dan_1392

exon [dana_GLEANR_4068:4]; CDS [Dana\GF20818-cds]; exon [dana_GLEANR_4068:5]; CDS [Dana\GF20818-cds]; intron [Dana\GF20818-in]

Name	Class	Family	Strand
TART_DV	LINE	Jockey	-

##################################################------------------------------------------------------------------################################################## TCCACAAAGATCGAGATCTGTCAGGCCCCAGCCCCGCAGCAGCAACAACAGCAGCAGCAACAGAGCCAACAGCAGCAGCAACATCATCATCAGCAACAGCATCAGCAGCAACAGAGCCAACACCATCAGACTACGGGACTGCCAAGCACCGTTCATATCCAGCCGG ************************************************.................................((............................)).************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M044 female body	V055 head	M058 embryo	V105 male body	V039 embryo	V106 head
........GGTCGAGATCTTTCAGGCC...........................................................................................................................................	19	2	1	1.00	1	1	0	0	0	0	0
.............................................................................................CAACAGCATCAGCAGCAACA.....................................................	20	0	7	0.29	2	0	0	0	2	0	0
.............................................................AGAGCCCACACCAGCAGCA......................................................................................	19	2	6	0.17	1	0	1	0	0	0	0
...........................................................................................AGCAACAGCATCAGCAGCAACA.....................................................	22	0	6	0.17	1	0	0	1	0	0	0
.......................................................................................................................ACACCATCACACTCTGGGAC...........................	20	3	12	0.17	2	0	0	2	0	0	0
................................................................................................................................GACTACGGGGCTTCCACGC...................	19	3	7	0.14	1	0	1	0	0	0	0
..........................................CAACAACAGCAGCAGCAACAGA......................................................................................................	22	0	7	0.14	1	0	0	0	0	1	0
..................................................................................................GTATCAGCAGGAACATAGC.................................................	19	3	20	0.10	2	1	0	1	0	0	0
.....................................................................CAGCAGCTGCAACATCATCATCACCAGC.....................................................................	28	3	13	0.08	1	0	1	0	0	0	0
......................................................................AGCAGCAGCAACAAGATCATCAGCT.......................................................................	25	3	20	0.05	1	0	0	0	0	0	1
............................................ACAACAGCAGCAGCAACAG.......................................................................................................	19	0	20	0.05	1	0	0	0	0	0	1

AGGTGTTTCTAGCTCTAGACAGTCCGGGGTCGGGGCGTCGTCGTTGTTGTCGTCGTCGTTGTCTCGGTTGTCGTCGTCGTTGTAGTAGTAGTCGTTGTCGTAGTCGTCGTTGTCTCGGTTGTGGTAGTCTGATGCCCTGACGGTTCGTGGCAAGTATAGGTCGGCC ************************************************.................................((............................)).************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V039 embryo	V106 head	M044 female body	V105 male body	V055 head
..............................................................................................................TGCCTCAGTTGTGGTAGTC.....................................	19	2	1	3.00	3	2	0	1	0	0
..............................................................................................................TGCCTCAGTTGTGGTAGTCA....................................	20	3	6	1.33	8	0	3	3	2	0
.......................................................................................................................TGTGGTAGTGTGAGACCCTG...........................	20	3	12	1.25	15	1	14	0	0	0
........................CGGGGTCGGGGCGGTGTCGT..........................................................................................................................	20	2	2	0.50	1	1	0	0	0	0
............................................................................................................GCTGCCTCAGTTGTGGTAGTC.....................................	21	3	5	0.40	2	0	0	0	2	0
................................................................................................................................CTGTTGCTCTGACGTTTCGTG.................	21	3	3	0.33	1	0	0	0	0	1
.............................................................................................................CTGCCTCAGTTGTGGTAGTC.....................................	20	3	8	0.25	2	0	0	0	2	0
.........................................................................................................................TGGTAGTGTGATACCCTGG..........................	19	3	18	0.06	1	0	1	0	0	0

Species	Coordinate	ID	Alignment
droAna3	scaffold_13117:4806051-4806216 -	dan_1392	TCCA-------CAAAGATCGAGATCTGTCA----GGCCCCAGCCCCG---CAGCA--GCAACAAC------A----------------------GCA------------------------GCAGCAACAGAGCC---------A---------------A---------CAGCA--GCAGCAACATC------------ATCATCAGC---------------AAC------AG---CATCAGCAGCAAC-------------------------------AGA------------------------GCC------------------------A-----------------------ACA---CCATCA----------------GACTACGGGACT--GCCAAGCACCGT--TCATATCC-AGC--CGG
droBip1	scf7180000395508:51671-51821 +		TCCA-------CAAAGATCGAGATCTGCCA----GGCGCCCGCCTCC---CAACA--ACAGCAAC------A----GTC------------CCAGCA------------------------ACAGCAGCAGCA---------------G---CATCATCAT------CACCA-----TCAGCA------------------------GC---------------------------------------AAC-------------------------------AGA------------------------GCC------------------------A-----------------------ACA---CCATCA----------------GACCACCGGACT--GCCCAGCACGGT--GCACATCC-AGC--CGG
droKik1	scf7180000302544:880879-881041 +		TCCA-------CAAAGATTGAGATCTGCCA----GGCTCCTGCCCCG---CAG--CAACAACAAC------A----------------------ACA------------------------GCAGCAGCAGCATC---------A---C---CAGCAACAG------CA--------GCAGCA------------------------GC---------------ACCACCAGCAG------C------AGC----------------------------AACACC------------------------AT------------CA------CCAGCA-----------------------ACA---CCATCA----------------GACCAATG---T--ACCCAGCACCGT--TCATATAC-AGC--CAG
droFic1	scf7180000453927:598339-598474 -		TCCA-------CGAAGATCGAGATCTGCCA----GGCGCCAACCGCC---CAGCA--GCAGCACC----------------------------------------------------------------AGCA---------------G---CAGCAACAG------CAGCA-----GCAGCA------------------------GC---------------AGA------------------------------ACCA----------CCAGCAGC-----------------------------------------------------------------------------------A---CCACCA----------------GGCGACCCACTT--GCCGAGCACCGT--GCACATCC-AGC--CGG
droEle1	scf7180000491338:910759-910929 -		TCCA-------CGAGGATCAGC-GCTATCA----GCCCTA------CCAATAC--CAA------CAGCAGCAG-CAGCAGCAGCAGCA---TCATCA------------------------GCAACAGCAACATC---------A---------------GCAACACCA--------GCAGCA---CCA------------------GC---------------AAC---------------------ACC-------------------------------AGC------------GACAGCAGCAG---------------CAGCAACATCAGT------CGCACTACCC--------AC---------A--------------------------------GCAACACCA---GCAATTCC-AGC--CGA
droRho1	scf7180000776849:468884-469040 -		GCCGGATATACC---CATTGTCAGTGTCTC----GGAACTGGTCCTG-----------------CAGGAGCAG-CAGCA------------GCAACAGCAGCAGCA---------------GCAACAGCAACATC---------A---------------G---------CAACAGC--AGCAACACCA------------GCAGCAGC---------------AGC----------------------------------AACAG------------------CAAC------------------AG---------------CTAC------AACTGCAGCAG--------CAGCAACAA------------------------------------------------------------CGC-AGT--CTG
droBia1	scf7180000302428:281221-281378 +		CCCC-------TGGAGATAAAGACCGAGAA----G----CA-----G---CAG--CAA---CA---GCAGCGA----------------CAACA---------------------------GCAGCAGCAACATC---------A---------------G---------CAGCAGC--AGCAACACCA---GCAGCAACA------------TCA---------------GCAG------C------AGCAGCAATACCA----------GCAGCAGCACTATC------------------------AGCAA---------CA------TTATCA-----------------------GCA---GCA-----------------------------------------GC----ACTTGTACCAGC--A--
droTak1	scf7180000415179:112073-112208 -		TCCA-------CGAAGATCGAGATTTGCCA----GGCGCC------G---CAGCA--G----------------------------------CAGCA------------------------ACAGCAGCAGCA---------------G---CAGCAACAT------CACCA-----GCAGCA------------------------GC---------------AAC------------------------------ACCA----------GCAACAGCAGCACC------------------------AGCAACAC------CA---------CC---------------------------------------------------------------T--GCCCAGCACGGT--GCACATCC-AGC--CGG
droEug1	scf7180000409095:102354-102520 +		ACCA-------TTAAGCACAACAGCCAC-----------------------AGC--------------AAGCAGCAACA----------CAACAACA------------------------GCAGCCACAA---C---------A---G---TTCATACAA------GA--------TCAACA---------------------GCAATATCATCATCATCAGCAGC------AGCAGCAGCAGCAGGAGC-------------------------------AGG------------GGGTGCAGCAG---------------GC----------------------------------------------------------------ACTACGTCATT--GCGACGACGGGC--CCTTACAC-CGC--CAG
dm3	chrX:7936527-7936677 -		ACCA-------CCAACAGCAGCAGCAGC----------------------------------------AGCAA----CT------------------------------------------AACCCAGCAGCAGC---------TGCAGCAGCAGCAACAA------CAACA-----GCA---------------------------GC---------------AGC----------------------------------AACAA------------------CATC------------------TCCAAC---------------------AGCAGCAACAC--------CAACAGCAGCA---CCATCA----------------GGCGGCTA--------ACAAGTTGCTGATCATACCC-AAACCCAT
droSim2	2r:10622638-10622799 +		CCAA--------GAAGACCGACAAGAAGCTGCCCGATC----CCTCG---CAGCA--GCATCAGC----------------------------------------------------------AGCAGCAGCAGC---------A---G---CACCAACAG------CA--------GCAGCA------------------------GC---------------ACC------------------------------AGCA----------GCATCAGCAACATC------------------------AGCAACAC------C--------------------------------------------AGCAGGCCCAGACCATGTTAGCCGGAC-A-G-CTGCAGAGCAGTGT--T------C-ATG--TGG
droSec2	scaffold_21:363286-363426 -		TCCG-------CAAAT--------CCATCA--------CCA----------------C------CACCAACAG-CAGCA---------ACAGCAGCA------------------------GCAGCAACAG---C---------A---G---CAGCAACAG------AA--------ACAGCA---------GCAACATCA------------TAT---------------GCAG------C------AGC----------------------------AGCAGC------------------------AGCAGCA--------------------------------------GCAACAAC------------------CT-----------------T--TGTCACCACCTC--ACCCAC-C-CGG--CAG
droYak3	3R:2559200-2559361 +		ACCA-------CCACCATCCCAGTCAGCTA-CA-A-CTCCA-----A---CAA--CAA------CAGCAACAA-CAACA------------------------------------------ACAGCAGCAACACC---------A---------------A---------CAACAGC--CGCTACACC------------AACAACAGC---------------AAC----------------------------------TGCAA------------------CACCAGCAGCACC------------AACAACAC------CA-----------------------------CCAACAACA---CTATCA----------------G-----------CAG---CATGCCAT--TCAA---C-ACC--AGC
droEre2	scaffold_4845:15922789-15922929 -		CCCT-------CGCA-------------------------------G---CAG--CAT---CAGC---AGCAG-CAGCA---------TCAGCAGCAGCATCAGCA---------------GCAGCAGCAGCATC---------A------------GCAG------CA--------GCAGCAGCAGCA------------TCAGCAGC---------------AGC---------------------AT-------------------------CA------GCAGC------------------AG---------------CA------GCATCA-----------------------GCAGCACCAGCAGGCCCAGACCATGTT--------------------------------------AGC--C--
dp5	XL_group1a:3407263-3407409 -		TCCA-------CAT--------------------------------------------------CAGCAGCAG-CATCAACAGCAGCACCACCAGCA---------GCAGCAACACCACCAGGCGCAGCAGCACC---------ACCACCAGCAGCAGCAG------CA--------ACA------------------------ACAGC---------------AAC----------------------------------AG------------CA------CCACC------------------ACCAGC---------------------AACAGCAGCAC--------CAGCAACAG--------------------------------------------------CGT--TCCT---C-GCC--AGC
droPer2	scaffold_2351:2067-2222 +		GCCA-------AGGGGATCGGCATCAGC----------------------------------------AGCAG-CATCA---------GCAGCAGCA------------------------GCATCAGCAGCATC---------A---------GCAGCAG------CA--------GCAGCA---------------------GCAGC---------------ATCAGCATCAG----------------------------------------CAGCAGCAGC------------------------AGCAGCAG------CA---------CT------GGCACGGGCC--------AC---------A----------------GGGAGCCG--C-C--ATCGGGCCGTT--CGTCTCGC-AGG--AGG
droWil2	scf2_1100000004902:6527871-6528033 +		CACA-------ATAATATCCACCACCATCA----GCA---------G---CAG--CAA---CA------A-------CA------------ACAACA------------------------ACAGCAGCAACAACTCTTACAACA------GCAGCAGC--------------------AGCATTTACAACAGCAACATCA------------TCT---------------GCAG------C------AGC----------CGCCACCGCAGCAGC------AGC------------------------AGCAGCAGCACCAACA------TCATCA-----------------------ACA---GCA-----------------------------------------------------TC-AAT--CGG
droVir3	scaffold_12970:10373467-10373647 -		TCCA-------CAAAGATTGAAATCTGCCA----GGCACCAGCGCCA---CAGCA--GCAGCAGCAGCAACAA----CA------------ACAACA------------------------ACAGCAGCACCATC---------A---G---CAGCAACAC------CA--------TCA------------------------GCAGC---------------AACAGCACCAT------CAGCAGCAAC-------------------------------AGC------------------------AGC---AG------CA------TCATCA-----------------------GCA---GCATCA----------------GACAACCA--G-C--GGCAATACGGT--GCACATAC-AGG--CAG
droMoj3	scaffold_6473:11857795-11857947 +		GCTA-------CAACTATCCAGAGCAGCCA----CACAAGCA----A---CAC--CTG------CAGCAGCAG-CAGCA------------ACAGCA------------------------GCAGCAGCAGCAGC---------A---G---CAGCAACAG------CA--------GCAGCA------------------------GC---------------AAC------------------------------AGCA----------GCAGCAGCAGCAGC------------------------AGCAACAG------CA---------GG------AG--------------CAGCA---GGAG-----------------------------------------C-T--GGATTTTC-AGC--TGT
droGri2	scaffold_14853:6565996-6566145 +		TCCA-------CAGC--------ACTATCA----ACC--------------------------------GCAA----CA---------ACAGCAGCA------------------------GCAGCAACAGCA---------------G---CAGCAACAA------CAACA-----GCAGCA------------------------GC---------------AAC------------------------------AACA----------ACAGCAGCAGCAGC------------------------AGCAACAA------CA---------AA-----------------------AGCC-------------CAAAGGCGGC--GATGATAAGAAT--TTCAAGGAATAT--GCAT---C-GGC--TGG

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droAna3

TCCA-------CAAAGATCGAGATCTGTCA----GGCCCCAGCCCCG---CAGCA--GCAACAAC------A----------------------GCA------------------------GCAGCAACAGAGCC---------A---------------A---------CAGCA--GCAGCAACATC------------ATCATCAGC---------------AAC------AG---CATCAGCAGCAAC-------------------------------AGA------------------------GCC------------------------A-----------------------ACA---CCATCA----------------GACTACGGGACT--GCCAAGCACCGT--TCATATCC-AGC--CGG	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
................................................................................................................................................................................................................C---------------AAC------AG---CATCAGCAGCAAC-------------------------------A......................................................................................................................................................	20	7	0.29	2	0	0	0	0	2	0
..............................................................................................................................................................................................................AGC---------------AAC------AG---CATCAGCAGCAAC-------------------------------A......................................................................................................................................................	22	6	0.17	1	0	1	0	0	0	0
..........................................................CAACAAC------A----------------------GCA------------------------GCAGCAACAGA.............................................................................................................................................................................................................................................................................................................	22	7	0.14	1	0	0	1	0	0	0
............................................................ACAAC------A----------------------GCA------------------------GCAGCAACAG..............................................................................................................................................................................................................................................................................................................	19	20	0.05	1	0	0	0	0	0	1

droBip1

TCCA-------CAAAGATCGAGATCTGCCA----GGCGCCCGCCTCC---CAACA--ACAGCAAC------A----GTC------------CCAGCA------------------------ACAGCAGCAGCA---------------G---CATCATCAT------CACCA-----TCAGCA------------------------GC---------------------------------------AAC-------------------------------AGA------------------------GCC------------------------A-----------------------ACA---CCATCA----------------GACCACCGGACT--GCCCAGCACGGT--GCACATCC-AGC--CGG	Size	Hit Count	Total Norm	Total
No Reads

droKik1

TCCA-------CAAAGATTGAGATCTGCCA----GGCTCCTGCCCCG---CAG--CAACAACAAC------A----------------------ACA------------------------GCAGCAGCAGCATC---------A---C---CAGCAACAG------CA--------GCAGCA------------------------GC---------------ACCACCAGCAG------C------AGC----------------------------AACACC------------------------AT------------CA------CCAGCA-----------------------ACA---CCATCA----------------GACCAATG---T--ACCCAGCACCGT--TCATATAC-AGC--CAG	Size	Hit Count	Total Norm	Total
No Reads

droFic1

TCCA-------CGAAGATCGAGATCTGCCA----GGCGCCAACCGCC---CAGCA--GCAGCACC----------------------------------------------------------------AGCA---------------G---CAGCAACAG------CAGCA-----GCAGCA------------------------GC---------------AGA------------------------------ACCA----------CCAGCAGC-----------------------------------------------------------------------------------A---CCACCA----------------GGCGACCCACTT--GCCGAGCACCGT--GCACATCC-AGC--CGG	Size	Hit Count	Total Norm	Total
No Reads

droEle1

TCCA-------CGAGGATCAGC-GCTATCA----GCCCTA------CCAATAC--CAA------CAGCAGCAG-CAGCAGCAGCAGCA---TCATCA------------------------GCAACAGCAACATC---------A---------------GCAACACCA--------GCAGCA---CCA------------------GC---------------AAC---------------------ACC-------------------------------AGC------------GACAGCAGCAG---------------CAGCAACATCAGT------CGCACTACCC--------AC---------A--------------------------------GCAACACCA---GCAATTCC-AGC--CGA	Size	Hit Count	Total Norm	Total
No Reads

droRho1

GCCGGATATACC---CATTGTCAGTGTCTC----GGAACTGGTCCTG-----------------CAGGAGCAG-CAGCA------------GCAACAGCAGCAGCA---------------GCAACAGCAACATC---------A---------------G---------CAACAGC--AGCAACACCA------------GCAGCAGC---------------AGC----------------------------------AACAG------------------CAAC------------------AG---------------CTAC------AACTGCAGCAG--------CAGCAACAA------------------------------------------------------------CGC-AGT--CTG	Size	Hit Count	Total Norm	Total
No Reads

droBia1

CCCC-------TGGAGATAAAGACCGAGAA----G----CA-----G---CAG--CAA---CA---GCAGCGA----------------CAACA---------------------------GCAGCAGCAACATC---------A---------------G---------CAGCAGC--AGCAACACCA---GCAGCAACA------------TCA---------------GCAG------C------AGCAGCAATACCA----------GCAGCAGCACTATC------------------------AGCAA---------CA------TTATCA-----------------------GCA---GCA-----------------------------------------GC----ACTTGTACCAGC--A--	Size	Hit Count	Total Norm	Total
No Reads

droTak1

TCCA-------CGAAGATCGAGATTTGCCA----GGCGCC------G---CAGCA--G----------------------------------CAGCA------------------------ACAGCAGCAGCA---------------G---CAGCAACAT------CACCA-----GCAGCA------------------------GC---------------AAC------------------------------ACCA----------GCAACAGCAGCACC------------------------AGCAACAC------CA---------CC---------------------------------------------------------------T--GCCCAGCACGGT--GCACATCC-AGC--CGG	Size	Hit Count	Total Norm	Total
No Reads

droEug1

ACCA-------TTAAGCACAACAGCCAC-----------------------AGC--------------AAGCAGCAACA----------CAACAACA------------------------GCAGCCACAA---C---------A---G---TTCATACAA------GA--------TCAACA---------------------GCAATATCATCATCATCAGCAGC------AGCAGCAGCAGCAGGAGC-------------------------------AGG------------GGGTGCAGCAG---------------GC----------------------------------------------------------------ACTACGTCATT--GCGACGACGGGC--CCTTACAC-CGC--CAG	Size	Hit Count	Total Norm	Total
No Reads

dm3

ACCA-------CCAACAGCAGCAGCAGC----------------------------------------AGCAA----CT------------------------------------------AACCCAGCAGCAGC---------TGCAGCAGCAGCAACAA------CAACA-----GCA---------------------------GC---------------AGC----------------------------------AACAA------------------CATC------------------TCCAAC---------------------AGCAGCAACAC--------CAACAGCAGCA---CCATCA----------------GGCGGCTA--------ACAAGTTGCTGATCATACCC-AAACCCAT	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
.....................................................................................................................................................................................................................................................................................................................................................................................................................CAAGTTGCTGATCATACCC-AAAC....	23	1	6.00	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................................................................................................................................................................................................................................................AGTTGCTGATCATACCC-A.......	18	1	3.00	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...........................................................................................................................................................................................................................................................................................................................................................................................................A--------ACAAGTTGCTGATCATACCC-........	21	1	3.00	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
........................CAGC----------------------------------------AGCAA----CT------------------------------------------AACCCAGCAGCAGC---------.................................................................................................................................................................................................................................................................................................	25	1	3.00	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................................................................................................AACAC--------CAACAGCAGCA---CCATCA----------------GGCGGC.......................................	28	1	2.00	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
........................CAGC----------------------------------------AGCAA----CT------------------------------------------AACCCAGCAGCAG...........................................................................................................................................................................................................................................................................................................	24	1	2.00	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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...................................................................................................................................................AGCAGCAGCAACAA------CAACA-----G...............................................................................................................................................................................................................................................................	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
................................................................................................................................................TGCAGCAGCAGCAACAA------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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
......................................................................................................................................................AGCAGCAACAA------CAACA-----GCA---------------------------GC---------------AGC----------------------------------AACA........................................................................................................................................................................	28	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
......................................................................................................................................................AGCAGCAACAA------CAACA-----GCA---------------------------GC---------------AGC----------------------------------A...........................................................................................................................................................................	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	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droSim2

CCAA--------GAAGACCGACAAGAAGCTGCCCGATC----CCTCG---CAGCA--GCATCAGC----------------------------------------------------------AGCAGCAGCAGC---------A---G---CACCAACAG------CA--------GCAGCA------------------------GC---------------ACC------------------------------AGCA----------GCATCAGCAACATC------------------------AGCAACAC------C--------------------------------------------AGCAGGCCCAGACCATGTTAGCCGGAC-A-G-CTGCAGAGCAGTGT--T------C-ATG--TGG	Size	Hit Count	Total Norm	Total	M023 Head	M024 Male-body	M025 Embryo	M053 Female-body	O001 Testis	O002 Head	SRR553485 Ovary	SRR553486 Ovary	SRR553487 Ovary	SRR553488 Ovary	SRR618934 Ovary	V044 Embryo	SRR902008 Ovary	SRR902009 Testis	SRR1275487 Male larvae	SRR1275485 Male prepupae	SRR1275483 Male prepupae
.................................................................................................................................AGCAGC---------A---G---CACCAACAG------C.........................................................................................................................................................................................................................................................................	18	15	1.13	17	0	0	0	0	17	0	0	0	0	0	0	0	0	0	0	0	0
...................GACAAGAAGCTGCCCGATC----CCTCG---C..............................................................................................................................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0
..........................................................................................................................................................................................................................................................................................................................................................................................GACCATGTTAGCCGGA.......................................	16	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
.................................................................................................................................................................................................................................................................................................................................................................................................TTAGCCGGAC-A-G-CTGCAGAGC........................	21	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.................................................................................................................................................................................................................................................................................................................................................................................................TTAGCCGGAC-A-G-CTGCAGAGCAGTGT--.................	26	1	1.00	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
........................................................................................................................................................CACCAACAG------CA--------GCAGCA------------------------GC---------------A................................................................................................................................................................................................................	20	20	0.05	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..............................................................AGC----------------------------------------------------------AGCAGCAGCAGC---------A---G---C........................................................................................................................................................................................................................................................................................	18	20	0.05	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
........................................................................................................................................................................A--------GCAGCA------------------------GC---------------ACC------------------------------AGCA----------GC................................................................................................................................................................	18	20	0.05	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0

droSec2

TCCG-------CAAAT--------CCATCA--------CCA----------------C------CACCAACAG-CAGCA---------ACAGCAGCA------------------------GCAGCAACAG---C---------A---G---CAGCAACAG------AA--------ACAGCA---------GCAACATCA------------TAT---------------GCAG------C------AGC----------------------------AGCAGC------------------------AGCAGCA--------------------------------------GCAACAAC------------------CT-----------------T--TGTCACCACCTC--ACCCAC-C-CGG--CAG	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
...............................................................................................................................ACAG---C---------A---G---CAGCAACAG------AA--------A...............................................................................................................................................................................................................................................................	19	3	0.33	1	0	0	1	0
..............................................................................A---------ACAGCAGCA------------------------GCAGCAACAG---C---------A---G---CAGC.....................................................................................................................................................................................................................................................................................	27	16	0.06	1	0	1	0	0
..........................................................................CAGCA---------ACAGCAGCA------------------------GCAGCAACAG---C---------A---.............................................................................................................................................................................................................................................................................................	26	18	0.06	1	0	0	1	0
.............................................................................................AGCA------------------------GCAGCAACAG---C---------A---G---CA.......................................................................................................................................................................................................................................................................................	19	20	0.05	1	0	0	1	0
.........................................................................................................................................................................................................................................AG------C------AGC----------------------------AGCAGC------------------------AGCAGCA--------------------------------------GCA............................................................................	22	20	0.05	1	0	0	1	0
..............................................................................A---------ACAGCAGCA------------------------GCAGCAACAG---C---------A---G---CA.......................................................................................................................................................................................................................................................................................	25	20	0.05	1	0	0	1	0

droYak3

ACCA-------CCACCATCCCAGTCAGCTA-CA-A-CTCCA-----A---CAA--CAA------CAGCAACAA-CAACA------------------------------------------ACAGCAGCAACACC---------A---------------A---------CAACAGC--CGCTACACC------------AACAACAGC---------------AAC----------------------------------TGCAA------------------CACCAGCAGCACC------------AACAACAC------CA-----------------------------CCAACAACA---CTATCA----------------G-----------CAG---CATGCCAT--TCAA---C-ACC--AGC	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
.................................................................AGCAACAA-CAACA------------------------------------------ACAGCAGC................................................................................................................................................................................................................................................................................................................	21	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0

droEre2

CCCT-------CGCA-------------------------------G---CAG--CAT---CAGC---AGCAG-CAGCA---------TCAGCAGCAGCATCAGCA---------------GCAGCAGCAGCATC---------A------------GCAG------CA--------GCAGCAGCAGCA------------TCAGCAGC---------------AGC---------------------AT-------------------------CA------GCAGC------------------AG---------------CA------GCATCA-----------------------GCAGCACCAGCAGGCCCAGACCATGTT--------------------------------------AGC--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------CA--------GCAGCAGCAGCA------------TCAGCA..................................................................................................................................................................................................................................	21	20	0.30	6	6	0	0	0	0	0	0
................................................................................................................................................A------------GCAG------CA--------GCAGCAGCAGCA------------TCAGCAGC---------------A................................................................................................................................................................................................................	28	18	0.22	4	2	0	0	0	1	1	0
..................................................................................................CATCAGCA---------------GCAGCAGCAGCATC---------A------------GC..................................................................................................................................................................................................................................................................................	25	5	0.20	1	0	0	0	0	0	1	0
.............................................................................................................................................................GCAG------CA--------GCAGCAGCAGCA------------TCAGCAGC---------------A................................................................................................................................................................................................................	27	19	0.16	3	3	0	0	0	0	0	0
......................................................................................................................................C---------A------------GCAG------CA--------GCAGCAGCAGCA------------TCAGC...................................................................................................................................................................................................................................	25	20	0.10	2	0	1	0	0	0	0	1
...................................................................................................................................................................................................................................................................................CA------GCAGC------------------AG---------------CA------GCATCA-----------------------GCA......................................................................	20	20	0.10	2	2	0	0	0	0	0	0
................................................................................................................................................A------------GCAG------CA--------GCAGCAGCAGCA------------TCAGCA..................................................................................................................................................................................................................................	25	20	0.10	2	0	0	0	0	2	0	0
................................................................................................................................................A------------GCAG------CA--------GCAGCAGCAGCA------------TC......................................................................................................................................................................................................................................	21	20	0.10	2	2	0	0	0	0	0	0
.............................................................CAGC---AGCAG-CAGCA---------TCAGCA...................................................................................................................................................................................................................................................................................................................................................	20	20	0.10	2	2	0	0	0	0	0	0
.............................................................................................AGCAGCATCAGCA---------------GCAGCA..................................................................................................................................................................................................................................................................................................................	19	20	0.10	2	1	0	0	0	0	1	0
..............................................................................................................................................................................................................AGC---------------AGC---------------------AT-------------------------CA------GCAGC------------------AG---------------CA------......................................................................................................	19	20	0.10	2	1	0	0	0	0	1	0
................................................................................................................................................A------------GCAG------CA--------GCAGCAGCAGCA------------TCAGC...................................................................................................................................................................................................................................	24	20	0.10	2	2	0	0	0	0	0	0
..............A-------------------------------G---CAG--CAT---CAGC---AGCAG-CA.....................................................................................................................................................................................................................................................................................................................................................................	19	20	0.10	2	1	0	0	0	0	1	0
.......................................................................AG-CAGCA---------TCAGCAGCAGCATCAGC........................................................................................................................................................................................................................................................................................................................................	24	11	0.09	1	1	0	0	0	0	0	0
......................................................................................................................................................................................AGCAGCA------------TCAGCAGC---------------AGC---------------------AT-------------------------CA------GC....................................................................................................................................................	24	11	0.09	1	1	0	0	0	0	0	0
............................................................................................................................................................................................A------------TCAGCAGC---------------AGC---------------------AT-------------------------CA------GCAGC------------------A..............................................................................................................................	22	12	0.08	1	0	0	0	0	0	1	0
..............................................................................A---------TCAGCAGCAGCATCAGCA---------------GCA.....................................................................................................................................................................................................................................................................................................................	22	12	0.08	1	0	0	0	0	0	1	0
...............................................................................................................................................................AG------CA--------GCAGCAGCAGCA------------TCAGCAGC---------------AGC---------------------.........................................................................................................................................................................................	27	17	0.06	1	0	0	0	0	0	1	0
......................................................................................................AGCA---------------GCAGCAGCAGCATC---------A------------GCAG------CA--------GC..............................................................................................................................................................................................................................................................	27	17	0.06	1	0	0	0	0	0	1	0
.........................................................................................................................................................................................AGCA------------TCAGCAGC---------------AGC---------------------AT-------------------------CA------......................................................................................................................................................	19	19	0.05	1	0	0	0	0	0	1	0
...........................................................................AGCA---------TCAGCAGCAGCATCA..........................................................................................................................................................................................................................................................................................................................................	19	19	0.05	1	0	0	0	0	0	1	0
.............................................................................................................................................................GCAG------CA--------GCAGCAGCAGCA------------TCAGCAGC---------------.................................................................................................................................................................................................................	26	20	0.05	1	1	0	0	0	0	0	0
...............................................................................................CAGCATCAGCA---------------GCAGCAGC................................................................................................................................................................................................................................................................................................................	19	20	0.05	1	0	0	0	0	1	0	0
................................................................................................................................................................................................................C---------------AGC---------------------AT-------------------------CA------GCAGC------------------AG---------------CA------GC....................................................................................................	19	20	0.05	1	0	0	0	0	1	0	0
........................................................................................................CA---------------GCAGCAGCAGCATC---------A------------GCAG------CA--------GC..............................................................................................................................................................................................................................................................	25	20	0.05	1	0	0	0	0	0	1	0
.......................................................................................................GCA---------------GCAGCAGCAGCATC---------A------------GCAG------CA--------GC..............................................................................................................................................................................................................................................................	26	20	0.05	1	1	0	0	0	0	0	0
...............................................................................................................................................................AG------CA--------GCAGCAGCAGCA------------TCAGCAGC---------------A................................................................................................................................................................................................................	25	20	0.05	1	1	0	0	0	0	0	0
...................................................................................................................................................................................AGCAGCAGCA------------TCAGCAGC---------------AGC---------------------.........................................................................................................................................................................................	21	20	0.05	1	1	0	0	0	0	0	0
....................................................................AGCAG-CAGCA---------TCAGCAGCAGC..............................................................................................................................................................................................................................................................................................................................................	21	20	0.05	1	1	0	0	0	0	0	0
..............................................................AGC---AGCAG-CAGCA---------TCAGCAGCAGCA.............................................................................................................................................................................................................................................................................................................................................	25	20	0.05	1	0	0	0	0	1	0	0
................................................................................................................................................................G------CA--------GCAGCAGCAGCA------------TCAGCAGC---------------AGC---------------------.........................................................................................................................................................................................	26	20	0.05	1	1	0	0	0	0	0	0
.......................................................................AG-CAGCA---------TCAGCAGCAGCA.............................................................................................................................................................................................................................................................................................................................................	19	20	0.05	1	0	0	0	0	0	1	0
...................................................................................................................................CATC---------A------------GCAG------CA--------GCAGCAGCAGC.....................................................................................................................................................................................................................................................	22	20	0.05	1	0	0	0	0	0	1	0
................................................................................................................................................................G------CA--------GCAGCAGCAGCA------------TCAGC...................................................................................................................................................................................................................................	20	20	0.05	1	0	0	0	0	0	1	0
.............................................................CAGC---AGCAG-CAGCA---------TCAGCAGCAG...............................................................................................................................................................................................................................................................................................................................................	24	20	0.05	1	1	0	0	0	0	0	0
.......................................................................................................................................................................CA--------GCAGCAGCAGCA------------TCAGCAGC---------------AGC---------------------.........................................................................................................................................................................................	25	20	0.05	1	0	0	0	0	0	1	0
................................................................................................................................CAGCATC---------A------------GCAG------CA--------GCAGC...........................................................................................................................................................................................................................................................	19	20	0.05	1	0	0	0	0	1	0	0
...........................................................................................................................AGCAGCAGCATC---------A------------GCAG------CA--------GC..............................................................................................................................................................................................................................................................	21	20	0.05	1	1	0	0	0	0	0	0

dp5

TCCA-------CAT--------------------------------------------------CAGCAGCAG-CATCAACAGCAGCACCACCAGCA---------GCAGCAACACCACCAGGCGCAGCAGCACC---------ACCACCAGCAGCAGCAG------CA--------ACA------------------------ACAGC---------------AAC----------------------------------AG------------CA------CCACC------------------ACCAGC---------------------AACAGCAGCAC--------CAGCAACAG--------------------------------------------------CGT--TCCT---C-GCC--AGC	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
...........................................................................ATCAACAGCAGCACCACCAGCA---------.......................................................................................................................................................................................................................................................................................................................................	22	1	1.00	1	0	1	0	0	0	0	0	0	0	0
....................................................................AGCAG-CATCAACAGCAGCACCACCAGCA---------.......................................................................................................................................................................................................................................................................................................................................	28	1	1.00	1	0	0	0	0	1	0	0	0	0	0
................................................................................................................................................ACCACCAGCAGCAGCAG------CA--------AC..............................................................................................................................................................................................................................................................	21	13	0.08	1	0	0	0	1	0	0	0	0	0	0
..................................................................GCAGCAG-CATCAACAGCAGCA.........................................................................................................................................................................................................................................................................................................................................................	21	14	0.07	1	0	1	0	0	0	0	0	0	0	0
........................................................................................................................................................CAGCAGCAG------CA--------ACA------------------------ACAGC---------------AAC----------------------------------A...........................................................................................................................................................................	23	20	0.05	1	0	1	0	0	0	0	0	0	0	0
.......................................................................................................................................................GCAGCAGCAG------CA--------ACA------------------------ACAGC---------------AAC----------------------------------AG------------CA------......................................................................................................................................................	27	20	0.05	1	0	1	0	0	0	0	0	0	0	0
............................................................................................................................................................AGCAG------CA--------ACA------------------------ACAGC---------------AAC----------------------------------A...........................................................................................................................................................................	19	20	0.05	1	0	1	0	0	0	0	0	0	0	0
.................................................................................AGCAGCACCACCAGCA---------GCAG...................................................................................................................................................................................................................................................................................................................................	20	20	0.05	1	0	0	0	1	0	0	0	0	0	0

droPer2

GCCA-------AGGGGATCGGCATCAGC----------------------------------------AGCAG-CATCA---------GCAGCAGCA------------------------GCATCAGCAGCATC---------A---------GCAGCAG------CA--------GCAGCA---------------------GCAGC---------------ATCAGCATCAG----------------------------------------CAGCAGCAGC------------------------AGCAGCAG------CA---------CT------GGCACGGGCC--------AC---------A----------------GGGAGCCG--C-C--ATCGGGCCGTT--CGTCTCGC-AGG--AGG	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
.............................................................................................................................................................................................................................................................................................................................................................GCC--------AC---------A----------------GGGAGCCG--C-C--ATCGGG........................	22	6	0.33	2	0	2	0	0	0	0
.............................................................................................................................................................................................................................................................................................................................................................GCC--------AC---------A----------------GGGAGCCG--C-C--ATCGGGCC......................	24	6	0.17	1	0	1	0	0	0	0
....................................................................................................................................................................................................................................................................................AGCAGCAGC------------------------AGCAGCAG------CA---------CT------GGC........................................................................................	24	7	0.14	1	0	0	0	0	1	0
........................................................................................................................................................................................................................................................................................................................AGCAG------CA---------CT------GGCACGGGCC--------AC---------A----------------GG...........................................	24	14	0.07	1	0	1	0	0	0	0
...............................................................................................................................................................................................................................................................................................................................................T------GGCACGGGCC--------AC---------A----------------GGGAGCCG--C-C--A.............................	25	14	0.07	1	0	1	0	0	0	0
...............................................................................................................................................................................................................................................................................................................................................T------GGCACGGGCC--------AC---------A----------------GGGAGCCG--C-.................................	23	14	0.07	1	0	1	0	0	0	0
......................................................................................................................................................................................................................................................................................................................................................GGCACGGGCC--------AC---------A----------------GGGAGA.......................................	19	15	0.07	1	0	1	0	0	0	0
...............................................................................................................................................................................................................................................................................................................................................T------GGCACGGGCC--------AC---------A----------------GGGAGC.......................................	20	15	0.07	1	0	1	0	0	0	0
..............................................................................................................................AGCAGCATC---------A---------GCAGCAG------CA--------GC..............................................................................................................................................................................................................................................................	21	20	0.05	1	0	0	1	0	0	0
........................CAGC----------------------------------------AGCAG-CATCA---------GCAGCAGCA------------------------G.......................................................................................................................................................................................................................................................................................................................	24	20	0.05	1	0	1	0	0	0	0
...................................................................................................................................................................................................................................AGCATCAG----------------------------------------CAGCAGCAGC------------------------AG..........................................................................................................................	20	20	0.05	1	0	1	0	0	0	0
..........................................................................................................................CATCAGCAGCATC---------A---------GCAGC..................................................................................................................................................................................................................................................................................	19	20	0.05	1	0	0	1	0	0	0

droWil2

CACA-------ATAATATCCACCACCATCA----GCA---------G---CAG--CAA---CA------A-------CA------------ACAACA------------------------ACAGCAGCAACAACTCTTACAACA------GCAGCAGC--------------------AGCATTTACAACAGCAACATCA------------TCT---------------GCAG------C------AGC----------CGCCACCGCAGCAGC------AGC------------------------AGCAGCAGCACCAACA------TCATCA-----------------------ACA---GCA-----------------------------------------------------TC-AAT--CGG	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
.................................................................................................................................AACAACTCTTACAACA------GCAGC.....................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	1	0	0	0
................................................................................................................................CAACAACTCTTACAACA------GCAGC.....................................................................................................................................................................................................................................................................................	22	1	1.00	1	0	0	0	1	0
.............................................................................................................................................AACA------GCAGCAGC--------------------AGCATT........................................................................................................................................................................................................................................................	18	9	0.11	1	0	0	0	1	0
.....................................................................A-------CA------------ACAACA------------------------ACAGCAGCAACAAC..........................................................................................................................................................................................................................................................................................................	23	20	0.10	2	0	0	0	2	0
..........................ATCA----GCA---------G---CAG--CAA---CA------A-------CA------------......................................................................................................................................................................................................................................................................................................................................................	19	20	0.05	1	0	0	0	1	0
...................................................................................................................................................................................................................................................................................C------AGC------------------------AGCAGCAGCACCAAC.............................................................................................................	19	20	0.05	1	0	0	0	1	0
..............................................................A------A-------CA------------ACAACA------------------------ACAGCAGCAACAAC..........................................................................................................................................................................................................................................................................................................	24	20	0.05	1	0	0	0	1	0

droVir3

TCCA-------CAAAGATTGAAATCTGCCA----GGCACCAGCGCCA---CAGCA--GCAGCAGCAGCAACAA----CA------------ACAACA------------------------ACAGCAGCACCATC---------A---G---CAGCAACAC------CA--------TCA------------------------GCAGC---------------AACAGCACCAT------CAGCAGCAAC-------------------------------AGC------------------------AGC---AG------CA------TCATCA-----------------------GCA---GCATCA----------------GACAACCA--G-C--GGCAATACGGT--GCACATAC-AGG--CAG	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
.......................................................................AA----CA------------ACAACA------------------------ACAGCAGCACCATC---------.................................................................................................................................................................................................................................................................................................	24	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
..................................................................................................................................................................................................................................................................................................................................................................................CA----------------GACAACCA--G-C--GGCAATACGGT--GCAC.............	27	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
.............................................................................................................................................................ACAC------CA--------TCA------------------------GCAGC---------------AACAGCACCAT------CA..............................................................................................................................................................................................	27	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.................................................................................................................................................................................................................................................................................................................................................................................TCA----------------GACAACCA--G-C--GGCAATACGGT--GCA..............	27	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
................................................................................................A------------------------ACAGCAGCACCATC---------A---G---C........................................................................................................................................................................................................................................................................................	18	2	0.50	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
.......................................................................................................................................................................CA--------TCA------------------------GCAGC---------------AACAGCACC........................................................................................................................................................................................................	19	4	0.25	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
..............................................................................................................................................................................................................AGC---------------AACAGCACCAT------CAGCAGCA........................................................................................................................................................................................	22	4	0.25	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
........................................................................................................................................................................................................................................................AAC-------------------------------AGC------------------------AGC---AG------CA------TCATCA-----------------------.........................................................................	19	6	0.17	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
...........................................................................................................................................................................................................................................................................................GC------------------------AGC---AG------CA------TCATCA-----------------------GCA---GCA................................................................	21	8	0.13	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
...........................................................AGCAGCAGCAACAA----CA------------ACAACA------------------------A.......................................................................................................................................................................................................................................................................................................................	23	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	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
.....................................................................................................................................................................................................................................................................................................................AGC---AG------CA------TCATCA-----------------------GCA---GCA................................................................	19	11	0.09	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
......................................................................CAA----CA------------ACAACA------------------------ACAGCAGCAC..............................................................................................................................................................................................................................................................................................................	21	13	0.08	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
........................................................................A----CA------------ACAACA------------------------ACAGCAGCAC..............................................................................................................................................................................................................................................................................................................	19	14	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	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
........................................................................................................................................................................................................................................CAT------CAGCAGCAAC-------------------------------AGC------------------------AGC---AG------CA------......................................................................................................	23	20	0.05	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.........................................................GCAGCAGCAGCAACAA----CA------------......................................................................................................................................................................................................................................................................................................................................................	18	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	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
........................................................................................................................................................................................................................................CAT------CAGCAGCAAC-------------------------------AGC------------------------AGC---A.....................................................................................................................	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	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
...............................................................GCAGCAACAA----CA------------ACAACA------------------------ACAGCAG.................................................................................................................................................................................................................................................................................................................	25	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
......................................................A--GCAGCAGCAGCAACAA----CA------------ACA...................................................................................................................................................................................................................................................................................................................................................	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	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
...................................................................................................................................................................................................................................................GCAGCAAC-------------------------------AGC------------------------AGC---AG------CA------T.....................................................................................................	19	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
............................................CCA---CAGCA--GCAGCAGCAGCAA...........................................................................................................................................................................................................................................................................................................................................................................	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	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

droMoj3

GCTA-------CAACTATCCAGAGCAGCCA----CACAAGCA----A---CAC--CTG------CAGCAGCAG-CAGCA------------ACAGCA------------------------GCAGCAGCAGCAGC---------A---G---CAGCAACAG------CA--------GCAGCA------------------------GC---------------AAC------------------------------AGCA----------GCAGCAGCAGCAGC------------------------AGCAACAG------CA---------GG------AG--------------CAGCA---GGAG-----------------------------------------C-T--GGATTTTC-AGC--TGT	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
...................................................AC--CTG------CAGCAGCAG-CAGCA------------ACAGC.................................................................................................................................................................................................................................................................................................................................................	24	2	0.50	1	0	0	0	0	1	0
...................................................................................................................................................................................................................................................................................CAGCAGCAGC------------------------AGCAACAG------C.............................................................................................................	19	20	0.20	4	0	2	0	0	2	0
...................................................................................................................................................................................................................................................................................CAGCAGCAGC------------------------AGCAACAG------CA---------GG------AG--------------C..........................................................................	25	14	0.07	1	0	0	0	0	0	1
................................................................................................................................................................................................................C---------------AAC------------------------------AGCA----------GCAGCAGCAGCAGC------------------------AG..........................................................................................................................	24	20	0.05	1	1	0	0	0	0	0
....................................................................................................................................................................................................................................................................A----------GCAGCAGCAGCAGC------------------------AGCAACAG------C.............................................................................................................	24	20	0.05	1	0	0	0	0	1	0
.......................................................CTG------CAGCAGCAG-CAGCA------------AC....................................................................................................................................................................................................................................................................................................................................................	19	20	0.05	1	0	0	0	0	1	0
...................................................................................................................................CAGC---------A---G---CAGCAACAG------CA--------GCAGCA------------------------GC---------------A................................................................................................................................................................................................................	26	20	0.05	1	1	0	0	0	0	0
.....................................................................................................................................GC---------A---G---CAGCAACAG------CA--------GCA.............................................................................................................................................................................................................................................................	18	20	0.05	1	0	0	0	0	1	0
...............................................................................................................................................................................................................GC---------------AAC------------------------------AGCA----------GCAGCAGCAGCAGC------------------------A...........................................................................................................................	24	20	0.05	1	1	0	0	0	0	0
........................................................................G-CAGCA------------ACAGCA------------------------GCAGCAGCAGCAGC---------.................................................................................................................................................................................................................................................................................................	26	20	0.05	1	0	0	0	0	1	0
..................................................................................................................................GCAGC---------A---G---CAGCAACAG------CA--------GCAGCA------------------------..................................................................................................................................................................................................................................	24	20	0.05	1	0	1	0	0	0	0

droGri2

TCCA-------CAGC--------ACTATCA----ACC--------------------------------GCAA----CA---------ACAGCAGCA------------------------GCAGCAACAGCA---------------G---CAGCAACAA------CAACA-----GCAGCA------------------------GC---------------AAC------------------------------AACA----------ACAGCAGCAGCAGC------------------------AGCAACAA------CA---------AA-----------------------AGCC-------------CAAAGGCGGC--GATGATAAGAAT--TTCAAGGAATAT--GCAT---C-GGC--TGG	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
...............................................................................................................................................................................................................................................................................................................................................A-----------------------AGCC-------------CAAAGGCGGC--GATGATAAG....................................	24	1	1.00	1	1	0
.............................................................................................................................................................ACAA------CAACA-----GCAGCA------------------------GC---------------AAC------------------------------AACA----------ACA...............................................................................................................................................................	27	20	0.10	2	2	0
.......................................................................AA----CA---------ACAGCAGCA------------------------GCAGC...................................................................................................................................................................................................................................................................................................................	18	20	0.05	1	1	0
...........................................................................................GCAGCA------------------------GCAGCAACAGCA---------------G---CAGCA....................................................................................................................................................................................................................................................................................	24	20	0.05	1	1	0

-4.6	-4.6	-4.2	-4.2

dan_1392

scaffold_13117:4806101-4806166 -

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