dpe_384

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------################################################## CTTTAACTTTGGCGGTGATTAGTGAAAGAAGTTTGTCCAAAATGCGCACATTTATTTGCCTCGTCCTGGCGGCCCTCGTCCTTGCCCTGGTCGCCAGCACCAACGCGGCCACTACGCTGCTCGATGTGGATGCAGGTGTCTCAGAGCCGATTTCTGTGCGTCAGGCTCGTCAATTCGGAGGATTCGGAGGAAGACCTGGAGGTGGTTTTGGCGGCGGTGGTTTCGGCGGGCCCGGCGGCTTTGGCGGTCGA *************************************************************************************************************************************************...(((((.((.(((...(((.........)))))).)).)))))*********************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M021 embryo	V057 head	V050 head	V111 male body
........................................................................................................................................................................................CGGAGGAAGACCTGGAGGTGGTTTTGGC.......................................	28	0	1	4.00	4	4	0	0	0
...................................................................................................................................................CGATTTCTGTGCGTCAGGCT....................................................................................	20	0	1	2.00	2	2	0	0	0
............................................................................................................................................................................ATTCGGAGGATTCGGAGGAA...........................................................	20	0	1	2.00	2	2	0	0	0
............................................................................................................................................TCAGAGCCGATTTCTGTGCGTCAGGCT....................................................................................	27	0	1	2.00	2	2	0	0	0
................................................................................................................................................................TCAGGCTCGTCAATTCGGAGG......................................................................	21	0	1	1.00	1	0	1	0	0
...........................................................................................................................ATGTGGATGCAGGTGTCTCA............................................................................................................	20	0	1	1.00	1	0	1	0	0
....................................................................................................................................................GATTTCTGTGCGTCAGGCC....................................................................................	19	1	1	1.00	1	1	0	0	0
....................................................................................................................................................GATTTCTGTGCGTCAGGCT....................................................................................	19	0	1	1.00	1	1	0	0	0
.....................................................ATTTGCCTCGTCCTGGCGGCC.................................................................................................................................................................................	21	0	1	1.00	1	0	0	1	0
................................................................................................................................................................................GGAGGATTCGGAGGAAGT.........................................................	18	1	2	0.50	1	0	1	0	0
...........................................................................................................................................................................................GGGAAGACCGGGTGGTGGTTT...........................................	21	3	2	0.50	1	0	1	0	0
.....................................................................................................................................................................................................GGAGGTGATTTTGGCTGCGGAGG...............................	23	3	3	0.33	1	0	1	0	0
..........................................................................................................................................TGGCAGAGCCGGTTTCTGTG.............................................................................................	20	3	14	0.07	1	0	1	0	0
.....................................................................................................................................................................................................GGTGGTGGGTTTGGCGGC....................................	18	2	20	0.05	1	0	0	0	1
.....................................................................................................................................................AGTTCTGTGCGTCTGGCCC...................................................................................	19	3	20	0.05	1	0	1	0	0

GAAATTGAAACCGCCACTAATCACTTTCTTCAAACAGGTTTTACGCGTGTAAATAAACGGAGCAGGACCGCCGGGAGCAGGAACGGGACCAGCGGTCGTGGTTGCGCCGGTGATGCGACGAGCTACACCTACGTCCACAGAGTCTCGGCTAAAGACACGCAGTCCGAGCAGTTAAGCCTCCTAAGCCTCCTTCTGGACCTCCACCAAAACCGCCGCCACCAAAGCCGCCCGGGCCGCCGAAACCGCCAGCT *********************************************************...(((((.((.(((...(((.........)))))).)).)))))*************************************************************************************************************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V057 head	M042 female body	V111 male body
................................AACAGGTTTTACGCGTGTAA.......................................................................................................................................................................................................	20	0	1	1.00	1	1	0	0
............................TTCAAACAGGTTTTAGGCGAGA.........................................................................................................................................................................................................	22	3	2	0.50	1	0	1	0
...........................................................................AGGAGGAACGGGAACAGCG.............................................................................................................................................................	19	2	9	0.22	2	0	0	2
......................................................................................GGCCAGCGGTCGTAGTTG...................................................................................................................................................	18	2	5	0.20	1	0	1	0
................................................................GGGACGCCGGGAGCAGGAAT.......................................................................................................................................................................	20	3	6	0.17	1	1	0	0
.........................TGGTTCAAACAGGTTTTA................................................................................................................................................................................................................	18	2	14	0.07	1	0	0	1
.........................TGGTTCAAACAGGTTTAAC...............................................................................................................................................................................................................	19	3	20	0.05	1	1	0	0

Species	Coordinate	ID	Alignment
droPer2	scaffold_0:3517363-3517613 +	dpe_384	CTTTAACTTTGGCGGTGATTAGTGAAAGAAGTTTG---TCCA--------------AAATGCGCACATTTATTTGCCTCGTCCTGGCGGCCCTCGTCCTTGCCCTGGTCGCCAGCAC---CAACGCGGCCAC---------------------TACGCTGCTCGATGTGGATGCAGGTGTCTCAGAGCCGATTTCTGTGCGTCAGGCTCGTCAATTCGGA---GGATTC------------GG------------------------------------------AGG---AAG------------ACCTGGA---GGTGGTTTTGGCGGCGGTGGTTTCGGCG---GGCC---CGGCGGCTTTGGCGGTCGA
dp5	2:16874157-16874407 -		CTTTAACTTTGGCGGTGATTAGTGAAAGAAGTTTG---TCCA--------------AAATGCGCACATTTACTTGCCTCGTCCTGGCGGCCCTTATCCTTGCCCTGGTCGCCAGCTC---CAACGCGGCCAC---------------------TACGCTGCTCGATGTGGATGCAGGTGTCTCAGAGCCGGTGTCTGTGCGTCAGGCCCGTCAATTCGGA---GGATTC------------GG------------------------------------------AGG---AAG------------ACCAGGA---GGAGGTTTTGGCGGCGGTGGTTTCGGCG---GGCC---CGGCGGCTTTGGCGGTCGA
droWil2	scf2_1100000003205:656-772 -		GGA------------------------------------------------------------------------------------------------------------------------------------------------------------------GGCGGTGGTCGTGGTGGCGG----------------------------------------CTTC------------GGTGG------------TCGTAGCCGTGGTGGAGGCGG------CGGTGGAGG------------TGGA---GGCGGTGGCGGTG---GCAATCGCTTT------GATCGCGGCGGCGGTGGTGGTGGCGGC
droVir3	scaffold_12963:10298185-10298257 +		CGGCGGCTTCGGCGGT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AG------------ACCCGGC---GGCGGTTTCGGTGGACCCGGATTCGGAG---------GCGGCGGCTTCGGCGGTAGA
droMoj3	scaffold_6308:2899616-2899770 +		CTGCTCGCTGTG-------------------------------------------------TG---------CAGCATGGCCCATGCGGGCTTCCTT---------GGCGGC-----------GGCAGCGCCCTCAGCTCCG------GT----------------------------------------------------------------------GGCGGCTATAGCGGTGGTCATGG------------CGGTGGCTA---CGGCGG------------------CGGCTATGGCGGCGGCCAT---GG---------------------------AGGCGGCTATGGCGGTGGCTACGGCGGCGG-
droGri2	scaffold_15074:2515927-2516026 -		TCTG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGCGGAGGTCTG------------GGCGGCGGTCTGGGCAGCGGTCTGAGTGGAGG------------------AGGTCTGGGCGGCGGTCTG---GG---------------------------CGGCGGTCTAGGCGGCGGTCTGGGCGGTGGT
droAna3	scaffold_13340:1987204-1987484 -		TCGAAACTTTGGCGGTGATTAGTGGCAGAAGTTTT---CCTG--------------AAATGCGCACATTCGTTTGTCTTGCCCTGGCGGCCGTCCTC------CTGGTCGCCAGCTCAACTTCGGCGGCTACATTCGATCCG------GCCGCTCAACTCCTGGCCGTAGATGCAGGTGTCCAGGCTCCGGTGGCAGCCCGTCAAGTTCGTCAGTTCGGAGGAGGCTTC------------GGAGG---------------ACC---TGGAGG---TGGTTTTGG------AGG------------ACCT---GGAGGTGGTTTCGGA---GGTGGTTTCGGAG---GACCTGGAGGTGGCTTCGGAGG---A
droBip1	scf7180000396712:2344853-2345145 +		TCGAAACTTTGGTGGTGATTAGTGGCAGAAGTTTT---CGTG--------------AAATGCGCACATTCGTTTGCCTCACCCTGGCGGCCGTCCTT------CTGGTCGCCGGCTCAACTTCGGCTGCTACATTCGATCCG------GCCGCCCAACTCCTGGCCGTGGATGCAGGTGTCCAGGCTCCGGTTGCTGCTCGTCAAGTTCGTCAGTTCGAAGGAGGCTTT------------GGAGG---------------TCC---TGGAGG---TGGCTTCGGAGG---ACG------------CCCT---GGAGGTGGTTTCGGAGGCGGTGGCTTTGGAGGAGGCCCTGGAGGTGGCTTCGGAGGAGGC
droKik1	scf7180000302392:367084-367324 +		TCGAAACTTTGCCGGTGATTAGTGGCAGAAGTTTC---CCCGAGTCCGAGCAAACGAAATGCGTACATTTGTTTGCCTTGCCCTGGCGGCCATTCTC------CTGGTCGCCGGCAC---TTCAGCGGCCACATATGATGCG------GCTGCCCAGCTTTTAGATGTGGATGCAGGTGTCCAAACACCGTTGGCCGCTCGGCAGGTTCGTCAATTTGGA------------------------------------------------------------------------GG------------TCCA---GGAGGCGGCTATG---------------GA---GGCTTTGG---------AGGCGGAAGA
droFic1	scf7180000453906:63228-63464 -		TCGAAACTTTGTCGGTGATTAGTGGCAGAAGTTTTTCCCCCCA-------------AAATGCGCACATTTGTTTGCCTCGCATTGGCGACCATTCTC------CTGGTCGCCGGCTC---CTCGGCCGCGGTATTTGAGCCCAGTGTGGCCGCCAAGCTCCTGGCTGTGGATGCAGGTGTCCAGGCTCCTTCGGCCGCCCGACAGGTTCGTCAGTTTGGCGGTGGCTTC------------GG------------------------------------------TGG---AGG------------TCCA---------------------------------------------GGTGGATTCGGCGGAGGT
droEle1	scf7180000491047:1762030-1762293 +		TCGAAACTTTGGCGGTGATAAGTGGCAGAAGTTTC---CTCG--------------AAATGCGCACATTTGTTAGCCTCGTCCTGGCGACCATCCTT------CTGGTCGCCGGCTG---CTCAGCAGGCACATATGATCCT------GCGGCCCAGCTGCTGGATGCGGATGCAGGGGTCCTGGCTCCTACGGCCGCTCGTCAAGTTCGTCAATATGGA---GGTTTC------------GGAGG---------------TCC---TGGAGG---AGGCTTTGG------CCG------------TCCA---GGAGGTGGCTTCG---------------GA---GGTCCTGGAGGCGGCTTCGGAGGTC--
droRho1	scf7180000762774:4244-4476 +		TCGAAACTTTGGCGGTGATTAGTGGCAGAAGTTTC---CTCG--------------AAATGCGTACATTTGTTTGCCTTGCCCTGGCGACCATCCTT------CTGGTCGCCGGCTC---TTCAGCAGCTACATTTGATCCT------GCGGCCCAGCTCCTGGCTGTGGATGCAGGTGTCCAGGCTCCACAGGCCGCTCGGCCAGTTCGTCAATTCGGCGGAGGATTT------------GG------------------------------------------AGG---AAG------------GCCAGGA---G------------------------------------GAGGCGGTTTCGGAGGAGGG
droBia1	scf7180000302402:2162109-2162315 -		TCGAAACTTTGGCGGTGATTAGTGGCAGAAGTTTT---ACTCG-------------AAATGCGCACATTTCTTTGCCTCGCCGTGGCGGCCGTCCTC------TTGGTCGCCGGCTC---CTCTGCAGCCACATATGATCCG------GCGGCCCAACTCCTGGCCGTGGATGCAGGTGTCCAGGCTCCGGCTGCCGCTCGCCAGGTTCGCCAGTTCGCA---------------------------------------------------------------------------------------------------------------------------------------GGCGGCTTTGGAGGAGGA
droTak1	scf7180000415380:232637-232853 -		TCGAAACTTTGTCGGTGATTAGTGGCAGAAGTTTC---ATCG--------------AAATGCGCACATTTGTTTGCCTCGCCCTGGCGACCATCCTT------TTGGTCGCCGGCTC---TTCAGCAGCCACATATGATCCT------GCGGCCCAACTCCTGGCCGTGGATGCAGGTGTCCAGGCTCCAGTGGCCGCACGGCAAGTTCGTCAGTTTGGAGGCGGATTC------------GG------------------------------------------AGG---AGG------------TCCTGGA---GGAGG----------------------------------------------------
droEug1	scf7180000409802:542843-543109 +		TCGAAACTTTGTCGGTGATTAGTGGCAGAAGTTTC---CTCGA-------------ATATGCGCACATTCGTTTGCCTCGCCCTGGCGACCATTCTT------CTGGTCGCCGGCTC---CTCAGCAGCCACATTTGATCCT------GCGGCTCAACTTCTGGCCGTGGATGCCGGTGTCCAGGCACCAGTGGCAGCACGGCAAGCTCGTCAATTTGGAGG---ATTCGGCTTT------G---G---------------TCC---AGGAGG---CGGATTCGGCGG---TGG------------TCCA---GGAGGTGGCTTCG---------------GAG---------GCGGCGGTTTCGGCGGTGGC
dm3	chr3R:9437871-9438141 -		TCGAAACTTTGCCGGTGATTAGTAGCAGAAGTTTC---CTCGA-------------AAATGCGCACATTTGTTTGCCTTGCCCTGGCGACCATTCTC------CTGGTCGCCGGCTC---ATCAGCAGCCACATATGATCCT---GTGGCGGCGCAACTTCTGGATGTGGATGCAGGTGTCCAGGCTCCGGTGGCAGCACGCCAAGCACGTCAGTTTGGCGGCGGCTTT------------GGCGG---------------TCC---GGGAGG---CGGTTTCGG------AGG------------TCCA---GGCGGCGGATTCG---------------GA---GGTCAAGGCGGCGGATTCGGAGGTC--
droSim2	3r:11741456-11741710 +		TCGAAACTTTGCCGGTGATTAGTAGCAGAAGTTTC---CTCGA-------------AAATGCGCACATTTGTTTGCCTTGCCCTGGCGACCATTCTC------CTGGTCGCCGGCTC---ATCAGCAGCCACATATGATCCT---GTGGCGGCGCAACTTCTGGATGTGGATGCAGGTGTCCAGGCTCCGGTGGCAGAACGTCAAGCTCGCCAGTTTGGCGGTGGCTTT------------GG------------------------------------------AGG---AAG------------TCCAGGC---GGCGGCTTTG---------------GC---GGTCCGGGAGGCGGTTTTGGAGGACGT
droSec2	scaffold_0:12569044-12569322 +		TCGAAACTTTGCCTGTGATTAGTAGCAGAAGTTTC---CTCGA-------------AAATGCGCACATTTGTTTGCCTTGCCCTGGCGACCATTCTC------CTAGTCGCCGGCTC---ATCAGCAGCCACATATGATCCT---GTGGCGGCGCAACTTCTGGATGTGGATGCAAGTGTCCAGGCTCCGGTGGCAGAACGTCAAGCTCGCCAGTTTGGCGGTGGCTTT------------GGAGG------------ACGTCC---AGGCGG---CGGCTTTGGAGG---AAA------------TCCA---GGCGGCGGCTTCG---------------GC---GGTCCGGGAGGCGGTTTTGGAGGACGT
droYak3	3R:13746936-13747166 -		TCGAAACTTTGCCGGTGATTAGTAGCAGGAGTTTT---CTCGA-------------ATATGCGCACATTTGTTTGCCTCGCCCTGGCGACCATCCTC------CTGGTCGCCGGCTC---CTCAGCAGCCACATATGATCCT---GTGGCGGCGCAACTTCTGGATGTGGATGCTGGTGTCCAGGCTCCGGCGGCAGCACGGCAAGTTCGTCAGTTCGGC---GGCTTC------------GG------------------------------------------AGG---AGG------------TCCA------------------------------------------GGAGGCGGCTTCGGAGGAGGT
droEre2	scaffold_4770:12196871-12197131 +		TCGAAACTTTGCCGGTGATTAGTAGCAGAAGTTTT---CACGA-------------ATATGCGCACATTTGTTTGCCTTGTCTTGGCGACCATCCTC------CTGGTCGCCGGCTC---CTCAGCTGCCACATATGATCCT---GTGGCGGCGCAACTTCTGGATGTGGATGCAGGTGTCCAGGCTCCGTCGGCAGCGCGGCAAGTTCGTCAGTTTGG------CTTC------------GGACG---------------TCC---TG---------GCTTTGA------ACG------------TCC---------TGGCTTTGAACGTCCTGGTTTTGAAC---GTCC------TGGCTTTGGAG---GT

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droPer2

CTTTAACTTTGGCGGTGATTAGTGAAAGAAGTTTG---TCCA--------------AAATGCGCACATTTATTTGCCTCGTCCTGGCGGCCCTCGTCCTTGCCCTGGTCGCCAGCAC---CAACGCGGCCAC---------------------TACGCTGCTCGATGTGGATGCAGGTGTCTCAGAGCCGATTTCTGTGCGTCAGGCTCGTCAATTCGGA---GGATTC------------GG------------------------------------------AGG---AAG------------ACCTGGA---GGTGGTTTTGGCGGCGGTGGTTTCGGCG---GGCC---CGGCGGCTTTGGCGGTCGA	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
....................................................................................................................................................................................................................................C------------GG------------------------------------------AGG---AAG------------ACCTGGA---GGTGGTTTTGGC.............................................	28	1	4.00	4	4	0	0	0	0	0
............................................................................................................................................................................................CGATTTCTGTGCGTCAGGCT.....................................................................................................................................................................	20	1	2.00	2	2	0	0	0	0	0
.....................................................................................................................................................................................................................ATTCGGA---GGATTC------------GG------------------------------------------AGG---AA................................................................................	20	1	2.00	2	2	0	0	0	0	0
.....................................................................................................................................................................................TCAGAGCCGATTTCTGTGCGTCAGGCT.....................................................................................................................................................................	27	1	2.00	2	2	0	0	0	0	0
.........................................................................................................................................................................................................TCAGGCTCGTCAATTCGGA---GG....................................................................................................................................................	21	1	1.00	1	0	0	0	0	1	0
....................................................................................................................................................................ATGTGGATGCAGGTGTCTCA.............................................................................................................................................................................................	20	1	1.00	1	0	0	0	0	1	0
.............................................................................................................................................................................................GATTTCTGTGCGTCAGGCC.....................................................................................................................................................................	19	1	1.00	1	1	0	0	0	0	0
.............................................................................................................................................................................................GATTTCTGTGCGTCAGGCT.....................................................................................................................................................................	19	1	1.00	1	1	0	0	0	0	0
......................................................................ATTTGCCTCGTCCTGGCGGCC..........................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	1	0	0
.........................................................................................................................................................................................................................GGA---GGATTC------------GG------------------------------------------AGG---AAG------------T..................................................................	18	2	0.50	1	0	0	0	0	1	0

dp5

CTTTAACTTTGGCGGTGATTAGTGAAAGAAGTTTG---TCCA--------------AAATGCGCACATTTACTTGCCTCGTCCTGGCGGCCCTTATCCTTGCCCTGGTCGCCAGCTC---CAACGCGGCCAC---------------------TACGCTGCTCGATGTGGATGCAGGTGTCTCAGAGCCGGTGTCTGTGCGTCAGGCCCGTCAATTCGGA---GGATTC------------GG------------------------------------------AGG---AAG------------ACCAGGA---GGAGGTTTTGGCGGCGGTGGTTTCGGCG---GGCC---CGGCGGCTTTGGCGGTCGA	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
......................................................................................................................................................................................................................TTCGGA---GGATTC------------GG------------------------------------------AGG---AAG------------A..................................................................	21	1	1.00	1	0	1	0	0	0	0	0	0	0	0
..................................................................................................................................................................CGATGTGGATGCAGGTGT.................................................................................................................................................................................................	18	1	1.00	1	0	1	0	0	0	0	0	0	0	0
...........................................................................................................................................................................................CCGGTGTCTGTGCGTCAGGCC.....................................................................................................................................................................	21	1	1.00	1	0	0	0	1	0	0	0	0	0	0
....................................................................................................................................................................................................................................................................................................................CAGGA---GGAGGTTTTGGCGGCGGTGGT....................................	26	1	1.00	1	0	1	0	0	0	0	0	0	0	0
...................TAGTGAAAGAAGTTTG---AA.............................................................................................................................................................................................................................................................................................................................................	18	20	0.05	1	0	1	0	0	0	0	0	0	0	0

droWil2

GGA------------------------------------------------------------------------------------------------------------------------------------------------------------------GGCGGTGGTCGTGGTGGCGG----------------------------------------CTTC------------GGTGG------------TCGTAGCCGTGGTGGAGGCGG------CGGTGGAGG------------TGGA---GGCGGTGGCGGTG---GCAATCGCTTT------GATCGCGGCGGCGGTGGTGGTGGCGGC	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
.................................................................................................................................................................................................................................................................................................GGAGG------------TGGA---GGCGGTGGC...................................................	18	4	1.75	7	0	3	0	1	3
...................................................................................................................................................................................................................................................................................GCGG------CGGTGGAGG------------TGGA---GGCGGTGGC...................................................	26	3	1.67	5	0	2	2	0	1
..............................................................................................................................................................................................................................................................................................GGTGGAGG------------TGGA---GGCGGTGGC...................................................	21	4	1.50	6	0	2	1	0	3
...................................................................................................................................................................................................................................................................................GCGG------CGGTGGAGG------------TGGA---GGCGGTGG....................................................	25	3	1.33	4	0	1	0	1	2
.....................................................................................................................................................................GGCGGTGGTCGTGGTGGC..............................................................................................................................................................................................	18	2	1.00	2	0	0	0	2	0
............................................................................................................................................................................................................................................................................GGTGGAGGCGG------CGGTGGA.................................................................................	18	2	1.00	2	0	1	0	0	1
............................................................................................................................................................................................................................................................................GGTGGAGGCGG------CGGTGGAGG------------TGGA---G...........................................................	25	2	1.00	2	0	1	0	0	1
.............................................................................................................................................................................................................................................................................................CGGTGGAGG------------TGGA---GGCGGTGGCGG.................................................	24	2	1.00	2	0	1	0	1	0
......................................................................................................................................................................................................................................................................................G------CGGTGGAGG------------TGGA---GGCGGTGGC...................................................	23	3	0.67	2	0	0	1	0	1
.....................................................................................................................................................................................................................................................................................GG------CGGTGGAGG------------TGGA---GGCGGTGGC...................................................	24	3	0.67	2	0	2	0	0	0
................................................................................................................................................................................................................................................................................GAGGCGG------CGGTGGAGG------------TGGA---GGCGGTG.....................................................	27	3	0.67	2	0	0	2	0	0
..................................................................................................................................................................................................................................................................................GGCGG------CGGTGGAGG------------TGGA---GGCGGT......................................................	24	3	0.67	2	0	2	0	0	0
...............................................................................................................................................................................................................................................................................................GTGGAGG------------TGGA---GGCGGTGGCGG.................................................	22	2	0.50	1	0	1	0	0	0
................................................................................................................................................................................................................................................................................................................................................CTTT------GATCGCGGCGGCGGTGG..........	21	2	0.50	1	0	1	0	0	0
.....................................................................................................................................................................................................................................................................................................................................G---GCAATCGCTTT------GATCGCGGCGGCGGTG...........	28	2	0.50	1	0	0	0	1	0
.............................................................................................................................................................................................................................................................................GTGGAGGCGG------CGGTGGAGG------------TGG................................................................	22	2	0.50	1	0	0	0	1	0
...................................................................................................................................................................................................................................................................CGTAGCCGTGGTGGAGGC................................................................................................	18	2	0.50	1	0	0	0	1	0
............................................................................................................................................................................................................................................................................GGTGGAGGCGG------CGGTGGAGG------------TGGA---............................................................	24	2	0.50	1	0	1	0	0	0
..............................................................................................................................................................................................................................................................................................................................................CGCTTT------GATCGCGGCGGCG..............	19	2	0.50	1	0	0	0	1	0
.....................................................................................................................................................................................................................................................................................................................................G---GCAATCGCTTT------GATCGCGGCGGCGGT............	27	2	0.50	1	0	0	1	0	0
....................................................................................................................................................................................................................................................................................CGG------CGGTGGAGG------------TGGA---GGCGGTGGCG..................................................	26	2	0.50	1	0	0	0	1	0
......................................................................................................................................................................................................................................................................................G------CGGTGGAGG------------TGGA---GGCGGTGGCG..................................................	24	2	0.50	1	0	0	0	0	1
...............................................................................................................................................................................................................................................................................................GTGGAGG------------TGGA---GGCGGTGGCG..................................................	21	2	0.50	1	0	1	0	0	0
.....................................................................................................................................................................GGCGGTGGTCGTGGTGGCGG----------------------------------------C...................................................................................................................................................	21	2	0.50	1	0	1	0	0	0
..........................................................................................................................................................................................................................................................................GTGGTGGAGGCGG------CGGTGGAGG------------TGGA---............................................................	26	2	0.50	1	0	0	0	1	0
...............................................................................................................................................................................................................................................................................................................................................GCTTT------GATCGCGGCGGCGGT............	20	2	0.50	1	0	0	1	0	0
..................................................................................................................................................................................................................................................GTGG------------TCGTAGCCGTGGTGGA...................................................................................................	20	2	0.50	1	0	0	0	1	0
.........................................................................................................................................................................................................................................................................................................................................GCAATCGCTTT------GATCGCGGCGG................	22	2	0.50	1	1	0	0	0	0
.............................................................................................................................................................................................................................................................................GTGGAGGCGG------CGGTGGAGG------------TGGA---GG..........................................................	25	2	0.50	1	0	1	0	0	0
..................................................................................................................................................................................................................................................................................................................................GGTG---GCAATCGCTTT------GATCGCG....................	22	2	0.50	1	0	0	0	1	0
.............................................................................................................................................................................................................................................................................GTGGAGGCGG------CGGTGGAGG------------TGGA---............................................................	23	2	0.50	1	0	1	0	0	0
.....................................................................................................................................................................................................................................................................................GG------CGGTGGAGG------------TGGA---GGCGGTGGCG..................................................	25	2	0.50	1	0	1	0	0	0
..................................................................................................................................................................................................................................................................TCGTAGCCGTGGTGGAGGCGG------........................................................................................	21	2	0.50	1	0	0	0	0	1
...................................................................................................................................................................................................................................................................................................................................GTG---GCAATCGCTTT------GATCGCG....................	21	2	0.50	1	0	1	0	0	0
...........................................................................................................................................................................................................................................................................................................................................AATCGCTTT------GATCGCGGCGGCGGT............	24	2	0.50	1	0	0	0	1	0
...................................................................................................................................................................................................................................................TGG------------TCGTAGCCGTGGTGGAGG.................................................................................................	21	2	0.50	1	0	0	1	0	0
......................................................................................................................................................................................................................................................................................G------CGGTGGAGG------------TGGA---GGCGGTGGCGG.................................................	25	2	0.50	1	0	0	0	1	0
.............................................................................................................................................................................................................................................................................................................................................................CGCGGCGGCGGTGGTGGTGG....	20	3	0.33	1	0	0	0	0	1
.................................................................................................................................................................................................................................................................................AGGCGG------CGGTGGAGG------------TGGA---GGCGGTGG....................................................	27	3	0.33	1	0	0	1	0	0
...................................................................................................................................................................................................................................................................................GCGG------CGGTGGAGG------------TGGA---GGCGGT......................................................	23	3	0.33	1	0	0	0	0	1
.....................................................................................................................................................................................................................................................................................GG------CGGTGGAGG------------TGGA---GGCGGT......................................................	21	3	0.33	1	0	1	0	0	0
....................................................................................................................................................................................................................................................................................CGG------CGGTGGAGG------------TGGA---GGCGGTGGC...................................................	25	3	0.33	1	0	0	0	0	1
..................................................................................................................................................................................................................................................................................GGCGG------CGGTGGAGG------------TGGA---GGC.........................................................	21	3	0.33	1	0	0	0	0	1
................................................................................................................................................................................................................................................................................GAGGCGG------CGGTGGAGG------------TGGA---GGCGGT......................................................	26	3	0.33	1	0	1	0	0	0
...........................................................................................................................................................................................................................................................................................................................................................ATCGCGGCGGCGGTGGTGGT......	20	3	0.33	1	0	1	0	0	0
...............................................................................................................................................................................................................................................................................GGAGGCGG------CGGTGGAGG------------TGGA---GGCG........................................................	25	3	0.33	1	0	1	0	0	0
...........................................................................................................................................................................................................................................................................................................................................................ATCGCGGCGGCGGTGGTGGTGG....	22	3	0.33	1	0	0	0	0	1
....................................................................................................................................................................................................................................................................................CGG------CGGTGGAGG------------TGGA---GGCG........................................................	20	3	0.33	1	0	0	0	0	1
...................................................................................................................................................................................................................................................................................GCGG------CGGTGGAGG------------TGGA---GGC.........................................................	20	3	0.33	1	0	1	0	0	0
.....................................................................................................................................................................................................................................................................................................G------------TGGA---GGCGGTGGCGGTG---GCA.........................................	21	3	0.33	1	0	1	0	0	0
..................................................................................................................................................................................................................................................................................GGCGG------CGGTGGAGG------------TGGA---GGCGGTG.....................................................	25	3	0.33	1	0	1	0	0	0
................................................................................................................................................................................................................................................................................................................................................................GGCGGCGGTGGTGGTGGCGGC	21	7	0.29	2	0	2	0	0	0
................................................................................................................................................................................................................................................................................GAGGCGG------CGGTGGAGG------------TGGA---GG..........................................................	22	4	0.25	1	0	1	0	0	0
................................................................................................................................................................................................................................................................................................TGGAGG------------TGGA---GGCGGTGGC...................................................	19	4	0.25	1	0	1	0	0	0
...................................................................................................................................................................................................................................................................................GCGG------CGGTGGAGG------------TGGA---GGCGGTGGT...................................................	26	4	0.25	1	0	1	0	0	0
...............................................................................................................................................................................................................................................................................GGAGGCGG------CGGTGGAGG------------TGGA---............................................................	21	4	0.25	1	0	1	0	0	0
....................................................................................................................................................................................................................................................................................CGG------CGGTGGAGG------------TGGA---GGCGGTGGCT..................................................	26	4	0.25	1	0	1	0	0	0
................................................................................................................................................................................................................................................................................GAGGCGG------CGGTGGAGG------------TGGA---............................................................	20	5	0.20	1	0	1	0	0	0
..........................................................................................................................................................................................................................................................................GTGGTGGAGGCGG------CGGTGG..................................................................................	19	5	0.20	1	0	0	0	1	0
.........................................................................................................................................................................................................................................................................CGTGGTGGAGGCGG------CGGTGGT.................................................................................	21	5	0.20	1	0	1	0	0	0
................................................................................................................................................................................................................................................................................................................................................................GGCGGCGGTGGTGGTGGC...	18	19	0.11	2	0	1	0	0	1
................................................................................................................................................................................................................................................................................................................................................................GGCGGCGGTGGTGGTGGCG..	19	13	0.08	1	0	1	0	0	0
.................................................................................................................................................................................................................................................................................................................................................................GCGGCGGTGGTGGTGGCG..	18	14	0.07	1	0	1	0	0	0
..............................................................................................................................................................................................................................................................................................................................................................GCGGCGGCGGTGGTGGTGG....	19	20	0.05	1	0	0	0	0	1
...................................................................................................................................................................................................................................................................CGTAGCCGTGGTGGAATA................................................................................................	18	20	0.05	1	0	1	0	0	0
...............................................................................................................................................................................................................................................................................................................................................................CGGCGGCGGTGGTGGTGG....	18	20	0.05	1	0	1	0	0	0

droVir3

CGGCGGCTTCGGCGGT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AG------------ACCCGGC---GGCGGTTTCGGTGGACCCGGATTCGGAG---------GCGGCGGCTTCGGCGGTAGA	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
..................................................................................................................................................................................................................................................................................................................................TTCGGTGGACCCGGATTCGGAG---------GC..................	24	1	2.00	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
......................................................................................................................................................................................................................................................................................................................................GTGGACCCGGATTCGGAG---------GC..................	20	1	1.00	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................................................................................................................TTCGGTGGACCCGGATTCGGAG---------GCGGC...............	27	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0

droMoj3

CTGCTCGCTGTG-------------------------------------------------TG---------CAGCATGGCCCATGCGGGCTTCCTT---------GGCGGC-----------GGCAGCGCCCTCAGCTCCG------GT----------------------------------------------------------------------GGCGGCTATAGCGGTGGTCATGG------------CGGTGGCTA---CGGCGG------------------CGGCTATGGCGGCGGCCAT---GG---------------------------AGGCGGCTATGGCGGTGGCTACGGCGGCGG-	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
............................................................................................................................................................................................................................................................................................................................................................CTATGGCGGTGGCTACGC.......	18	4	0.25	1	0	0	0	0	1	0

droGri2

TCTG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGCGGAGGTCTG------------GGCGGCGGTCTGGGCAGCGGTCTGAGTGGAGG------------------AGGTCTGGGCGGCGGTCTG---GG---------------------------CGGCGGTCTAGGCGGCGGTCTGGGCGGTGGT	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

droAna3

TCGAAACTTTGGCGGTGATTAGTGGCAGAAGTTTT---CCTG--------------AAATGCGCACATTCGTTTGTCTTGCCCTGGCGGCCGTCCTC------CTGGTCGCCAGCTCAACTTCGGCGGCTACATTCGATCCG------GCCGCTCAACTCCTGGCCGTAGATGCAGGTGTCCAGGCTCCGGTGGCAGCCCGTCAAGTTCGTCAGTTCGGAGGAGGCTTC------------GGAGG---------------ACC---TGGAGG---TGGTTTTGG------AGG------------ACCT---GGAGGTGGTTTCGGA---GGTGGTTTCGGAG---GACCTGGAGGTGGCTTCGGAGG---A	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
................GATTAGTGGCAGAAGTTTT---CCT............................................................................................................................................................................................................................................................................................................................................	22	1	3.00	3	0	0	0	0	0	3
................................TTT---CCTG--------------AAATGCGCACATT................................................................................................................................................................................................................................................................................................................	20	1	2.00	2	0	2	0	0	0	0
......................................................................................................................................................CGCTCAACTCCTGGCCGTAGATGCAGG....................................................................................................................................................................................................	27	1	1.00	1	0	1	0	0	0	0
.............GGTGATTAGTGGCAGAAGTTTT---CC.............................................................................................................................................................................................................................................................................................................................................	24	1	1.00	1	0	0	1	0	0	0
..GAAACTTTGGCGGTGATTAGTGGCA..........................................................................................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	1	0	0	0	0
................................TTT---CCTG--------------AAATGCGCACATC................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0
............................................................................................................................................................................................................AGTTCGTCAGTTCGGAGGAGGCTTC------------....................................................................................................................................	25	1	1.00	1	0	1	0	0	0	0
..............................................................................................................................GGCTACATTCGATCCG------GCC..............................................................................................................................................................................................................................	19	1	1.00	1	0	1	0	0	0	0
..GAAACTTTGGCGGTGATTAGTGGCAGA........................................................................................................................................................................................................................................................................................................................................................	27	1	1.00	1	0	1	0	0	0	0
.........................................................................................................................................................................................................................................................................................TTGG------AGG------------ACCT---GGAGGTGGT...................................................	20	1	1.00	1	0	0	0	0	1	0
............................................................................CTTGCCCTGGCGGCCGTCCTC------C.............................................................................................................................................................................................................................................................................	22	1	1.00	1	0	1	0	0	0	0
................................................................................................................................................................................................................................................................................................................................................................GGAGGTGGCTTCGGAGG---A	18	3	0.33	1	1	0	0	0	0	0

droBip1

TCGAAACTTTGGTGGTGATTAGTGGCAGAAGTTTT---CGTG--------------AAATGCGCACATTCGTTTGCCTCACCCTGGCGGCCGTCCTT------CTGGTCGCCGGCTCAACTTCGGCTGCTACATTCGATCCG------GCCGCCCAACTCCTGGCCGTGGATGCAGGTGTCCAGGCTCCGGTTGCTGCTCGTCAAGTTCGTCAGTTCGAAGGAGGCTTT------------GGAGG---------------TCC---TGGAGG---TGGCTTCGGAGG---ACG------------CCCT---GGAGGTGGTTTCGGAGGCGGTGGCTTTGGAGGAGGCCCTGGAGGTGGCTTCGGAGGAGGC	Size	Hit Count	Total Norm	Total
No Reads

droKik1

TCGAAACTTTGCCGGTGATTAGTGGCAGAAGTTTC---CCCGAGTCCGAGCAAACGAAATGCGTACATTTGTTTGCCTTGCCCTGGCGGCCATTCTC------CTGGTCGCCGGCAC---TTCAGCGGCCACATATGATGCG------GCTGCCCAGCTTTTAGATGTGGATGCAGGTGTCCAAACACCGTTGGCCGCTCGGCAGGTTCGTCAATTTGGA------------------------------------------------------------------------GG------------TCCA---GGAGGCGGCTATG---------------GA---GGCTTTGG---------AGGCGGAAGA	Size	Hit Count	Total Norm	Total
No Reads

droFic1

TCGAAACTTTGTCGGTGATTAGTGGCAGAAGTTTTTCCCCCCA-------------AAATGCGCACATTTGTTTGCCTCGCATTGGCGACCATTCTC------CTGGTCGCCGGCTC---CTCGGCCGCGGTATTTGAGCCCAGTGTGGCCGCCAAGCTCCTGGCTGTGGATGCAGGTGTCCAGGCTCCTTCGGCCGCCCGACAGGTTCGTCAGTTTGGCGGTGGCTTC------------GG------------------------------------------TGG---AGG------------TCCA---------------------------------------------GGTGGATTCGGCGGAGGT	Size	Hit Count	Total Norm	Total
No Reads

droEle1

TCGAAACTTTGGCGGTGATAAGTGGCAGAAGTTTC---CTCG--------------AAATGCGCACATTTGTTAGCCTCGTCCTGGCGACCATCCTT------CTGGTCGCCGGCTG---CTCAGCAGGCACATATGATCCT------GCGGCCCAGCTGCTGGATGCGGATGCAGGGGTCCTGGCTCCTACGGCCGCTCGTCAAGTTCGTCAATATGGA---GGTTTC------------GGAGG---------------TCC---TGGAGG---AGGCTTTGG------CCG------------TCCA---GGAGGTGGCTTCG---------------GA---GGTCCTGGAGGCGGCTTCGGAGGTC--	Size	Hit Count	Total Norm	Total
No Reads

droRho1

TCGAAACTTTGGCGGTGATTAGTGGCAGAAGTTTC---CTCG--------------AAATGCGTACATTTGTTTGCCTTGCCCTGGCGACCATCCTT------CTGGTCGCCGGCTC---TTCAGCAGCTACATTTGATCCT------GCGGCCCAGCTCCTGGCTGTGGATGCAGGTGTCCAGGCTCCACAGGCCGCTCGGCCAGTTCGTCAATTCGGCGGAGGATTT------------GG------------------------------------------AGG---AAG------------GCCAGGA---G------------------------------------GAGGCGGTTTCGGAGGAGGG	Size	Hit Count	Total Norm	Total
No Reads

droBia1

TCGAAACTTTGGCGGTGATTAGTGGCAGAAGTTTT---ACTCG-------------AAATGCGCACATTTCTTTGCCTCGCCGTGGCGGCCGTCCTC------TTGGTCGCCGGCTC---CTCTGCAGCCACATATGATCCG------GCGGCCCAACTCCTGGCCGTGGATGCAGGTGTCCAGGCTCCGGCTGCCGCTCGCCAGGTTCGCCAGTTCGCA---------------------------------------------------------------------------------------------------------------------------------------GGCGGCTTTGGAGGAGGA	Size	Hit Count	Total Norm	Total
No Reads

droTak1

TCGAAACTTTGTCGGTGATTAGTGGCAGAAGTTTC---ATCG--------------AAATGCGCACATTTGTTTGCCTCGCCCTGGCGACCATCCTT------TTGGTCGCCGGCTC---TTCAGCAGCCACATATGATCCT------GCGGCCCAACTCCTGGCCGTGGATGCAGGTGTCCAGGCTCCAGTGGCCGCACGGCAAGTTCGTCAGTTTGGAGGCGGATTC------------GG------------------------------------------AGG---AGG------------TCCTGGA---GGAGG----------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droEug1

TCGAAACTTTGTCGGTGATTAGTGGCAGAAGTTTC---CTCGA-------------ATATGCGCACATTCGTTTGCCTCGCCCTGGCGACCATTCTT------CTGGTCGCCGGCTC---CTCAGCAGCCACATTTGATCCT------GCGGCTCAACTTCTGGCCGTGGATGCCGGTGTCCAGGCACCAGTGGCAGCACGGCAAGCTCGTCAATTTGGAGG---ATTCGGCTTT------G---G---------------TCC---AGGAGG---CGGATTCGGCGG---TGG------------TCCA---GGAGGTGGCTTCG---------------GAG---------GCGGCGGTTTCGGCGGTGGC	Size	Hit Count	Total Norm	Total
No Reads

dm3

TCGAAACTTTGCCGGTGATTAGTAGCAGAAGTTTC---CTCGA-------------AAATGCGCACATTTGTTTGCCTTGCCCTGGCGACCATTCTC------CTGGTCGCCGGCTC---ATCAGCAGCCACATATGATCCT---GTGGCGGCGCAACTTCTGGATGTGGATGCAGGTGTCCAGGCTCCGGTGGCAGCACGCCAAGCACGTCAGTTTGGCGGCGGCTTT------------GGCGG---------------TCC---GGGAGG---CGGTTTCGG------AGG------------TCCA---GGCGGCGGATTCG---------------GA---GGTCAAGGCGGCGGATTCGGAGGTC--	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
.................................................................................................................................CACATATGATCCT---GTGGCGGC............................................................................................................................................................................................................................	21	1	2.00	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	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	1	0	0	0	0	0	0	0	0	0	0	0
...................TAGTAGCAGAAGTTTC---CTCGA-------------AAATG........................................................................................................................................................................................................................................................................................................................	26	1	2.00	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	0	0	0	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
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.........................................................................................................................................................................................................................................................................................TCGG------AGG------------TCCA---GGCGGCGGATTCG---------------GA---...........................	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	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
....................................................................................................................................................................................................................................................................................................GG------------TCCA---GGCGGCGGATTCG---------------GA---G..........................	22	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
.................................................................................................................................................GTGGCGGCGCAACTTCTGGATGTG............................................................................................................................................................................................................	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	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
..........GCCGGTGATTAGTAGCAGAAGT.....................................................................................................................................................................................................................................................................................................................................................	22	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
.................................................................................................................................................................................................GCAGCACGCCAAGCACGTCAG...............................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
.............................................................................................................................................................................................................................................................................................................................GCGGATTCG---------------GA---GGTCAAG....................	18	4	0.75	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	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
.................................................................................................................................................................................................................................................................................................................................ATTCG---------------GA---GGTCAAGGCGGC...............	19	3	0.33	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
............................................................................................................................................................................................................................................................................................................................GGCGGATTCG---------------GA---GGTCAAG....................	19	4	0.25	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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

droSim2

TCGAAACTTTGCCGGTGATTAGTAGCAGAAGTTTC---CTCGA-------------AAATGCGCACATTTGTTTGCCTTGCCCTGGCGACCATTCTC------CTGGTCGCCGGCTC---ATCAGCAGCCACATATGATCCT---GTGGCGGCGCAACTTCTGGATGTGGATGCAGGTGTCCAGGCTCCGGTGGCAGAACGTCAAGCTCGCCAGTTTGGCGGTGGCTTT------------GG------------------------------------------AGG---AAG------------TCCAGGC---GGCGGCTTTG---------------GC---GGTCCGGGAGGCGGTTTTGGAGGACGT	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
.......................................................................................GACCATTCTC------CTGGTCGCCGGC..................................................................................................................................................................................................................................................................	22	1	3.00	3	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.......................................................................................GACCATTCTC------CTGGTCGCCGGCTC---.............................................................................................................................................................................................................................................................	24	1	3.00	3	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.......................................................................................GACCATTCTC------CTGGTCGCCGGCT.................................................................................................................................................................................................................................................................	23	1	3.00	3	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0
................................................................................................................................................................CTGGATGTGGATGCAGGT...................................................................................................................................................................................................	18	1	2.00	2	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0
....................................................................................................................................................GCGGCGCAACTTCTGGATGTG............................................................................................................................................................................................................	21	1	2.00	2	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0
...................................................................................................................................................GGCGGCGCAACTTCTGGATGTG............................................................................................................................................................................................................	22	1	2.00	2	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0
........TTGCCGGTGATTAGTAGCAGAAGTTTC---C..............................................................................................................................................................................................................................................................................................................................................	28	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.................................................................................................................................CACATATGATCCT---GTGGC...............................................................................................................................................................................................................................	18	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.....................................................................................................................................................CGGCGCAACTTCTGGATGTG............................................................................................................................................................................................................	20	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
......................................................................................................................................................................GTGGATGCAGGTGTCCAGGCTCCGGT.....................................................................................................................................................................................	26	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0
..................TTAGTAGCAGAAGTTTC---CTCGA-------------AAA..........................................................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
............................................................................................TTCTC------CTGGTCGCCGGCTC---ATCAGCAGCC...................................................................................................................................................................................................................................................	29	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.................................................................................................................................................................................................GCAGAACGTCAAGCTCGCC.................................................................................................................................................................	19	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...........................................................................................ATTCTC------CTGGTCGCCGGCT.................................................................................................................................................................................................................................................................	19	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..................................................................................................................................ACATATGATCCT---GTGGCGGGC...........................................................................................................................................................................................................................	21	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...............TGATTAGTAGCAGAAGTTTC---CTCGA-------------AAA..........................................................................................................................................................................................................................................................................................................................	28	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
.........................................................................................................................................................................GATGCAGGTGTCCAGGCT..........................................................................................................................................................................................	18	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...........CCGGTGATTAGTAGCAGAAGT.....................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..........................................................................................CATTCTC------CTGGTCGCCGGCTC---.............................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droSec2

TCGAAACTTTGCCTGTGATTAGTAGCAGAAGTTTC---CTCGA-------------AAATGCGCACATTTGTTTGCCTTGCCCTGGCGACCATTCTC------CTAGTCGCCGGCTC---ATCAGCAGCCACATATGATCCT---GTGGCGGCGCAACTTCTGGATGTGGATGCAAGTGTCCAGGCTCCGGTGGCAGAACGTCAAGCTCGCCAGTTTGGCGGTGGCTTT------------GGAGG------------ACGTCC---AGGCGG---CGGCTTTGGAGG---AAA------------TCCA---GGCGGCGGCTTCG---------------GC---GGTCCGGGAGGCGGTTTTGGAGGACGT	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
No Reads

droYak3

TCGAAACTTTGCCGGTGATTAGTAGCAGGAGTTTT---CTCGA-------------ATATGCGCACATTTGTTTGCCTCGCCCTGGCGACCATCCTC------CTGGTCGCCGGCTC---CTCAGCAGCCACATATGATCCT---GTGGCGGCGCAACTTCTGGATGTGGATGCTGGTGTCCAGGCTCCGGCGGCAGCACGGCAAGTTCGTCAGTTCGGC---GGCTTC------------GG------------------------------------------AGG---AGG------------TCCA------------------------------------------GGAGGCGGCTTCGGAGGAGGT	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
...........................................................................................ATCCTC------CTGGTCGCCGGCTC---CTCAGCT......................................................................................................................................................................................................................................................	27	1	4.00	4	0	0	0	0	0	0	0	0	0	0	4
...........................................................................................ATCCTC------CTGGTCGCCGGCTC---C............................................................................................................................................................................................................................................................	21	1	4.00	4	4	0	0	0	0	0	0	0	0	0	0
................GATTAGTAGCAGGAGTTTT---CT.............................................................................................................................................................................................................................................................................................................................................	21	1	2.00	2	0	0	2	0	0	0	0	0	0	0	0
........................................................................................................................................................CGCAACTTCTGGATGTGGATGC.......................................................................................................................................................................................................	22	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0
....................................................................................................................................................................ATGTGGATGCTGGTGTCCAGG............................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	1	0	0	0	0	0
....AACTTTGCCGGTGATTAGTAGCAGGAC......................................................................................................................................................................................................................................................................................................................................................	27	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0
........................................................................................................................................................................................................................CGGC---GGCTTC------------GG------------------------------------------AGG---AGG------------...................................................................	18	1	1.00	1	0	0	0	0	0	1	0	0	0	0	0
..........................................................................................CATCCTC------CTGGTCGCCGGCTC---.............................................................................................................................................................................................................................................................	21	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0
....................................................................TTGTTTGCCTCGCCCTGGC..............................................................................................................................................................................................................................................................................................	19	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0
......................................................................GTTTGCCTCGCCCTGGCGACC..........................................................................................................................................................................................................................................................................................	21	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0
..........................................................................................................................................................................................................CAAGTTCGTCAGTTCGGC---GGC...................................................................................................................................................	21	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0
..................................................................ATTTGTTTGCCTCGCCCTGGC..............................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0
.........................................................................................................................................................GCAACTTCTGGATGTGGATGCTGGT...................................................................................................................................................................................................	25	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0
..................................................................................................................................................TGGCGGCGCAACTTCTGGATG..............................................................................................................................................................................................................	21	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0
.........................................................................................CCATCCTC------CTGGTCGCCGGCT.................................................................................................................................................................................................................................................................	21	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0
..GAAACTTTGCCGGTGATTAGTAGC...........................................................................................................................................................................................................................................................................................................................................................	24	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0
.....ACTTTGCCGGTGATTAGTAGC...........................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0
...................................................................................................................................................GGCGGCGCAACTTCTGGATGG.............................................................................................................................................................................................................	21	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0
..............................................................................................................................................................TTCTGGATGTGGATGCTGG....................................................................................................................................................................................................	19	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0
................................................................................................C------CTGGTCGCCGGCTC---CTCAGC.......................................................................................................................................................................................................................................................	21	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0
.....................................................................................................................................................CGGCGCAACTTCTGGATGTG............................................................................................................................................................................................................	20	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0
..................................................................................................................................................................................................................................TTC------------GG------------------------------------------AGG---AGG------------TCCA------------------------------------------GGAGGTTT.............	23	2	1.00	2	2	0	0	0	0	0	0	0	0	0	0
............................GAGTTTT---CTCGA-------------ATATGCGCA....................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	1	0	0	0	0	0
....................................................................................................................................................................................................................................................................................................................CA------------------------------------------GGAGGCGGCTTCGGAGGAGG.	22	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
.........................................................................................................................................................................................................................GGC---GGCTTC------------GG------------------------------------------AGG---AGG------------T..................................................................	18	2	0.50	1	0	0	0	0	1	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................................................................................................................GGCGGCTTCGGAGGAGGT	18	2	0.50	1	0	0	0	0	1	0	0	0	0	0	0
..................................................................................................................................................................................................................................TTC------------GG------------------------------------------AGG---AGG------------TCCA------------------------------------------GGAGGCG..............	22	2	0.50	1	1	0	0	0	0	0	0	0	0	0	0
...............................................................................................................................................................................................................................................................................................G---AGG------------TCCA------------------------------------------GGAGGCGGCTTCGA.......	22	3	0.33	1	0	0	0	0	1	0	0	0	0	0	0
....................................................................................................................................................................................................................................C------------GG------------------------------------------AGG---AGG------------TCCA------------------------------------------GGAGT................	18	4	0.25	1	1	0	0	0	0	0	0	0	0	0	0
.................................................................................................................................................................................................................................................GG------------------------------------------AGG---AGG------------TCCA------------------------------------------GGAGGCGGC............	21	4	0.25	1	1	0	0	0	0	0	0	0	0	0	0

droEre2

TCGAAACTTTGCCGGTGATTAGTAGCAGAAGTTTT---CACGA-------------ATATGCGCACATTTGTTTGCCTTGTCTTGGCGACCATCCTC------CTGGTCGCCGGCTC---CTCAGCTGCCACATATGATCCT---GTGGCGGCGCAACTTCTGGATGTGGATGCAGGTGTCCAGGCTCCGTCGGCAGCGCGGCAAGTTCGTCAGTTTGG------CTTC------------GGACG---------------TCC---TG---------GCTTTGA------ACG------------TCC---------TGGCTTTGAACGTCCTGGTTTTGAAC---GTCC------TGGCTTTGGAG---GT	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
............................................................................CTTGTCTTGGCGACCATCCTC------CTGGC.........................................................................................................................................................................................................................................................................	26	1	2.00	2	0	2	0	0	0	0	0
.................................................................................................................................CACATATGATCCT---GTGGCGGC............................................................................................................................................................................................................................	21	1	2.00	2	0	2	0	0	0	0	0
......CTTTGCCGGTGATTAGTAGCAGA........................................................................................................................................................................................................................................................................................................................................................	23	1	2.00	2	0	0	0	2	0	0	0
........................................................................................................................................................................................................GGCAAGTTCGTCAGTTTGG------CTTC------------....................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0	0
...................................................................TTTGTTTGCCTTGTCTTGG...............................................................................................................................................................................................................................................................................................	19	1	1.00	1	0	0	0	1	0	0	0
..................................T---CACGA-------------ATATGCGCACATTTGTTTGCC........................................................................................................................................................................................................................................................................................................	27	1	1.00	1	0	1	0	0	0	0	0
.......................................................................................................CTGGTCGCCGGCTC---CTCAGCTGCCAC.................................................................................................................................................................................................................................................	26	1	1.00	1	0	1	0	0	0	0	0
.......................................................................TTTGCCTTGTCTTGGCGACC..........................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0	0
................................................................ACATTTGTTTGCCTTGTCTTGGC..............................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0	0
..........................................................................................................................................................................ATGCAGGTGTCCAGGCTCCGTCGGCAGC...............................................................................................................................................................................	28	1	1.00	1	0	1	0	0	0	0	0
..................................................................ATTTGTTTGCCTTGTCTTGG...............................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0	0
..........GCCGGTGATTAGTAGCAGAAGT.....................................................................................................................................................................................................................................................................................................................................................	22	1	1.00	1	0	1	0	0	0	0	0
.................................................................................................................................................................................................................GTCAGTTTGG------CTTC------------GGAC................................................................................................................................	18	1	1.00	1	0	1	0	0	0	0	0
.........................................................................................................................................................................GATGCAGGTGTCCAGGCTCCGTC.....................................................................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0	0
..................................................................................................................................................................................................................................................................................................................................................TTGAAC---GTCC------TGGCTTTGGA......	20	1	1.00	1	0	0	0	1	0	0	0
..................................................................ATTTGTTTGCCTTGTCTTGGC..............................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	1	0	0	0	0	0
..........................................................................................................................................................CAACTTCTGGATGTGGATGC.......................................................................................................................................................................................................	20	1	1.00	1	0	0	0	1	0	0	0
.......................................................................................GACCATCCTC------CTGGTCGCCGGCT.................................................................................................................................................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0	0
..................................................................................................................................ACATATGATCCT---GTGGCGG.............................................................................................................................................................................................................................	19	1	1.00	1	0	1	0	0	0	0	0
..................................................................ATTTGTTTGCCTTGTCTTGGCGA............................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0	0
.........................................................................................CCATCCTC------CTGGTCGCCGGCTC---CTC..........................................................................................................................................................................................................................................................	25	1	1.00	1	0	1	0	0	0	0	0
.......................................................................................GACCATCCTC------CTGGTCGCCGGC..................................................................................................................................................................................................................................................................	22	1	1.00	1	0	1	0	0	0	0	0
................................................................................................................................................................................GTGTCCAGGCTCCGTCGGCA.................................................................................................................................................................................	20	1	1.00	1	0	0	0	1	0	0	0
................................................................................................................................................................................GTGTCCAGGCTCCGTCGGCAGCGC.............................................................................................................................................................................	24	1	1.00	1	0	1	0	0	0	0	0
.......TTTGCCGGTGATTAGTAGCA..........................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	0	0	1	0	0	0
........TTGCCGGTGATTAGTAGCA..........................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	1	0	0	0	1	0	0	0
.................................................................................................................................................................................................................GTCAGTTTGG------CTTC------------GGACG---------------TCC---..........................................................................................................	22	1	1.00	1	0	1	0	0	0	0	0
................................................................................................................................................................................................................CGTCAGTTTGG------CTTC------------GGA.................................................................................................................................	18	1	1.00	1	0	0	0	1	0	0	0
...................................................................................................................................................................GATGTGGATGCAGGTGTCC...............................................................................................................................................................................................	19	1	1.00	1	0	0	0	1	0	0	0
............CGGTGATTAGTAGCAGAAGT.....................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	0	0	1	0	0	0
.........................................................................................................................................................GCAACTTCTGGATGTGGATGCAGGT...................................................................................................................................................................................................	25	1	1.00	1	0	1	0	0	0	0	0
................................................................................................................................................................................................................CGTCAGTTTGG------CTTC------------GGAC................................................................................................................................	19	1	1.00	1	0	1	0	0	0	0	0
....................................................................................................................................ATATGATCCT---GTGGCGGCGC..........................................................................................................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0	0
..................................................................................................................................ACATATGATCCT---GTGGCGGCGC..........................................................................................................................................................................................................................	22	1	1.00	1	0	1	0	0	0	0	0
.....................................................................................................................................TATGATCCT---GTGGCGGCGCA.........................................................................................................................................................................................................................	20	1	1.00	1	0	0	0	1	0	0	0
...........................................................................................................................................................................................CCGTCGGCAGCGCGGCAAGTTCGTCA................................................................................................................................................................	26	1	1.00	1	0	0	0	1	0	0	0
............................................................................................................................................................................................................AGTTCGTCAGTTTGG------CTTC------------GGA.................................................................................................................................	22	1	1.00	1	0	0	0	1	0	0	0
.............................................................................................................................................................CTTCTGGATGTGGATGCAGGT...................................................................................................................................................................................................	21	1	1.00	1	0	0	0	1	0	0	0
....................................................................................................................................................................................................................................................CG---------------TCC---TG---------GCTTTGA------ACG------------TCC---------TGG....................................................	23	2	0.50	1	0	1	0	0	0	0	0
....................................................................................................................................................................................................................................................................................................CG------------TCC---------TGGCTTTGAACGTCCTGG.....................................	23	2	0.50	1	0	1	0	0	0	0	0

dpe_384

scaffold_0:3517413-3517563 +

Candidate

Unknown

Predicted structure

Flybase annnotation

Sense Strand Reads

Anti-sense strand reads

Re-alignment of all predicted orthologs

Re-alignment of all predicted orthologs with sRNA reads

-7.3	-7.1	-7.1