dse_1133

Name	Class	Family	Strand
DNAREP1_DYak	RC	Helitron	+

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------################################################## TTGAAAAGTATGTAAGCGTTTCCGACCGAATAAACATTATTTATTCTTGATTAGGATCAATAGCCGAGTCGATCAAGCCATGTCCGTCTGTCCAAACCATTTATTTACCCCACCCTATCGTGTTGACTGTTTTTGGCCACTATTCATTTATTTTCTGTGCAGCTAGTTCGCCAATTGTACTTAACCTCTTTAAATTCTCAGGTGGATAGCAGACGATTGGAGCACTTGCAGCCGCCTTTGTGGTCACGGCT ************************************************...((((.........((.((..((.....))..)).))))))............................(((((......(((((.(((((((((.........))).)).))))..)))))......)))))................************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V114 embryo	M054 female body
....................................................................................................................................................................................TTAACCTCTTTAAATTCTCAGGTGGA.............................................	26	0	1	1.00	1	0	1
..................................................................................................................................................................................................TTTTCAGGTCGATAGCAGA......................................	19	2	1	1.00	1	1	0
.............................................................................................................................................................TACAGCTAGTTCGGCACTTGT.........................................................................	21	3	3	0.33	1	0	1
.......GTATGTAAGCGTTACCGGT.................................................................................................................................................................................................................................	19	3	14	0.21	3	3	0
.....ATGTATGTAAGCGTTACCGG..................................................................................................................................................................................................................................	20	3	5	0.20	1	1	0
...............................................TGATTAGGATCAATAGCCGAGTCGAT..................................................................................................................................................................................	26	0	6	0.17	1	1	0
..................................................................................................................................................................................................TTCTAAGGGGTATAGCAGA......................................	19	3	18	0.06	1	0	1
........................................................TCAATAGCCGAGTCGATCAAGCCA...........................................................................................................................................................................	24	0	20	0.05	1	0	1
....................................................AGGATCAATAGCCGAGTAGATCAAGC.............................................................................................................................................................................	26	1	20	0.05	1	0	1

AACTTTTCATACATTCGCAAAGGCTGGCTTATTTGTAATAAATAAGAACTAATCCTAGTTATCGGCTCAGCTAGTTCGGTACAGGCAGACAGGTTTGGTAAATAAATGGGGTGGGATAGCACAACTGACAAAAACCGGTGATAAGTAAATAAAAGACACGTCGATCAAGCGGTTAACATGAATTGGAGAAATTTAAGAGTCCACCTATCGTCTGCTAACCTCGTGAACGTCGGCGGAAACACCAGTGCCGA ************************************************...((((.........((.((..((.....))..)).))))))............................(((((......(((((.(((((((((.........))).)).))))..)))))......)))))................************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V113 male body	M054 female body	V114 embryo
.....................................................................................CAGACAGGTTTGGTAAAGA...................................................................................................................................................	19	1	1	1.00	1	1	0	0
.................................................................CTCAGCTAGTTCGGTACAGGC.....................................................................................................................................................................	21	0	2	0.50	1	0	1	0
...............................................ACTAATCCTAGTTATCGGCTCAGCT...................................................................................................................................................................................	25	0	6	0.33	2	0	2	0
.................................................TAATCCTAGTTATCGGCTCAGCT...................................................................................................................................................................................	23	0	7	0.14	1	0	0	1
....................................................................................................AATAAAGAGGGTGGAATAG....................................................................................................................................	19	3	20	0.10	2	2	0	0
....................................................TCCTAGTTATCGGCTCAGCTAGTT...............................................................................................................................................................................	24	0	19	0.05	1	0	1	0
............................................................ATCGGCTCAGCTAGTTCGGTA..........................................................................................................................................................................	21	0	20	0.05	1	0	0	1

Species	Coordinate	ID	Alignment
droSec2	scaffold_28:256087-256337 +	dse_1133	TTGA-AA-----------------------AGTATGTA-------------AGCGTTTCCGACCGA-ATAAACATTATTTATTCTTGATTAGGATCAATAGCCGAGTCGA-----TCAAGCCATGTCCGTCTGTCCAA-----------------------ACCATTTATTTACCC-----------------------CACCCTATCGT--G-----TTGA-CT--GT---------T-TTT--GGCC-------ACTATTCATTTATTTTC-TGTGC--A-GCTAGTTCG-----------------------CC-----AATTGT--ACTT---------AAC------------------------------------------CTCTTTAA-------------------------------------------------------ATTCTCAGGTGGATAGCAGACGATTGGAGCACTTGCAGCCGCCTTTGTGGTCACGGCT
droSim2	2l:20983235-20983499 +	dsi_15942	TTGA-AA-----------------------AGTATGTAACAGCCAGGTGGAAGCGTTTCCGACCGA-ATAAAGATTATTTATTCTTGATTAGGATCAATAGCCGAGTCGA-----TCAAGCCATGTCCGTCTGTCCAA-----------------------ACCATTTATTTACCC-----------------------CACCCTATCGT-TG-----TTGA-CT--GT---------T-TTT--GACC-------ACTATTCATTTATTTTC-TGTGC--A-GCTAGTTCG-----------------------CC-----AATTGT--ACTT---------AAC------------------------------------------GTCTTTAA-------------------------------------------------------ATTCTCAGGTGGATAGCAGACGATTGGAGCACTTGCAGCCGCCTTTGTGGTCACGGCT
dm3	chr2L:21710861-21711130 +		TTGA-AA-----------------------AGTATTTAACAGGCAGGGGGAAACGTTTCCGACCAAAATAAAGAATATTTATTTTTGATTAGGATCAATGGCCGAGTCGA-----ACTGCCCCTGTCCGTCTGTCCTA-----------------------ACCATTTATTTTCCC-----------------------CACCCTATCGT--GTGCCATTGA-CT--GC---------T-TAT--GGCC-------ACTATTCATTTATTTTC-TGTGC--A-GCTAGTTCG-----------------------CC-----AATTGT--ACTT---------AAC------------------------------------------ATCTTTAA-------------------------------------------------------ATTCTTAGGTGGATAGCAGACGATTGGAGCACTTGCAGCCGCCTTTGTGGTCACGGCT
droEre2	scaffold_4929:6504089-6504246 +		TTGA-AA-----------------------AGAATGTAACAGGTAGAAGAAAGCGTTTCCGACCCT-GTAAGGTAAATATACTCTTAATTAAGATCAATAGCCGAGTCGA-----TCTGGCCATGTTCGTCCGCCTGTCCGTCTTTTTAT------------------------TA------------------------------------------TAAA-TT--AT---------TCTTT--GCTT-------ATTATTTATTATTTGTC-TG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droYak3	3L:23896740-23896928 -		TTGA-AG-----------------------AGTATGTAACAGGCAGAAGGAAGCGTTTCCGACCAT-ATAAAGAATATATATTCTTGATCAGGATCAATAGCCTAGTCGA-----TCTGGCCATGTCCGTCTCTCCGTATGAACGTC-------------------------------------------------------------------------GA-AT--GTTTTGATATTT-TTCTATTAGACTTGTAAATATCTATCTATTTTC-AGAAT--A-GCTT-TTCG-----------------------CC-----TACTCT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A
droEug1	scf7180000409176:46001-46156 +		TTGA-TA-----------------------AGTATGTAACAGGTAGAAGGAAGTGTTTCCGGCCCT-ATAAAGTTTATATATTCTAGATAAGGATCAATACCGAAGTTGA-----TTGACCCATGTCCGTCTGTCCGTCCATTCGTCTGT------------------------CC-----------------------GTACTGGA-----------TAGA-CT--GT---------T-T---------------AGTGTTCGTTCTTTT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T
droBia1	scf7180000301750:11292-11537 -		TTTC-A------------------GTCAGAAGTTTGCAACGCAGTTAAGGA-ACGTTTCCGACCCG-ATAAAGTATAAATATTTTTGATCAGCATCACTAGAGGAGTCGT-----TCTTGCCGTGTTCGTCTGTTTCT-----------------------------------------------------------------------------------------------------------------------------------------ACGC--AAACTAGTCTC-----------------------TC-----AGTTTAAAAGCT---------ATC------------------------------------------GGACTGAAAATTTCCGAAAAATCCTTTTTTTTTTGCAGGTACATTTAACATTTTGAATTTTAAATT-TTTTATAAAAATCAGACGAATGTATCATAGGCTGC------------------C
droTak1	scf7180000415765:379211-379418 +		TTGC-AGAGGGTATAATGATTTCAGTCAGAA------------------------------------------GTTATATATTCTTAATCAGCATCACTAGACGAGTCGA-----TCTAGCCATGACCGTCTGTCTGTCCGTTCGTCTGTCCGTTCGTCTGTCTGTTCGT----CTGTCTGTTC----GTCTGTCTGTT-----------------------------------------------------CGTC--TGTCTGTCCG-TTT-CTAAGC--AAACTAGTCTT-----------------------TC-----AGTTTTCAAGCT---------ATC------------------------------------------GTCTTAAAACTTTC-----------------------------------------------------------------------------------------------------------
droEle1	scf7180000491113:164645-164842 -		GTCA-GA-----------------------AGTTTGCAACGCAGTGAAGGAGACATTTCCGACCCT-ATAAAGTATATATATTATTCATCAGAATCACTAGGAGAGTCGA-----TCTAGCCATGTCCGTCTGTCCGTCCGTCTGTTAGT------------------------CTGTCA------------GTCTGTC-----------------------------------------------------TGT--CTGTCCGTCCG-TTT-CTACGC--AAGCTAGTCTC-----------------------TC-----AGTTTTACAGCT---------ATC------------------------------------------TGCATGAAATTTTC-----------------------------------------------------------------------------------------------------------
droRho1	scf7180000777424:4316-4505 -		GTCA-AA-----------------------AGTT--CAA------------CGCATTTCCGACCCT-ATA-AGTATATATATTCTTGATCAGGATCATCAGAAGAGTCGA-----TGTAGCCATGTCCGTCTGTCCGTCCGTCTGTCCGT------------------------CCGTCTGTCC----GTCTGTCCGTC-----------------------------------------------------CGTC--CGTCCGTCCA-TTT-CTACGC--T-ACTAGTCCC-----------------------TC-----AGTTTTAAAGCT---------ATC------------------------------------------TGCTTGAAACTTTC-----------------------------------------------------------------------------------------------------------
droFic1	scf7180000453973:545131-545299 -		TTTG-TT------------------------------------------------------------------------------TGACCCAAA--------------------------------------------------------------------CCACTT-----------------------------------------------------A-CT--GC---------C-GCT--GGCA-------ACTACTCATTTACTTTC-TGTTC--C-GCCGACTCGCGATGAACGCCCTGACTGACCGACC-----ACTTGC--ACTC---------AAC------------------------------------------CT-TGTGA-------------------------------------------------------ATCCGCAGCTGGATAACCGACGACTGGAGCACTTGCAGCCGGCTCTGTGGCCACGGCT
droKik1	scf7180000302281:145821-146025 +		TCGC-AA------------------------------------GTGAAGGAGACCTTTCCGACCCA-ATAA--TATATATATTCTTGATCATCATCAACAGCCGAGTCGA-----TCTAGCCATGTCCGTCTATGCAA-------------------------------------------------------------------------------------------------------------------------------------------------ACTAGTCCC-----------------------TCGACAAAATTTTATAGCTTGGTTGTTTATCAACATTTTTGCTCCATTTTTGAAATA-TGGCCATTTTATATTATTTTTCA-------------------------------------------------------ACTTTCA--TGAAAAGCGGACGAC---------------------------------T
droAna3	scaffold_9449:3404-3648 +		GTCA-AA-----------------------AGTGTGCAACGCAGTGAAGGAGACATCTCCGACCCT-ATAAAGTATATATATTCTTGATCAGGATCACCTCCTGAGTCGA-----TATAAGCATGTCCGTCTGTCCGTCTGTCCGTCTGTCCGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCCGTCTGTCTGTCTGTC-----------------------------------------------------CGTC--TGTCTGTCTG-TTT-CTACGC--AAACTAGTCTC-----------------------TC-----AGTTTTAAAGCT---------ATC------------------------------------------GAGTTGAAACTTTG------------------------------------------------------------------------------------CACACACCCT------------T
droBip1	scf7180000396621:107832-108041 +		GTCA-AA-----------------------AGTGTGCAACGCAGTGAAGGAGAATTCTCCGACCCT-ATAAAGTATATATATTCTTGATCAGGATCACCTCCTGAGTTTA-----TATAAGCATGTCCGTCTGTCCTG-----------------------TCTGTCTGTCTGTCCGTCTGTCCGTCTGTCTGTCCGTC-----------------------------------------------------TGTC--TGTCTTTCCG-TTT-CTACGC--GAACTAGTCTG-----------------------TC-----AGTTTTGAAGCT---------ATC------------------------------------------GTCTTGAAACTTT------------------------------------------------------------------------------------------------------------
dp5	Unknown_singleton_1398:3003-3159 +		ATAT-T---------------------------------------------ACCGTTTCCGACCCC-ATAAAGTATATATATTCTTGATCAGCATCAATAGCCGAGTTGAGCCAATTGAGCCCTGTCTGTCTGTCCGACCGTCCGTCTGT------------------------CC-----------------------GTCCCTATCA-GC--GCC---TA-GT--G-------------------------------------------------------------CTC-----------------------AA-----AGACTTTAAACA---------ATT------------------------------------------T-------------------------------------------------------------------------------------------------CATTCGTTCT------------C
droPer2	scaffold_87:180496-180632 +		TGGTAAA-----------------------AGTGG---A--TCCAGAAGGAATCGTTTCCGACCCC-ATAAAGTATATATATTCTTGATCAGCATCAATAGCCGAGTCGA-----TTGAGTCATGTCTGTCTGTCCGTCTGACCTC------------------------------------------------------------------C-----TCTA-TT--GC---------T-TTG--GCCC-------GCCATTCA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil2	scf2_1100000004962:393077-393293 -		TTTT-G------------------GTCAGAAGTGTGCAACGCATAGAAGGAAGCATCTCCGACCAT-ATAAAGTATATATATTCTTGATCAGCATGACGAGACGAGTTCA-----TATAGCCATGTCCGTCCGTCCTTCCGTCTGTCCGT------------------------CCGTCTGT-------------------CAACAGTG-ACT-----TTGATCAATATC------------------------------TTCGTTTT-TTCC-TATGCTAA-GATTGTTGG-----------------------CC-----GTTCTT--TCGC---------A------------------------AGCATTAGC-----------CTTTTTAG-------------------------------------------------------A--------------------------------------------------------T
droVir3	scaffold_12528:152458-152618 -		A---------------------------------------------------GTATCTCCGACCCC-ATAAAATGTATGTATTCTTGATCAGCATCAATAGCCGAGTCGA-----TCCAGCGATGTCCGTCTGTCTGTCCGTTCGTCCGT------------------------CT-----------------------GTCCGCAGCA-GCT-----TTGA-CA--AT---------T-TCT--GTACACATGTA--CACATATACA-TTC-ATGCGC--G-TCTGCTTCG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C
droMoj3	scaffold_6496:25466860-25466999 +		TTGA-AA-----------------------TGTATGTAACAGGCAAAAGGAGGCGTGGCAGACCCC-ACAAAGTATATATATTCTTGATCAGGGCGACGAGCTGAGTTGA-----TTTAGCACTGTCCGTCTGTCCTT-----------------------GAAATTTGTTTTCCT-----------------------AGGTCC----------------------------------------------------------ATGTGTTTG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CT
droGri2	scaffold_15252:3890383-3890490 -		TGCA-AA-----------------------GGT--------------AAAAGGAGTCTCCGACACC-ATAAACTATATATATTCTTGATCAGGTTCTACAGCCGAGTCGA-----TATAGCCATGTCCGTCTGTCCGTCCGTCCGTCCAC------------------------CC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droSec2

TTGA-AA-----------------------AGTATGTA-------------AGCGTTTCCGACCGA-ATAAACATTATTTATTCTTGATTAGGATCAATAGCCGAGTCGA-----TCAAGCCATGTCCGTCTGTCCAA-----------------------ACCATTTATTTACCC-----------------------CACCCTATCGT--G-----TTGA-CT--GT---------T-TTT--GGCC-------ACTATTCATTTATTTTC-TGTGC--A-GCTAGTTCG-----------------------CC-----AATTGT--ACTT---------AAC------------------------------------------CTCTTTAA-------------------------------------------------------ATTCTCAGGTGGATAGCAGACGATTGGAGCACTTGCAGCCGCCTTTGTGGTCACGGCT	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
............................................................................................................................................................................................................................................................................................................................................TT---------AAC------------------------------------------CTCTTTAA-------------------------------------------------------ATTCTCAGGTGGA.............................................	26	1	1.00	1	1	0	0	0
.....................................................................................TGATTAGGATCAATAGCCGAGTCGA-----T.........................................................................................................................................................................................................................................................................................................................................................................................................	26	6	0.17	1	0	0	1	0
..............................................................................................TCAATAGCCGAGTCGA-----TCAAGCCA..................................................................................................................................................................................................................................................................................................................................................................................................	24	20	0.05	1	1	0	0	0

droSim2

TTGA-AA-----------------------AGTATGTAACAGCCAGGTGGAAGCGTTTCCGACCGA-ATAAAGATTATTTATTCTTGATTAGGATCAATAGCCGAGTCGA-----TCAAGCCATGTCCGTCTGTCCAA-----------------------ACCATTTATTTACCC-----------------------CACCCTATCGT-TG-----TTGA-CT--GT---------T-TTT--GACC-------ACTATTCATTTATTTTC-TGTGC--A-GCTAGTTCG-----------------------CC-----AATTGT--ACTT---------AAC------------------------------------------GTCTTTAA-------------------------------------------------------ATTCTCAGGTGGATAGCAGACGATTGGAGCACTTGCAGCCGCCTTTGTGGTCACGGCT	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
..............................................................................................TCAATAGCCGAGTCGA-----TCAAGCCA..................................................................................................................................................................................................................................................................................................................................................................................................	24	8	8.63	69	0	0	0	0	0	0	25	35	0	2	5	0	2	0	0	0	0
...........................................................................................................................................................................................................................TGA-CT--GT---------T-TTT--GACC-------ACTATTCATT...................................................................................................................................................................................................................................................	25	4	2.00	8	0	0	0	0	0	0	3	0	3	2	0	0	0	0	0	0	0
.........................................................................................TAGGATCAATAGCCGAGTCGA-----TC........................................................................................................................................................................................................................................................................................................................................................................................................	23	12	1.33	16	0	0	0	0	0	0	8	4	3	0	1	0	0	0	0	0	0
................................TATGTAACAGCCAGGTGGAAGCGTT....................................................................................................................................................................................................................................................................................................................................................................................................................................................................	25	4	1.00	4	0	0	0	2	0	0	0	0	0	0	2	0	0	0	0	0	0
...............................................................................................CAATAGCCGAGTCGA-----TCAA......................................................................................................................................................................................................................................................................................................................................................................................................	19	10	1.00	10	0	0	0	0	9	0	0	0	0	0	0	1	0	0	0	0	0
.......................................................................................................................................................................................................................................................................................................................................................................................................TTTAA-------------------------------------------------------ATTCTCAGGTGGATAGCAGA......................................	25	4	1.00	4	0	0	0	0	0	0	1	1	2	0	0	0	0	0	0	0	0
.........................................................................................TAGGATCAATAGCCGAGTC.................................................................................................................................................................................................................................................................................................................................................................................................................	19	15	0.93	14	0	0	0	0	0	14	0	0	0	0	0	0	0	0	0	0	0
.........................................................................................TAGGATCAATAGCCGAGTCGA-----TCAAG.....................................................................................................................................................................................................................................................................................................................................................................................................	26	5	0.80	4	0	0	0	0	0	0	3	0	1	0	0	0	0	0	0	0	0
.........................................................................................TAGGATCAATAGCCGAGTCGA-----TCAAGC....................................................................................................................................................................................................................................................................................................................................................................................................	27	5	0.80	4	0	0	0	0	0	0	1	1	2	0	0	0	0	0	0	0	0
...A-AA-----------------------AGTATGTAACAGCCAGGTGGA..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................	24	4	0.75	3	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................................................................................................A-GCTAGTTCG-----------------------CC-----AATTGT--ACTT---------AAC------------------------------------------GTC......................................................................................................................	28	4	0.75	3	0	0	0	0	0	0	0	0	2	1	0	0	0	0	0	0	0
................................TATGTAACAGCCAGGTGGAAGCGT.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................	24	4	0.75	3	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0
...............................................................................................CAATAGCCGAGTCGA-----TCAAGCCATG................................................................................................................................................................................................................................................................................................................................................................................................	25	8	0.75	6	0	0	0	0	0	0	1	0	0	0	5	0	0	0	0	0	0
.............................................................................................ATCAATAGCCGAGTCGA-----TCAAGCCA..................................................................................................................................................................................................................................................................................................................................................................................................	25	8	0.75	6	0	0	0	0	0	0	4	2	0	0	0	0	0	0	0	0	0
...............................................................................................CAATAGCCGAGTCGA-----TCAAGCCAT.................................................................................................................................................................................................................................................................................................................................................................................................	24	9	0.67	6	0	0	0	1	0	0	0	0	1	0	3	0	1	0	0	0	0
...................................................................................................AGCCGAGTCGA-----TCAAGCCATG................................................................................................................................................................................................................................................................................................................................................................................................	21	8	0.63	5	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0
.........................................................................................TAGGATCAATAGCCGAGTCGA-----T.........................................................................................................................................................................................................................................................................................................................................................................................................	22	13	0.62	8	0	0	0	0	0	0	3	0	4	1	0	0	0	0	0	0	0
...............................................................................................CAATAGCCGAGTCGA-----TCAAGCCA..................................................................................................................................................................................................................................................................................................................................................................................................	23	9	0.56	5	0	0	0	1	0	0	0	1	1	1	1	0	0	0	0	0	0
.....................................................................................................CCGAGTCGA-----TCAAGCCATGT...............................................................................................................................................................................................................................................................................................................................................................................................	20	6	0.50	3	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0
..........................................................................................................................................................................................................CCTATCGT-TG-----TTGA-CT--GT---------T-TTT--GACC-------A............................................................................................................................................................................................................................................................	27	4	0.50	2	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0
.........................................................................................TAGGATCAATAGCCGAGTCGA-----TCAA......................................................................................................................................................................................................................................................................................................................................................................................................	25	5	0.40	2	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0
...................................................................................................AGCCGAGTCGA-----TCAAGCCATGTCCGTC..........................................................................................................................................................................................................................................................................................................................................................................................	27	5	0.40	2	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0
..................................................................................................TAGCCGAGTCGA-----TCAAGCCATGTC..............................................................................................................................................................................................................................................................................................................................................................................................	24	6	0.33	2	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0
...............................................................................................CAATAGCCGAGTCGA-----TCAAGCCATGT...............................................................................................................................................................................................................................................................................................................................................................................................	26	6	0.33	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0
...................................................................................................AGCCGAGTCGA-----TCAAGCCATGTC..............................................................................................................................................................................................................................................................................................................................................................................................	23	6	0.33	2	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0
.........................................................................................................GTCGA-----TCAAGCCATGTCCGTC..........................................................................................................................................................................................................................................................................................................................................................................................	21	7	0.29	2	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0
..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTGGAGCACTTGCAGCC..................	17	4	0.25	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
....................................TAACAGCCAGGTGGAAGCGTTTCCG................................................................................................................................................................................................................................................................................................................................................................................................................................................................	25	4	0.25	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
......................................................................................................................................................................TTATTTACCC-----------------------CACCCTATCGT-TG-----TT.................................................................................................................................................................................................................................................................................................	25	4	0.25	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
..............................................................................................................................................................................................................................................................................................AGTTCG-----------------------CC-----AATTGT--ACTT---------AAC------------------------------------------GTCT.....................................................................................................................	25	4	0.25	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
....................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTCTCAGGTGGATAG..........................................	15	4	0.25	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
................................................................................................................................................................................................................................................TTT--GACC-------ACTATTCATTTATTTTC-TGT........................................................................................................................................................................................................................................	27	4	0.25	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AGCAGACGATTGGAGCACTTGCAGC...................	25	4	0.25	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
.........................................GCCAGGTGGAAGCGTT....................................................................................................................................................................................................................................................................................................................................................................................................................................................................	16	4	0.25	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
............................................................................................................................................................................................................................................................................................................................................TT---------AAC------------------------------------------GTCTTTAA-------------------------------------------------------ATTCTCAGGTGGA.............................................	26	4	0.25	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
.............................................................................................................................................................................................................................................................................................TAGTTCG-----------------------CC-----AATTGT--ACTT---------AAC------------------------------------------GTCTT....................................................................................................................	27	4	0.25	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
.............................................................................................................................................................................................................................................................................................................................................T---------AAC------------------------------------------GTCTTTAA-------------------------------------------------------ATTCTCAGGTGGA.............................................	25	4	0.25	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
...................................................................................................................................TGTCCAA-----------------------ACCATTTATTTACCC-----------------------CACCC.................................................................................................................................................................................................................................................................................................................	27	4	0.25	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
..........................................................................................................................................................................................................................................................................TATTTTC-TGTGC--A-GCTAGTTCG-----------------------CC-----AA.........................................................................................................................................................................................	26	4	0.25	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
...............................................................................................................................................................................................................................................................................TC-TGTGC--A-GCTAGTTCG-----------------------CC-----AATTGT--ACT................................................................................................................................................................................	28	4	0.25	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
..............................................................................................TCAATAGCCGAGTCGA-----TCAAGCC...................................................................................................................................................................................................................................................................................................................................................................................................	23	8	0.25	2	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0
................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TAGCAGACGATTGGAGCACTTGCAGC...................	26	4	0.25	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TAGCAGACGATTGGAGCACTTGC......................	23	4	0.25	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AGACGATTGGAGCACTTGCAGCCGCCTT.............	28	4	0.25	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CTTGCAGCCGCCTTTGTGG........	19	4	0.25	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
..............................................................................................TCAATAGCCGAGTCGA-----TC........................................................................................................................................................................................................................................................................................................................................................................................................	18	20	0.25	5	0	0	0	0	0	0	0	3	0	0	2	0	0	0	0	0	0
.........................................................................................................................................................................................................................................................................................................................................................................................................TAA-------------------------------------------------------ATTCTCAGGTGGATAGCAGACGA...................................	26	4	0.25	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
.....................................................................................................................................................................................................................................................................................................................................TGT--ACTT---------AAC------------------------------------------GTCTTTAA-------------------------------------------------------ATTCTCAGG.................................................	27	4	0.25	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................TCAGGTGGATAGCAGACGATTGGAGC............................	26	4	0.25	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
.................................................................................TTCTTGATTAGGATCAATAGCCGAGT..................................................................................................................................................................................................................................................................................................................................................................................................................	26	8	0.25	2	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0
............................................................................................................................................................................................................................................................................TTTTC-TGTGC--A-GCTAGTTCG-----------------------CC-----AA.........................................................................................................................................................................................	24	4	0.25	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTCTCAGGTGGATAGCAGACGATTGG...............................	26	4	0.25	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTCTCAGGTGGATAGCAGA......................................	19	4	0.25	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
.......................................................................................................................................................................................................................................................................................................................................T--ACTT---------AAC------------------------------------------GTCTTTAA-------------------------------------------------------ATTCTCAGGTGGA.............................................	29	4	0.25	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
........................................................................................................................................................................................................................................................................TTTATTTTC-TGTGC--A-GCTAGTTCG-----------------------CC-----AAT........................................................................................................................................................................................	29	4	0.25	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
.............................................................................TTTATTCTTGATTAGGATCAATAGCCGAGT..................................................................................................................................................................................................................................................................................................................................................................................................................	30	4	0.25	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
..............................................................................................TCAATAGCCGAGTCGA-----TCAAGCCATG................................................................................................................................................................................................................................................................................................................................................................................................	26	8	0.25	2	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0
...........................................................................................GGATCAATAGCCGAGTCGA-----TCAAGCCA..................................................................................................................................................................................................................................................................................................................................................................................................	27	8	0.25	2	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CGATTGGAGCACTTGCAGCCGCCTT.............	25	4	0.25	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................................................................................................................................................................................GTCTTTAA-------------------------------------------------------ATTCTCAGGTGGATAGCAGA......................................	28	4	0.25	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
...........................................................................................................................................................................TACCC-----------------------CACCCTATCGT-TG-----TTGA-CT--GT---------T-.............................................................................................................................................................................................................................................................................	27	4	0.25	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
...A-AA-----------------------AGTATGTAACAGCCAGG..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	4	0.25	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
.............................................................................................................................................................................................................................................................................................TAGTTCG-----------------------CC-----AATTGT--ACTT---------AAC------------------------------------------GTCT.....................................................................................................................	26	4	0.25	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
............................................................................................................................................................................................................................................................................................................................................................................................................................................................................TGGATAGCAGACGATTGGAGCACTTGCAGC...................	30	4	0.25	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AGACGATTGGAGCACTTGCAGCCGCC...............	26	4	0.25	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TAGCAGACGATTGGAGCACTTGCAGCA..................	27	4	0.25	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
.........................................................................................................................................................................TTTACCC-----------------------CACCCTATCGT-TG-----TTGA-C.............................................................................................................................................................................................................................................................................................	25	4	0.25	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
............................................................................................................................................................................................................................................................................................................................................................................................................................................................................TGGATAGCAGACGATTGGAGCACTTGC......................	27	4	0.25	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
........................................................................................................................................................................................................................................................................................................................................................................................................................................................................CAGGTGGATAGCAGACGATTGGAGCACT.........................	28	4	0.25	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
................................TATGTAACAGCCAGGTGGAAGC.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................	22	4	0.25	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
................................................................................................AATAGCCGAGTCGA-----TCAAGCCAT.................................................................................................................................................................................................................................................................................................................................................................................................	23	9	0.22	2	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0
..............................................................................................TCAATAGCCGAGTCGA-----TCAA......................................................................................................................................................................................................................................................................................................................................................................................................	20	9	0.22	2	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0
....................................................................................................GCCGAGTCGA-----TCAAGCCATGTCCGT...........................................................................................................................................................................................................................................................................................................................................................................................	25	5	0.20	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
.........................................................................................TAGGATCAATAGCCGAGTCGA-----TCAAGTT...................................................................................................................................................................................................................................................................................................................................................................................................	28	5	0.20	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
....................................................................................................GCCGAGTCGA-----TCAAGCCATGTCCGTC..........................................................................................................................................................................................................................................................................................................................................................................................	26	5	0.20	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
.........................................................................................................GTCGA-----TCAAGCCATGTCCGTCTGTC......................................................................................................................................................................................................................................................................................................................................................................................	25	6	0.17	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
.......................................................................................................GAGTCGA-----TCAAGCCATGTCCGTCTG........................................................................................................................................................................................................................................................................................................................................................................................	25	6	0.17	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
.........................................................................................TAGGATCAATAGCCGAGTCGA-----TCAAGA....................................................................................................................................................................................................................................................................................................................................................................................................	27	6	0.17	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
......................................................................................................CGAGTCGA-----TCAAGCCATGTCCGTCTG........................................................................................................................................................................................................................................................................................................................................................................................	26	6	0.17	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
......................................................................................................CGAGTCGA-----TCAAGCCATGTCCGTCT.........................................................................................................................................................................................................................................................................................................................................................................................	25	6	0.17	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
......................................................................................................CGAGTCGA-----TCAAGCCATGTCCGT...........................................................................................................................................................................................................................................................................................................................................................................................	23	6	0.17	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
..........................................................................................AGGATCAATAGCCGAGTCGA-----TCAAGCCA..................................................................................................................................................................................................................................................................................................................................................................................................	28	8	0.13	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
..................................................................................TCTTGATTAGGATCAATAGCCGAGT..................................................................................................................................................................................................................................................................................................................................................................................................................	25	8	0.13	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
.........................................................................................................GTCGA-----TCAAGCCATGTCCGTCTGTTA.....................................................................................................................................................................................................................................................................................................................................................................................	26	8	0.13	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
.............................................................................................................A-----TCAAGCCATGTCCGTCT.........................................................................................................................................................................................................................................................................................................................................................................................	18	8	0.13	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
..............................................................................................TCAATAGCCGAGTCGA-----TCAAGC....................................................................................................................................................................................................................................................................................................................................................................................................	22	8	0.13	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
..............................................................................................TCAATAGCCGAGTCGA-----TCAAG.....................................................................................................................................................................................................................................................................................................................................................................................................	21	8	0.13	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
..........................................................................................AGGATCAATAGCCGAGTCGA-----TCAAGT....................................................................................................................................................................................................................................................................................................................................................................................................	26	8	0.13	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
....................................................................TAAAGATTATTTATT..........................................................................................................................................................................................................................................................................................................................................................................................................................................	15	8	0.13	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
..................................................................................TCTTGATTAGGATCAATAGCCGAGTCGA-----..........................................................................................................................................................................................................................................................................................................................................................................................................	28	8	0.13	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
...........................................................................................GGATCAATAGCCGAGTCGA-----TCAAGC....................................................................................................................................................................................................................................................................................................................................................................................................	25	8	0.13	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
..........................................................................................AGGATCAATAGCCGAGTCGA-----TCAA......................................................................................................................................................................................................................................................................................................................................................................................................	24	8	0.13	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0
...............................................................................................CAATAGCCGAGTCGA-----TCAAGCC...................................................................................................................................................................................................................................................................................................................................................................................................	22	9	0.11	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
....................................................................................TTGATTAGGATCAATAGCCGAGT..................................................................................................................................................................................................................................................................................................................................................................................................................	23	9	0.11	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
....................................................................................................GCCGAGTCGA-----TCAAGCCAT.................................................................................................................................................................................................................................................................................................................................................................................................	19	11	0.09	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
....................................................................................................GCCGAGTCGA-----TCAAGCC...................................................................................................................................................................................................................................................................................................................................................................................................	17	11	0.09	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
....................................................................................................GCCGAGTCGA-----TCAAGCCA..................................................................................................................................................................................................................................................................................................................................................................................................	18	11	0.09	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
...............................................................................TATTCTTGATTAGGATCAATAGC.......................................................................................................................................................................................................................................................................................................................................................................................................................	23	11	0.09	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
................................................................................................AATAGCCGAGTCGA-----TCAAGCCT..................................................................................................................................................................................................................................................................................................................................................................................................	22	14	0.07	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
..........................................................................................AGGATCAATAGCCGAGTCGA-----TCAT......................................................................................................................................................................................................................................................................................................................................................................................................	24	14	0.07	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
.....................................................................................TGATTAGGATCAATAGCC......................................................................................................................................................................................................................................................................................................................................................................................................................	18	16	0.06	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
................................................................................................AATAGCCGAGTCGA-----TCA.......................................................................................................................................................................................................................................................................................................................................................................................................	17	16	0.06	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
.........................................................................................................................................................................................................CCCTATCGT-TG-----TTGA-..............................................................................................................................................................................................................................................................................................	15	17	0.06	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
......................................................................................................CGAGTCGA-----TCAAGCCAC.................................................................................................................................................................................................................................................................................................................................................................................................	17	17	0.06	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
.................................................GAAGCGTTTCCGACC.............................................................................................................................................................................................................................................................................................................................................................................................................................................................	15	20	0.05	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
...............................................................................TATTCTTGATTAGGATC.............................................................................................................................................................................................................................................................................................................................................................................................................................	17	20	0.05	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
..........................................................................................AGGATCAATAGCCGAGTCGA-----..........................................................................................................................................................................................................................................................................................................................................................................................................	20	20	0.05	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0

dm3

TTGA-AA-----------------------AGTATTTAACAGGCAGGGGGAAACGTTTCCGACCAAAATAAAGAATATTTATTTTTGATTAGGATCAATGGCCGAGTCGA-----ACTGCCCCTGTCCGTCTGTCCTA-----------------------ACCATTTATTTTCCC-----------------------CACCCTATCGT--GTGCCATTGA-CT--GC---------T-TAT--GGCC-------ACTATTCATTTATTTTC-TGTGC--A-GCTAGTTCG-----------------------CC-----AATTGT--ACTT---------AAC------------------------------------------ATCTTTAA-------------------------------------------------------ATTCTTAGGTGGATAGCAGACGATTGGAGCACTTGCAGCCGCCTTTGTGGTCACGGCT	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
..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................GGTGGATAGCAGACGATTGG...............................	20	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
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..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................GGTGGATAGCAGACGATTGGAGCACT.........................	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
............................................................................................................................................................................................................................................................................TTTTC-TGTGC--A-GCTAGTTCG-----------------------CC-----AA.........................................................................................................................................................................................	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	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
.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................TCTTAGGTGGATAGCAGACGATTG................................	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	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
.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................TCTTAGGTGGATAGCAGACGATTGGA..............................	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	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
...........................................................................................................................................................................TTCCC-----------------------CACCCTATCGT--GTGCCATTGA-..............................................................................................................................................................................................................................................................................................	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	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
.................................................................................TTTTTGATTAGGATCAATGGCCGAG...................................................................................................................................................................................................................................................................................................................................................................................................................	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
.....................................................................................................................................TCCTA-----------------------ACCATTTATTTTT...............................................................................................................................................................................................................................................................................................................................................	18	2	0.50	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
..........................................................................................AGGATCAATGGCCGAGTCGA-----..........................................................................................................................................................................................................................................................................................................................................................................................................	20	9	0.22	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droEre2

TTGA-AA-----------------------AGAATGTAACAGGTAGAAGAAAGCGTTTCCGACCCT-GTAAGGTAAATATACTCTTAATTAAGATCAATAGCCGAGTCGA-----TCTGGCCATGTTCGTCCGCCTGTCCGTCTTTTTAT------------------------TA------------------------------------------TAAA-TT--AT---------TCTTT--GCTT-------ATTATTTATTATTTGTC-TG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
...................................GTAACAGGTAGAAGAAAGCGT.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	8	0.25	2	0	0	0	0	0	2	0
....................................TAACAGGTAGAAGAAAGC.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	14	0.07	1	1	0	0	0	0	0	0

droYak3

TTGA-AG-----------------------AGTATGTAACAGGCAGAAGGAAGCGTTTCCGACCAT-ATAAAGAATATATATTCTTGATCAGGATCAATAGCCTAGTCGA-----TCTGGCCATGTCCGTCTCTCCGTATGAACGTC-------------------------------------------------------------------------GA-AT--GTTTTGATATTT-TTCTATTAGACTTGTAAATATCTATCTATTTTC-AGAAT--A-GCTT-TTCG-----------------------CC-----TACTCT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A	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
.............................................................................TATATTCTTGATCAGGATCAATAGCCT.....................................................................................................................................................................................................................................................................................................................................................................................................................	27	20	0.10	2	0	0	2	0	0	0	0	0	0	0	0
.................................................................................TTCTTGATCAGGATCAATAGCCTAG...................................................................................................................................................................................................................................................................................................................................................................................................................	25	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
.........................................................................................................GTCGA-----TCTGGCCATGTCCGTC..........................................................................................................................................................................................................................................................................................................................................................................................	21	20	0.05	1	0	0	0	0	0	0	1	0	0	0	0
...........................................................................................GGATCAATAGCCTAGTCGA-----TCTGGCC...................................................................................................................................................................................................................................................................................................................................................................................................	26	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0

droEug1

TTGA-TA-----------------------AGTATGTAACAGGTAGAAGGAAGTGTTTCCGGCCCT-ATAAAGTTTATATATTCTAGATAAGGATCAATACCGAAGTTGA-----TTGACCCATGTCCGTCTGTCCGTCCATTCGTCTGT------------------------CC-----------------------GTACTGGA-----------TAGA-CT--GT---------T-T---------------AGTGTTCGTTCTTTT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T	Size	Hit Count	Total Norm	Total
No Reads

droBia1

TTTC-A------------------GTCAGAAGTTTGCAACGCAGTTAAGGA-ACGTTTCCGACCCG-ATAAAGTATAAATATTTTTGATCAGCATCACTAGAGGAGTCGT-----TCTTGCCGTGTTCGTCTGTTTCT-----------------------------------------------------------------------------------------------------------------------------------------ACGC--AAACTAGTCTC-----------------------TC-----AGTTTAAAAGCT---------ATC------------------------------------------GGACTGAAAATTTCCGAAAAATCCTTTTTTTTTTGCAGGTACATTTAACATTTTGAATTTTAAATT-TTTTATAAAAATCAGACGAATGTATCATAGGCTGC------------------C	Size	Hit Count	Total Norm	Total
No Reads

droTak1

TTGC-AGAGGGTATAATGATTTCAGTCAGAA------------------------------------------GTTATATATTCTTAATCAGCATCACTAGACGAGTCGA-----TCTAGCCATGACCGTCTGTCTGTCCGTTCGTCTGTCCGTTCGTCTGTCTGTTCGT----CTGTCTGTTC----GTCTGTCTGTT-----------------------------------------------------CGTC--TGTCTGTCCG-TTT-CTAAGC--AAACTAGTCTT-----------------------TC-----AGTTTTCAAGCT---------ATC------------------------------------------GTCTTAAAACTTTC-----------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droEle1

GTCA-GA-----------------------AGTTTGCAACGCAGTGAAGGAGACATTTCCGACCCT-ATAAAGTATATATATTATTCATCAGAATCACTAGGAGAGTCGA-----TCTAGCCATGTCCGTCTGTCCGTCCGTCTGTTAGT------------------------CTGTCA------------GTCTGTC-----------------------------------------------------TGT--CTGTCCGTCCG-TTT-CTACGC--AAGCTAGTCTC-----------------------TC-----AGTTTTACAGCT---------ATC------------------------------------------TGCATGAAATTTTC-----------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droRho1

GTCA-AA-----------------------AGTT--CAA------------CGCATTTCCGACCCT-ATA-AGTATATATATTCTTGATCAGGATCATCAGAAGAGTCGA-----TGTAGCCATGTCCGTCTGTCCGTCCGTCTGTCCGT------------------------CCGTCTGTCC----GTCTGTCCGTC-----------------------------------------------------CGTC--CGTCCGTCCA-TTT-CTACGC--T-ACTAGTCCC-----------------------TC-----AGTTTTAAAGCT---------ATC------------------------------------------TGCTTGAAACTTTC-----------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droFic1

TTTG-TT------------------------------------------------------------------------------TGACCCAAA--------------------------------------------------------------------CCACTT-----------------------------------------------------A-CT--GC---------C-GCT--GGCA-------ACTACTCATTTACTTTC-TGTTC--C-GCCGACTCGCGATGAACGCCCTGACTGACCGACC-----ACTTGC--ACTC---------AAC------------------------------------------CT-TGTGA-------------------------------------------------------ATCCGCAGCTGGATAACCGACGACTGGAGCACTTGCAGCCGGCTCTGTGGCCACGGCT	Size	Hit Count	Total Norm	Total
No Reads

droKik1

TCGC-AA------------------------------------GTGAAGGAGACCTTTCCGACCCA-ATAA--TATATATATTCTTGATCATCATCAACAGCCGAGTCGA-----TCTAGCCATGTCCGTCTATGCAA-------------------------------------------------------------------------------------------------------------------------------------------------ACTAGTCCC-----------------------TCGACAAAATTTTATAGCTTGGTTGTTTATCAACATTTTTGCTCCATTTTTGAAATA-TGGCCATTTTATATTATTTTTCA-------------------------------------------------------ACTTTCA--TGAAAAGCGGACGAC---------------------------------T	Size	Hit Count	Total Norm	Total
No Reads

droAna3

GTCA-AA-----------------------AGTGTGCAACGCAGTGAAGGAGACATCTCCGACCCT-ATAAAGTATATATATTCTTGATCAGGATCACCTCCTGAGTCGA-----TATAAGCATGTCCGTCTGTCCGTCTGTCCGTCTGTCCGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCCGTCTGTCTGTCTGTC-----------------------------------------------------CGTC--TGTCTGTCTG-TTT-CTACGC--AAACTAGTCTC-----------------------TC-----AGTTTTAAAGCT---------ATC------------------------------------------GAGTTGAAACTTTG------------------------------------------------------------------------------------CACACACCCT------------T	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
.................................................................................TTCTTGATCAGGATCACCTC........................................................................................................................................................................................................................................................................................................................................................................................................................	20	20	1.10	22	0	0	22	0	0	0
..........................................................................................................TCGA-----TATAAGCATGTCCGTCTGTCCGTC..................................................................................................................................................................................................................................................................................................................................................................................	28	20	0.90	18	0	18	0	0	0	0
...................................................................................................................TATAAGCATGTCCGTCTGTCCGTCTGT...............................................................................................................................................................................................................................................................................................................................................................................	27	20	0.35	7	0	7	0	0	0	0
.......................................................................................................GAGTCGA-----TATAAGCATGTC..............................................................................................................................................................................................................................................................................................................................................................................................	19	20	0.25	5	0	0	0	0	5	0
...........................................................................................................CGA-----TATAAGCATGTCCGTCTG........................................................................................................................................................................................................................................................................................................................................................................................	21	20	0.20	4	2	0	0	0	2	0
.......................................................................AGTATATATATTCTTGATCAG.................................................................................................................................................................................................................................................................................................................................................................................................................................	21	20	0.20	4	4	0	0	0	0	0
...................................GCAACGCAGTGAAGGAGACAT.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	20	0.15	3	0	0	0	0	3	0
....................................................................................................................................................GTCCGTCTGTCTGTCTGTCTG....................................................................................................................................................................................................................................................................................................................................................	21	20	0.15	3	3	0	0	0	0	0
........................................GCAGTGAAGGAGACATCTCCGACC.............................................................................................................................................................................................................................................................................................................................................................................................................................................................	24	20	0.10	2	2	0	0	0	0	0
..................................................................................................................................................................................CTGTCCGTCTGTCTGTCTG........................................................................................................................................................................................................................................................................................................................	19	20	0.10	2	0	0	0	0	0	2
.................................................................................................................................TCTGTCCGTCTGTCCGTCTGTCCGT...................................................................................................................................................................................................................................................................................................................................................................	25	20	0.10	2	0	2	0	0	0	0
...................................................................................................................................................................TGTCTGTCTGTCTGTCTGTCCGTCTGT...............................................................................................................................................................................................................................................................................................................................	27	20	0.05	1	1	0	0	0	0	0
...............................................................................TATTCTTGATCAGGATCACC..........................................................................................................................................................................................................................................................................................................................................................................................................................	20	20	0.05	1	0	0	0	0	0	1
...........................................................................................................CGA-----TATAAGCATGTCCGTCTGT.......................................................................................................................................................................................................................................................................................................................................................................................	22	20	0.05	1	0	0	0	0	1	0
.....................................................................................................................................................................................................................................................................................................................................TTTAAAGCT---------ATC------------------------------------------GAGTTGAAACTTTG------------------------------------------------------------------------------------C......................	27	20	0.05	1	0	0	0	0	1	0
...............................................................................................CACCTCCTGAGTCGA-----TATAAGCAT.................................................................................................................................................................................................................................................................................................................................................................................................	24	20	0.05	1	1	0	0	0	0	0
........................................................................................................................................GTCTGTCCGTCTGTCCGTCT.................................................................................................................................................................................................................................................................................................................................................................	20	20	0.05	1	0	1	0	0	0	0
..................................................................................................................................................................................................................................................................................................................................AGTTTTAAAGCT---------ATC------------------------------------------GAGTTG...................................................................................................................	21	20	0.05	1	0	0	0	0	0	1
.......................................................................................................GAGTCGA-----TATAAGCATGTCCGTCTGT.......................................................................................................................................................................................................................................................................................................................................................................................	26	20	0.05	1	1	0	0	0	0	0
....................................................................................................................................GTCCGTCTGTCCGTCTGTCCG....................................................................................................................................................................................................................................................................................................................................................................	21	20	0.05	1	1	0	0	0	0	0
............................................................................................................................................................................GTCTGTCTGTCCGTCTGTCTGTCTGTC-----------------------------------------------------.................................................................................................................................................................................................................................................................	27	20	0.05	1	0	1	0	0	0	0
...........................................................................................GGATCACCTCCTGAGTCGA-----TATAAG....................................................................................................................................................................................................................................................................................................................................................................................................	25	20	0.05	1	1	0	0	0	0	0
..................................................................................................CTCCTGAGTCGA-----TATAAGCATGTCC.............................................................................................................................................................................................................................................................................................................................................................................................	25	20	0.05	1	0	1	0	0	0	0
...........................................................................................................................................TGTCCGTCTGTCCGTCTGTC..............................................................................................................................................................................................................................................................................................................................................................	20	20	0.05	1	0	0	1	0	0	0
........................................................................................................................................................................................................................................................................................................................................AAAGCT---------ATC------------------------------------------GAGTTGAAACTTTG------------------------------------------------------------------------------------CAC....................	26	20	0.05	1	0	1	0	0	0	0
............................................................................................................................................................................................................................................................CGTC--TGTCTGTCTG-TTT-CTACGC--AAA.................................................................................................................................................................................................................................	26	20	0.05	1	0	0	0	0	1	0
............................................................................................................................................................GTCTGTCTGTCTGTCTGTCTGTCT.........................................................................................................................................................................................................................................................................................................................................	24	20	0.05	1	1	0	0	0	0	0
.....................................................CATCTCCGACCCT-ATAAAGTATATATA............................................................................................................................................................................................................................................................................................................................................................................................................................................	27	20	0.05	1	0	1	0	0	0	0
.............................................................................TATATTCTTGATCAGGATCACCTCCTGAG...................................................................................................................................................................................................................................................................................................................................................................................................................	29	20	0.05	1	1	0	0	0	0	0
......................................................................................................................AAGCATGTCCGTCTGTCCGTCT.................................................................................................................................................................................................................................................................................................................................................................................	22	20	0.05	1	0	0	0	0	1	0
.............................................................................................................................................................................................................................................................GTC--TGTCTGTCTG-TTT-CTACGC--....................................................................................................................................................................................................................................	22	20	0.05	1	0	0	1	0	0	0

droBip1

GTCA-AA-----------------------AGTGTGCAACGCAGTGAAGGAGAATTCTCCGACCCT-ATAAAGTATATATATTCTTGATCAGGATCACCTCCTGAGTTTA-----TATAAGCATGTCCGTCTGTCCTG-----------------------TCTGTCTGTCTGTCCGTCTGTCCGTCTGTCTGTCCGTC-----------------------------------------------------TGTC--TGTCTTTCCG-TTT-CTACGC--GAACTAGTCTG-----------------------TC-----AGTTTTGAAGCT---------ATC------------------------------------------GTCTTGAAACTTT------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

dp5

ATAT-T---------------------------------------------ACCGTTTCCGACCCC-ATAAAGTATATATATTCTTGATCAGCATCAATAGCCGAGTTGAGCCAATTGAGCCCTGTCTGTCTGTCCGACCGTCCGTCTGT------------------------CC-----------------------GTCCCTATCA-GC--GCC---TA-GT--G-------------------------------------------------------------CTC-----------------------AA-----AGACTTTAAACA---------ATT------------------------------------------T-------------------------------------------------------------------------------------------------CATTCGTTCT------------C	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
....................................................................................TTGATCAGCATCAATAGCCGAGTT.................................................................................................................................................................................................................................................................................................................................................................................................................	24	10	1.50	15	0	9	2	0	3	0	0	1	0	0
....................................................................................TTGATCAGCATCAATAGCCGAGTTG................................................................................................................................................................................................................................................................................................................................................................................................................	25	8	1.25	10	0	10	0	0	0	0	0	0	0	0
....................................................................................TTGATCAGCATCAATAGCCGAGTTGAG..............................................................................................................................................................................................................................................................................................................................................................................................................	27	1	1.00	1	0	0	0	0	0	0	1	0	0	0
.....................................................................................................................GAGCCCTGTCTGTCTGTCCG....................................................................................................................................................................................................................................................................................................................................................................................	20	20	0.55	11	0	10	0	0	0	0	1	0	0	0
................................................................................ATTCTTGATCAGCATCAATAGCCGAGT..................................................................................................................................................................................................................................................................................................................................................................................................................	27	20	0.40	8	0	0	0	0	0	0	0	8	0	0
.....................................................................................TGATCAGCATCAATAGCCGAGTT.................................................................................................................................................................................................................................................................................................................................................................................................................	23	11	0.27	3	0	3	0	0	0	0	0	0	0	0
...................................................................................................................TTGAGCCCTGTCTGTCTGTC......................................................................................................................................................................................................................................................................................................................................................................................	20	20	0.20	4	0	4	0	0	0	0	0	0	0	0
....................................................................................TTGATCAGCATCAATAGCCGAGTTGA...............................................................................................................................................................................................................................................................................................................................................................................................................	26	5	0.20	1	0	1	0	0	0	0	0	0	0	0
.....................................................................................TGATCAGCATCAATAGCCGAG...................................................................................................................................................................................................................................................................................................................................................................................................................	21	20	0.20	4	0	0	0	0	0	4	0	0	0	0
................................................................................ATTCTTGATCAGCATCAATAGCCGAGTT.................................................................................................................................................................................................................................................................................................................................................................................................................	28	8	0.13	1	0	1	0	0	0	0	0	0	0	0
.................................................................................................................AATTGAGCCCTGTCTGTCTGT.......................................................................................................................................................................................................................................................................................................................................................................................	21	14	0.07	1	0	0	0	0	0	0	1	0	0	0
.............................................................................................................................................TCCGTCTGT------------------------CC-----------------------GTCCCTATCA-G..........................................................................................................................................................................................................................................................................................................	22	20	0.05	1	0	1	0	0	0	0	0	0	0	0
......................................................................AAGTATATATATTCTTGATCAGCATCA............................................................................................................................................................................................................................................................................................................................................................................................................................	27	20	0.05	1	0	0	0	0	0	0	0	1	0	0
.................................................................C-ATAAAGTATATATATTCTT.......................................................................................................................................................................................................................................................................................................................................................................................................................................	20	20	0.05	1	0	0	0	0	0	0	0	0	1	0
..........................................................................................................................................CCGTCCGTCTGT------------------------CC-----------------------GTCCCTATCA-G..........................................................................................................................................................................................................................................................................................................	25	20	0.05	1	0	0	0	0	0	0	0	0	1	0
......................................................................................................................................................................................................................GCC---TA-GT--G-------------------------------------------------------------CTC-----------------------AA-----AGACT......................................................................................................................................................................................	18	20	0.05	1	0	1	0	0	0	0	0	0	0	0
................................................................CC-ATAAAGTATATATATTCTT.......................................................................................................................................................................................................................................................................................................................................................................................................................................	21	20	0.05	1	0	0	1	0	0	0	0	0	0	0
.........................................................TCCGACCCC-ATAAAGTATATATA............................................................................................................................................................................................................................................................................................................................................................................................................................................	23	20	0.05	1	0	1	0	0	0	0	0	0	0	0
....................................................................................TTGATCAGCATCAATAGCCGAGTTT................................................................................................................................................................................................................................................................................................................................................................................................................	25	20	0.05	1	0	1	0	0	0	0	0	0	0	0

droPer2

TGGTAAA-----------------------AGTGG---A--TCCAGAAGGAATCGTTTCCGACCCC-ATAAAGTATATATATTCTTGATCAGCATCAATAGCCGAGTCGA-----TTGAGTCATGTCTGTCTGTCCGTCTGACCTC------------------------------------------------------------------C-----TCTA-TT--GC---------T-TTG--GCCC-------GCCATTCA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
........................................................................................TCAGCATCAATAGCCGAGTCGA-----TT........................................................................................................................................................................................................................................................................................................................................................................................................	24	20	0.20	4	0	4	0	0	0	0
.........................................................................................................................CATGTCTGTCTGTCCGTC..................................................................................................................................................................................................................................................................................................................................................................................	18	20	0.15	3	3	0	0	0	0	0
......................................A--TCCAGAAGGAATCGTTTCCGACCCC-..........................................................................................................................................................................................................................................................................................................................................................................................................................................................	26	13	0.08	1	0	1	0	0	0	0
..........................................................................................................................ATGTCTGTCTGTCCGTCTG................................................................................................................................................................................................................................................................................................................................................................................	19	20	0.05	1	0	0	0	1	0	0
..............................................................................................TCAATAGCCGAGTCGA-----TTGAGT....................................................................................................................................................................................................................................................................................................................................................................................................	22	20	0.05	1	0	1	0	0	0	0
....................................................TCGTTTCCGACCCC-ATAAAGTATATA..............................................................................................................................................................................................................................................................................................................................................................................................................................................	26	20	0.05	1	0	1	0	0	0	0
.....................................................................AAAGTATATATATTCTTGATCAGCA...............................................................................................................................................................................................................................................................................................................................................................................................................................	25	20	0.05	1	0	1	0	0	0	0

droWil2

TTTT-G------------------GTCAGAAGTGTGCAACGCATAGAAGGAAGCATCTCCGACCAT-ATAAAGTATATATATTCTTGATCAGCATGACGAGACGAGTTCA-----TATAGCCATGTCCGTCCGTCCTTCCGTCTGTCCGT------------------------CCGTCTGT-------------------CAACAGTG-ACT-----TTGATCAATATC------------------------------TTCGTTTT-TTCC-TATGCTAA-GATTGTTGG-----------------------CC-----GTTCTT--TCGC---------A------------------------AGCATTAGC-----------CTTTTTAG-------------------------------------------------------A--------------------------------------------------------T	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
..............................................................................................................................CCGTCCGTCCTTCCGTCTGTC..........................................................................................................................................................................................................................................................................................................................................................................	21	5	0.20	1	0	0	0	1	0
.......................................................................................................................................................................................................................................................................................TAA-GATTGTTGG-----------------------CC-----GTTCTT--TCGC---------A------------------------AG...........................................................................................................................................	27	14	0.14	2	0	0	0	2	0
........................................................................................................................................TTCCGTCTGTCCGT------------------------CCGTCTG........................................................................................................................................................................................................................................................................................................................................	21	10	0.10	1	0	1	0	0	0
..............................................AAGGAAGCATCTCCGACCAT-A.........................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	20	0.10	2	0	0	0	2	0
..........................................................................................................TTCA-----TATAGCCATGTCCGTCCGTCC.....................................................................................................................................................................................................................................................................................................................................................................................	25	20	0.10	2	0	0	0	2	0
....................................................................................................................ATAGCCATGTCCGTCCGTCCT....................................................................................................................................................................................................................................................................................................................................................................................	21	14	0.07	1	0	1	0	0	0
.......................................................................................................................................................................................................................................................................................TAA-GATTGTTGG-----------------------CC-----GTTCTT--TCGC---------A------------------------AGC..........................................................................................................................................	28	14	0.07	1	0	1	0	0	0
...................................................................................................................................................................................................................................................................................................................................TTCTT--TCGC---------A------------------------AGCATTAGC-----------CTTTTTAG-------------------------------------------------------A--------------------------------------------------------.	28	18	0.06	1	0	1	0	0	0
............................................................................................................................................................................................................................................................................................ATTGTTGG-----------------------CC-----GTTCTT--TCG................................................................................................................................................................................	19	20	0.05	1	0	0	0	0	1
.........................................................................TATATATATTCTTGATCAGCATGACG..........................................................................................................................................................................................................................................................................................................................................................................................................................	26	20	0.05	1	1	0	0	0	0
................................................................................................................................................................................................................................................................................................TTGG-----------------------CC-----GTTCTT--TCGC---------A------------------------AGCA.........................................................................................................................................	21	20	0.05	1	0	1	0	0	0
......................................................................................GATCAGCATGACGAGACGAG...................................................................................................................................................................................................................................................................................................................................................................................................................	20	20	0.05	1	0	0	1	0	0
TTTT-G------------------GTCAGAAGTGTGCAACGCATA................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	26	20	0.05	1	0	0	0	1	0
..............................................................................................................................................................................................................................................................................TCC-TATGCTAA-GATTGTTGG-----------------------CC-----...........................................................................................................................................................................................	22	20	0.05	1	0	0	0	1	0
........................................................................................TCAGCATGACGAGACGAGTTC................................................................................................................................................................................................................................................................................................................................................................................................................	21	20	0.05	1	0	0	1	0	0

droVir3

A---------------------------------------------------GTATCTCCGACCCC-ATAAAATGTATGTATTCTTGATCAGCATCAATAGCCGAGTCGA-----TCCAGCGATGTCCGTCTGTCTGTCCGTTCGTCCGT------------------------CT-----------------------GTCCGCAGCA-GCT-----TTGA-CA--AT---------T-TCT--GTACACATGTA--CACATATACA-TTC-ATGCGC--G-TCTGCTTCG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C	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
.......................................................................AATGTATGTATTCTTGATCAGCATCA............................................................................................................................................................................................................................................................................................................................................................................................................................	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	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
..............................................................................GTATTCTTGATCAGCATCAATAGCC......................................................................................................................................................................................................................................................................................................................................................................................................................	25	19	0.74	14	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	1	3	0	1	2	0	2	1	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
..............................................................................GTATTCTTGATCAGCATCAATAG........................................................................................................................................................................................................................................................................................................................................................................................................................	23	20	0.60	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	2	2	2	0	3	1	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
..............................................................................GTATTCTTGATCAGCATCAATAGC.......................................................................................................................................................................................................................................................................................................................................................................................................................	24	19	0.53	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	7	0	1	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
....................................................................................TTGATCAGCATCAATAGCCGAG...................................................................................................................................................................................................................................................................................................................................................................................................................	22	20	0.35	7	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	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	0	0	0	0	0	0
.............................................................................TGTATTCTTGATCAGCATCAATAG........................................................................................................................................................................................................................................................................................................................................................................................................................	24	19	0.32	6	0	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	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...........................................................................TATGTATTCTTGATCAGCATCAATA.........................................................................................................................................................................................................................................................................................................................................................................................................................	25	18	0.22	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	2	0	0	1	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
.............................................................................TGTATTCTTGATCAGCATCAATA.........................................................................................................................................................................................................................................................................................................................................................................................................................	23	19	0.21	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	0	0	0	1	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..............................................................................GTATTCTTGATCAGCATCAATA.........................................................................................................................................................................................................................................................................................................................................................................................................................	22	20	0.20	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	0	1	2	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
.........................................................................TGTATGTATTCTTGATCAGCA...............................................................................................................................................................................................................................................................................................................................................................................................................................	21	5	0.20	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
..........................................................................GTATGTATTCTTGATCAGCATCAATA.........................................................................................................................................................................................................................................................................................................................................................................................................................	26	10	0.20	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	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
...............................................................................TATTCTTGATCAGCATCAATAGCCGAG...................................................................................................................................................................................................................................................................................................................................................................................................................	27	20	0.15	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.............................................................................TGTATTCTTGATCAGCATCAAT..........................................................................................................................................................................................................................................................................................................................................................................................................................	22	20	0.10	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	1	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
..........................................................................................................................ATGTCCGTCTGTCTGTCCGT...............................................................................................................................................................................................................................................................................................................................................................................	20	20	0.10	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	2	0
...........................................................................TATGTATTCTTGATCAGCATCAATAGCC......................................................................................................................................................................................................................................................................................................................................................................................................................	28	17	0.06	1	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
...........................................................................TATGTATTCTTGATCAGCATCAATAG........................................................................................................................................................................................................................................................................................................................................................................................................................	26	18	0.06	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
............................................................................ATGTATTCTTGATCAGCATCAATAGCC......................................................................................................................................................................................................................................................................................................................................................................................................................	27	18	0.06	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	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
...................................................................................................................................TGTCTGTCCGTTCGTCCGT------------------------C..............................................................................................................................................................................................................................................................................................................................................	20	20	0.05	1	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
.............................................................................TGTATTCTTGATCAGCATCAA...........................................................................................................................................................................................................................................................................................................................................................................................................................	21	20	0.05	1	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
.....................................................................................TGATCAGCATCAATAGCCGAG...................................................................................................................................................................................................................................................................................................................................................................................................................	21	20	0.05	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
...........................................................................TATGTATTCTTGATCAGCATCAA...........................................................................................................................................................................................................................................................................................................................................................................................................................	23	20	0.05	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
............................................................................ATGTATTCTTGATCAGCATCA............................................................................................................................................................................................................................................................................................................................................................................................................................	21	20	0.05	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

TTGA-AA-----------------------TGTATGTAACAGGCAAAAGGAGGCGTGGCAGACCCC-ACAAAGTATATATATTCTTGATCAGGGCGACGAGCTGAGTTGA-----TTTAGCACTGTCCGTCTGTCCTT-----------------------GAAATTTGTTTTCCT-----------------------AGGTCC----------------------------------------------------------ATGTGTTTG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CT	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
.............................................................ACCCC-ACAAAGTATATATATTCTTGATCA..................................................................................................................................................................................................................................................................................................................................................................................................................................	29	20	0.40	8	8	0	0	0	0	0
..............................................................................ATATTCTTGATCAGGGCGACGAGCTGAG...................................................................................................................................................................................................................................................................................................................................................................................................................	28	20	0.15	3	3	0	0	0	0	0
.............................................................................TATATTCTTGATCAGGGCGACGA.........................................................................................................................................................................................................................................................................................................................................................................................................................	23	20	0.05	1	1	0	0	0	0	0
...........................................CAAAAGGAGGCGTGGCAG................................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	20	0.05	1	1	0	0	0	0	0
....................................................................................TTGATCAGGGCGACGAGCTGAGTTGA-----..........................................................................................................................................................................................................................................................................................................................................................................................................	26	20	0.05	1	1	0	0	0	0	0
................................TATGTAACAGGCAAAAGGAGG........................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	20	0.05	1	1	0	0	0	0	0
................................TATGTAACAGGCAAAAGGAGGCG......................................................................................................................................................................................................................................................................................................................................................................................................................................................................	23	20	0.05	1	1	0	0	0	0	0

droGri2

TGCA-AA-----------------------GGT--------------AAAAGGAGTCTCCGACACC-ATAAACTATATATATTCTTGATCAGGTTCTACAGCCGAGTCGA-----TATAGCCATGTCCGTCTGTCCGTCCGTCCGTCCAC------------------------CC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
...............................................................................................................................CGTCTGTCCGTCCGTCCGTCC.........................................................................................................................................................................................................................................................................................................................................................................	21	7	0.14	1	1	0

dse_1133

scaffold_28:256137-256287 +

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

-13.91	-13.8	-13.6