dan_2574

exon [dana_GLEANR_8836:7]; exon [dana_GLEANR_8836:6]; CDS [Dana\GF24084-cds]; CDS [Dana\GF24084-cds]; intron [Dana\GF24084-in]

Name	Class	Family	Strand
TART_DV	LINE	Jockey	-

##################################################---------------------------------------------------------------------------------------------------################################################## ACAGCAGCAGCAGCAGCAGCAACGTCGTCTGCTGCTGGACGTCAATTCGGGTAACAGCAATAGCAACAACAGCAACTGCAACTGCAACTGCAACATCAACAATCACAACCACAACAGCAACACTAACATCAGCAACAGTGACGATATAGCCTGGCAACTCGGCAACTCATGCTACTACTCCACACAATGCTTGTCCAGC ************************************************......((....)).......(((..(((....)))..))).............................((((............)))).........************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M058 embryo	V106 head
....CAGCAGCAGCAGCAGCAACGTCGTCTGC.......................................................................................................................................................................	28	0	1	1.00	1	0	1
......................................................................................................................AACACTAACATCAGCAACAGT............................................................	21	0	1	1.00	1	1	0
......................................................................................................ACACAACCACACCAGCAACA.............................................................................	20	2	16	0.06	1	1	0

TGTCGTCGTCGTCGTCGTCGTTGCAGCAGACGACGACCTGCAGTTAAGCCCATTGTCGTTATCGTTGTTGTCGTTGACGTTGACGTTGACGTTGTAGTTGTTAGTGTTGGTGTTGTCGTTGTGATTGTAGTCGTTGTCACTGCTATATCGGACCGTTGAGCCGTTGAGTACGATGATGAGGTGTGTTACGAACAGGTCG ************************************************......((....)).......(((..(((....)))..))).............................((((............)))).........************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M044 female body	V039 embryo	V105 male body	V055 head
..............................................................CGTTGTTGTCGTTGACGTT......................................................................................................................	19	0	3	0.33	1	1	0	0	0
.............................................AAGCCCAGTGTCGTTATG........................................................................................................................................	18	2	4	0.25	1	0	1	0	0
.......................................GTAGATAAGCCCAGTGTCGT............................................................................................................................................	20	3	6	0.17	1	0	0	1	0
...........................................................................................TTGTAGTTGTGAGTGATG..........................................................................................	18	2	8	0.13	1	0	0	0	1
...........................................................................................CTGTAGTAGTTAGTGTTG..........................................................................................	18	2	18	0.06	1	1	0	0	0
.......................................GTAGATAAGCCCAGTGTCG.............................................................................................................................................	19	3	19	0.05	1	0	0	1	0

Species	Coordinate	ID	Alignment
droAna3	scaffold_13337:11559658-11559856 -	dan_2574	ACAGCAGCAGCAGCA---GCAG-CAACGTCGTC---TGCTGCTGGA---CGTC----A--ATTCGGGTAACA--------------------GC-AA--------------TA---G------------------------CA------ACAA------CAGCAACTGCAA--------------------------CTG------CAAC---TGC------------------AACATCAACAATCACAACCACAACAGCAAC---------ACT-----------AACATCAGCAACAGTGACGA---TAT---------------------------------------AGCCTGGCAACTCGGCA----------------------------------------------------------------------------------ACTCATGCTACTACTCCACACAATG------------------CT-TGTC-CAGC
droBip1	scf7180000396589:2415449-2415635 +		GCAGAACCAGAACCAGCAGCAG-CAACGTCGCC---TGCTGCTGGA---CGTC----A--ATTCGGGTA----------------------------------------AC-AGCCA------TAGCCA------------CA------GCAA------CTGCAA-----------------------------------------------------------------------------CAATCACAACCACAACAGCAAC---------ACT-----------AACATCAGCAAC---------------A---GTGACG--------ATC---TACT----------AGCCTGGCAGCTCGGCA---------------ACC----------------------------------------------------------------ACTCATGCTACTACTCCACACAATG------------------CT-TGTC-CAGC
droKik1	scf7180000302392:163638-163812 +		GCAGCCATGGCGGCA---GCAG-CTGCAGCGGCCTTCAATGC--GG---C----------------GCAACA--------------------GC-AG--------------CA---GCAGCAACAGCATCAGCAG------CA------GCAA--------------------------------------------CAC---------------------------------CAGCAA---TCCCAGCAGCAGCAACAGCAAACCCCAC---AAC-----------AGCAGC---------------------A---GCAATC------GCAG---CAGCA---------------------------------GCA------GCTGC-A---------------------------------------------------------------------ACAGCATGCCCACA------------------GTCT-GGCC-CAGC
droFic1	scf7180000453901:790938-791138 -		GCCGCCGCAGTAGCA---GCAG-CAACGTTTGC------TGCCAGC---CAACAG------CA---A---------------------------CAGC---------A-GC-AACTT------CAGCAC------------CA------GCAA------CAGCAACAACA--------------------------ACAG------CAGC---AGCAG------------------------CAGCAACAACAGCAACAGCATC---------TCC-----------TACAGTACC------------------AGCAG---CAT------CAGC---AACT---------------------------------GCA------TTTGCA----GAA------------------TAGCAGC---A-----------------------GCAACTATGCGGCAACGCTGCTCGATGCTG------------------CCTT-TTGC
droEle1	scf7180000491006:2461947-2462149 -		GCAGCAACCGCAGCA---ACAG-CAACAGCCGG---AGTTGC--AA---CAGCA------------A---------------------------CATC---------A-GC-AATAT------------------CAACAGCA------GCAA------CAGCAACAGAAGC--AGCTACCACAAAAGGAACTGAAGC------------------AGCAACAGCAGCAACTCAATCAT---------CAA------CAGCAAC---------ACC---ATA-----------------------------ACAATCAG---CAA------CAGC---AGCA---------------------------ACAGATGCAACAACAGCAGC-A-----------------------------------------------------------------------------ACACAATT---------------AT-CAG-CAA-CAGC
droRho1	scf7180000779985:553162-553354 -		GCAGCAGCAGCAGCA---GCAG-CAACATCTGC---AGCAGC----------------------------------------------------------------------AGCAAC------------------AGTTGCA------ACTA------CAGCAGCAGCA--------------------------GCAG------------------CAGCAG------------------CAACAGCAGCTGCAACAGCAAC---------ACTATCATAAC---TACAGC---------------------G---G---CA------ATAGCAACAATT------------------------------------------AC----AAAA------TGCATTT-------------------AACTACCACATCGAGCAATTC-------------------------AACGGCATCTAATGCCAACAA-TAA-TAA-CAAC
droBia1	scf7180000301760:4501508-4501697 +		ACAGCAGCAGCAGCA---ACAG-CAACTGCAAC---AGCGGC----------------------------------------------------------------------AGGAC------------------GGGCAGCA------GCAA------CAGCAACAGTTTAGAA--GAGAGCAAAA--GACTTGAGC------------------ATCAACAA------------------CAACAGCAACCACAACAGCATC---------AG-----------------------------------------------CATCAGCAGCAGC---------------------------------------AGCA------AC----AATA------TACATCA-------------------ATACTACACA-CGGCC----------TTAATGTCACAGCG--------TT------------------CC-CTGC-CAGC
droTak1	scf7180000415769:748990-749161 -		ACAGCAGCACCAGCA---GTAG-TAGCAACTTC---ATCGAT--------GGCCA------CCA-----------------------------C-CAC--------------A---ACAACAAAAGC---------------A------GCAG------CAGCAACCA-----------------------------CAC---------------------------------CAGCAA---CAACAACAA---CAACAACCAG---------TCA-----------T--GCCACC-----------GAC----A---GCAGCAA------CAG---CAACAGTAACAACAA--CATGGC--------------CC-----------------------A---------------------------------------------------TCCCATTC----ATC-------------------------CC-TCG-CAG-CAGC
droEug1	scf7180000408176:347039-347226 +		ACAATATCAACGGTG---GCAG-CAGCATCAGT---AGCAGCAACA---CGCT----G--AAT---A-------------------CAACTAGC-AAC---------G-GC-AACAC------------------------CA------GCAACAGCAACAGCAA--------------------------------CAC------CATC---AGC---------------------AG---CAGCAACAACAACAACAGCGAT---------TGC-----------AACTATAGC------------------AACAG---TGT---------------------------GGGCAGACAGAATTGCA---ACTGTA------ATTGCA----ATA---------------------------------------------------------TC---------------TGC-----------------AA-CAA-TAT-CAAC
dm3	chrX:8949691-8949866 -		GAAAGAGGAGCAGCA---GCAG-CAACAGCATCCAGAGTTGC--AG---CAACAG------CA---A---------------------------CAGC---------A-GC-AGCAA------CAGCAA------------CA------GCAA------CAGCAACAGCA--------------------------ACAG------C------AACAGCAACAG------------------------------CAACAGCAAC---------AGC--------------AAC---------------------A---GCAACA------ACAGCAGCAACA---------------------------GCAGCAACA------GCA----------------------------------------------------------------ACTCAAGCAACAACATC------AG------------------CC-CGAC-CAGC
droSim2	2l:7522991-7523177 -	dsi_7724	-CAGCAGCAGCAGCA---ACAG-CAGCAGCAAC---TGTTGC--AA---CAGCAG------CAGG------------------------------AGCAGCAACAATTC--CT---G------------------------CA------GCAA------CAGCAACTGAA--------------------------ACTG------C------AGATCCTGCAG------------------CAACAGCGACTGCAACAGCAGG---------TCC-----------TGCAGC---------------------A---G---CA------GCAGCTGCAACA---------------------------ACAAGTGCA------ACTGCA----ACATCC--------------------TCAGCA--------------------------------------------ACTTC----------------AA-CT-TCCC-CAGC
droSec2	scaffold_0:6865501-6865692 -		ACAGCAACAGCAGCA---GCAAGCAATGACAGTGAGCGGTGC--GA---CGG----------TCGGACAAGT-------------------------------------GC-AACAA------------------------CAGGTGCAGCAA------GTGCAGCAGCA--------------------------GGTCCAGCAGCAACAGCAGCAG---------------------------------CAGCAACAACAAC---------AAC-----------AACAGC---------------------T---G---CA------ACATCACCAA------------------------------------AT------CATAG--ACT------CGTCGGG---CAACATTACAACAGCA--------------------------------------------ACAACG------------------AG-TGCTCAAGC
droYak3	3L:9059654-9059874 +		ACATCAACAGCAGCA---GCAG-CAACAGCAACAG--CCAGC--GG------CCGC--------------------------------------CACC---------G-GC-AACAC------------------CAACGGCA------ACAG------CAGCAGCAGCAAC--AACTGCAACAACGGCAACAGCAAC------------------AACGGCAACAACAGCAACGCCGA---------CGG------CAGCAAT---------ACC---ACGGTTCCAGCGCC-----------------CCTGGGCAG---CAG------CAG---CAACA---------------------------GCAGCAGCA------A--------------------------------------------------------------------CCATGCTAATGCTGCAAGTGGTG----------GC---AACAA-TGGC-CAGC
droEre2	scaffold_4784:3526938-3527144 +		TCAGCATCAGCAGCA---ACAT-CACGGCCATC---CGTTGC--ATCCGCATCAT------AC---A---------------------------CACC---------A-GC-AACAG------------------CAACAACA------GCAG------CAGCAGCAGCAGC--AGCC------------------GCCGCAACACC------------ACCAG------------------CAGCAGCAGCAGCAACAGCAGC---------ACG-----------CACAGC---------------------A---G---C---------------AGCA------------------------------------------GCAGC-AGCATC---ATGCCGCCCAG----------------CTGGCCC------------------ACACACTCTCCTCGGCCGC-CGC-----------------TG-CCG-CTG-CAGC
dp5	XR_group6:162609-162783 -		GCATCCACAACAGCA---GCAG-CCCCGTCGCC---TGCTGCTTGA---TGTC----A--ATTCGGGT--------------------------------------------AGTTA------TATCGC------------TG------GAC--------------------------------------------TCAC------------------CAACA---------------------------------------------------CT-----------AACAGCAGCGAC---------------------------------------------------CA--CCTGGC--------------GGTG------CC----CAGA------CACGCCT-------------------TCTCTCTACA-CGAACCGCTCAACCATTCATGCTACTACTCGACACAATG------------------CT-TGAC-CAGC
droPer2	scaffold_4:6640718-6640909 -		ACAACAGCAGCAACA---TCAG-CATCTGAATCTCCAACTGC--ATCCGCAG---------CACT------------------------------TGGGCCTACACCTG--CA---ACAGCAACAGCAA---------------------CTG------CAACTGCAA-----------------------------CAC---------------------------------AATGCA---CAGGCGCAACAGCAGCAGCAGATACAAG---TGC--------------AAC---------------------A---GCAGCA------ACAGCAACAACA---------------------------GCAGCAGCA------GCA-------GC-------------------------------------------------------ACTCTCCCT----------ACAATG------------------CC-AACC-TGGG
droWil2	scf2_1100000002399:894-1078 +		ACAGCAACATCAGCA---GCAG-CAACAACAAC---TGCAGCT--------AC----A--ATTGA------------------------------TGCAACAACAATT--------G------------------------CA------GCCA------CAGCAACAACA--------------------------ACAA------CAGC---AAGAAAAGCCA------------------GAGCAACAACAGCAGGAGCCAC---------AGC-----------AACATC---------------------A---G---CAG------CAGCAACAACA---------------------------ACTGCAGCA------ACTGCA----GCTACA---------------------------------------------------ATTGATGCAAC-----------------------------AA-CAA-TTG-CAGC
droVir3	scaffold_13049:15007310-15007517 -		TCAGCAGCAGTCGCAGGCGGAG-CAACATCCTC---AGCATTGGGA---TTAC----T--ATGCGCGA--CAGCAACCCGCCGCGCCAGCCAAC-AAT---------A-GC-AACAA---CAGTAAC---------------A------GCAG------CGGCAACAA-----------------------------CAA---------------------------------CAGCAG---CAATAACAACAACAGCGGCAAC---------GCC-----------AACGGC---------------------A---G---CA------ACAGTGACAACA---------------------------ACAACAGCA------ACAA----T----------------------------------------------------------ACAAATGTTGCAACA--------------------------CCTT-TGGG-CAGC
droMoj3	scaffold_6654:1115912-1116101 +		GCAGCAGCAGCAGCA---GCAA-CAACAGCAAC---AGGAGC--AA------GCGCCTCCAGCTGCACAACA-------------------------------------GC-AACAAC------------------AACAACA------TCAA------CAACAACAGCA--------------------------GCAG---------------C------------------AACAA---CAACAGCAGCAGCAACAGCAGCAG---C---AAC-----------AACAAC---------------------A---G---CA------GGAGCAACAACA------------------------------------------ACAAC------------------------------------AG--CAACA-----------------AGTCGCGCCACCTCCTCGC----CG------------------CT-CGCC-CAAC
droGri2	scaffold_15074:4570053-4570229 +		GCAGCAGCAGCAGCA---GCGA-CGTCGACGTC---GG------AA---TGGG---------------AACA--------------------GC-TG--------------CA---ACAACAACAGCAACAACAC------CT------GCAA--------------------------------------------CAC---------------------------------CAACAA---CACCAACATCAGCAACACCA---A---CAACACC--------------AGC---------------------A---GCAACA------CCATC---AACA---------------------------------ACA------CTTGC-AACA------TGCCGCC----------------------------------------------TCACTTTA---CACAGCCAAA-----------------AG-CAG-CAG-CAGC

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droAna3

ACAGCAGCAGCAGCA---GCAG-CAACGTCGTC---TGCTGCTGGA---CGTC----A--ATTCGGGTAACA--------------------GC-AA--------------TA---G------------------------CA------ACAA------CAGCAACTGCAA--------------------------CTG------CAAC---TGC------------------AACATCAACAATCACAACCACAACAGCAAC---------ACT-----------AACATCAGCAACAGTGACGA---TAT---------------------------------------AGCCTGGCAACTCGGCA----------------------------------------------------------------------------------ACTCATGCTACTACTCCACACAATG------------------CT-TGTC-CAGC	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
....CAGCAGCAGCA---GCAG-CAACGTCGTC---TGC...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	28	1	1.00	1	0	0	0	0	0	1
.....................................................................................................................................................................................................................................................................AAC---------ACT-----------AACATCAGCAACAGT............................................................................................................................................................................................................	21	1	1.00	1	0	1	0	0	0	0

droBip1

GCAGAACCAGAACCAGCAGCAG-CAACGTCGCC---TGCTGCTGGA---CGTC----A--ATTCGGGTA----------------------------------------AC-AGCCA------TAGCCA------------CA------GCAA------CTGCAA-----------------------------------------------------------------------------CAATCACAACCACAACAGCAAC---------ACT-----------AACATCAGCAAC---------------A---GTGACG--------ATC---TACT----------AGCCTGGCAGCTCGGCA---------------ACC----------------------------------------------------------------ACTCATGCTACTACTCCACACAATG------------------CT-TGTC-CAGC	Size	Hit Count	Total Norm	Total
No Reads

droKik1

GCAGCCATGGCGGCA---GCAG-CTGCAGCGGCCTTCAATGC--GG---C----------------GCAACA--------------------GC-AG--------------CA---GCAGCAACAGCATCAGCAG------CA------GCAA--------------------------------------------CAC---------------------------------CAGCAA---TCCCAGCAGCAGCAACAGCAAACCCCAC---AAC-----------AGCAGC---------------------A---GCAATC------GCAG---CAGCA---------------------------------GCA------GCTGC-A---------------------------------------------------------------------ACAGCATGCCCACA------------------GTCT-GGCC-CAGC	Size	Hit Count	Total Norm	Total
No Reads

droFic1

GCCGCCGCAGTAGCA---GCAG-CAACGTTTGC------TGCCAGC---CAACAG------CA---A---------------------------CAGC---------A-GC-AACTT------CAGCAC------------CA------GCAA------CAGCAACAACA--------------------------ACAG------CAGC---AGCAG------------------------CAGCAACAACAGCAACAGCATC---------TCC-----------TACAGTACC------------------AGCAG---CAT------CAGC---AACT---------------------------------GCA------TTTGCA----GAA------------------TAGCAGC---A-----------------------GCAACTATGCGGCAACGCTGCTCGATGCTG------------------CCTT-TTGC	Size	Hit Count	Total Norm	Total
No Reads

droEle1

GCAGCAACCGCAGCA---ACAG-CAACAGCCGG---AGTTGC--AA---CAGCA------------A---------------------------CATC---------A-GC-AATAT------------------CAACAGCA------GCAA------CAGCAACAGAAGC--AGCTACCACAAAAGGAACTGAAGC------------------AGCAACAGCAGCAACTCAATCAT---------CAA------CAGCAAC---------ACC---ATA-----------------------------ACAATCAG---CAA------CAGC---AGCA---------------------------ACAGATGCAACAACAGCAGC-A-----------------------------------------------------------------------------ACACAATT---------------AT-CAG-CAA-CAGC	Size	Hit Count	Total Norm	Total
No Reads

droRho1

GCAGCAGCAGCAGCA---GCAG-CAACATCTGC---AGCAGC----------------------------------------------------------------------AGCAAC------------------AGTTGCA------ACTA------CAGCAGCAGCA--------------------------GCAG------------------CAGCAG------------------CAACAGCAGCTGCAACAGCAAC---------ACTATCATAAC---TACAGC---------------------G---G---CA------ATAGCAACAATT------------------------------------------AC----AAAA------TGCATTT-------------------AACTACCACATCGAGCAATTC-------------------------AACGGCATCTAATGCCAACAA-TAA-TAA-CAAC	Size	Hit Count	Total Norm	Total
No Reads

droBia1

ACAGCAGCAGCAGCA---ACAG-CAACTGCAAC---AGCGGC----------------------------------------------------------------------AGGAC------------------GGGCAGCA------GCAA------CAGCAACAGTTTAGAA--GAGAGCAAAA--GACTTGAGC------------------ATCAACAA------------------CAACAGCAACCACAACAGCATC---------AG-----------------------------------------------CATCAGCAGCAGC---------------------------------------AGCA------AC----AATA------TACATCA-------------------ATACTACACA-CGGCC----------TTAATGTCACAGCG--------TT------------------CC-CTGC-CAGC	Size	Hit Count	Total Norm	Total
No Reads

droTak1

ACAGCAGCACCAGCA---GTAG-TAGCAACTTC---ATCGAT--------GGCCA------CCA-----------------------------C-CAC--------------A---ACAACAAAAGC---------------A------GCAG------CAGCAACCA-----------------------------CAC---------------------------------CAGCAA---CAACAACAA---CAACAACCAG---------TCA-----------T--GCCACC-----------GAC----A---GCAGCAA------CAG---CAACAGTAACAACAA--CATGGC--------------CC-----------------------A---------------------------------------------------TCCCATTC----ATC-------------------------CC-TCG-CAG-CAGC	Size	Hit Count	Total Norm	Total
No Reads

droEug1

ACAATATCAACGGTG---GCAG-CAGCATCAGT---AGCAGCAACA---CGCT----G--AAT---A-------------------CAACTAGC-AAC---------G-GC-AACAC------------------------CA------GCAACAGCAACAGCAA--------------------------------CAC------CATC---AGC---------------------AG---CAGCAACAACAACAACAGCGAT---------TGC-----------AACTATAGC------------------AACAG---TGT---------------------------GGGCAGACAGAATTGCA---ACTGTA------ATTGCA----ATA---------------------------------------------------------TC---------------TGC-----------------AA-CAA-TAT-CAAC	Size	Hit Count	Total Norm	Total
No Reads

dm3

GAAAGAGGAGCAGCA---GCAG-CAACAGCATCCAGAGTTGC--AG---CAACAG------CA---A---------------------------CAGC---------A-GC-AGCAA------CAGCAA------------CA------GCAA------CAGCAACAGCA--------------------------ACAG------C------AACAGCAACAG------------------------------CAACAGCAAC---------AGC--------------AAC---------------------A---GCAACA------ACAGCAGCAACA---------------------------GCAGCAACA------GCA----------------------------------------------------------------ACTCAAGCAACAACATC------AG------------------CC-CGAC-CAGC	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
............................................................................................................................................................................................................................................................................................................................................AGCAGCAACA---------------------------GCAGCAACA------GCA----------------------------------------------------------------ACT....................................................	25	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
.....................G-CAACAGCATCCAGAGTT..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................................................................................................ACA---------------------------GCAGCAACA------GCA----------------------------------------------------------------ACTCAAGCAACAAC.........................................	29	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
.AAAGAGGAGCAGCA---GCAG-CAA................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
.........................ACAGCATCCAGAGTTGC--AG---CA.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
...................................................................................................................................................................................................................................................................................................................................................ACA---------------------------GCAGCAACA------GCA----------------------------------------------------------------ACTCAAGCAACAACA........................................	30	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
...................CAG-CAACAGCATCCAGAGTTG.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
.................................................CAACAG------CA---A---------------------------CAGC---------A-GC-AGCAA------CAGCAA------------.............................................................................................................................................................................................................................................................................................................................................................................	27	4	0.25	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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
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droSim2

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..................................................................................................................................................................CAACTGAA--------------------------ACTG------C------AGATCCT..............................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
...........AGCA---ACAG-CAGCAGCAAC---TG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	8	0.13	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.............CA---ACAG-CAGCAGCAAC---TG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	19	0.11	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

droSec2

ACAGCAACAGCAGCA---GCAAGCAATGACAGTGAGCGGTGC--GA---CGG----------TCGGACAAGT-------------------------------------GC-AACAA------------------------CAGGTGCAGCAA------GTGCAGCAGCA--------------------------GGTCCAGCAGCAACAGCAGCAG---------------------------------CAGCAACAACAAC---------AAC-----------AACAGC---------------------T---G---CA------ACATCACCAA------------------------------------AT------CATAG--ACT------CGTCGGG---CAACATTACAACAGCA--------------------------------------------ACAACG------------------AG-TGCTCAAGC	Size	Hit Count	Total Norm	Total	M054 Female-body	V113 Male-body	V114 Embryo	V115 Head
..............................AGTGAGCGGTGC--GA---CGG----------TC..........................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	1	1	0	0	0
...........AGCA---GCAAGCAATGACAGTGAGCGGTG.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	27	1	1.00	1	0	1	0	0
......................................GTGC--GA---CGG----------TCGGACAAGT-------------------------------------GC-..........................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	1	0
...............................................................................................................................................................................................................................................................................................................................................ACCAA------------------------------------AT------CATAG--ACT------CGTCGGG---C...............................................................................................	23	1	1.00	1	0	0	1	0

droYak3

ACATCAACAGCAGCA---GCAG-CAACAGCAACAG--CCAGC--GG------CCGC--------------------------------------CACC---------G-GC-AACAC------------------CAACGGCA------ACAG------CAGCAGCAGCAAC--AACTGCAACAACGGCAACAGCAAC------------------AACGGCAACAACAGCAACGCCGA---------CGG------CAGCAAT---------ACC---ACGGTTCCAGCGCC-----------------CCTGGGCAG---CAG------CAG---CAACA---------------------------GCAGCAGCA------A--------------------------------------------------------------------CCATGCTAATGCTGCAAGTGGTG----------GC---AACAA-TGGC-CAGC	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
.......................................................................................................................................................................GCAAC--AACTGCAACAACGGCAAC..........................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0
.................................................................................................................................................................................................................................................................................................................................................CAACA---------------------------GCAGCAGCA------A--------------------------------------------------------------------CCATGCTAATGCT........................................	28	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0
.........................................................................................................................................................................................................................ACGGCAACAACAGCAACGCCGA---------CG................................................................................................................................................................................................................................................................	24	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................................................................................AG------CAG---CAACA---------------------------GCAGCAGCA------A--------------------------------------------------------------------CC...................................................	22	9	0.11	1	0	1	0	0	0	0	0	0	0	0	0
.............................................................................................................................................................................................................................................................................................................................AG---CAG------CAG---CAACA---------------------------GCAGCAGC.................................................................................................................................	21	20	0.10	2	2	0	0	0	0	0	0	0	0	0	0
............................................................................................................................................................................................................................................................................................................................................AG---CAACA---------------------------GCAGCAGCA------A--------------------------------------------------------------------CC...................................................	19	11	0.09	1	0	0	0	0	0	1	0	0	0	0	0
..ATCAACAGCAGCA---GCAG-CAA................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	14	0.07	1	0	1	0	0	0	0	0	0	0	0	0
..............................................................................................................................................................................................................................................................................................................................G---CAG------CAG---CAACA---------------------------GCAGCAGCA------A--------------------------------------------------------------------C....................................................	23	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0
...........................................................................................................................................................................................................................................................................................................................GCAG---CAG------CAG---CAACA---------------------------GCAGC....................................................................................................................................	20	20	0.05	1	0	1	0	0	0	0	0	0	0	0	0

droEre2

TCAGCATCAGCAGCA---ACAT-CACGGCCATC---CGTTGC--ATCCGCATCAT------AC---A---------------------------CACC---------A-GC-AACAG------------------CAACAACA------GCAG------CAGCAGCAGCAGC--AGCC------------------GCCGCAACACC------------ACCAG------------------CAGCAGCAGCAGCAACAGCAGC---------ACG-----------CACAGC---------------------A---G---C---------------AGCA------------------------------------------GCAGC-AGCATC---ATGCCGCCCAG----------------CTGGCCC------------------ACACACTCTCCTCGGCCGC-CGC-----------------TG-CCG-CTG-CAGC	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
..............A---ACAT-CACGGCCATC---CGTTGC--ATCCG.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................	26	1	1.00	1	1	0	0	0	0	0	0
............................................................................................................................................................................................................................................................AGCAACAGCAGC---------ACG-----------CACAGC---------------------A---G---C---------------AGC.....................................................................................................................................................................	27	1	1.00	1	1	0	0	0	0	0	0
.............................................................................................................................................................................................................................................................GCAACAGCAGC---------ACG-----------CACAG......................................................................................................................................................................................................................	19	1	1.00	1	0	0	0	0	0	1	0
.......................CACGGCCATC---CGTTGC--ATCCGCATC.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................	25	1	1.00	1	1	0	0	0	0	0	0
...................................................................................................................................................................................................................................................................GCAGC---------ACG-----------CACAGC---------------------A---G---C---------------AGCA------------------------------------------GCA.......................................................................................................................	24	1	1.00	1	0	0	0	0	1	0	0
....................................................................................................................................................................................................................................................................................................................................................................................................................................................................CACACTCTCCTCGGCCGC-CGC-----------------T..............	22	1	1.00	1	0	0	1	0	0	0	0
.....ATCAGCAGCA---ACAT-CACGGCC............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	1	0
..................ACAT-CACGGCCATC---CGTTGC--..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1	1	0	0	0	0	0	0
...............................................................................................................................................................................................................................................................AACAGCAGC---------ACG-----------CACAGC---------------------A---G---C---------------AGCA------------------------------------------GC........................................................................................................................	27	1	1.00	1	0	0	0	0	1	0	0
......................................................................................................................................................................................................CGCAACACC------------ACCAG------------------CAGCAGC.................................................................................................................................................................................................................................................................	21	2	0.50	1	1	0	0	0	0	0	0
...........................................................................................................................................AACA------GCAG------CAGCAGCAGCA................................................................................................................................................................................................................................................................................................................................................	19	20	0.15	3	0	0	0	0	0	3	0
.............................................................................................................GC-AACAG------------------CAACAACA------GCAG------C..........................................................................................................................................................................................................................................................................................................................................................	20	20	0.10	2	1	1	0	0	0	0	0
.......................................................................................................................................CAACAACA------GCAG------CAGCAGCA...................................................................................................................................................................................................................................................................................................................................................	20	20	0.10	2	0	0	0	0	0	2	0
..............................................................................................................................................................................................................C------------ACCAG------------------CAGCAGCAGCAGCAACAGCA....................................................................................................................................................................................................................................................	26	13	0.08	1	1	0	0	0	0	0	0
.......................................................................................................................................................................................................................................................GCAGCAGCAACAGCAGC---------AC.......................................................................................................................................................................................................................................	19	19	0.05	1	1	0	0	0	0	0	0
...................................................................................................................AG------------------CAACAACA------GCAG------CAGCA......................................................................................................................................................................................................................................................................................................................................................	19	20	0.05	1	1	0	0	0	0	0	0
..............................................................................................................................................................................................................................AG------------------CAGCAGCAGCAGCAACAGCAGC---------.........................................................................................................................................................................................................................................	24	20	0.05	1	0	1	0	0	0	0	0
.............................................................................................................................................................................................................CC------------ACCAG------------------CAGCAGCAGCAGCA..........................................................................................................................................................................................................................................................	21	20	0.05	1	0	0	0	0	0	1	0
................................................................................................................AACAG------------------CAACAACA------GCAG------CAGCA......................................................................................................................................................................................................................................................................................................................................................	22	20	0.05	1	0	0	0	0	0	1	0
.............................................................................................................................................................................................................CC------------ACCAG------------------CAGCAGCAGCAGC...........................................................................................................................................................................................................................................................	20	20	0.05	1	0	0	0	1	0	0	0
....................................................................................................................................................................................................................................................GCAGCAGCAGCAACAGCA....................................................................................................................................................................................................................................................	18	20	0.05	1	1	0	0	0	0	0	0
........................................................................................................................................AACAACA------GCAG------CAGCAGCA...................................................................................................................................................................................................................................................................................................................................................	19	20	0.05	1	0	0	0	0	1	0	0
................................................................................................................AACAG------------------CAACAACA------GCAG------CAGC.......................................................................................................................................................................................................................................................................................................................................................	21	20	0.05	1	0	0	1	0	0	0	0
.........................................................................................................................................ACAACA------GCAG------CAGCAGCAGC.................................................................................................................................................................................................................................................................................................................................................	20	20	0.05	1	0	0	0	1	0	0	0
......................................................................................................................................................................................................................................................AGCAGCAGCAACAGCAGC---------A........................................................................................................................................................................................................................................	19	20	0.05	1	0	0	0	1	0	0	0
...............................................................................................................................................................................................................................................................................................CACAGC---------------------A---G---C---------------AGCA------------------------------------------GCAGC-AGC.................................................................................................................	21	20	0.05	1	0	0	0	0	0	1	0
........................................................................................................................................AACAACA------GCAG------CAGCAGCAGCAG...............................................................................................................................................................................................................................................................................................................................................	23	20	0.05	1	0	1	0	0	0	0	0
...........................................................................................................A-GC-AACAG------------------CAACAACA------GCAG------...........................................................................................................................................................................................................................................................................................................................................................	20	20	0.05	1	1	0	0	0	0	0	0
...................................................................................................................AG------------------CAACAACA------GCAG------CAGCAGCAGCA................................................................................................................................................................................................................................................................................................................................................	25	20	0.05	1	0	0	0	0	0	1	0
....................................................................................................................G------------------CAACAACA------GCAG------CAGCAGCA...................................................................................................................................................................................................................................................................................................................................................	21	20	0.05	1	0	0	0	0	1	0	0
...........................................................................................................................................................................................................CACC------------ACCAG------------------CAGCAGCAGC..............................................................................................................................................................................................................................................................	19	20	0.05	1	1	0	0	0	0	0	0

dp5

GCATCCACAACAGCA---GCAG-CCCCGTCGCC---TGCTGCTTGA---TGTC----A--ATTCGGGT--------------------------------------------AGTTA------TATCGC------------TG------GAC--------------------------------------------TCAC------------------CAACA---------------------------------------------------CT-----------AACAGCAGCGAC---------------------------------------------------CA--CCTGGC--------------GGTG------CC----CAGA------CACGCCT-------------------TCTCTCTACA-CGAACCGCTCAACCATTCATGCTACTACTCGACACAATG------------------CT-TGAC-CAGC	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
........AACAGCA---GCAG-CCCCGTCGCC---......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	1	0	0	0
..........................................TTGA---TGTC----A--ATTCGGGT--------------------------------------------AGTTA------T..............................................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0	0	0	0	0
..............................................................................................................................................G------GAC--------------------------------------------TCAC------------------CAACA---------------------------------------------------CT-----------AACAGC.....................................................................................................................................................................................................................	21	1	1.00	1	0	1	0	0	0	0	0	0	0	0
...........................................................................................................................TATCGC------------TG------GAC--------------------------------------------TCAC------------------CAACA---------------------------------------------------C.......................................................................................................................................................................................................................................	21	1	1.00	1	0	1	0	0	0	0	0	0	0	0

droPer2

ACAACAGCAGCAACA---TCAG-CATCTGAATCTCCAACTGC--ATCCGCAG---------CACT------------------------------TGGGCCTACACCTG--CA---ACAGCAACAGCAA---------------------CTG------CAACTGCAA-----------------------------CAC---------------------------------AATGCA---CAGGCGCAACAGCAGCAGCAGATACAAG---TGC--------------AAC---------------------A---GCAGCA------ACAGCAACAACA---------------------------GCAGCAGCA------GCA-------GC-------------------------------------------------------ACTCTCCCT----------ACAATG------------------CC-AACC-TGGG	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
No Reads

droWil2

ACAGCAACATCAGCA---GCAG-CAACAACAAC---TGCAGCT--------AC----A--ATTGA------------------------------TGCAACAACAATT--------G------------------------CA------GCCA------CAGCAACAACA--------------------------ACAA------CAGC---AAGAAAAGCCA------------------GAGCAACAACAGCAGGAGCCAC---------AGC-----------AACATC---------------------A---G---CAG------CAGCAACAACA---------------------------ACTGCAGCA------ACTGCA----GCTACA---------------------------------------------------ATTGATGCAAC-----------------------------AA-CAA-TTG-CAGC	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
...........................................................................................................................................................................................................................AGCCA------------------GAGCAACAACAGCAGG........................................................................................................................................................................................................................................................	21	13	10.08	131	0	56	1	74	0
...........................................................................................................................................................................................................................AGCCA------------------GAGCAACAACAGCAGGA.......................................................................................................................................................................................................................................................	22	13	4.77	62	0	55	0	7	0
.........................................................A--ATTGA------------------------------TGCAACAACAATT--------G------------------------CA------GC...................................................................................................................................................................................................................................................................................................................................................................	24	13	2.69	35	0	35	0	0	0
...............................................................................................................................................................................................................................................................................................................................................................................................................A---------------------------------------------------ATTGATGCAAC-----------------------------AA-CAA-TTG-CAGC	24	13	2.69	35	0	35	0	0	0
...........................................................................................................................................................................................................................AGCCA------------------GAGCAACAACAGCAGGAG......................................................................................................................................................................................................................................................	23	13	2.31	30	0	27	2	1	0
...........................................................................................................................................................................................................................AGCCA------------------GAGCAACAACAGCAG.........................................................................................................................................................................................................................................................	20	13	1.62	21	0	10	0	11	0
...........................................................................................................................................................................................................................AGCCA------------------GAGCAACAACAGCAGGAGC.....................................................................................................................................................................................................................................................	24	13	1.15	15	0	7	0	7	1
...........................................................................................................................................................................................................................AGCCA------------------GAGCAACAACAGCAGGAGCCA...................................................................................................................................................................................................................................................	26	13	1.00	13	0	12	0	1	0
.......................CAACAACAAC---TGCAGCT--------AC----A--ATTGA------------------------------...........................................................................................................................................................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	1	0	0	0
...........................................................................................................................................................................................................................AGCCA------------------GAGCAACAACAGCAGGAGCC....................................................................................................................................................................................................................................................	25	13	0.69	9	0	8	0	1	0
.........................................................A--ATTGA------------------------------TGCAACAACAATT--------G------------------------CA------GCC..................................................................................................................................................................................................................................................................................................................................................................	25	13	0.69	9	0	9	0	0	0
...............................................................................................................................................................................................................................................................................................................................................................................................................A---------------------------------------------------ATTGATGCAAC-----------------------------AA-CAA-TTG-CAG.	23	13	0.54	7	0	7	0	0	0
.........................................................A--ATTGA------------------------------TGCAACAACAATT--------G------------------------CA------GCCA------...........................................................................................................................................................................................................................................................................................................................................................	26	13	0.54	7	0	7	0	0	0
...........................................................................................................................................................................................................................AGCCA------------------GAGCAACAACAGCAGGAGCCAC---------.........................................................................................................................................................................................................................................	27	13	0.54	7	0	7	0	0	0
..............................................................................................................................................................................................................................CA------------------GAGCAACAACAGCAGGAGC.....................................................................................................................................................................................................................................................	21	13	0.54	7	0	4	0	3	0
.........................................................A--ATTGA------------------------------TGCAACAACAATT--------G------------------------CA------G....................................................................................................................................................................................................................................................................................................................................................................	23	13	0.54	7	0	7	0	0	0
..............................................................................................................................................................................................................................CA------------------GAGCAACAACAGCAGGAGCCA...................................................................................................................................................................................................................................................	23	13	0.46	6	0	6	0	0	0
...................................................................................................................................................................................................................................................AGCAACAACAGCAGGAGCCAC---------AG.......................................................................................................................................................................................................................................	23	13	0.38	5	0	5	0	0	0
............................................................ATTGA------------------------------TGCAACAACAATT--------G------------------------CA------GC...................................................................................................................................................................................................................................................................................................................................................................	23	13	0.38	5	0	5	0	0	0
...................................................................................................................................................................................................................................................................................................................................................................................................................................................................ATTGATGCAAC-----------------------------AA-CAA-TTG-CAGC	23	13	0.38	5	0	5	0	0	0
...........................................................................................................................................................................................................................AGCCA------------------GAGCAACAACAGCA..........................................................................................................................................................................................................................................................	19	14	0.36	5	0	1	0	3	1
............................................................................................................................................................................................................................GCCA------------------GAGCAACAACAGCAGGAGCCA...................................................................................................................................................................................................................................................	25	13	0.31	4	0	4	0	0	0
...........................................................................................................................................................................................................................AGCCA------------------GAGCAACAACAGC...........................................................................................................................................................................................................................................................	18	14	0.29	4	0	1	0	3	0
..............................................................................................................................................................................................................................CA------------------GAGCAACAACAGCAGGAGCC....................................................................................................................................................................................................................................................	22	13	0.23	3	0	2	0	1	0
............................................................ATTGA------------------------------TGCAACAACAATT--------G------------------------CA------GCCA------...........................................................................................................................................................................................................................................................................................................................................................	25	13	0.23	3	0	3	0	0	0
...................................................................................................................................................................................................................................................................................................................................................................................................................................................................ATTGATGCAAC-----------------------------AA-CAA-TTG-CAG.	22	13	0.23	3	0	3	0	0	0
.........................................................................................................................................................................................................................................................AACAGCAGGAGCCAC---------AGC-----------AACATC---------------------................................................................................................................................................................................................	24	13	0.23	3	0	3	0	0	0
.........................................................A--ATTGA------------------------------TGCAACAACAATT--------G------------------------CA------.....................................................................................................................................................................................................................................................................................................................................................................	22	13	0.23	3	0	3	0	0	0
............................................................ATTGA------------------------------TGCAACAACAATT--------G------------------------CA------G....................................................................................................................................................................................................................................................................................................................................................................	22	13	0.23	3	0	3	0	0	0
...............................................................................................................................................................................................................................................................................................................................................................................................................A---------------------------------------------------ATTGATGCAAC-----------------------------AA-CAA-TTG-CA..	22	13	0.23	3	0	3	0	0	0
........ATCAGCA---GCAG-CAACAACAAC---TG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	23	6	0.17	1	0	1	0	0	0
..................................................................................................................................................................................................................................................................AGCCAC---------AGC-----------AACATC---------------------A---G---CAG------CAGCAAC........................................................................................................................................................................	27	12	0.17	2	0	1	0	1	0
..................................................................................................................................................................................................................................................................................................ATC---------------------A---G---CAG------CAGCAACAACA---------------------------ACTG.....................................................................................................................................	23	6	0.17	1	0	1	0	0	0
...................................................................................................................................................................................................................................................AGCAACAACAGCAGGAGCCAC---------A........................................................................................................................................................................................................................................	22	13	0.15	2	0	2	0	0	0
..............................................................TGA------------------------------TGCAACAACAATT--------G------------------------CA------GC...................................................................................................................................................................................................................................................................................................................................................................	21	13	0.15	2	0	2	0	0	0
.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................TGATGCAAC-----------------------------AA-CAA-TTG-CAGC	21	13	0.15	2	0	2	0	0	0
............................................................................................................................................................................................................................GCCA------------------GAGCAACAACAGCAGGAG......................................................................................................................................................................................................................................................	22	13	0.15	2	0	2	0	0	0
........................................................................................................................................................................................................................AAAAGCCA------------------GAGCAACAACAGCAG.........................................................................................................................................................................................................................................................	23	13	0.15	2	0	2	0	0	0
............................................................................................................................................................................................................................GCCA------------------GAGCAACAACAGCAGG........................................................................................................................................................................................................................................................	20	13	0.15	2	0	2	0	0	0
........................................................................................................................................................................................................................AAAAGCCA------------------GAGCAACAACAGCA..........................................................................................................................................................................................................................................................	22	13	0.15	2	0	1	0	1	0
.........................................................................................................................................................................................................................................................AACAGCAGGAGCCAC---------AGC-----------AACA.......................................................................................................................................................................................................................	22	13	0.15	2	0	2	0	0	0
.....................................................................................................................................................................................................................................................CAACAACAGCAGGAGCCAC---------AG.......................................................................................................................................................................................................................................	21	13	0.15	2	0	0	0	2	0
..................................................................................................................................................................CAACAACA--------------------------ACAA------CAGC---AAGAAA...............................................................................................................................................................................................................................................................................................	22	20	0.10	2	0	0	0	2	0
.......................................................................................................................................................CA------CAGCAACAACA--------------------------ACAA------CAGC---AAGAA................................................................................................................................................................................................................................................................................................	26	12	0.08	1	0	1	0	0	0
..........................................................................................................................................................................................................................................................................................................................................................................................................GCTACA---------------------------------------------------ATTGATGCAAC-----------------------------AA-CAA-TTG-....	25	12	0.08	1	0	0	0	1	0
.......................................................................................................................................................CA------CAGCAACAACA--------------------------ACAA------CAGC---AAG..................................................................................................................................................................................................................................................................................................	24	12	0.08	1	0	1	0	0	0
........................................GCT--------AC----A--ATTGA------------------------------TGCAACAACAATT--------G------------------------.............................................................................................................................................................................................................................................................................................................................................................................	25	12	0.08	1	0	0	0	1	0
................................................................................................................................................................AGCAACAACA--------------------------ACAA------CAGC---AAGAAA...............................................................................................................................................................................................................................................................................................	24	12	0.08	1	0	0	0	1	0
..................................................................................................................................................................CAACAACA--------------------------ACAA------CAGC---AAGAAAAGCC...........................................................................................................................................................................................................................................................................................	26	12	0.08	1	0	0	0	1	0
.........................................................................................................................................................................................................................................................AACAGCAGGAGCCAC---------AGC-----------AA.........................................................................................................................................................................................................................	20	13	0.08	1	0	0	0	0	1
.......................................................................................................................................................................................................A------CAGC---AAGAAAAGCCA------------------GAGCAACAAC..............................................................................................................................................................................................................................................................	26	13	0.08	1	0	1	0	0	0
...................................................................................................................................................................................................................................................AGCAACAACAGCAGGAGCCA...................................................................................................................................................................................................................................................	20	13	0.08	1	0	1	0	0	0
..............................................................................................................................................................................................................................CA------------------GAGCAACAACAGCAGGA.......................................................................................................................................................................................................................................................	19	13	0.08	1	0	1	0	0	0
...............................................................................................................................................................................................................................A------------------GAGCAACAACAGCAGGAGCCAC---------.........................................................................................................................................................................................................................................	23	13	0.08	1	0	1	0	0	0
...............................................................................................................................................................................................................................................................................................................................................................................................................A---------------------------------------------------ATTGATGCAAC-----------------------------AA-CAA-TTG-C...	21	13	0.08	1	0	1	0	0	0
.........................................................................................................................................................................................................................AAAGCCA------------------GAGCAACAACAGCA..........................................................................................................................................................................................................................................................	21	13	0.08	1	0	0	0	1	0
............................................................ATTGA------------------------------TGCAACAACAATT--------G------------------------CA------GCC..................................................................................................................................................................................................................................................................................................................................................................	24	13	0.08	1	0	1	0	0	0
......................................................................................................................................................................................................................................................AACAACAGCAGGAGCCAC---------AGC-----------AAC........................................................................................................................................................................................................................	24	13	0.08	1	0	1	0	0	0
..............................................................................................................................................................................................................................CA------------------GAGCAACAACAGCAGGAGCCAC---------A........................................................................................................................................................................................................................................	25	13	0.08	1	0	1	0	0	0
...................................................................................................................................................................................................................................................AGCAACAACAGCAGGAGCCAC---------AGC-----------A..........................................................................................................................................................................................................................	25	13	0.08	1	0	1	0	0	0
...................................................................................................................................................................................................................................................AGCAACAACAGCAGGAGCCAC---------AGC-----------AACA.......................................................................................................................................................................................................................	28	13	0.08	1	0	1	0	0	0
...................................................................................................................................................................................................................................................AGCAACAACAGCAGGAGCCAC---------AGC-----------...........................................................................................................................................................................................................................	24	13	0.08	1	0	0	0	1	0
...............................................................GA------------------------------TGCAACAACAATT--------G------------------------CA------GC...................................................................................................................................................................................................................................................................................................................................................................	20	13	0.08	1	0	1	0	0	0
...........................................................................................................................................................................................................................AGCCA------------------GAGCAACAACAGCAGGAGT.....................................................................................................................................................................................................................................................	24	13	0.08	1	0	0	1	0	0
.........................................................A--ATTGA------------------------------TGCAACAACAATT--------G------------------------C............................................................................................................................................................................................................................................................................................................................................................................	21	13	0.08	1	0	1	0	0	0
............................................................ATTGA------------------------------TGCAACAACAATT--------G------------------------.............................................................................................................................................................................................................................................................................................................................................................................	19	13	0.08	1	0	1	0	0	0
............................................................................................................................................................................................................................GCCA------------------GAGCAACAACAGCAG.........................................................................................................................................................................................................................................................	19	13	0.08	1	0	1	0	0	0
.........................................................A--ATTGA------------------------------TGCAACAACAATT--------G------------------------CA------GCA..................................................................................................................................................................................................................................................................................................................................................................	25	13	0.08	1	0	1	0	0	0
..............................................................................................................................................................................................................................CA------------------GAGCAACAACAGCAGGAGCCAC---------AG.......................................................................................................................................................................................................................................	26	13	0.08	1	0	0	0	1	0
...................................................................................................................................................................................................................................................................................................................................................................................................................................................................ATTGATGCAAC-----------------------------AA-CAA-TTG-....	19	13	0.08	1	0	1	0	0	0
.........................................................A--ATTGA------------------------------TGCAACAACAATT--------G------------------------CA------GCCA------CA.........................................................................................................................................................................................................................................................................................................................................................	28	13	0.08	1	0	1	0	0	0
......................................................................................................................................................................................................................AGAAAAGCCA------------------GAGCAACAACAGCA..........................................................................................................................................................................................................................................................	24	13	0.08	1	0	0	0	0	1
.....................................................................................................................................................................................................................................................CAACAACAGCAGGAGCCAC---------AGC-----------AA.........................................................................................................................................................................................................................	24	13	0.08	1	0	0	0	1	0
............................................................................................................................................................................................................................GCCA------------------GAGCAACAACAGCAGGAGCCAC---------.........................................................................................................................................................................................................................................	26	13	0.08	1	0	1	0	0	0
.........................................................................................................................................................................................................................AAAGCCA------------------GAGCAACAACAGCAGGAGC.....................................................................................................................................................................................................................................................	26	13	0.08	1	0	0	0	1	0
..............................................................................................................................................................................................................................CA------------------GAGCAACAACAGCAGGAGCCAC---------AGC-----------...........................................................................................................................................................................................................................	27	13	0.08	1	0	0	0	1	0
...................................................................................................................................................................................................................................................AGCAACAACAGCAGGAGCCAC---------AGC-----------AAC........................................................................................................................................................................................................................	27	13	0.08	1	0	1	0	0	0
..............................................................................................................................................................................................................................CA------------------GAGCAACAACAGCAGGAGCCG...................................................................................................................................................................................................................................................	23	13	0.08	1	0	1	0	0	0
...........................................................................................................................................................................................................................AGCCA------------------GAGCAACAACAGCAGGAGCCAC---------A........................................................................................................................................................................................................................................	28	13	0.08	1	0	1	0	0	0
........................................................................................................................................................................................................................AAAAGCCA------------------GAGCAACAACAGCAGGAGC.....................................................................................................................................................................................................................................................	27	13	0.08	1	0	1	0	0	0
........................................................................................................................................................................................................................AAAAGCCA------------------GAGCAACAACAGCAGG........................................................................................................................................................................................................................................................	24	13	0.08	1	0	1	0	0	0
.........................................................................................................................................................................................................................AAAGCCA------------------GAGCAACAACAGCAGGA.......................................................................................................................................................................................................................................................	24	13	0.08	1	0	1	0	0	0
............................................................................................................................................................................................................................GCCA------------------GAGCAACAACAGCAGGA.......................................................................................................................................................................................................................................................	21	13	0.08	1	0	1	0	0	0
............................................................ATTGA------------------------------TGCAACAACAATT--------G------------------------CA------GCCA------T..........................................................................................................................................................................................................................................................................................................................................................	26	13	0.08	1	0	1	0	0	0
..............................................................................................................................................................................................................................CA------------------GAGCAACAACAGCAGGAG......................................................................................................................................................................................................................................................	20	13	0.08	1	0	1	0	0	0
......................................................................................................................................................................................................................................................AACAACAGCAGGAGCCAC---------AGT-----------...........................................................................................................................................................................................................................	21	13	0.08	1	0	1	0	0	0
......................................................................................................................................................................................................................................................................................................................................................................................................................................................................GATGCAAC-----------------------------AA-CAA-TTG-CAGC	20	13	0.08	1	0	1	0	0	0
..................................................................................................................................................................................................................................................GAGCAACAACAGCAGGAG......................................................................................................................................................................................................................................................	18	13	0.08	1	0	1	0	0	0
.....................................................................................................................................................................................................................................................CAACAACAGCAGGAGCCAC---------AGC-----------A..........................................................................................................................................................................................................................	23	13	0.08	1	0	1	0	0	0
...............................................................................................................................................................................................................................................................AGGAGCCAC---------AGC-----------AACATC---------------------A---G---CA......................................................................................................................................................................................	22	14	0.07	1	0	0	0	1	0
...............................................................................................................................................................................................................................A------------------GAGCAACAACAGCAGGA.......................................................................................................................................................................................................................................................	18	14	0.07	1	0	1	0	0	0
...............................................................................................................................................................................................................................................................AGGAGCCAC---------AGC-----------AACATC---------------------A---G---........................................................................................................................................................................................	20	14	0.07	1	0	1	0	0	0
..............................................................................................................................................A------GCCA------CAGCAACAACA--------------------------ACAA------CA..........................................................................................................................................................................................................................................................................................................	22	15	0.07	1	0	1	0	0	0
......................................................................................................................................................CCA------CAGCAACAACA--------------------------ACAA------CAGC---.....................................................................................................................................................................................................................................................................................................	22	16	0.06	1	0	0	0	1	0
...........................................................................................................................................................................................................................AGCCA------------------GAGCAACAACAGCAGC........................................................................................................................................................................................................................................................	21	17	0.06	1	0	0	0	1	0
...............................................................................................................................................................................................................................................................................................AACATC---------------------A---G---CAG------CAGCAACAACA---------------------------AC.......................................................................................................................................	24	19	0.05	1	0	1	0	0	0
.....AACATCAGCA---GCAG-CAACAACAAC---......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	24	19	0.05	1	0	1	0	0	0
.......................................................................................................................................................................................................................................................................C---------AGC-----------AACATC---------------------A---G---CAG------CAGC...........................................................................................................................................................................	19	20	0.05	1	0	0	0	1	0
....................................................................................................................................................................................................................................................................................................C---------------------A---G---CAG------CAGCAACAACA---------------------------ACT......................................................................................................................................	20	20	0.05	1	0	0	1	0	0
.CAGCAACATCAGCA---GCAG-C..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	20	0.05	1	0	0	0	1	0
..........CAGCA---GCAG-CAACAACAAC---T.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	20	0.05	1	0	0	1	0	0
.................................................................................................................................................................................................................................................................................AGC-----------AACATC---------------------A---G---CAG------CAGCAACAAT.....................................................................................................................................................................	24	20	0.05	1	0	1	0	0	0
....CAACATCAGCA---GCAG-CAACAAC............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	22	20	0.05	1	0	1	0	0	0
...................................................................................................................................................................................................................................................................................C-----------AACATC---------------------A---G---CAG------CAGCAACAAC.....................................................................................................................................................................	22	20	0.05	1	0	1	0	0	0
......................................................................................................................................................CCA------CAGCAACAACA--------------------------ACAA------C...........................................................................................................................................................................................................................................................................................................	19	20	0.05	1	0	0	0	1	0
.......................................................................................................................................................CA------CAGCAACAACA--------------------------ACAA------CAGC---.....................................................................................................................................................................................................................................................................................................	21	20	0.05	1	0	1	0	0	0
......ACATCAGCA---GCAG-CAACAAC............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	20	0.05	1	0	0	0	1	0
..AGCAACATCAGCA---GCAG-CAACAAT............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	24	20	0.05	1	0	1	0	0	0
..................................................................................................................................................................CAACAACA--------------------------ACAA------CAGC---AAGA.................................................................................................................................................................................................................................................................................................	20	20	0.05	1	0	1	0	0	0
.CAGCAACATCAGCA---GCAG-CA.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	20	0.05	1	0	0	0	1	0
.......................................................................................................................................................................................................................................................................C---------AGC-----------AACATC---------------------A---G---CAG------CAGCA..........................................................................................................................................................................	20	20	0.05	1	0	0	0	1	0

droVir3

TCAGCAGCAGTCGCAGGCGGAG-CAACATCCTC---AGCATTGGGA---TTAC----T--ATGCGCGA--CAGCAACCCGCCGCGCCAGCCAAC-AAT---------A-GC-AACAA---CAGTAAC---------------A------GCAG------CGGCAACAA-----------------------------CAA---------------------------------CAGCAG---CAATAACAACAACAGCGGCAAC---------GCC-----------AACGGC---------------------A---G---CA------ACAGTGACAACA---------------------------ACAACAGCA------ACAA----T----------------------------------------------------------ACAAATGTTGCAACA--------------------------CCTT-TGGG-CAGC	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
.................................................................................................................................................................................................................................................................................GCC-----------AACGGC---------------------A---G---CA------ACAGTGACATTC---------------------------.........................................................................................................................................	25	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
....................................................................................................................................................................ACAA-----------------------------CAA---------------------------------CAGCAG---CAATAA..................................................................................................................................................................................................................................................................	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
.................................................................................................................................................................GCAACAA-----------------------------CAA---------------------------------CAGCAG---CAA.....................................................................................................................................................................................................................................................................	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	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

droMoj3

GCAGCAGCAGCAGCA---GCAA-CAACAGCAAC---AGGAGC--AA------GCGCCTCCAGCTGCACAACA-------------------------------------GC-AACAAC------------------AACAACA------TCAA------CAACAACAGCA--------------------------GCAG---------------C------------------AACAA---CAACAGCAGCAGCAACAGCAGCAG---C---AAC-----------AACAAC---------------------A---G---CA------GGAGCAACAACA------------------------------------------ACAAC------------------------------------AG--CAACA-----------------AGTCGCGCCACCTCCTCGC----CG------------------CT-CGCC-CAAC	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
............................GCAAC---AGGAGC--AA------GCGCCTCC..............................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	1	0	0	0	0
....................AA-CAACAGCAAC---AGGAGC--AA------GCG...................................................................................................................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	1
.....................................................CGCCTCCAGCTGCACAACA-------------------------------------GC-AACAAC------------------A.................................................................................................................................................................................................................................................................................................................................................................................	28	1	1.00	1	1	0	0	0	0	0
................................................................................................................................................................................................................................................................................................ACAAC---------------------A---G---CA------GGAGCAACAACA------------------------------------------..........................................................................................................................	21	6	0.17	1	0	0	0	1	0	0
...................................................................................................................................................................................................................................................................................C-----------AACAAC---------------------A---G---CA------GGAGCAACA.......................................................................................................................................................................	20	7	0.14	1	0	0	0	0	0	1
..............................................................................................................................................................................................................................................................................................................................G---CA------GGAGCAACAACA------------------------------------------ACAAC------------------------------------.................................................................................	20	9	0.11	1	0	0	0	0	0	1
..............................................................................................................................................................................................................................................A---CAACAGCAGCAGCAACA.......................................................................................................................................................................................................................................................	18	20	0.10	2	0	0	0	0	2	0
..................................................................................................................................................................CAACAGCA--------------------------GCAG---------------C------------------AACAA---CA......................................................................................................................................................................................................................................................................	20	20	0.10	2	2	0	0	0	0	0
...........................................................................................................................................................................................................................................ACAA---CAACAGCAGCAGCA..........................................................................................................................................................................................................................................................	18	20	0.10	2	0	0	0	0	2	0
....................................................................................................................................................................ACAGCA--------------------------GCAG---------------C------------------AACAA---CAACAGC.................................................................................................................................................................................................................................................................	23	20	0.10	2	0	0	0	0	2	0
.............................................................................................................................................................................................................................................................................C---AAC-----------AACAAC---------------------A---G---CA------GGAGC...........................................................................................................................................................................	19	11	0.09	1	0	0	0	0	0	1
....................................................................................................................AC------------------AACAACA------TCAA------CAACAACAGC.................................................................................................................................................................................................................................................................................................................................................	23	16	0.06	1	0	0	0	0	1	0
..............................................................................................................................................A------TCAA------CAACAACAGCA--------------------------GCAG---------------C------------------A...............................................................................................................................................................................................................................................................................	22	18	0.06	1	1	0	0	0	0	0
..............................................................................................................................................A------TCAA------CAACAACAGCA--------------------------GCAG---------------C------------------................................................................................................................................................................................................................................................................................	21	18	0.06	1	1	0	0	0	0	0
............................................................................................................................................................................................................................................................AGCAACAGCAGCAG---C---AAC-----------A..........................................................................................................................................................................................................................	19	20	0.05	1	0	0	0	0	1	0
..............................................................................................................................................................................................................................................A---CAACAGCAGCAGCAACAGCAGCAG---.............................................................................................................................................................................................................................................	25	20	0.05	1	1	0	0	0	0	0
.........................................................................................................................................................................................................................................................AGCAGCAACAGCAGCAG---C---AAC-----------AA.........................................................................................................................................................................................................................	23	20	0.05	1	1	0	0	0	0	0
..............................................................................................................................................................................................................................................................CAACAGCAGCAG---C---AAC-----------AACAAC---------------------A---G---CA------G...............................................................................................................................................................................	27	20	0.05	1	0	0	0	0	1	0
....................................................................................................................................................................................................................................................ACAGCAGCAGCAACAGCAGCA.................................................................................................................................................................................................................................................	21	20	0.05	1	0	1	0	0	0	0
..................................................................................................................CAAC------------------AACAACA------TCAA------CAACAAC....................................................................................................................................................................................................................................................................................................................................................	22	20	0.05	1	0	0	0	0	1	0
........AGCAGCA---GCAA-CAACAGCA...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	20	0.05	1	0	0	1	0	0	0
.....................................................................................................................................................TCAA------CAACAACAGCA--------------------------GCAG---------------...................................................................................................................................................................................................................................................................................................	19	20	0.05	1	1	0	0	0	0	0
.....AGCAGCAGCA---GCAA-CAACAGCA...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	22	20	0.05	1	0	1	0	0	0	0
..................................................................................................................................................................................................................................................................AGCAGCAG---C---AAC-----------AACAAC---------------------A---G---........................................................................................................................................................................................	20	20	0.05	1	0	0	0	0	1	0
.......................................................................................................................................................................................................................................................GCAGCAGCAACAGCAGCAG---C---.........................................................................................................................................................................................................................................	20	20	0.05	1	0	0	0	0	1	0
.............................................................................................................................................................................................................................................................................................................................................GCAACAACA------------------------------------------ACAAC------------------------------------AG--CAACA-----------------AGT....................................................	24	20	0.05	1	1	0	0	0	0	0
...........................................................................................................................................................................................................................................ACAA---CAACAGCAGCAGCAACAGC.....................................................................................................................................................................................................................................................	23	20	0.05	1	1	0	0	0	0	0
............................................................................................................................................................................................................................................................................................................................................AGCAACAACA------------------------------------------ACAAC------------------------------------AG--CAACA-----------------AGT....................................................	25	20	0.05	1	1	0	0	0	0	0
......................................................................................................................................................................................................AG---------------C------------------AACAA---CAACAGCAGCAGCAACAGC.....................................................................................................................................................................................................................................................	27	20	0.05	1	1	0	0	0	0	0
..................................................................................................................................................................CAACAGCA--------------------------GCAG---------------C------------------AACAA---CAACAGCAG...............................................................................................................................................................................................................................................................	27	20	0.05	1	0	0	0	0	1	0
.......................................................................................................................................................................................................G---------------C------------------AACAA---CAACAGCAGCAGCAACA.......................................................................................................................................................................................................................................................	24	20	0.05	1	1	0	0	0	0	0
.................................................................................................................................................................ACAACAGCA--------------------------GCAG---------------C------------------AACAA---CAACAGCA................................................................................................................................................................................................................................................................	27	20	0.05	1	0	0	0	0	1	0
............................................................................................................................................................................................................................................................................................................................................AGCAACAACA------------------------------------------ACAAC------------------------------------AG--CAACA-----------------AG.....................................................	24	20	0.05	1	1	0	0	0	0	0
...........................................................................................................................................................................................................................................................CAGCAACAGCAGCAG---C---AAC-----------A..........................................................................................................................................................................................................................	20	20	0.05	1	1	0	0	0	0	0
.................................................................................................................................................................ACAACAGCA--------------------------GCAG---------------C------------------AACAA---C.......................................................................................................................................................................................................................................................................	20	20	0.05	1	1	0	0	0	0	0
...................................................................................................................AAC------------------AACAACA------TCAA------CAACAACA...................................................................................................................................................................................................................................................................................................................................................	22	20	0.05	1	0	1	0	0	0	0
.........GCAGCA---GCAA-CAACAGCAAC---A.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	20	0.05	1	0	0	0	0	1	0
GCAGCAGCAGCAGCA---GCAA-CA.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	20	0.05	1	0	1	0	0	0	0
......................................................................................................................................................................AGCA--------------------------GCAG---------------C------------------AACAA---CAACAGC.................................................................................................................................................................................................................................................................	21	20	0.05	1	0	0	0	0	1	0

droGri2

GCAGCAGCAGCAGCA---GCGA-CGTCGACGTC---GG------AA---TGGG---------------AACA--------------------GC-TG--------------CA---ACAACAACAGCAACAACAC------CT------GCAA--------------------------------------------CAC---------------------------------CAACAA---CACCAACATCAGCAACACCA---A---CAACACC--------------AGC---------------------A---GCAACA------CCATC---AACA---------------------------------ACA------CTTGC-AACA------TGCCGCC----------------------------------------------TCACTTTA---CACAGCCAAA-----------------AG-CAG-CAG-CAGC	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
.....................A-CGTCGACGTC---GG------AA---TGG......................................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	1	1	0
................................................................................................................................ACAACAC------CT------GCAA--------------------------------------------CAC---------------------------------CAACAA---CACC....................................................................................................................................................................................................................................................................	26	1	1.00	1	1	0
.................................................................................................................................CAACAC------CT------GCAA--------------------------------------------CAC---------------------------------CAACAA---CACCAACA................................................................................................................................................................................................................................................................	29	1	1.00	1	1	0
.......................CGTCGACGTC---GG------AA---TGGG---------------AACA--------------------GC-...........................................................................................................................................................................................................................................................................................................................................................................................................................	24	1	1.00	1	1	0
...............................................................................................................................................................................................................................................................AACACCA---A---CAACACC--------------AGC---------------------A---............................................................................................................................................................................................	19	9	0.11	1	1	0
......................................................................................................................................................................................................................................................AACATCAGCAACACCA---A---CA...........................................................................................................................................................................................................................................	19	9	0.11	1	1	0
.......................................................................A--------------------GC-TG--------------CA---ACAACAACAGCA..........................................................................................................................................................................................................................................................................................................................................................................................	19	20	0.05	1	1	0

dan_2574

scaffold_13337:11559708-11559806 -

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

-7.0	-7.0	-6.7