dan_2348

CDS [Dana\GF25020-cds]; exon [dana_GLEANR_9701:2]; exon [dana_GLEANR_9701:3]; CDS [Dana\GF25020-cds]; intron [Dana\GF25020-in]

Name	Class	Family	Strand
(CAG)n	Simple_repeat	Simple_repeat	+
TART_DV	LINE	Jockey	+

##################################################------------------------------------------------------------------################################################## ATCTGCGCAACACCTCATCGATTGCCGAACTGGCTGCAGCAGCCAGTGCGGTAAACGAGCAACATCAGCAGCACCAGCAACAGCAGCAGCAGCAACACCAACAGCTGCAACAACAGCGACCGGCCAGCAATCTCTCCAGCGCGAGCAGCAGCCATGCCAGCCTCTC ************************************************((...............(((((...............................)))))....))..************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M058 embryo	M044 female body	V106 head	V039 embryo
.............................................TTGCGGTAAATGAGCAACAT.....................................................................................................	20	2	2	1.50	3	0	3	0	0
...........................................CATTGCGGTAAATGAGCAACACC....................................................................................................	23	3	1	1.00	1	1	0	0	0
..................................TGCAGCAGCCAGTGCGGTA.................................................................................................................	19	0	1	1.00	1	0	0	1	0
............................................................................................................AACAACAGCGACCGGCCAG.......................................	19	0	1	1.00	1	1	0	0	0
........................................................................ACCAGCAACAGCAGCAGCAGCA........................................................................	22	0	20	0.15	3	1	0	2	0
.........................................................................CCAGCAACAGCAGCAGCAGCA........................................................................	21	0	20	0.15	3	0	0	2	1
........................................................................ACCAGCAACAGCAGCAGCAGCAA.......................................................................	23	0	7	0.14	1	0	1	0	0
........................................................................ACCAGCAACAGCAGCAGCAGC.........................................................................	21	0	20	0.10	2	0	0	2	0
.........................................................................CCAGCAACAGCAGCAGCAGC.........................................................................	20	0	20	0.10	2	2	0	0	0
...............................................................................ACAGCAGCAGCAGCAACAC....................................................................	19	0	20	0.05	1	0	1	0	0
.................................................................................ATCAGCAGCAGCAACACCAACAGC.............................................................	24	1	20	0.05	1	1	0	0	0
.........................................................................CCAGCAAAAGCAGCAGCAGCAA.......................................................................	22	1	20	0.05	1	1	0	0	0
..............................................................................AACAGCAGCAGCAGCAACAC....................................................................	20	0	20	0.05	1	1	0	0	0
..........................................................................CAGCAACAGCAGCAGCAGC.........................................................................	19	0	20	0.05	1	0	0	0	1

TAGACGCGTTGTGGAGTAGCTAACGGCTTGACCGACGTCGTCGGTCACGCCATTTGCTCGTTGTAGTCGTCGTGGTCGTTGTCGTCGTCGTCGTTGTGGTTGTCGACGTTGTTGTCGCTGGCCGGTCGTTAGAGAGGTCGCGCTCGTCGTCGGTACGGTCGGAGAG ************************************************((...............(((((...............................)))))....))..************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M058 embryo	M044 female body	V039 embryo
...........................................GTAACGCCATTTACTCGTTG.......................................................................................................	20	2	2	1.00	2	2	0	0
..........................................GGTAACGCCATTTACTCGTTG.......................................................................................................	21	2	1	1.00	1	0	1	0
...........................................GTAACGCCATTTACTCGTTGT......................................................................................................	21	2	1	1.00	1	1	0	0
...........................................GCAACGCCATTTACTCGTTG.......................................................................................................	20	3	3	0.33	1	1	0	0
..................................................................................................................................................TCGTCGGTATGGTCGAAGA.	19	2	4	0.25	1	0	1	0
....................................GTCGTCGGTCACGCACTTGGC.............................................................................................................	21	3	8	0.13	1	0	0	1

Species	Coordinate	ID	Alignment
droAna3	scaffold_13337:1833387-1833552 +	dan_2348	ATCTGCGC-AACAC-------CT------------------------------------------------------CATCGATTGCCG--------------AA-------CTG-----GCTGCA----G------CAGCCA------------------GTGCGGTAAACG--------------------------------AG---CAACATCAGCAGCAC---CAGCAA----CAGCAGCA------GCAGCAAC------AC---------------CAACAGCTGCAACAACAGCGA---------------------------------CCG-GCCAGC---AATC---------------TCTCCAGCGCGA-------GCAGCAGCCATGCCAG------CCTCTC-----------
droBip1	scf7180000396569:1883550-1883712 +		ATCTGCGC-AGCAC-------CT------------------------------------------------------CATCGATTGCCG--------------AA-------CTG-----GCTGCA----G------CAGCCA------------------GTGCGGTGAACG--------------------------------AG---CAACATCAGCAGCAC---CAG-------CAACAGCA------GCAGCAAC------AC---------------CAGCAGTTGCAACAACAGCGC---------------------------------CCG-GCCAGC---AATC---------------TCTCCAGCGCGA-------GCAGCAGTCACGCCAG------CCTCTC-----------
droKik1	scf7180000302274:154994-155168 -		ATCTGCGGTG-A-CCA------------------------------------------------------ACAACAATGTGAAT-GCCTGGG------------C-------C-----TTGCAGCA----G------CAG---CAACAGA------------------CAGCAGCCC----------------------------TG---CATCATCACCAGCAA---CAA-------C---AGCA------GCAGCAACAAC---AC---------------CAACAGCACTTGCAGCAGCAG---------------------------------CAG---CAGC---ATGC---------------TCACCAGCAACATGTGGCTGCTGTT-ATGCAGCAG------CAACAG-----------
droFic1	scf7180000453841:461471-461628 -		GCAACA-------G----------------------------------------------------------------------------GCCGTTGTCG----C------------CCAGCAGCA----G------CAG------CAGCAGGTT--------GCTGTCGTCG-CCCAG-------------------------CAG---CAGCATCACCAGCAA---CAG-------C---AGCA------GCAGCAACAGCAGGCG---------------GTGCAGCAGCAACAACAGCAG---------------------------------CAG---CAGC---AACA---------------CCAACAGCAACA-------GCAGCAGCAACAACAG------C----------------
droEle1	scf7180000491272:883393-883559 +		ATCACGCC-GCCAC-------AC------------------------------------------------------CATCAATTGCCG--------------CT-------TTC-----CGTGCA----G------CTG---CAACAC-------------------------------------------CAGC---TGCACCAG---CAACATCAGCTGCAT---CAGCAA----CATCAGCA------ACATCAGC------AA---------------CATCAGCAGCAACACCAGCAA---------------------------------CAT---CAGC---AACG---CT----------GCTCCAGTGTGG-------GCAGCACCAGCAGCAG------CGGCAC-----------
droRho1	scf7180000777200:277430-277584 -		AGTTCTGC-GATTGCA---------------------------------------------------------------ACGAT-GCCAAGCA-----CG----C------------GCCGCAGCC----G------CA------TCTGC------------------CAACGAGCCAATATCA----------TCCACAGC---AGCAACAGCAACAGCAGCAG---C-------------------------------------AG---------------CAACAGCAGCAGCAGCAGCAA---------------------------------CTG---CAGC---AGCA---------------A------CAGCA-------GCAACAACTGCAACAG------CAACTG-----------
droBia1	scf7180000301592:106012-106180 -		AGTTCTGC-GATTGCA---------------------------------------------------------------ACGAT-GCCAAGCA-----CG----C------------GCCGCAGCC----G------CA------TCTGC------------------CAACGAGCCAATACCA----------TCCACAGC---AG---CAA---CAGCAGCAG----------------------------CAGCATC------AGCAACAACTGCAACAGCAGCAGCAGCTGCAACAGCAACTG------------------------------CAG---CAGC---AA------------------------CAGAT-------GCTGCAGATGCACCAG------CGTCT------------
droTak1	scf7180000410580:130496-130659 +		ACCTGCTGCA-CTA------CCA---------------------------------------------------------GACT-GACTCGCC-----CG----A------------CCTGCAGCA----G------CAG------CACC------------------AGGCGATGCAA-------------------------CAG---CAACAGCAGCAGCAA---CAG-------CACCTCCCGCA---GCAACACC------TC---------------CCGCAGCAGCACCAACAGATC---------------------------------CCG---CAGC---AACA---------------CCA---GACGAT-------GCAGCAGCAGCAGCAG------CAACAC-----------
droEug1	scf7180000409804:1107879-1108028 +		ATCCATACCAGCAG---------------------------------------------------------CAAC---TGGAA-----------------------------------AAGCAGCA----G------CAG---CAACAT-------------------------------------------CAGC---AGCAACAA---CAACATCAGC----------------------AGCA------ACAGCAAC------AT---------------CAGCAGCAGCAACAACATCAC---------------------------------CAG---CAGC---AACA-----TCAACCTCAACCGCCAACTC-A-------GCAGCAGC---AACCG-----ACTCCTC-----------
dm3	chr3R:11239680-11239849 +		AACTGCGACA---G-------TT------------------------------------------------------TGGC-------CAGG------------ACTTCCAACTG-----GC------------------------------------------------------CCCGAGCAACACTTCACCGC---CCC---AG---CAGCAACAGCAGCAG---CAGCAG----CAGCAGCA------GCAGCATC------AA---------------GTGCAGCAGCAGCAACAGCGA---------------------------------GCGTTGCAGC---AATCTG-CC----------TCGCCACC-GCA-------ACAGCAGCAGCAGCAG------CAGCAA-----------
droSim2	x:10052424-10052600 +		ATCTCCGC-CGC-TCAACGATCAGATCAGCTTGCTATTCCCCAAGTGCCGACCC----------------------------------------------------------------AAACAGCA----G------C-------------------------------------------------------------------AG---CAGCAGCAGCAGCAG---CAGCAG----CAGCAGCA------GCAGCAGC------AA---------------CAGCAGCAGCAGCAACAGCAA---------------------------------CAG---CAGC---AACT-----TCA---------ACCAGC-----------ACAACAGCAGCAGCAG------CAGCATGTCCTTCCCAC
droSec2	scaffold_2:6867778-6867950 +		AGCAGCGGCA-CAG-------CT------------------------------------------------------CGTC-------CAG---------------------------TTGCAGCA----G------CAG----------------------------------------------------------------------------CAACAGCAG---CAGCTA----CAGCAACA------GCAGCACC------TA---------------CAGCTGCAGCAGCAACAGCAACTGCAGCAGCAACAGCAGCTGCAACTCAATCAACAG---CAGCAGCAACT---------------CTACCAACAGCA-------GCAACAGCAATACCTGCTG--ACCTTTC-----------
droYak3	2L:8786107-8786266 +		CTGC--AC-AA---------CCAAAT----------------AAATTCCAGCCCAATAGCACTGCCATCGGCAAC---GGCAA-----------------------------------TCGC-----------------------------------------------------------------------------------AG---CAATATCTGCAGCGG---CAACAG----CAGCAGCA------GCACCACC------AC---------------CAGCAACAGCAACACCAGGCA---------------------------------CCG---CAGC---AACC---------------GCA---GCAGCT-------GCAGCAGCAACAGCAG------CAGCAG-----------
droEre2	scaffold_4690:6767329-6767485 +		ACCTCCGGCA---A-------CT------------------------------C----------------AC-----CC-GACTTGCTG--------------AGCTACCAGATGGAGCAGCAGCT----G------CAG------C----------------------------------------------------------AC---CAGCAGCAGCAGCAG---CAACAG----CAGCAGCA------GCAGCAGC------AA---------------CAGCAGCAGCAACACCAGTCC---------------------------------CAG---CAGC---AACA---------------TCTCCACCAGCA-------ACACCAGGCGAACCAG------C----------------
dp5	XL_group1e:5881179-5881330 -		GTGGTGCC-AACTG---------------------------------------------------------CAGC---AACGAT----------------------------CTG-----GCGGCCAGCTC------------------------------TCGCGGTG-------GAG-------------------------CGG-----GCAGTGTGGGCCC---CACCTCCCAGCAGCAGCA------GCAGCCAC------AC---------------CAACAGCTGCAGCAGCTGCAA---------------------------------CAG---CAGC---AGTC---------------G-GGCAGCGGGA-------GCAGCAGCGCAGCCAG------C----------------
droPer2	scaffold_0:634986-635143 +		ATCAGCAGCAACAG---------------------------------------------------------CAGC---AGCAAC-----------------------------------AGCAGCA----G------CAG---CAACAA-------------------------------------------CAGC---AGC---AG---CAGCAACATCAGCAA---CAG-------CAACATCA------GCAGCAAC------AG---------------CAGCAGCAGCAACAACAGCAG---------------------------------CAG---CAGC---AACA---------------TCAGCAACAGCA-------ACAGCAACAACAGCAGCTGCAGCCCCCC-----------
droWil2	scf2_1100000003523:1030-1199 +		ATCAGCAACA---GCA------------------------------------------------------ACAGCAGCAACAATGGCA--------------------------------GCAACT----GCAGCAGCAA---CAACAA-------------------------------------------CAAC---AGC---AG---CAACAACAACAGCAGCAGC---AA----CAACAGCA------GCAACAAC------AA---------------CAGCAGCAGCAACAACAGCAT---------------------------------CAGCAACAGC---AACA---------------GCAGCAACAATG-------GCAGCAGCAACAACAG------CAACAT-----------
droVir3	scaffold_13047:11419254-11419410 +		ATCCGCAC-AACAGCA---------------------------------------------------------GC------TAT----------------------------------------CC----G------CA------TCAGCTGGCCGCCATG--GCGGCAT----TCC----------------------------AA---CAACATCAGCAGCAG---CAGCAG----CAACAACAACAACATCACCACC------AC---------------CAGCAGCAGCAGCAGCAGCAG---------------------------------------CAGC---AGCG--ACT----------GCAGCAA-------------CGTCTGCCCTGTCAG------CCACT------------
droMoj3	scaffold_6540:5209920-5210078 -		ATCAGCAC-AACAC------------------------------------------------------------------CAAA-ATCGAGCA-----TGCCGAC-------TCC-----ACAACG----A------CAGCCG------------------CTGCTGCAC-----------------------------------AG---CACCATCATCAGCAG---CAGCAA----CAACAGCA------GCAGCAAC------AA---------------CAGCAGCAGCAACAACAGCAA---------------------------------CAG---CAGC---AACA---------------ACAGCAGCACCA-------ACAACAACAGCAGCAG------C----------------
droGri2	scaffold_15500:1125-1294 -		AGCAGCAGCAGCAG---------------------------------------------------------CAGCAGCAGCG------G--------------CA-------GCA-----GCAGCA----G------CAGCAG------------------GAGCGGCAG---------CA-------------GC---AGC---AG---CAGCAGCAGCAGCAG---CAG-------CAGCAGCAGTA---GCAGCATC------AG---------------CAGCGGCAGCAGCAGCAGCAG---------------------------------CGGCAGCAGC---AGCA---------------GCAGCAGCGGCA-------GCAGCAGCAGCAGCAG------CGGCAG-----------

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droAna3

ATCTGCGC-AACAC-------CT------------------------------------------------------CATCGATTGCCG--------------AA-------CTG-----GCTGCA----G------CAGCCA------------------GTGCGGTAAACG--------------------------------AG---CAACATCAGCAGCAC---CAGCAA----CAGCAGCA------GCAGCAAC------AC---------------CAACAGCTGCAACAACAGCGA---------------------------------CCG-GCCAGC---AATC---------------TCTCCAGCGCGA-------GCAGCAGCCATGCCAG------CCTCTC-----------	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
..........................................................................................................................TGCA----G------CAGCCA------------------GTGCGGTA..................................................................................................................................................................................................................................................................	19	1	1.00	1	0	0	0	0	0	1
.....................................................................................................................................................................................................................................................................................................AACAACAGCGA---------------------------------CCG-GCCAG.................................................................................	19	1	1.00	1	0	1	0	0	0	0
...............................................................................................................................................................................................................................AC---CAGCAA----CAGCAGCA------GCAGCA.........................................................................................................................................................................	22	20	0.15	3	0	1	0	0	0	2
................................................................................................................................................................................................................................C---CAGCAA----CAGCAGCA------GCAGCA.........................................................................................................................................................................	21	20	0.15	3	0	0	1	0	0	2
...............................................................................................................................................................................................................................AC---CAGCAA----CAGCAGCA------GCAGCAA........................................................................................................................................................................	23	7	0.14	1	1	0	0	0	0	0
...............................................................................................................................................................................................................................AC---CAGCAA----CAGCAGCA------GCAGC..........................................................................................................................................................................	21	20	0.10	2	0	0	0	0	0	2
................................................................................................................................................................................................................................C---CAGCAA----CAGCAGCA------GCAGC..........................................................................................................................................................................	20	20	0.10	2	0	2	0	0	0	0
.........................................................................................................................................................................................................................................A----CAGCAGCA------GCAGCAAC------AC---------------................................................................................................................................................	19	20	0.05	1	1	0	0	0	0	0
........................................................................................................................................................................................................................................AA----CAGCAGCA------GCAGCAAC------AC---------------................................................................................................................................................	20	20	0.05	1	0	1	0	0	0	0
....................................................................................................................................................................................................................................CAGCAA----CAGCAGCA------GCAGC..........................................................................................................................................................................	19	20	0.05	1	0	0	1	0	0	0

droBip1

ATCTGCGC-AGCAC-------CT------------------------------------------------------CATCGATTGCCG--------------AA-------CTG-----GCTGCA----G------CAGCCA------------------GTGCGGTGAACG--------------------------------AG---CAACATCAGCAGCAC---CAG-------CAACAGCA------GCAGCAAC------AC---------------CAGCAGTTGCAACAACAGCGC---------------------------------CCG-GCCAGC---AATC---------------TCTCCAGCGCGA-------GCAGCAGTCACGCCAG------CCTCTC-----------	Size	Hit Count	Total Norm	Total
No Reads

droKik1

ATCTGCGGTG-A-CCA------------------------------------------------------ACAACAATGTGAAT-GCCTGGG------------C-------C-----TTGCAGCA----G------CAG---CAACAGA------------------CAGCAGCCC----------------------------TG---CATCATCACCAGCAA---CAA-------C---AGCA------GCAGCAACAAC---AC---------------CAACAGCACTTGCAGCAGCAG---------------------------------CAG---CAGC---ATGC---------------TCACCAGCAACATGTGGCTGCTGTT-ATGCAGCAG------CAACAG-----------	Size	Hit Count	Total Norm	Total
No Reads

droFic1

GCAACA-------G----------------------------------------------------------------------------GCCGTTGTCG----C------------CCAGCAGCA----G------CAG------CAGCAGGTT--------GCTGTCGTCG-CCCAG-------------------------CAG---CAGCATCACCAGCAA---CAG-------C---AGCA------GCAGCAACAGCAGGCG---------------GTGCAGCAGCAACAACAGCAG---------------------------------CAG---CAGC---AACA---------------CCAACAGCAACA-------GCAGCAGCAACAACAG------C----------------	Size	Hit Count	Total Norm	Total
No Reads

droEle1

ATCACGCC-GCCAC-------AC------------------------------------------------------CATCAATTGCCG--------------CT-------TTC-----CGTGCA----G------CTG---CAACAC-------------------------------------------CAGC---TGCACCAG---CAACATCAGCTGCAT---CAGCAA----CATCAGCA------ACATCAGC------AA---------------CATCAGCAGCAACACCAGCAA---------------------------------CAT---CAGC---AACG---CT----------GCTCCAGTGTGG-------GCAGCACCAGCAGCAG------CGGCAC-----------	Size	Hit Count	Total Norm	Total
No Reads

droRho1

AGTTCTGC-GATTGCA---------------------------------------------------------------ACGAT-GCCAAGCA-----CG----C------------GCCGCAGCC----G------CA------TCTGC------------------CAACGAGCCAATATCA----------TCCACAGC---AGCAACAGCAACAGCAGCAG---C-------------------------------------AG---------------CAACAGCAGCAGCAGCAGCAA---------------------------------CTG---CAGC---AGCA---------------A------CAGCA-------GCAACAACTGCAACAG------CAACTG-----------	Size	Hit Count	Total Norm	Total
No Reads

droBia1

AGTTCTGC-GATTGCA---------------------------------------------------------------ACGAT-GCCAAGCA-----CG----C------------GCCGCAGCC----G------CA------TCTGC------------------CAACGAGCCAATACCA----------TCCACAGC---AG---CAA---CAGCAGCAG----------------------------CAGCATC------AGCAACAACTGCAACAGCAGCAGCAGCTGCAACAGCAACTG------------------------------CAG---CAGC---AA------------------------CAGAT-------GCTGCAGATGCACCAG------CGTCT------------	Size	Hit Count	Total Norm	Total
No Reads

droTak1

ACCTGCTGCA-CTA------CCA---------------------------------------------------------GACT-GACTCGCC-----CG----A------------CCTGCAGCA----G------CAG------CACC------------------AGGCGATGCAA-------------------------CAG---CAACAGCAGCAGCAA---CAG-------CACCTCCCGCA---GCAACACC------TC---------------CCGCAGCAGCACCAACAGATC---------------------------------CCG---CAGC---AACA---------------CCA---GACGAT-------GCAGCAGCAGCAGCAG------CAACAC-----------	Size	Hit Count	Total Norm	Total
No Reads

droEug1

ATCCATACCAGCAG---------------------------------------------------------CAAC---TGGAA-----------------------------------AAGCAGCA----G------CAG---CAACAT-------------------------------------------CAGC---AGCAACAA---CAACATCAGC----------------------AGCA------ACAGCAAC------AT---------------CAGCAGCAGCAACAACATCAC---------------------------------CAG---CAGC---AACA-----TCAACCTCAACCGCCAACTC-A-------GCAGCAGC---AACCG-----ACTCCTC-----------	Size	Hit Count	Total Norm	Total
No Reads

dm3

AACTGCGACA---G-------TT------------------------------------------------------TGGC-------CAGG------------ACTTCCAACTG-----GC------------------------------------------------------CCCGAGCAACACTTCACCGC---CCC---AG---CAGCAACAGCAGCAG---CAGCAG----CAGCAGCA------GCAGCATC------AA---------------GTGCAGCAGCAGCAACAGCGA---------------------------------GCGTTGCAGC---AATCTG-CC----------TCGCCACC-GCA-------ACAGCAGCAGCAGCAG------CAGCAA-----------	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
..................................................................................................................................................................................................................................................................................................AGCAGCAACAGCGA---------------------------------GCGTTGC...................................................................................	21	1	5.00	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0
...............................................................................................................................................................................................................................................................................................AGCAGCAGCAACAGCGA---------------------------------GCGTTG....................................................................................	23	1	5.00	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................................................................................................GTTGCAGC---AATCTG-CC----------TCGCCACC-GCA-------.......................................	27	1	4.00	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...TGCGACA---G-------TT------------------------------------------------------TGGC-------CAGG------------ACTTCCAAC..........................................................................................................................................................................................................................................................................................................................	27	1	4.00	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	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	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	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
..........................................................................................................................................................................................................................................................................................................CAGCGA---------------------------------GCGTTGCAGC---AATCTG-CC----------TC........................................................	26	1	4.00	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
................................................................................................................................................................................................................................................................................................GCAGCAGCAACAGCGA---------------------------------GCGTTGC...................................................................................	23	1	4.00	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0
............................................................................................................................................................................................................................................................................................TGCAGCAGCAGCAACAGCGA---------------------------------GCGTTG....................................................................................	26	1	4.00	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	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	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
............................................................................................................................................................................................................................................................................................TGCAGCAGCAGCAACAGCGA---------------------------------GCGTT.....................................................................................	25	1	4.00	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	2	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
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.....................................................................................................................................................................................................................................................A------GCAGCAGC------AA---------------CAGCAGCAGCAGC...................................................................................................................................	24	20	0.05	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droSec2

AGCAGCGGCA-CAG-------CT------------------------------------------------------CGTC-------CAG---------------------------TTGCAGCA----G------CAG----------------------------------------------------------------------------CAACAGCAG---CAGCTA----CAGCAACA------GCAGCACC------TA---------------CAGCTGCAGCAGCAACAGCAACTGCAGCAGCAACAGCAGCTGCAACTCAATCAACAG---CAGCAGCAACT---------------CTACCAACAGCA-------GCAACAGCAATACCTGCTG--ACCTTTC-----------	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
..........................................................................................................................................................................................................................................................................................................CAGCAACTGCAGCAGCAACA.............................................................................................................	20	18	0.06	1	0	0	1	0
.........................................................................................................................CAGCA----G------CAG----------------------------------------------------------------------------CAACAGCAG---C......................................................................................................................................................................................................	19	20	0.05	1	0	0	1	0
.........................................................................................................................................................................................................................................................................................................ACAGCAACTGCAGCAGCA................................................................................................................	18	20	0.05	1	0	0	1	0

droYak3

CTGC--AC-AA---------CCAAAT----------------AAATTCCAGCCCAATAGCACTGCCATCGGCAAC---GGCAA-----------------------------------TCGC-----------------------------------------------------------------------------------AG---CAATATCTGCAGCGG---CAACAG----CAGCAGCA------GCACCACC------AC---------------CAGCAACAGCAACACCAGGCA---------------------------------CCG---CAGC---AACC---------------GCA---GCAGCT-------GCAGCAGCAACAGCAG------CAGCAG-----------	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
.............................................................................................................................................................................................................................................................................................................GCA---------------------------------CCG---CAGC---AACC---------------GCA---GCAGCT-------.......................................	23	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................AATATCTGCAGCGG---CAACAG----CAGC.........................................................................................................................................................................................	24	1	1.00	1	0	0	0	1	0	0	0	0	0	0	0
....................................................................................................................................................................................................................ATATCTGCAGCGG---CAACAG----CAGC.........................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
......................................................AATAGCACTGCCATCGGCAAC---GG...........................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
..............................................................................................................................................................................................................................................................................................................CA---------------------------------CCG---CAGC---AACC---------------GCA---GCAGCT-------.......................................	22	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................AATATCTGCAGCGG---CAACAG----CAGCA........................................................................................................................................................................................	25	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0
....................................................................................................................................................................................................................................................................................................................................................................................................GCAGCAGCAACAGCAG------CAGC.............	20	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0

droEre2

ACCTCCGGCA---A-------CT------------------------------C----------------AC-----CC-GACTTGCTG--------------AGCTACCAGATGGAGCAGCAGCT----G------CAG------C----------------------------------------------------------AC---CAGCAGCAGCAGCAG---CAACAG----CAGCAGCA------GCAGCAGC------AA---------------CAGCAGCAGCAACACCAGTCC---------------------------------CAG---CAGC---AACA---------------TCTCCACCAGCA-------ACACCAGGCGAACCAG------C----------------	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
...................................................................................................................................................................................................................................................................................................................................................G---CAGC---AACA---------------TCTCCACCAGCA-------.......................................	21	1	1.00	1	1	0	0	0	0	0	0
.........A---A-------CT------------------------------C----------------AC-----CC-GACTTGCTG--------------A...................................................................................................................................................................................................................................................................................................................................	19	1	1.00	1	0	0	0	0	1	0	0
..................................................................................................................................................C----------------------------------------------------------AC---CAGCAGCAGCAGCAG---C......................................................................................................................................................................................................	19	20	0.10	2	0	0	0	2	0	0	0
..................................................................................................................................................C----------------------------------------------------------AC---CAGCAGCAGCAGCAG---CAACAG----CA...........................................................................................................................................................................................	26	13	0.08	1	1	0	0	0	0	0	0
...............................................................................................................................................................................................................................AG---CAACAG----CAGCAGCA------GCAGCAGC------A................................................................................................................................................................	25	20	0.05	1	0	0	0	0	0	1	0
...................................................................................................................................................................................................................AGCAGCAGCAGCAG---CAACAG----CAGC.........................................................................................................................................................................................	24	20	0.05	1	0	1	0	0	0	0	0
.........................................................................................................................................................................................................................AGCAGCAG---CAACAG----CAGCA........................................................................................................................................................................................	19	20	0.05	1	0	0	0	1	0	0	0
.........................................................................................................................................................................................................................................G----CAGCAGCA------GCAGCAGC------AA---------------CA..............................................................................................................................................	21	20	0.05	1	0	0	0	0	1	0	0
........................................................................................................................................................................................................................................AG----CAGCAGCA------GCAGCAGC------AA---------------CA..............................................................................................................................................	22	20	0.05	1	0	0	0	1	0	0	0
.........................................................................................................................................................................................................................................G----CAGCAGCA------GCAGCAGC------AA---------------CAGCAGCA........................................................................................................................................	27	20	0.05	1	0	1	0	0	0	0	0
.................................................................................................................................................................................................................................................................AGC------AA---------------CAGCAGCAGCAACA..................................................................................................................................	19	20	0.05	1	0	0	0	1	0	0	0

dp5

GTGGTGCC-AACTG---------------------------------------------------------CAGC---AACGAT----------------------------CTG-----GCGGCCAGCTC------------------------------TCGCGGTG-------GAG-------------------------CGG-----GCAGTGTGGGCCC---CACCTCCCAGCAGCAGCA------GCAGCCAC------AC---------------CAACAGCTGCAGCAGCTGCAA---------------------------------CAG---CAGC---AGTC---------------G-GGCAGCGGGA-------GCAGCAGCGCAGCCAG------C----------------	Size	Hit Count	Total Norm	Total	M022 Male-body	M040 Female-body	M059 Embryo	M062 Head	V043 Embryo	V051 Head	V112 Male-body	SRR902010 Ovary	SRR902011 Testis	SRR902012 CNS imaginal disc
....................................................................................................................................................................................................................................................................................................................................................................................GCAGCGGGA-------GCAGCAGCG..............................	18	3	0.33	1	0	1	0	0	0	0	0	0	0	0

droPer2

ATCAGCAGCAACAG---------------------------------------------------------CAGC---AGCAAC-----------------------------------AGCAGCA----G------CAG---CAACAA-------------------------------------------CAGC---AGC---AG---CAGCAACATCAGCAA---CAG-------CAACATCA------GCAGCAAC------AG---------------CAGCAGCAGCAACAACAGCAG---------------------------------CAG---CAGC---AACA---------------TCAGCAACAGCA-------ACAGCAACAACAGCAGCTGCAGCCCCCC-----------	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
..................................................................................................................................................................................................................................................ATCA------GCAGCAAC------AG---------------CAGCAGCAGC......................................................................................................................................	24	9	0.11	1	0	1	0	0	0	0
.....................................................................................................................................................................................................................................................A------GCAGCAAC------AG---------------CAGCAGCAGC......................................................................................................................................	21	20	0.05	1	0	0	1	0	0	0
...............................................................................................................................................CAACAA-------------------------------------------CAGC---AGC---AG---CAGCAA...................................................................................................................................................................................................................	21	20	0.05	1	0	0	1	0	0	0
...................................................................................................................................................................................................................................................................................................GCAACAACAGCAG---------------------------------CAG---CAGC---AACA---------------..........................................................	24	20	0.05	1	0	0	1	0	0	0
.................................................................................................................................................................................................................................................................AAC------AG---------------CAGCAGCAGCAACA..................................................................................................................................	19	20	0.05	1	0	1	0	0	0	0
..........ACAG---------------------------------------------------------CAGC---AGCAAC-----------------------------------AGCAGCA----.........................................................................................................................................................................................................................................................................................................	21	20	0.05	1	0	0	1	0	0	0
...........................................................................................................................................G---CAACAA-------------------------------------------CAGC---AGC---AG---CAGC.....................................................................................................................................................................................................................	20	20	0.05	1	0	0	1	0	0	0
...........................................................................................................................................................................................................................................................................G---------------CAGCAGCAGCAACAACAGCAG---------------------------------CA........................................................................................	24	20	0.05	1	0	0	1	0	0	0
........................................................................................................................GCAGCA----G------CAG---CAACAA-------------------------------------------CAGC---AGC---A.............................................................................................................................................................................................................................	24	20	0.05	1	0	0	1	0	0	0
..........................................................................C---AGCAAC-----------------------------------AGCAGCA----G------CAG---CAACA.......................................................................................................................................................................................................................................................................................	23	20	0.05	1	0	1	0	0	0	0
....................................................................................................................................................................................................................................................................................................CAACAACAGCAG---------------------------------CAG---CAGC---AA...........................................................................	21	20	0.05	1	0	0	1	0	0	0
....GCAGCAACAG---------------------------------------------------------CAGC---AGCAAC-----------------------------------AGCAGCA----.........................................................................................................................................................................................................................................................................................................	27	20	0.05	1	0	0	1	0	0	0
...........................................................................................................................................G---CAACAA-------------------------------------------CAGC---AGC---AG---CAGCAACA.................................................................................................................................................................................................................	24	20	0.05	1	0	0	1	0	0	0
..........................................................................................................................................AG---CAACAA-------------------------------------------CAGC---AGC---AG---CAGC.....................................................................................................................................................................................................................	21	20	0.05	1	0	0	1	0	0	0
..............................................................................................................................................................................................................................................................AGCAAC------AG---------------CAGCAGCAGCAA....................................................................................................................................	20	20	0.05	1	0	0	1	0	0	0
..................................................................................................................................................................................................................................................................................................AGCAACAACAGCAG---------------------------------CAG---CAGC---.............................................................................	21	20	0.05	1	0	0	1	0	0	0

droWil2

ATCAGCAACA---GCA------------------------------------------------------ACAGCAGCAACAATGGCA--------------------------------GCAACT----GCAGCAGCAA---CAACAA-------------------------------------------CAAC---AGC---AG---CAACAACAACAGCAGCAGC---AA----CAACAGCA------GCAACAAC------AA---------------CAGCAGCAGCAACAACAGCAT---------------------------------CAGCAACAGC---AACA---------------GCAGCAACAATG-------GCAGCAGCAACAACAG------CAACAT-----------	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
..................................................................................................................................................................................................................................................................AC------AA---------------CAGCAGCAGCAACA..................................................................................................................................	18	20	0.20	4	0	0	0	4	0
...............................................................................................................................................................................................................................................................................................................T---------------------------------CAGCAACAGC---AACA---------------GCAGCAACAAT...............................................	26	6	0.17	1	0	1	0	0	0
.TCAGCAACA---GCA------------------------------------------------------ACAGCAGCAACAAT.......................................................................................................................................................................................................................................................................................................................................................	26	6	0.17	1	0	1	0	0	0
.....................................................................................................................................................................................................................................................................................................................................................AACAGC---AACA---------------GCAGCAACAATG-------G......................................	23	20	0.10	2	0	2	0	0	0
.....................................................................................................................................................................................................................................................................................................................................................AACAGC---AACA---------------GCAGCAACAATG-------GC.....................................	24	20	0.10	2	0	2	0	0	0
...............................................................................................................................................................................................................................................................................................................T---------------------------------CAGCAACAGC---AACA---------------GCAGCAACA.................................................	24	10	0.10	1	0	0	0	1	0
..................................................................................................................................................................................................................CAACAACAACAGCAGCAGC---AA----CA...........................................................................................................................................................................................	23	20	0.10	2	0	0	0	1	1
......AACA---GCA------------------------------------------------------ACAGCAGCAACAATGGC....................................................................................................................................................................................................................................................................................................................................................	24	20	0.10	2	0	2	0	0	0
..................................................................................................................................................................................................................CAACAACAACAGCAGCAGC---AA----C............................................................................................................................................................................................	22	20	0.10	2	0	0	0	2	0
.............................................................................................................................................................................................................................................................CAACAAC------AA---------------CAGCAGCAGCAAC...................................................................................................................................	22	20	0.10	2	0	0	0	2	0
................................................................................................................................................................................................CAAC---AGC---AG---CAACAACAACA..............................................................................................................................................................................................................	20	20	0.10	2	0	0	0	2	0
......AACA---GCA------------------------------------------------------ACAGCAGCAACAATGG.....................................................................................................................................................................................................................................................................................................................................................	23	20	0.10	2	0	2	0	0	0
.TCAGCAACA---GCA------------------------------------------------------ACAGCAGCAACA.........................................................................................................................................................................................................................................................................................................................................................	24	10	0.10	1	0	0	0	1	0
.........................................................................................................................................CAA---CAACAA-------------------------------------------CAAC---AGC---AG---C........................................................................................................................................................................................................................	19	20	0.10	2	0	2	0	0	0
..................................................................................................................................................................................................................CAACAACAACAGCAGCAGC---A..................................................................................................................................................................................................	20	20	0.10	2	0	0	0	2	0
.......................................................................................................................................................................................................................................................................................................CAACAGCAT---------------------------------CAGCAACAGC---AACA---------------GCAG......................................................	27	12	0.08	1	0	0	0	1	0
...................................................................................................................................................................................................................................................................C------AA---------------CAGCAGCAGCAACAACAGCAT---------------------------------CAG.......................................................................................	27	12	0.08	1	0	0	0	1	0
....................................................................................................................................................................................................................................................................................................CAACAACAGCAT---------------------------------CAGCAACAGC---AACA---------------G.........................................................	27	12	0.08	1	0	1	0	0	0
....................................................................................................................................................................................................................................................................................................CAACAACAGCAT---------------------------------CAGCAACAGC---.............................................................................	22	14	0.07	1	0	0	0	1	0
...........................................................................................................................................................................................................................................................................................................AGCAT---------------------------------CAGCAACAGC---AACA---------------GCAG......................................................	23	17	0.06	1	0	1	0	0	0
.......................................................................................................................................................................................................................................................................................................CAACAGCAT---------------------------------CAGCAACAGC---.............................................................................	19	17	0.06	1	0	0	0	1	0
ATCAGCAACA---GCA------------------------------------------------------ACAGCAGCAAC..........................................................................................................................................................................................................................................................................................................................................................	24	19	0.05	1	0	1	0	0	0
..............................................................................................................................................................................................................................................................................................................AT---------------------------------CAGCAACAGC---AACA---------------GCAGCAAC..................................................	24	19	0.05	1	0	1	0	0	0
..............................................................................................................................................................................................................................................................................................................AT---------------------------------CAGCAACAGC---AACA---------------GCAGC.....................................................	21	20	0.05	1	0	1	0	0	0
.........A---GCA------------------------------------------------------ACAGCAGCAACAATGG.....................................................................................................................................................................................................................................................................................................................................................	20	20	0.05	1	0	1	0	0	0
........................................................................................................................................GCAA---CAACAA-------------------------------------------CAAC---AGC---AG---CA.......................................................................................................................................................................................................................	21	20	0.05	1	0	0	0	1	0
.....................................................................................................................................................................................................................CAACAACAGCAGCAGC---AA----CAACAG.......................................................................................................................................................................................	24	20	0.05	1	0	1	0	0	0
.......................................................................................................................................................................................................AGC---AG---CAACAACAACAGCAGCAGC---AA----.............................................................................................................................................................................................	26	20	0.05	1	0	1	0	0	0
.......................................................................................................................................................................................................................ACAACAGCAGCAGC---AA----CAACA........................................................................................................................................................................................	21	20	0.05	1	0	1	0	0	0
...................................................................................................................................................................................................................AACAACAACAGCAGCAGC---AA----.............................................................................................................................................................................................	20	20	0.05	1	0	0	1	0	0
................................................................................................................................................AACAA-------------------------------------------CAAC---AGC---AG---CAACAACAACAG.............................................................................................................................................................................................................	26	20	0.05	1	0	0	0	1	0
....................................................................................................................................................................................................................................................................................................................................................CAACAGC---AACA---------------GCAGCAACAATG-------GC.....................................	25	20	0.05	1	0	1	0	0	0
.......................................................................................................................................AGCAA---CAACAA-------------------------------------------CAAC---AGC---AG---C........................................................................................................................................................................................................................	21	20	0.05	1	0	1	0	0	0
...........................................................................................................................................................................................................................CAGCAGCAGC---AA----CAACAGCA------GCA............................................................................................................................................................................	23	20	0.05	1	0	1	0	0	0
............................................................................................................................................................................................................................................................GCAACAAC------AA---------------CAGCAGCAGCA.....................................................................................................................................	21	20	0.05	1	0	1	0	0	0
.................................................................................................................................................................................................AAC---AGC---AG---CAACAACAACAGCA...........................................................................................................................................................................................................	22	20	0.05	1	0	0	0	0	1
.....CAACA---GCA------------------------------------------------------ACAGCAGCAACAATGGC....................................................................................................................................................................................................................................................................................................................................................	25	20	0.05	1	0	1	0	0	0
ATCAGCAACA---GCA------------------------------------------------------ACAGCAGC.............................................................................................................................................................................................................................................................................................................................................................	21	20	0.05	1	0	1	0	0	0
..................................................................................................................................................................................................................................................AGCA------GCAACAAC------AA---------------CAGCAGCAGCAA....................................................................................................................................	26	20	0.05	1	0	1	0	0	0
......................................................................................................................................CAGCAA---CAACAA-------------------------------------------CAAC---AGC---AG---CAAC.....................................................................................................................................................................................................................	25	20	0.05	1	0	0	0	1	0
.......................................................................................................................................AGCAA---CAACAA-------------------------------------------CAAC---AGC---AG---CAAC.....................................................................................................................................................................................................................	24	20	0.05	1	0	0	0	1	0
.....................................................................................................................................GCAGCAA---CAACAA-------------------------------------------CAAC---AGC---AG---CA.......................................................................................................................................................................................................................	24	20	0.05	1	0	0	0	1	0
................................................................................................................................................................................................................................GCAGC---AA----CAACAGCA------GCAAC..........................................................................................................................................................................	20	20	0.05	1	0	0	0	1	0
......................................................................................................................................CAGCAA---CAACAA-------------------------------------------CAAC---AGC---A.............................................................................................................................................................................................................................	20	20	0.05	1	0	0	0	1	0
.............................................................................................................................................................................................................................................................CAACAAC------AA---------------CAGCAGCAGCAACA..................................................................................................................................	23	20	0.05	1	0	0	0	1	0
........................................................................................................................................GCAA---CAACAA-------------------------------------------CAAC---AGC---A.............................................................................................................................................................................................................................	18	20	0.05	1	0	1	0	0	0
..........................................................................................................................................................................................................................................................................AA---------------CAGCAGCAGCAACAACAGCA............................................................................................................................	22	20	0.05	1	0	1	0	0	0
.............................................................................................................................................................................................................................................................................................................CAT---------------------------------CAGCAACAGC---AACA---------------GCA.......................................................	20	20	0.05	1	0	0	0	1	0
............................................................................................................................................................................................................................................................GCAACAAC------AA---------------CAGCAGCAGCAACA..................................................................................................................................	24	20	0.05	1	0	0	0	1	0
........................................................................................................................................................................................................................................................................................................................................................AGC---AACA---------------GCAGCAACAATG-------G......................................	20	20	0.05	1	0	1	0	0	0
...................................................................................................................................................AA-------------------------------------------CAAC---AGC---AG---CAACAACA.................................................................................................................................................................................................................	19	20	0.05	1	0	0	0	1	0
....................................................................................................................................AGCAGCAA---CAACAA-------------------------------------------CAAC---AGC---AG---.........................................................................................................................................................................................................................	23	20	0.05	1	0	0	0	1	0
..................................................................................................................................................................................................................................................................AC------AA---------------CAGCAGCAGCAACAA.................................................................................................................................	19	20	0.05	1	0	0	0	1	0
..................................................................................................................................................................................................................................................................AC------AA---------------CAGCAGCAGCAACAACA...............................................................................................................................	21	20	0.05	1	0	1	0	0	0
...............................................................................................................................................................................................................................................AACAGCA------GCAACAAC------AA---------------CAGC............................................................................................................................................	21	20	0.05	1	0	0	0	1	0
.........................................................................................................................................................................................................................AACAGCAGCAGC---AA----CAACAGCA------...............................................................................................................................................................................	22	20	0.05	1	0	1	0	0	0
.............................................................................................................................................................................................................AG---CAACAACAACAGCAGCAGC---AA----CA...........................................................................................................................................................................................	25	20	0.05	1	0	0	0	1	0
....................................................................................................................................................................................................................................................CA------GCAACAAC------AA---------------CAGCAGCAG.......................................................................................................................................	21	20	0.05	1	0	0	0	1	0
..................................................................................................................................................CAA-------------------------------------------CAAC---AGC---AG---CAACAACAACA..............................................................................................................................................................................................................	23	20	0.05	1	0	0	0	0	1
..............................................................................................................................................................................................................G---CAACAACAACAGCAGCAGC---AA----CA...........................................................................................................................................................................................	24	20	0.05	1	0	0	0	1	0
................................................................................................................................................................................................CAAC---AGC---AG---CAACAACAACAGC............................................................................................................................................................................................................	22	20	0.05	1	0	1	0	0	0
....................................................................................................................................AGCAGCAA---CAACAA-------------------------------------------CAAC---AGC---A.............................................................................................................................................................................................................................	22	20	0.05	1	0	0	0	1	0
................................................................................................................................................................................................................................................ACAGCA------GCAACAAC------AA---------------CAGCAG..........................................................................................................................................	22	20	0.05	1	0	1	0	0	0
........................................................................................................................................................................................................GC---AG---CAACAACAACAGCAGCAGC---A..................................................................................................................................................................................................	24	20	0.05	1	0	0	0	1	0
...................................................................................................................................................................................................................................................GCA------GCAACAAC------AA---------------CAGCAGCAGCA.....................................................................................................................................	24	20	0.05	1	0	0	0	1	0
......................................................................................................................................................................................................................AACAACAGCAGCAGC---AA----CAACAGCA------...............................................................................................................................................................................	25	20	0.05	1	0	0	0	1	0

droVir3

ATCCGCAC-AACAGCA---------------------------------------------------------GC------TAT----------------------------------------CC----G------CA------TCAGCTGGCCGCCATG--GCGGCAT----TCC----------------------------AA---CAACATCAGCAGCAG---CAGCAG----CAACAACAACAACATCACCACC------AC---------------CAGCAGCAGCAGCAGCAGCAG---------------------------------------CAGC---AGCG--ACT----------GCAGCAA-------------CGTCTGCCCTGTCAG------CCACT------------	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
........................................................................................................................................................................................................................................................................................................................................................AGC---AGCG--ACT----------GCAGCAA-------------CGTCT.................................	22	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..............................................................................................................................................................................................................................................................................................................................................................AGCG--ACT----------GCAGCAA-------------CGTCT.................................	19	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
..............................................................................................................................................................................................................................................................................................................................................................AGCG--ACT----------GCAGCAA-------------CGTCTGCCCTGTCAG------.................	29	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................................................................................................................................AGCAGCAGCAG---------------------------------------CAGC---AGCG--ACT----------..........................................................	22	20	0.15	3	0	0	2	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
......................................................................................................................................................................................................................................................................................................GCAGCAGCAG---------------------------------------CAGC---AGCG--ACT----------G.........................................................	22	18	0.11	2	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
.............................................................................................................................................................................................................AA---CAACATCAGCAGCAG---CAG....................................................................................................................................................................................................	20	20	0.10	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
................................................................................................................................................................................C----------------------------AA---CAACATCAGCAGCAG---CAG....................................................................................................................................................................................................	21	20	0.10	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................................................GCAGCAGCAGCAG---------------------------------------CAGC---AGCG--ACT----------G.........................................................	25	11	0.09	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................................................CATCAGCAGCAG---CAGCAG----CAACAAC......................................................................................................................................................................................	25	15	0.07	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................................AGCAGCAG---CAGCAG----CAACAAC......................................................................................................................................................................................	21	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
.............................................................................................................................................................................................................................................................................................GCAGCAGCAGCAGCAGCAG---------------------------------------CA..................................................................................	21	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
.............................................................................................................................................................................................................AA---CAACATCAGCAGCAG---CAGCAG----CA...........................................................................................................................................................................................	25	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
...............................................................................................................................................................................................................................................................CCACC------AC---------------CAGCAGCAGCAGC...................................................................................................................................	20	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
...................................................................................................................................................................................................................................................................C------AC---------------CAGCAGCAGCAGCAGCA...............................................................................................................................	20	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
................................................................................................................................................................................C----------------------------AA---CAACATCAGCAGCAG---CAGC...................................................................................................................................................................................................	22	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
......................................................................................................................................................................................................................................GCAG----CAACAACAACAACATCA............................................................................................................................................................................	21	20	0.05	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................................................................AGCAG----CAACAACAACAACATCA............................................................................................................................................................................	22	20	0.05	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.............................................................................................................................................................................................................AA---CAACATCAGCAGCAG---CAGC...................................................................................................................................................................................................	21	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
...............................................................................................................................................................................................................................AG---CAGCAG----CAACAACAACAAC................................................................................................................................................................................	21	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
............................................................................................................................................................................................................................AGCAG---CAGCAG----CAACAACAACAAC................................................................................................................................................................................	24	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
...............................................................................................................................................................................................................................................................................................AGCAGCAGCAGCAGCAG---------------------------------------CA..................................................................................	19	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
...................................................................................................................................................................................................................AACATCAGCAGCAG---CAGCAG----CA...........................................................................................................................................................................................	22	20	0.05	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................................................CATCAGCAGCAG---CAGCAG----CA...........................................................................................................................................................................................	20	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
......................................................................................................................................................................................................................ATCAGCAGCAG---CAGCAG----CAACAA.......................................................................................................................................................................................	23	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droMoj3

ATCAGCAC-AACAC------------------------------------------------------------------CAAA-ATCGAGCA-----TGCCGAC-------TCC-----ACAACG----A------CAGCCG------------------CTGCTGCAC-----------------------------------AG---CACCATCATCAGCAG---CAGCAA----CAACAGCA------GCAGCAAC------AA---------------CAGCAGCAGCAACAACAGCAA---------------------------------CAG---CAGC---AACA---------------ACAGCAGCACCA-------ACAACAACAGCAGCAG------C----------------	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
.......................................................................................................................................................................................................................................................................................................................................................................................GCACCA-------ACAACAACAGCAGC.........................	20	6	0.17	1	1	0	0	0	0	0
........................................................................................................................................................................................................................................................................................................................................................................................CACCA-------ACAACAACAGCAGCAG------C----------------	22	14	0.07	1	1	0	0	0	0	0
.........................................................................................................................................................................................................................................................................................................................................................................................ACCA-------ACAACAACAGCAGCAG------C----------------	21	18	0.06	1	0	0	0	1	0	0
...........................................................................................................................................................................................................................CAGCAG---CAGCAA----CAACAGCA------GCA............................................................................................................................................................................	23	20	0.05	1	1	0	0	0	0	0
.................................................................................................................................................................................................................................................CAGCA------GCAGCAAC------AA---------------CAGCAGCA........................................................................................................................................	23	20	0.05	1	1	0	0	0	0	0
................................................................................................................................................................................................................................G---CAGCAA----CAACAGCA------GCAGCAAC------A................................................................................................................................................................	24	20	0.05	1	1	0	0	0	0	0
...........................................................................................................................................................................................................................................................................................................AGCAA---------------------------------CAG---CAGC---AACA---------------ACAGCAG...................................................	23	20	0.05	1	1	0	0	0	0	0
................................................................................................................................................................................................................................G---CAGCAA----CAACAGCA------GCAGCA.........................................................................................................................................................................	21	20	0.05	1	1	0	0	0	0	0
.....................................................................................................................................................................................................................................................................................................AACAACAGCAA---------------------------------CAG---CAGC---A............................................................................	19	20	0.05	1	0	0	0	0	1	0

droGri2

AGCAGCAGCAGCAG---------------------------------------------------------CAGCAGCAGCG------G--------------CA-------GCA-----GCAGCA----G------CAGCAG------------------GAGCGGCAG---------CA-------------GC---AGC---AG---CAGCAGCAGCAGCAG---CAG-------CAGCAGCAGTA---GCAGCATC------AG---------------CAGCGGCAGCAGCAGCAGCAG---------------------------------CGGCAGCAGC---AGCA---------------GCAGCAGCGGCA-------GCAGCAGCAGCAGCAG------CGGCAG-----------	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
...................................................................................................................................................................................................................AGCAGCAGCAGCAG---CAG-------CAGCAGCA.....................................................................................................................................................................................	25	20	0.10	2	2	0
.................................................................................................................................................................................................................................................................................................CAGCAGCAGCAGCAG---------------------------------CGGCA.....................................................................................	20	20	0.05	1	0	1

dan_2348

scaffold_13337:1833437-1833502 +

Candidate

Unknown

Predicted structure

Flybase annnotation

Repeatable elements

Sense Strand Reads

Anti-sense strand reads

Re-alignment of all predicted orthologs

Re-alignment of all predicted orthologs with sRNA reads

-9.1	-8.4