................................................................ATTGCATGAAGAAAGAGAATC...............................................................................................................................................	21	0	1	1.00	1	1	0	0	0	0	0
............................................................................................................................................................................AGTGGTGAGTTCCAGTTGTT...........................................................	20	0	1	1.00	1	0	1	0	0	0	0
..............................TGTCGAGTTCGTCGATGATTGTG......................................................................................................................................................................................................	23	0	1	1.00	1	1	0	0	0	0	0
........................................................................................................................AATAACAACACACAACTGC................................................................................................................	19	1	2	0.50	1	0	0	1	0	0	0
...............................................................................................................GTGACAATGAATAACGATACA.......................................................................................................................	21	3	3	0.33	1	0	0	0	0	0	1
.........................................................................................TGCTTGAAGAATGAGAAGCT..............................................................................................................................................	20	3	6	0.17	1	0	0	0	0	1	0
.......................................................................................ATGGCATGAGGAAAGAGA..................................................................................................................................................	18	2	7	0.14	1	1	0	0	0	0	0
.....................................................................................................................................................................AACATAAAGTGGTAAGTT....................................................................	18	2	9	0.11	1	0	0	0	0	1	0
...........................................................................................................................................................................................................AATCCTATGTAACACAATAAA...........................	21	3	10	0.10	1	0	0	1	0	0	0
.................................................................................................................AACAACGACTAACAACACACAA....................................................................................................................	22	3	12	0.08	1	0	0	1	0	0	0

ACCTGCGTTCCCAGTAAAGGGTAAGTGCGTACAGCTCAAGCAGCTACTAACACTAAATTAGCTATTGAGATTTAAAAAATTACAAAGTAACGTACTTCTTTCTCTTAGATACCCTGTTACTTATTGTTGTGTGTTGACATAAATTATAATTTAAATTTTACTTAATTGTAATTCACCACTCAAGGTCAACAATTATATAAATTTTATGATACATTGTTTTTTTTTTACCTACATAAAATAAACCCTCAGCT ******************************************************.......................(((((((....((((.((((((((.((((.((......)).)))).))))))))...))))...)))))))..*************************************************************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V055 head	V039 embryo	M058 embryo	M044 female body
...TGGGTTTCCAGTAATGGGTAA...................................................................................................................................................................................................................................	21	3	2	0.50	1	1	0	0	0
.......TTCCCAATATAGGGTTAGTG................................................................................................................................................................................................................................	20	3	6	0.17	1	1	0	0	0
...........................................................................................................................TTGTTGTGGGTTGGCATA..............................................................................................................	18	2	7	0.14	1	0	1	0	0
.............................................................................................................................................................................CACCACTTAAGGTCAACTAG..........................................................	20	3	9	0.11	1	0	0	1	0
...........................................................................................................................TTGTTGTGTGTTGGTATA..............................................................................................................	18	2	20	0.10	2	0	2	0	0
...............AAAGGGTTAGTACGTGCAG.........................................................................................................................................................................................................................	19	3	20	0.05	1	0	1	0	0
..............................................................................................................................................................................ACCACTCAAGGGGCACAA...........................................................	18	3	20	0.05	1	0	0	0	1

Species	Coordinate	ID	Alignment
droAna3	scaffold_13034:1711321-1711571 +	dan_1106	TGGACGCAAGGG---------------T-CATTTCCCAT-TCACGCATGTCGAGTTCGTCGA---------------------------------------------TGATTGTGATTTAATCGATAACTCTAAATTTTTTAATGTTTCATTGCATGAA-----------GAAAGAGAATCTATGGGACAATGAATAA-------CAACACAC-----AA------CT---GTATTTAATA----------------TTAAA-----TTTAAAATGAATT------------AACATTAAGTGGTGAGTTCCAGTTGTTAATA----TATTTAAAATACTATGTA--------ACAAA----------AAA----AAAA----TGGATGTATTTTATTTGGGAGTCGA
droBip1	scf7180000395637:2382-2594 -		TGGGCGCAAGGG---------------T-CACTTTCCAT-TTACGCATGTTGAGTTTGTCGA---------------------------------------------TGATTGTGATTTAAGCGATAACTCTAAATTTTTAAATGTTCGAATGCATGAA----------------GAAAA-----GGACAATGAATAA-CA----TAAAATAA-----AA------AT---------GTAT----------------TTGAAATAAATTTAT-------A------------AAGATAA-------------AGTTGTTAATA----TATTTAAAATACTATGTA--------ATCAA----------TAAAAAAAT-ATT-GTGGATGTAT---------------T
droKik1	scf7180000301925:10512-10690 -		TGGTCGAAACGG---------------T-CACTTCCCAT-TTACGCACGTTGAATTCGTCGA---------------------------------------------CGACTGTGATTTAG------------CA------GAGTTACGTTCAAATGGCA-----CCAGTAAAAGTGAATGGG---AACAATAAG-AAAAAAAAATA------TGTTCA--------TCTAATTCTTATT-----------------TAAAGTTAAATGTAT-------T--------------------------TAAAACAATTGTTAATA----TAATCAAGA------------------------------------------------------------------------
droFic1	scf7180000454086:120268-120491 -		TGGAAGAAACGG---------------A-CACTTTCCAT-TCACGCACGTTGAATTTGTCGA---------------------------------------------CGATTGTGATTTAGGCAATAACTCCTCA------GAATTACGATAA-GAGACGATAAGGC---AAGAACGATGGGATAGAAAATTAACTA--------A--------------TTTTCCAGATCTTATGTATTT----------------TGAAGTTAAATGTAT-------T------------AAACCTAAGTTGTGAAAATTAATTGTTAAAA----TAATCAGGAAATTAAATA--------TTCAA----------TATAA--------A-------------------------A
droEle1	scf7180000491238:1236881-1237105 -		TGGGAGAAATGG---------------T-CACTTCCCAT-TCACGCACGTTGAATTTGTCGA---------------------------------------------TGATTGTGATTTAGGCAATAACTCCGCG------GAGATACGGTAA-ATGGCA--------GTAAAAGTGAATGGG----GCATTGAATC--------T--------------TTTTCTGAATCATTTTAACTT----------------TTAAATTAAATGTAA-------T------------AAACCTAAGTTGTGCAAACCAATTGTTAACA----TAATCAGAAAAGTAAATA--------AATA------TTG---------GAAATAAACGGGTA------------------T
droRho1	scf7180000779182:17980-18147 -		TGGGAGAAATGG---------------T-CACTTTCCAT-TCACGCACGTTGAATTTGTCGA---------------------------------------------TGATTGTGATTAA-----------------------------------------------------------------------TGAATC--------T--------------TATTCTCTATAATTTTAATTT----------------GTAAGTTAAATGTAT-------T------------AAACCTAAGTTGTGCAAACCAATTGTTATCA----TAATCAAAAAATTAAATA--------AACAT----------TAA----------------------------ATGAGTTTA
droBia1	scf7180000302087:82746-82953 -		TGGAAGAAATGG---------------T-CACTTCCCAT-TCACGCACGTTGAATTTGTCGA---------------------------------------------TGATTGTGATTTAGGCAATAACTCCACA------GAAATACGGTAA-ATGCCG--------GTACGACCGAATGGATAAAACAATGAACC--------T----------------ACCCGCATCATTTTTGTTT----------------TTAAGTTAACTGTAT-------A------------AAAATTAAGTT--GCAAACCAATTGTTAACA----TAATCAGAAAATTAAATA--------ATCA--------------------------------------------------A
droTak1	scf7180000415295:7549-7772 +		CGGGAGACATGG---------------T-CACTTCCCAT-TCACGCACGTTGAATTTGTCGA---------------------------------------------TGATTGTGATTTAGGTAATAACTCCACA------GAAATACGGTAA-ATGATG--------GTAGGAGCGAACGGGTAGAACAGTGAATC--------T--------------TTCTTCGGATCATTTTTATTT----------------TTAAGTTAGATGTAT-------G------------AAAATTAAGTTGTGTAAACCAATTGTTAACA----TAATCGGAAAATTAAATA--------ATCAA----------TAA----------------------------TTTATTTGG
droEug1	scf7180000406964:170123-170193 +		TGGAAGAATGGG---------------C-CATTTTCCAT-TCACGCATGTTGAATTTGTTGA---------------------------------------------TGATTGTGATTTATTTAAAACCTCCA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
dm3	chr4:233557-233774 +		TGGAAAAAATGG---------------T-CATTTTCCCT-TCACGCACGTTGAATTTGTCGA---------------------------------------------TGATTGTGATTTAAGCAAAAACTCCACA------GAAATATGCTAA-AT--------------AGGAAGGAATGGAA-------GGAA----------T--------------TTCTTTTGATAATTTTGATTT----------------TTGAGCTAATTGTAT-------G------------ATTAATAAGTTGTGCATACCAATTGTTAACA----TAATCAGAAAATTAAAATCTTATTAA-----GTAAAATA---------AAAATAAACG-----------------------
droSim2	4:181336-181553 +		TGGAAAAAATGG---------------T-CATTTTCCGT-TCACACACGTTGAATTTGTCGA---------------------------------------------TGATTGTGATTTAAGCAAAAACTCTACA------GAAATACGCTAA-AT--------------AGGAAGGAATGGAA-------TAAATA--------T--------------TCCTTTCGATAATTTTAATTT----------------TAAAGCTAATTGTAT-------G------------AATAATAAGTTGTGCATACCAATTGTTACCA----TAATCAGAAAATTAAAATCCTTATAA-----GTGAAATA---------AAAATAA-------------------------A
droSec2	scaffold_52:180796-181013 +		TGGAAAAAATGG---------------T-CATTTTCCGT-TCACACACGTTGAATTTGTCGA---------------------------------------------TGATTGTGATTTAAGCAAAAACTCTACA------GAAATACGCTAA-AT--------------AGGAAGGAATGGAA-------TAAATA--------T--------------TCCTTTCGATAATTTTAATTT----------------TTAAGCTAATTGTAT-------G------------AATAATAAGTTGTGCATACCAATTGTTACCA----TAATCAGAAAATTAAAATCCTTATAA-----GTGAAATA---------AAAATAA-------------------------A
droYak3	4:216550-216765 +		TGGAAAAAATGG---------------T-CACTTTCCCT-TCACGCACGTTGAATTTGTCGA---------------------------------------------TGATTGTGATTTAAGCAAAAACTCAACA------GAAATACGCTAA-CT--------------AAGAACGAATTGAA-------TACATT--------T--------------TTCTTTGGACCATTTCAATTT----------------TTAAGCTAATTGTAT-------G------------AATAATAAGTTGTGGAAATCAATTGTTAACA----AAATCAGAAAATTATACATTTAATAA-----CTAAAATG---------GAAATA---------------------------
droEre2	scaffold_4512:1076899-1077120 -		TGGAAAAAATGG---------------C-CACTTTCCCT-TCACGCACGTTGAATTTGTTGA---------------------------------------------TAATTGTGATTTAAGCAAAAACTCCACA------GAAATACGCTAG-CT--------------AAGAACAAATGGAA-------TAAATA--------T--------------TTCTTTGGACCATTTCGATTT----------------TTAAGCTAATTGTAT-------G------------AATAATAAGTTGTGAAAACCAATTGTTAACA----TAATCAGAAAATTAAATA--------ATTAACTGAAATG---------GAAATAAACGGGTA------------------T
dp5	Unknown_group_15:7095-7322 +		TGGACGCAAGGG---------------C-CACTTCCCAT-TCACTCACGTTGAATTTGTCGA---------------------------------------------TGATTGTGATTTAGGAAATAACTGTGGA------GAGGTACGTTTAAATAGCG-----CC---AGTAACGATTGGGTGGAACAATAA-----------TA------TTTTCA---TTTTGTATAATTTTTATTTAAATTTATGA-----------CAAAATGTATCAAGAAAT------------AACAGTAAGTGGTGCATACCAATTGTTAATACATATATTTAAAATATTTAATA------------------------------------A-------------------------A
droPer2	scaffold_42:37627-37854 -		TGGACGCAAGGG---------------C-CACTTCCCAT-TCACTCACGTTGAATTTGTCGA---------------------------------------------TGATTGTGATTTAGGAAATAACTGTGGA------GAGGTACGTTTAAATAGCG-----CC---AGTAACGATTGGGTGGAACAATAA-----------TA------TTTTCA---TTTTGTATAATTTTTATTTAAATTTATGA-----------CAAAATGTATCAAGAAAT------------AACAGTAAGTGGTGCATACCAATTGTTAATACATATATTTAAAATATTTAATA------------------------------------A-------------------------A
droWil2	scf2_1100000004943:1130751-1130983 -		AGGACGCAAAGG---------------C-CACTTTCCAT-TTACCCATGTTGAGTTTGTCGA---------------------------------------------TGATTGTGATTTAGGCAATAACAGTTCG------GACATTCGGATAAATACGG-CC-TCC---AGCAACGATTGGGTGGAACAATAA-----------TA---CGCATGTCATTTCTCTGGGTAATTTGTATTTAACAT-----------TAAGTTCAAATGTATCAAAAACT-----------TGCTAGTAGGTGGTGCATACCAATTGTTAATA----TATTAAACATATTGATTA--------------------------------------------------------------A
droVir3	scaffold_13052:1422473-1422702 -		TGGACGCAAGGG---------------C-CATTTTCCAT-TTACGCACGTCGAATTTGTCGA---------------------------------------------TGATTGTGATGTAA---ATAATTGTGCG------GATATTCGATTAAATAA-----------------CGATTGGGCGGAACAACAA-----------TAA-----TTTTCA------ATTATAACTTATATT-----------------TTAAGTTAAGAGAAT-------ATATTAAATTGTAATGAATAAGTGATGTTTACCAATTGTTAAAA----TATTAAACATATTGATTA--ATCTTA-----GAAAATTCAAAAGAA--------A-------------------------A
droMoj3	scaffold_6498:374179-374382 -		TGGGCGAAAAGG---------------T-CATTTTCCTT-TTACGCACGTTGAATTTATCGA---------------------------------------------TGATTGTGATTTAACCAATATTTGCGCA------GATGTTCGATTAAATAC-----------------TGATTGGGTGGATCAACAAA----AA----TAATATTC-----AA------TT---ATATTT----------GTCGTGTATTGTAGCTTAA--GAAT-------A------------TATATTAAGTGATGTTTACCAATTGTTAAAA----TATTAAACATATTGATTA--------------------------------------------------------------A
droGri2	scaffold_15203:7587597-7587788 -		TGCTTGCAAATTAATTAATAGTTTAGTCCGACTTTCAATGTTATACACTATAAACTATAAGATATAATATAATTATGTAAATAATATAATATAAAATGCATGCATTATAATTGTAATTAGT------------CC------AACTTAA--------------------------------------------------------------------------CTTTG-----------------------------------------------------------------------------------------------------------AATA--ATACTCAATTTTA-----GTAAAAAA---------AAAAAGA-AAGATGTATTTTTTATATACGTCAA

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droAna3

TGGACGCAAGGG---------------T-CATTTCCCAT-TCACGCATGTCGAGTTCGTCGA---------------------------------------------TGATTGTGATTTAATCGATAACTCTAAATTTTTTAATGTTTCATTGCATGAA-----------GAAAGAGAATCTATGGGACAATGAATAA-------CAACACAC-----AA------CT---GTATTTAATA----------------TTAAA-----TTTAAAATGAATT------------AACATTAAGTGGTGAGTTCCAGTTGTTAATA----TATTTAAAATACTATGTA--------ACAAA----------AAA----AAAA----TGGATGTATTTTATTTGGGAGTCGA	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
.......................................................................................................................................................................................................................................................................................................ATTAAGTGGTGAGTTCCAGTTGTTAAT......................................................................................	27	1	2.00	2	0	0	0	0	1	1
............................................................................................................................................................................AAGAGAATCTATGGGACAATGAATAA-------CA.........................................................................................................................................................................................................	28	1	1.00	1	0	0	0	0	1	0
.....................................................GTTCGTCGA---------------------------------------------TGATTGTGAT...................................................................................................................................................................................................................................................................................................	19	1	1.00	1	0	0	1	0	0	0
........................................................................................................................................................................................................................................................................................................TTAAGTGGTGAGTTCCAGTTGTTAAT......................................................................................	26	1	1.00	1	0	0	1	0	0	0
...........................................................................................................................................................................................................................................................................................................AGTGGTGAGTTCCAGTTGTTAATA----T................................................................................	25	1	1.00	1	0	0	0	0	0	1
..........................................................................................................................................................ATGAA-----------GAAAGAGAATCTATGG..............................................................................................................................................................................................................................	21	1	1.00	1	0	1	0	0	0	0
.............................................................................................................................................AATGTTTCATTGCATGAA-----------GAAAGAGA......................................................................................................................................................................................................................................	26	1	1.00	1	0	0	0	0	1	0
.....................................................GTTCGTCGA---------------------------------------------TGATTGTGATTTAAT..............................................................................................................................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	1
.....................................................................................................................................................ATTGCATGAA-----------GAAAGAGA......................................................................................................................................................................................................................................	18	1	1.00	1	0	0	0	1	0	0
..........................................................................................................................................................ATGAA-----------GAAAGAGAATCTATGGGA............................................................................................................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0
...........................................................CGA---------------------------------------------TGATTGTGATTTAATCGATAACC......................................................................................................................................................................................................................................................................................	26	1	1.00	1	0	1	0	0	0	0
..............................................ATGTCGAGTTCGTCGA---------------------------------------------TGATTGTGA....................................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	0	0	0	0	1
.....................................................................................................................................................ATTGCATGAA-----------GAAAGAGAATC...................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	1
...........................................................................................................................................................................................................................................................................................................AGTGGTGAGTTCCAGTTGTT.........................................................................................	20	1	1.00	1	0	0	0	0	1	0
...............................................TGTCGAGTTCGTCGA---------------------------------------------TGATTGTG.....................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	1
.................................................................................................................................................................................................AATAA-------CAACACAC-----AA------CT---GC...............................................................................................................................................................................	19	2	0.50	1	0	1	0	0	0	0

droBip1

TGGGCGCAAGGG---------------T-CACTTTCCAT-TTACGCATGTTGAGTTTGTCGA---------------------------------------------TGATTGTGATTTAAGCGATAACTCTAAATTTTTAAATGTTCGAATGCATGAA----------------GAAAA-----GGACAATGAATAA-CA----TAAAATAA-----AA------AT---------GTAT----------------TTGAAATAAATTTAT-------A------------AAGATAA-------------AGTTGTTAATA----TATTTAAAATACTATGTA--------ATCAA----------TAAAAAAAT-ATT-GTGGATGTAT---------------T	Size	Hit Count	Total Norm	Total
No Reads

droKik1

TGGTCGAAACGG---------------T-CACTTCCCAT-TTACGCACGTTGAATTCGTCGA---------------------------------------------CGACTGTGATTTAG------------CA------GAGTTACGTTCAAATGGCA-----CCAGTAAAAGTGAATGGG---AACAATAAG-AAAAAAAAATA------TGTTCA--------TCTAATTCTTATT-----------------TAAAGTTAAATGTAT-------T--------------------------TAAAACAATTGTTAATA----TAATCAAGA------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droFic1

TGGAAGAAACGG---------------A-CACTTTCCAT-TCACGCACGTTGAATTTGTCGA---------------------------------------------CGATTGTGATTTAGGCAATAACTCCTCA------GAATTACGATAA-GAGACGATAAGGC---AAGAACGATGGGATAGAAAATTAACTA--------A--------------TTTTCCAGATCTTATGTATTT----------------TGAAGTTAAATGTAT-------T------------AAACCTAAGTTGTGAAAATTAATTGTTAAAA----TAATCAGGAAATTAAATA--------TTCAA----------TATAA--------A-------------------------A	Size	Hit Count	Total Norm	Total
No Reads

droEle1

TGGGAGAAATGG---------------T-CACTTCCCAT-TCACGCACGTTGAATTTGTCGA---------------------------------------------TGATTGTGATTTAGGCAATAACTCCGCG------GAGATACGGTAA-ATGGCA--------GTAAAAGTGAATGGG----GCATTGAATC--------T--------------TTTTCTGAATCATTTTAACTT----------------TTAAATTAAATGTAA-------T------------AAACCTAAGTTGTGCAAACCAATTGTTAACA----TAATCAGAAAAGTAAATA--------AATA------TTG---------GAAATAAACGGGTA------------------T	Size	Hit Count	Total Norm	Total
No Reads

droRho1

TGGGAGAAATGG---------------T-CACTTTCCAT-TCACGCACGTTGAATTTGTCGA---------------------------------------------TGATTGTGATTAA-----------------------------------------------------------------------TGAATC--------T--------------TATTCTCTATAATTTTAATTT----------------GTAAGTTAAATGTAT-------T------------AAACCTAAGTTGTGCAAACCAATTGTTATCA----TAATCAAAAAATTAAATA--------AACAT----------TAA----------------------------ATGAGTTTA	Size	Hit Count	Total Norm	Total
No Reads

droBia1

TGGAAGAAATGG---------------T-CACTTCCCAT-TCACGCACGTTGAATTTGTCGA---------------------------------------------TGATTGTGATTTAGGCAATAACTCCACA------GAAATACGGTAA-ATGCCG--------GTACGACCGAATGGATAAAACAATGAACC--------T----------------ACCCGCATCATTTTTGTTT----------------TTAAGTTAACTGTAT-------A------------AAAATTAAGTT--GCAAACCAATTGTTAACA----TAATCAGAAAATTAAATA--------ATCA--------------------------------------------------A	Size	Hit Count	Total Norm	Total
No Reads

droTak1

CGGGAGACATGG---------------T-CACTTCCCAT-TCACGCACGTTGAATTTGTCGA---------------------------------------------TGATTGTGATTTAGGTAATAACTCCACA------GAAATACGGTAA-ATGATG--------GTAGGAGCGAACGGGTAGAACAGTGAATC--------T--------------TTCTTCGGATCATTTTTATTT----------------TTAAGTTAGATGTAT-------G------------AAAATTAAGTTGTGTAAACCAATTGTTAACA----TAATCGGAAAATTAAATA--------ATCAA----------TAA----------------------------TTTATTTGG	Size	Hit Count	Total Norm	Total
No Reads

droEug1

TGGAAGAATGGG---------------C-CATTTTCCAT-TCACGCATGTTGAATTTGTTGA---------------------------------------------TGATTGTGATTTATTTAAAACCTCCA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

dm3

TGGAAAAAATGG---------------T-CATTTTCCCT-TCACGCACGTTGAATTTGTCGA---------------------------------------------TGATTGTGATTTAAGCAAAAACTCCACA------GAAATATGCTAA-AT--------------AGGAAGGAATGGAA-------GGAA----------T--------------TTCTTTTGATAATTTTGATTT----------------TTGAGCTAATTGTAT-------G------------ATTAATAAGTTGTGCATACCAATTGTTAACA----TAATCAGAAAATTAAAATCTTATTAA-----GTAAAATA---------AAAATAAACG-----------------------	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
......................................................................................................................................................TAA-AT--------------AGGAAGGAATGGAA-------GGAA----------T--------------T...........................................................................................................................................................................................	25	1	11.00	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	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	0	0	0	0	0	0	0	0	0	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
................................................................................................................................................................................................................................................T----------------TTGAGCTAATTGTAT-------G------------ATTAATAAGT..........................................................................................................	27	1	10.00	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	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	1	0	0	0	4	0	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
.............................................................................................................................................................................................................................TCTTTTGATAATTTTGATTT----------------TTGAGC.................................................................................................................................................	26	1	10.00	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	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	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	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	2	0	0	0	2	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
......................................................................................................................................................TAA-AT--------------AGGAAGGAATGGAA-------GGAA----------T--------------TTC.........................................................................................................................................................................................	27	1	9.00	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	4	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	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	1	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
.............................................................................................................................................................................................................T--------------TTCTTTTGATAATTTTGATTT----------------TTGAGC.................................................................................................................................................	28	1	8.00	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	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	1	0	0	0	0	0	0	0	0	0	0	1	1	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
..........................................................TCGA---------------------------------------------TGATTGTGATTTAAGCAAAAAC.......................................................................................................................................................................................................................................................................................	26	1	7.00	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	5	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
...............................................................................................................................................................................................................................TTTTGATAATTTTGATTT----------------TTGAGC.................................................................................................................................................	24	1	7.00	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	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	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0
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.....................................................................................................................................................................................................................................TAATTTTGATTT----------------TTGAGCTAATTG...........................................................................................................................................	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
.............................................................A---------------------------------------------TGATTGTGATTTAAGCAAAAA........................................................................................................................................................................................................................................................................................	22	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
.....................................................ATTTGTCGA---------------------------------------------TGATTGTGATTTAAGCA............................................................................................................................................................................................................................................................................................	26	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	0	0	0	0	0	0	0	1	0	0	0	0	0

droSim2

TGGAAAAAATGG---------------T-CATTTTCCGT-TCACACACGTTGAATTTGTCGA---------------------------------------------TGATTGTGATTTAAGCAAAAACTCTACA------GAAATACGCTAA-AT--------------AGGAAGGAATGGAA-------TAAATA--------T--------------TCCTTTCGATAATTTTAATTT----------------TAAAGCTAATTGTAT-------G------------AATAATAAGTTGTGCATACCAATTGTTACCA----TAATCAGAAAATTAAAATCCTTATAA-----GTGAAATA---------AAAATAA-------------------------A	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
...............................................................................................................................................AATACGCTAA-AT--------------AGGAAG........................................................................................................................................................................................................................................	18	1	3.00	3	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...................................................................................................................................TACA------GAAATACGCTAA-AT--------------AGGAAGGAA.....................................................................................................................................................................................................................................	27	1	2.00	2	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0
........................................................................................................................AGCAAAAACTCTACA------GAAATACGC..................................................................................................................................................................................................................................................................	24	1	2.00	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0
............................................................................................................................................................................................................................................AATTT----------------TAAAGCTAATTGTAT-------G------------AATA................................................................................................................	25	1	1.00	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0
....................................................................................................................................ACA------GAAATACGCTAA-A.............................................................................................................................................................................................................................................................	16	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
.................................................................................................................................................TACGCTAA-AT--------------AGGAAGGAATGGAA-------TAA......................................................................................................................................................................................................................	27	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
..............................................................................................................................................................................................................................................................................................................TGTGCATACCAATTGTTACCA----TAATCAGA.........................................................................	29	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
...........................................................................................................................................................................................................................................................................................................................................CAGAAAATTAAAATCCTTATAA-----GT................................................	24	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
...............................................................................................................................................................................................................................................TT----------------TAAAGCTAATTGTAT-------G------------AATAATAAGT..........................................................................................................	28	1	1.00	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0
................................................................................................................................................................................................................................................T----------------TAAAGCTAATTGTAT-------G------------AATAATAAGT..........................................................................................................	27	1	1.00	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0
......................................................TTTGTCGA---------------------------------------------TGATTGTGATTTAAGCAAA..........................................................................................................................................................................................................................................................................................	27	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
..........................................ACACACGTTGAATTTGTCGA---------------------------------------------TGATTGT......................................................................................................................................................................................................................................................................................................	27	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.......................................................TTGTCGA---------------------------------------------TGATTGTGATTTAAGCAAA..........................................................................................................................................................................................................................................................................................	26	1	1.00	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
.............................................................................................................................................................................................................................................................................................................................................................ATAA-----GTGAAATA---------AAAATAA-------------------------A	20	1	1.00	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
.........................................CACACACGTTGAATTTGTCGA---------------------------------------------TGATTG.......................................................................................................................................................................................................................................................................................................	27	1	1.00	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
.................................................................................................................................TCTACA------GAAATACGCTAA-AT--------------AGGAAGGA......................................................................................................................................................................................................................................	28	1	1.00	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
...............................................CGTTGAATTTGTCGA---------------------------------------------TGATTG.......................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
.......................................................................................................................................................................................................................................................................TAATTGTAT-------G------------AATAATAAGTTGTGCA....................................................................................................	26	1	1.00	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................................................................................................TACCAATTGTTACCA----TAATCAGAAAA......................................................................	26	1	1.00	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
...............................................................................................................................................................................................................................................................................T-------G------------AATAATAAGTTGTGCATACCAAT.............................................................................................	25	1	1.00	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
.................................................................................................................................TCTACA------GAAATACGCTAA-AT--------------AGGAAGGAA.....................................................................................................................................................................................................................................	29	1	1.00	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
................................................................................................................................................ATACGCTAA-AT--------------AGGAAGG.......................................................................................................................................................................................................................................	18	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
........................................................................................................................................................................................................................................TTTTAATTT----------------TAAAGCTAATTGTAT-------G------------A...................................................................................................................	26	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
...................................................................................................................................TACA------GAAATACGCTAA-AT--------------AGGAAGGA......................................................................................................................................................................................................................................	26	1	1.00	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0

droSec2

TGGAAAAAATGG---------------T-CATTTTCCGT-TCACACACGTTGAATTTGTCGA---------------------------------------------TGATTGTGATTTAAGCAAAAACTCTACA------GAAATACGCTAA-AT--------------AGGAAGGAATGGAA-------TAAATA--------T--------------TCCTTTCGATAATTTTAATTT----------------TTAAGCTAATTGTAT-------G------------AATAATAAGTTGTGCATACCAATTGTTACCA----TAATCAGAAAATTAAAATCCTTATAA-----GTGAAATA---------AAAATAA-------------------------A	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
............................................................GA---------------------------------------------TGATTGTGATTTAAGCA............................................................................................................................................................................................................................................................................................	19	1	1.00	1	0	0	1	0
.....................................................ATTTGTCGA---------------------------------------------TGATTGTGATTTAAGC.............................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	0	1	0
................................................................................................................................................................................................................................................T----------------TTAAGCTAATTGTAT-------G------------AATAAT..............................................................................................................	23	1	1.00	1	1	0	0	0
....................................................................................................................................................GCTAA-AT--------------AGGAAGGAATGG..................................................................................................................................................................................................................................	19	1	1.00	1	0	1	0	0
.................................................TTGAATTTGTCGA---------------------------------------------TGATTGTG.....................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	1	0
..................................................................................................................................CTACA------GAAATACGCTAA-AT--------------AGGAAGGA......................................................................................................................................................................................................................................	27	1	1.00	1	0	0	1	0
......................................................................................................................................A------GAAATACGCTAA-AT--------------AGGAAGGA......................................................................................................................................................................................................................................	23	1	1.00	1	0	0	1	0

droYak3

TGGAAAAAATGG---------------T-CACTTTCCCT-TCACGCACGTTGAATTTGTCGA---------------------------------------------TGATTGTGATTTAAGCAAAAACTCAACA------GAAATACGCTAA-CT--------------AAGAACGAATTGAA-------TACATT--------T--------------TTCTTTGGACCATTTCAATTT----------------TTAAGCTAATTGTAT-------G------------AATAATAAGTTGTGGAAATCAATTGTTAACA----AAATCAGAAAATTATACATTTAATAA-----CTAAAATG---------GAAATA---------------------------	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
........................................................................................................................................................................................................................................................................................................ATAAGTTGTGGAAATCAATT............................................................................................	20	1	2.00	2	0	0	0	0	0	0	2	0	0	0	0
..............................ACTTTCCCT-TCACGCACGTTG....................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................................................................................................................................AATAAGTTGTGGAAATCAAT.............................................................................................	20	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
........................................................................................................................................................................................................................................................................................................................AATTGTTAACA----AAATCAGAAA.......................................................................	21	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
...............................................................................................................................................................................................................................................TT----------------TTAAGCTAATTGTAT-------G------------AATA................................................................................................................	22	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
.......................................................................................................................................................................................................................................................................................G------------AATAATAAGTTGTGGAAATCAATT............................................................................................	25	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
.............................................................................................................................................GAAATACGCTAA-CT--------------AAGAAC........................................................................................................................................................................................................................................	20	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0
.....................................................ATTTGTCGA---------------------------------------------TGATTGTGATTTAA...............................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
..........................................................................................................................................................................................................................................................................................................AAGTTGTGGAAATCAATT............................................................................................	18	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
...........................................................CGA---------------------------------------------TGATTGTGATTTAAGCAAAA.........................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
.......................................................................................................................................................................................................................................ATTTCAATTT----------------TTAAGCTAATT............................................................................................................................................	21	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
..................................................................................................................................CAACA------GAAATACGCTAA-CT--------------AAGAACGAA.....................................................................................................................................................................................................................................	28	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
............................................................GA---------------------------------------------TGATTGTGATTTAAGCA............................................................................................................................................................................................................................................................................................	19	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0

droEre2

TGGAAAAAATGG---------------C-CACTTTCCCT-TCACGCACGTTGAATTTGTTGA---------------------------------------------TAATTGTGATTTAAGCAAAAACTCCACA------GAAATACGCTAG-CT--------------AAGAACAAATGGAA-------TAAATA--------T--------------TTCTTTGGACCATTTCGATTT----------------TTAAGCTAATTGTAT-------G------------AATAATAAGTTGTGAAAACCAATTGTTAACA----TAATCAGAAAATTAAATA--------ATTAACTGAAATG---------GAAATAAACGGGTA------------------T	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
..................................................................................................................................CCACA------GAAATACGCTAG-CT--------------AA............................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	1	0	0	0
................................................................................................................................................ATACGCTAG-CT--------------AAGAACAAATGGA.................................................................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	1	0
.................................TTCCCT-TCACGCACGTTGAATTTGT.............................................................................................................................................................................................................................................................................................................................................................	25	1	1.00	1	1	0	0	0	0	0	0
.....................................................................................................................TTAAGCAAAAACTCCACA------GA.........................................................................................................................................................................................................................................................................	20	1	1.00	1	0	0	0	1	0	0	0
..............................ACTTTCCCT-TCACGCACGTTG....................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	1	0	0
........................................................................................................................................................................................................................................................................AATTGTAT-------G------------AATAATAAGTTGT.......................................................................................................	22	1	1.00	1	0	0	0	0	1	0	0
..................................................................................................................................................ACGCTAG-CT--------------AAGAACAAATGGAA-------TAAAA....................................................................................................................................................................................................................	28	1	1.00	1	1	0	0	0	0	0	0
................................................................................................................................................................................................................................TTGGACCATTTCGATTT----------------TTAAGCT................................................................................................................................................	24	1	1.00	1	0	0	0	0	1	0	0
.......................................................................................................................................................................................................................................................................................................AATAAGTTGTGAAAACCAATT............................................................................................	21	1	1.00	1	0	0	0	0	0	1	0
........ATGG---------------C-CACTTTCCCT-TCACGCACGTT.....................................................................................................................................................................................................................................................................................................................................................................	26	1	1.00	1	0	1	0	0	0	0	0

dp5

TGGACGCAAGGG---------------C-CACTTCCCAT-TCACTCACGTTGAATTTGTCGA---------------------------------------------TGATTGTGATTTAGGAAATAACTGTGGA------GAGGTACGTTTAAATAGCG-----CC---AGTAACGATTGGGTGGAACAATAA-----------TA------TTTTCA---TTTTGTATAATTTTTATTTAAATTTATGA-----------CAAAATGTATCAAGAAAT------------AACAGTAAGTGGTGCATACCAATTGTTAATACATATATTTAAAATATTTAATA------------------------------------A-------------------------A	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
.................................................................................................................TGATTTAGGAAATAACTGTGGA------GAGG.......................................................................................................................................................................................................................................................................	26	1	10.00	10	0	0	0	0	0	0	0	0	9	1
......................................................................................................................TAGGAAATAACTGTGGA------GAGGTA.....................................................................................................................................................................................................................................................................	23	1	10.00	10	0	0	0	0	0	0	0	0	10	0
......................................................................................................................TAGGAAATAACTGTGGA------GAGGTACGTT.................................................................................................................................................................................................................................................................	27	1	7.00	7	0	0	0	0	0	0	1	0	6	0
......................................................................................................................TAGGAAATAACTGTGGA------GAGGTAC....................................................................................................................................................................................................................................................................	24	1	3.00	3	0	0	0	0	0	0	0	0	3	0
......................................................................................................................TAGGAAATAACTGTGGA------GAGGTACG...................................................................................................................................................................................................................................................................	25	1	2.00	2	0	0	0	0	0	0	0	0	2	0
............................................................GA---------------------------------------------TGATTGTGATTTAGGAA............................................................................................................................................................................................................................................................................................	19	1	2.00	2	0	0	0	0	0	0	0	0	0	2
..........................................................................................................................................................................................................................................................................................................................TTGTTAATACATATATTTAAAATATT....................................................................	26	1	2.00	2	0	0	0	0	0	0	0	0	2	0
........................................................................................................................GGAAATAACTGTGGA------GAGGTA.....................................................................................................................................................................................................................................................................	21	1	2.00	2	0	0	0	0	0	0	0	0	2	0
..................................................TGAATTTGTCGA---------------------------------------------TGATTGTGATT..................................................................................................................................................................................................................................................................................................	23	1	2.00	2	0	0	0	0	0	0	0	0	2	0
......................................................................................................................TAGGAAATAACTGTGGA------GAGGT......................................................................................................................................................................................................................................................................	22	1	2.00	2	0	0	0	0	0	0	0	0	2	0
.............................................................................................................................................................GCG-----CC---AGTAACGATTGGGTGGA.............................................................................................................................................................................................................................	22	1	1.00	1	0	1	0	0	0	0	0	0	0	0
......................................T-TCACTCACGTTGAATTTGTC............................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	1	0	0	0	0	0	0	0	0
......................................................................................................................TAGGAAATAACTGTGGA------GAGGTACGT..................................................................................................................................................................................................................................................................	26	1	1.00	1	0	0	0	0	0	0	0	0	1	0
...ACGCAAGGG---------------C-CACTTCCCAT-T...............................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	1	0	0	0	0	0	0	0	0
...............................................................................................................................................................................CGATTGGGTGGAACAATAA-----------T..........................................................................................................................................................................................................	20	1	1.00	1	0	0	0	0	1	0	0	0	0	0
.....................................................................................................................TTAGGAAATAACTGTGGA------GAGGTACGT..................................................................................................................................................................................................................................................................	27	1	1.00	1	0	0	0	0	0	0	0	0	1	0
.......................................................................................................................................................TAAATAGCG-----CC---AGTAACGATTGGGTGA..............................................................................................................................................................................................................................	27	1	1.00	1	0	0	0	0	0	0	1	0	0	0
.....................................................................................................................TTAGGAAATAACTGTGGA------GAGGTACT...................................................................................................................................................................................................................................................................	26	1	1.00	1	0	0	0	0	0	0	0	0	1	0
......................................................................................................................TAGGAAATAACTGTGGA------GAGG.......................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	1	0
............................................................GA---------------------------------------------TGATTGTGATTTAGGA.............................................................................................................................................................................................................................................................................................	18	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.................................................................................................................................................................................................................................................................................AAGAAAT------------AACAGTAAGTGGTG......................................................................................................	21	1	1.00	1	0	1	0	0	0	0	0	0	0	0
......................................................................................................................TAGGAAATAACTGTGGA------GAGGTACGA..................................................................................................................................................................................................................................................................	26	1	1.00	1	0	0	0	0	0	0	0	0	1	0
....................................................................................................................................................................................................................................................................................................AACAGTAAGTGGTGCATACCAATTGTT.........................................................................................	27	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.......................................................................................................................................................TAAATAGCG-----CC---AGTAACGATTGGG.................................................................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	0	1	0	0	0
..................................................TGAATTTGTCGA---------------------------------------------TGATTGTGATTT.................................................................................................................................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	0	0	0	1	0
........................................................................................................................................................................................................................................................................................................GTAAGTGGTGCATACCAATT............................................................................................	20	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.....................................................................................................................TTAGGAAATAACTGTGGA------GAGGTA.....................................................................................................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	0	0	0	1	0
............................................................................................................................................................................TAACGATTGGGTGGAACAATAA-----------TA------TT.................................................................................................................................................................................................	26	1	1.00	1	0	0	0	0	0	0	0	0	1	0
.........................................................................................................................GAAATAACTGTGGA------GAGGTACG...................................................................................................................................................................................................................................................................	22	1	1.00	1	0	0	0	0	0	0	0	0	0	1
.....................................................................................................................TTAGGAAATAACTGTGGA------GAGGC......................................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	0	0	0	1	0
..................................................................................................................................................................................................................................................AATTTATGA-----------CAAAATGTATC.......................................................................................................................................	20	1	1.00	1	0	0	0	0	0	1	0	0	0	0

droPer2

TGGACGCAAGGG---------------C-CACTTCCCAT-TCACTCACGTTGAATTTGTCGA---------------------------------------------TGATTGTGATTTAGGAAATAACTGTGGA------GAGGTACGTTTAAATAGCG-----CC---AGTAACGATTGGGTGGAACAATAA-----------TA------TTTTCA---TTTTGTATAATTTTTATTTAAATTTATGA-----------CAAAATGTATCAAGAAAT------------AACAGTAAGTGGTGCATACCAATTGTTAATACATATATTTAAAATATTTAATA------------------------------------A-------------------------A	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
...............................................................................................................................................GGTACGTTTAAATAGCG-----CC---A.............................................................................................................................................................................................................................................	20	1	1.00	1	0	0	1	0	0	0
................................................................................................................................................................................................................................................................................................................TGCATACCAATTGTTAATACA...................................................................................	21	1	1.00	1	0	1	0	0	0	0
.....................................................ATTTGTCGA---------------------------------------------TGATTGTGATTTAGG..............................................................................................................................................................................................................................................................................................	24	1	1.00	1	0	0	1	0	0	0

droWil2

AGGACGCAAAGG---------------C-CACTTTCCAT-TTACCCATGTTGAGTTTGTCGA---------------------------------------------TGATTGTGATTTAGGCAATAACAGTTCG------GACATTCGGATAAATACGG-CC-TCC---AGCAACGATTGGGTGGAACAATAA-----------TA---CGCATGTCATTTCTCTGGGTAATTTGTATTTAACAT-----------TAAGTTCAAATGTATCAAAAACT-----------TGCTAGTAGGTGGTGCATACCAATTGTTAATA----TATTAAACATATTGATTA--------------------------------------------------------------A	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
............................................................................................................................................................................................................................................................................GTATCAAAAACT-----------TGCTAGTAGGT..........................................................................................................	23	1	2.00	2	0	1	0	1	0
.............................................................................................................................................................................AACGATTGGGTGGAACAATA.......................................................................................................................................................................................................................	20	1	2.00	2	0	0	2	0	0
...........................................................CGA---------------------------------------------TGATTGTGATTTAGGC.............................................................................................................................................................................................................................................................................................	19	1	1.00	1	0	0	0	0	1
..................................................................................................................................GTTCG------GACATTCGGATAAATACGG-CC-....................................................................................................................................................................................................................................................	26	1	1.00	1	1	0	0	0	0
...................................................................................................................................................................................................................................................................................AAACT-----------TGCTAGTAGGTGGTGCA....................................................................................................	22	1	1.00	1	0	0	1	0	0
............................................................................................................................ATAACAGTTCG------GACATTCGGAT................................................................................................................................................................................................................................................................	22	1	1.00	1	0	0	1	0	0
............................................................GA---------------------------------------------TGATTGTGATTTAGGCAAT..........................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	1	0
.............................................................................................................................................................................AACGATTGGGTGGAACAATAA-----------TA---......................................................................................................................................................................................................	23	1	1.00	1	0	0	1	0	0
.............................................................................................................................TAACAGTTCG------GACATTCGGAT................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	1	0	0
..............................................................................................................................................................................................ATAA-----------TA---CGCATGTCATTTCTCTGGGT..................................................................................................................................................................................	26	1	1.00	1	0	1	0	0	0
.......................................................................................................................................................................................................................................................................................T-----------TGCTAGTAGGTGGTGCATACCAATT............................................................................................	26	1	1.00	1	0	0	0	1	0
..........................................................TCGA---------------------------------------------TGATTGTGATTTAGGCA............................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	1	0	0	0
................................................................................................................GTGATTTAGGCAATAACAGTTCG------GA.........................................................................................................................................................................................................................................................................	25	1	1.00	1	0	0	0	1	0
......................................................................................................................................................................................................................................................................................CT-----------TGCTAGTAGGTGGTGCATACCAATT............................................................................................	27	1	1.00	1	0	0	1	0	0
............................................................................................................................ATAACAGTTCG------GACATTCGGATAA..............................................................................................................................................................................................................................................................	24	1	1.00	1	0	0	1	0	0
.............................................................................................................................TAACAGTTCG------GACATTCGGATAA..............................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	1	0
...................................................................................................................ATTTAGGCAATAACAGTTCG------GAC........................................................................................................................................................................................................................................................................	23	1	1.00	1	1	0	0	0	0
.................................................................................................................................................................................................................................................................TAAGTTCAAATGTATCAAAAACT-----------T....................................................................................................................	24	1	1.00	1	0	1	0	0	0
..................................................................................................................................................................................................................................................................................AAAACT-----------TGCTAGTAGGTGGTGCATACC................................................................................................	27	1	1.00	1	0	0	0	1	0
.............................................................................................................................TAACAGTTCG------GACATTCG...................................................................................................................................................................................................................................................................	18	1	1.00	1	0	0	0	1	0

droVir3

TGGACGCAAGGG---------------C-CATTTTCCAT-TTACGCACGTCGAATTTGTCGA---------------------------------------------TGATTGTGATGTAA---ATAATTGTGCG------GATATTCGATTAAATAA-----------------CGATTGGGCGGAACAACAA-----------TAA-----TTTTCA------ATTATAACTTATATT-----------------TTAAGTTAAGAGAAT-------ATATTAAATTGTAATGAATAAGTGATGTTTACCAATTGTTAAAA----TATTAAACATATTGATTA--ATCTTA-----GAAAATTCAAAAGAA--------A-------------------------A	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
....................................................................................................................................................GATTAAATAA-----------------CGATTGGGCGGAA............................................................................................................................................................................................................................	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
...........................................................CGA---------------------------------------------TGATTGTGATGTAA---ATA.........................................................................................................................................................................................................................................................................................	20	1	1.00	1	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
....................................................................................................................................................................................GGGCGGAACAACAA-----------TAA-----TTTTCA------AT.....................................................................................................................................................................................	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	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
....................................................................................................................................................GATTAAATAA-----------------CGATTGGGCGG..............................................................................................................................................................................................................................	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	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
.......................................................................................................................................................................................................................................................................................ATATTAAATTGTAATGAATAAGTGAT.......................................................................................................	26	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
................................................................................................................................................................................................................................................................................................................................................TATTGATTA--ATCTTA-----GAAAATT...........................................	22	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
..........................................................................................................................................................ATAA-----------------CGATTGGGCGGAACAACAA-----------TA.........................................................................................................................................................................................................	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	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
.................................................................................................................................TGTGCG------GATATTCGATTAAATAA-----------------CGAT.....................................................................................................................................................................................................................................	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	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
.............................................................................................................................................................................................................................................................................................AATTGTAATGAATAAGTGATGT.....................................................................................................	22	1	1.00	1	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
..................................................CGAATTTGTCGA---------------------------------------------TGATTGTGA....................................................................................................................................................................................................................................................................................................	21	1	1.00	1	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
.......................................................................................................................AA---ATAATTGTGCG------GATATTCG...................................................................................................................................................................................................................................................................	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	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
....CGCAAGGG---------------C-CATTTTCCAT-TTACGCAC........................................................................................................................................................................................................................................................................................................................................................................	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	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
..............................................................................................................................................ATATTCGATTAAATAA-----------------CGATT....................................................................................................................................................................................................................................	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
..............................................................................................................................................................................................................AA-----TTTTCA------ATTATAACTTATA..........................................................................................................................................................................	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
...................................................................................................................................TGCG------GATATTCGATTAAAT............................................................................................................................................................................................................................................................	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
................................................GTCGAATTTGTCGA---------------------------------------------TGATTGTGAT...................................................................................................................................................................................................................................................................................................	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
...ACGCAAGGG---------------C-CATTTTCCAT-TTACGCAC........................................................................................................................................................................................................................................................................................................................................................................	28	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
...........................................................................................................................................................................................................................................................................................................................................AAACATATTGATTA--ATCTT........................................................	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	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droMoj3

TGGGCGAAAAGG---------------T-CATTTTCCTT-TTACGCACGTTGAATTTATCGA---------------------------------------------TGATTGTGATTTAACCAATATTTGCGCA------GATGTTCGATTAAATAC-----------------TGATTGGGTGGATCAACAAA----AA----TAATATTC-----AA------TT---ATATTT----------GTCGTGTATTGTAGCTTAA--GAAT-------A------------TATATTAAGTGATGTTTACCAATTGTTAAAA----TATTAAACATATTGATTA--------------------------------------------------------------A	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
....................................................................................................................................................................................GGGTGGATCAACAAA----AA----T..........................................................................................................................................................................................................	18	1	1.00	1	1	0	0	0	0	0
..............................................................................................................................................................................................................AATATTC-----AA------TT---ATATTT----------GTCGTGT..........................................................................................................................................................	24	1	1.00	1	1	0	0	0	0	0
........................................................................................................................................................AAATAC-----------------TGATTGGGTGGAT............................................................................................................................................................................................................................	19	1	1.00	1	0	0	0	1	0	0
.........................................................................................................................................................AATAC-----------------TGATTGGGTGGATCAACAAA----A................................................................................................................................................................................................................	26	1	1.00	1	0	0	0	0	0	1
............................................................GA---------------------------------------------TGATTGTGATTTAACCA............................................................................................................................................................................................................................................................................................	19	1	1.00	1	0	0	0	0	0	1
...........G---------------T-CATTTTCCTT-TTACGCACGTTGAAT.................................................................................................................................................................................................................................................................................................................................................................	27	1	1.00	1	1	0	0	0	0	0
..........................................................................................................................................................................................................................................TTT----------GTCGTGTATTGTAGC..................................................................................................................................................	18	1	1.00	1	1	0	0	0	0	0
.......................................................TTATCGA---------------------------------------------TGATTGTGATTT.................................................................................................................................................................................................................................................................................................	19	1	1.00	1	1	0	0	0	0	0

droGri2

TGCTTGCAAATTAATTAATAGTTTAGTCCGACTTTCAATGTTATACACTATAAACTATAAGATATAATATAATTATGTAAATAATATAATATAAAATGCATGCATTATAATTGTAATTAGT------------CC------AACTTAA--------------------------------------------------------------------------CTTTG-----------------------------------------------------------------------------------------------------------AATA--ATACTCAATTTTA-----GTAAAAAA---------AAAAAGA-AAGATGTATTTTTTATATACGTCAA	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

dan_1106

scaffold_13034:1711371-1711521 +

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

-11.2	-11.2	-11.2