sblock109902- Best orthologs

sblock109902	chr3L:21200899-21201043 +	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	three_prime_UTR

Legend:

   mature strand at position 21200978-21200999
   star strand at position 21200911-21200931
   mutations
   read mismatches

20-way Fast Statistical Aligner (FSA) re-alignment

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr3L:21200884-21201058 +		1	TGCACTTAAAACATATT----TCTAGT----CTCCTAAGAGTCT----GTCGTTGCTCCT--------------AT---T-------------A--------TTTA------------------------GTTT--TTAA---------------CTACGCA---------------------------------------------A-----------GCT---------------------TTCTTATT-AACTAAAAACAT------------------------GAGCTTC-------------------------------------------------------------GGCATTCTTTTAGGGAATTAGCAATATTTAGTAGAGTAAAGACTTGCAGTTTGC--------------------------------------------AAA----------------------ATAATATACATAAGTA
droSim1	chr3L:20558975-20559146 +	LASTZ	3	TGCACTTAAAACATATT----TCTAGT----TTCCTAAAAGTCT----GTCGTTGCTCCT--------------AT---T-------------A--------TTTA------------------------GTTT--TTAA---------------CTACGCA---------------------------------------------A-----------GCT---------------------TTCTTATT-AACTAAAAACAT------------------------GAGCATCG------------------------------------------------------------GACATTCTTTTAGGGAATTAGTAATATTTGGTAGAGTAAAGACTTGCAGTTTGC--------------------------------------------ACA----------------------TT----AATATAAGTA
droSec1	super_11:1154364-1154534 +	LASTZ	4	TGCACTTAAAACATATT----T-TAGT----TTCCTAAAAGTCT----GTCGTTGCTCCT--------------AT---T-------------A--------TTTA------------------------GTTT--TTAA---------------CTACGCA---------------------------------------------A-----------GCT---------------------TTCTTATT-AACTAAAAATAT------------------------GAGCTTCG------------------------------------------------------------GACATTCTTTTAGGGAATTAGTAATATTTGGTAGAGTAAAGACTTGCAGTTTGC--------------------------------------------ACA----------------------TA----TATATAAGTA
droYak2	chr3L:19324761-19324962 -	LASTZ	1	TGCACTTAAAACATATT----CTTAGT----TCTCTAAAAGACT----GTCGTTACTCTT--------------TT---T-------------T--------TTTA------------------------GTT---ATAA---------------CTACGCAGGCTTTGGGA-----------------------------------A-----------ACGTTTAAATTCGAAAGGCTAAAAATCGAATT-AACTAAAATCAT------------------------GAGTTTC-------------------------------------------------------------GACATTCTTTTGTTGAATTAGTAATATTTACTAGAGTAAAGACTTGCAGTTTGC--------------------------------------------ACA----------------------TT---TAATATAAGTA
droEre2	scaffold_4784:20885185-20885365 +	LASTZ	1	TGCACTTAACGCATATT----CCTAGT----T-CCCAAAAGATC----GTCGTTGCTCTT---------------------------------T--------TTTA------------------------GTT---ATAA---------------CTACGCAGGATTAGGTG-----------------------------------A-----------GCTTTC-AATCTGAA----------------A-GGCTAAAAATCT------------------------GAGTTTC-------------------------------------------------------------GACACTCTTTTGTTGAATTAGTAATATTTTGTAGAGTAAAGACTTGCAGTTTGC--------------------------------------------ACA----------------------TT---TATTATAAGTA
droEug1	scf7180000408013:19257-19432 -	LASTZ	4	GGCACTTGACTATAGCG----TTTCTTCTTGTTTATATATGT------TTCCTAGCTTTT--------------T----A-------------CTT------TTGC------A--TGGGAACTACTATTA-------AGATTATTCCT---------------------------------------------------------------------------------------------------------------AATCC------------------------GTAAATCGG--------------TAA-----------------------------------AGT----------TTTTAAGAGAAA------------GTTTAGTCAGT------A------ATATTTCGCAAAATAACACTTGTTTGA-----------------ACC----------------------TGGATTCGTATATATT
droBia1	scf7180000302193:4832562-4832712 -	LASTZ	4	CA--CTTAAAGAATATT----TCTAGT----TTACTAGAAGGCT----GTCCTAGGTCTG--------------A----------------------------------------------------------------------------------------------------------AA---------------------------------------------------------------TAATT-AACTAAAAACATT-----------------TCTTACGATTTAT-------------------------------------------------------------GACATTCTTCTAGTAAATTAGCAATATAAAGTAGAGTAAAGACTTGCAGCTTGC--------------------------------------------ACT----------------------TT---TAATATAAGTA
droTak1	scf7180000414337:376691-376851 -	LASTZ	4	CA--CTTAGAACTTATT----TCTAGT----TTCCCAGAAGTCT----GTCGTTT------------------------T-------------A--------ATTC------------------------GTTT--T---------------------CGTA----------------------------C--------------------------------------------------------------------ATTT---------------------------AAAA-------------------------------------GTGTAATTATTTTTCACGAGTTTTCGACATTCTTTTGGTAAATTAGCCATAAAAAGTAGAGTAAAGACTTGCAGCTTGC--------------------------------------------ACT----------------------TT---TATTATAAGTA
droEle1	scf7180000490579:784550-784723 -	LASTZ	4	AT---GTAAAACATATTG---CCTAGT----TTATTA-----------------------------------------------------------------TTACGTTCGCAAGTGCGAAGCTTAATTT-------TAATTACTCTT---------------------------------------------------------------------------------------------------------------GATC---------------------------TAAA-------------------------------------ATCCATAAACAACTGAAAAGACGACAACATTTTATCACTGGTTCTATTAT----GGAAGAGTAT------TTG------------------------------------------AGGCTTACGGCCTT----------TAAATCT--TAAATAAATAT-AATA
droRho1	scf7180000780425:1014-1218 -	LASTZ	4	TGCACTTAAAACATATT----CCTAGT----TTTCTAGAAGTCT----GTCATAACTGAGAAAAGCTGTTCTCGTTTAAAAGTTTTACGAACCA--------TTTG--------------------G---ATGT--TAAA---------------CTA----------------------------------------------------------------------------------AAATTGTAATT-AACTAAAACACAT-----------------GGTAAAGAGTAAC-------------------------------------------------------------GACATTCTTTCAGTAAACTGGCAATATAAAGTAGAGTAAAGACTTGCAGTTTGC--------------------------------------------ACA----------------------TT---TATTATAAGTA
droFic1	scf7180000453929:352124-352311 +	LASTZ	4	TGCCCTTAAAACCTATT----TCTATT----TTCGAAGAGGTCT----GCCATAACTCAA--------------A----------------------------------------------------------------------------------------------------------CACATTTGGC---------AGTTAACA-----------GTT---------------------TACTCATT-A---AAAAATCTTAATTATATGTGTTTAACATTTTAGAGTTAT-------------------------------------------------------------GGCAGACTTTTAGCGAACGAACCATATATAGTAGAGTAAAGACTTGCAGTTTGC--------------------------------------------ACA----------------------TT---TATATTAAGTA
droKik1	scf7180000302180:9486-9662 -	LASTZ	0	TTTAGTCA---TGTTCG----TCCATG----TTCTTAAAGGCTT----AACGGC--TACT---------------T---A-------------ATTTGGTTACATA------------------------GTT----GCA---------------CCACGCC---------------------------------------------A-----------A--------------------------CTATG-AGCCAAAATCAT------------------------GGGATTTGAATGTCCA----------------------------------------------------------CTGATATCGAATAATAAGTCCTTAGTGAAGG---TACTCTTA------------------------------------------ACGTTTGAGC--------------TAAATCA--A-AAGATAAATGAGTA
droAna3	scaffold_13417:5151173-5151335 +	LASTZ	0	TTCATTTAAAAGGAATT----TTTATT----CTTATCGAAAACAATATATCGTTC----C--------------AA---T-------------T--------CTTA------------------------GTTT--CCGA---------------TTTAAGG-------------------------------------------------------------------------------------------------------------------------------------------------------G-----------------------------------AATTTTTGAAGTAATTTTATTGAATTTATTATAGGTGGTTAAACAATA-------------------------------TTTTCTTCAATTAAATTGGAGTTTTTAATCTC------------------------ATATTTTCAAA
droBip1	scf7180000391904:11169-11346 -	LASTZ	0	AAAACATA---CGTTTT--------TT----TCGCTCAGTGA-A----TTCTCTGCTCTC--------------AT---T-------------G--------TTT--------------------------TTC--TCTG---------------CTACGCA---------------------------------------------C-----------ACA---------------------CTCAAATT-TTAAACATGTGT------------------------TAGTTT-----------------------------------------------------------------TGCCCACCACTGGTTTAGATATACTCTCTCGAGTATAT----------------------------------------------CAAACACACAAAATATAATCTTCCGAAATAATCATACT---AATCCATAATA
dp4	chr2:26925016-26925184 -	LASTZ	0	CATT--TTAAATATATT----TTAAAT----CTGAATTCAGTCT----GG------ACCT--------------AT---C-------------A--------CTTA---------------CTTCTTTCA-------AGTCTATTCCG------------AA----------------------------TATATCTTCAATCCGACACCTTTTTGAAACCGTCTTGAATCGAAATTTT--TTTTTTTTTT-AATAAAAAAAAT------------------------TGGATTC----------------------------------------------------------------ATT-TTTTAG-------------------------------------TGCC--------------------------------------------ATT----------------------TT-----------TAT
droPer1	super_42:183057-183224 +	LASTZ	0	ATTTCTAA---TCTG-----------T----TTCCGATAAG--T----GACGATCCATAT--------------AA---T-------------A--------TTGCACACTGACTTACGG-GCACTGTTG-------TA------------------------------------------------------------------------------------------------------------------AGTACATACAA------------------------ACGTAAT-------------------------------------CGCATTTACATATGGAAATAT---GTACCTCATT----------------TATAGTAT------------------------ATAGTATATTCATAGAAGTTTGC-----------------ACA----------------------TAAATATATATATATA
droWil1	scaffold_181024:881694-881865 -	LASTZ	0	AAATCAAA---T----T----TACATT----CTTTTTCCAACTT----GGGCTTTTTCTT--------------TT---T-------------T--------TTTT------------------------GTTC--TTAC---------------CTACGCAAAAGTAATAAGAGGTTCGATT--------------------------------------------------------------------------------------------------------------------ATCGCAATATATCGCATTTTCCGTCTGACATT-----------GTTCACAATTTTGTGTCAGTATTA-AGTTAATTTGCAATGCAACACAAAT-------------------------------------------------------------------------------------------------GAAATA
droVir3	scaffold_13036:515447-515610 -	LASTZ	0	TCCAATTAAAACAGTTA----T--TTC----CTCATAACAGTCA----TTCT---CTTTG--------------AC---C-------------G-C------TTTC------------------------GTG---AGCA---------------CTATCCA---------------------------------------------A-----------ACT---------------------ATTTTATTAAGTTAGAGTCGT------------------------TAGTTTTA-------------------------------AGTT-----------GCTTACAATTAATCGGGCATATATCGGGAATTTAGC--------------TAAACAAT---------------------------------------------------------------------------TATTTT---ATATATAAGCA
droMoj3	scaffold_6500:14191327-14191493 +	LASTZ	0	GGCAAGCTTTGGAGCAT-ACAAGTTGT-----GCATAACTGACT----ATCATTGAACAT--------------AT---T-------------T--------TTTC------------------------CTATTCTTTC------CTATTA---TGTCGT--------------------------------------------------------------------------------------------ACAAATAATAT------------------------GTATTTTGT--------------GCA-----------------------------------AGC--------TTCCAAAAGGCATTCAACCCTATTTTGTAATAAAAAAAT----ATTTTTC--------------------------------------------AAA----------------------TA----AAAAATATAG
droGri2	scaffold_15110:22741833-22741988 -	LASTZ	0	TATGTGTA---TATATT----T--------------GAATATTT----AATTTC--TTTT---------------T---T-------------ATTTACTTATTTA------------------------ATG---TCAACTAAAGTC----AGTCTTCGCAAAAATTGCAAAAAGTCAGAAA----------------------------------------------------AACTTGAAATTAAATT-AAATGTAATATA-----------------CAATTTAAAATTAT-----------------------------------------------------------------------------------------------------------------AT--------------------------------------------ATA-------------TAAA----------TTACAAAATAA

Legend

0- The ortholog is absent. A better synthenic sequence candidate could not be found.
1- Reads w/ good pileup on mature and star strand & folds into hairpin structure.
2- Reads w/ good pileup on mature and star strand BUT does not fold into hairpin structure.
3- Sporadic reads & folds into a hairpin structure.
4- No reads but folds into a hairpin structure.
5- Ortholog is confident but miRNA appears absent (no reads and does not fold into a hairpin)

Re-alignment after removal of non-confident orthologs

Species	Alignment
dm3	TGCACTTAAAACATATTTCTAGTCTCCTAAGAGTCTGTCGTTGCTCCT-----------------------------------ATTATT--TAGTTTTTAACTACGCAAGC----------T------------T---------------------------TCTTATTA----------------------------ACTAAAAACA-------TGAGCT-TC-GGCATTCTT--------TTAGGGAATTAGCAATATTTAGTAGAGTA---AAGACTTGCAGTTTGCAAAATAAT------ATACATAAGTA
droSim1	TGCACTTAAAACATATTTCTAGTTTCCTAAAAGTCTGTCGTTGCTCCT-----------------------------------ATTATT--TAGTTTTTAACTACGCAAGC----------T------------T---------------------------TCTTATTA----------------------------ACTAAAAACA-------TGAGCA-TCGGACATTCTT--------TTAGGGAATTAGTAATATTTGGTAGAGTA---AAGACTTGCAGTTTGCACATTAA-------T---ATAAGTA
droSec1	TGCACTTAAAACATATTT-TAGTTTCCTAAAAGTCTGTCGTTGCTCCT-----------------------------------ATTATT--TAGTTTTTAACTACGCAAGC----------T------------T---------------------------TCTTATTA----------------------------ACTAAAAATA-------TGAGCT-TCGGACATTCTT--------TTAGGGAATTAGTAATATTTGGTAGAGTA---AAGACTTGCAGTTTGCACATATA-------T---ATAAGTA
droYak2	TGCACTTAAAACATATTCTTAGTTCTCTAAAAGACTGTCGTTACTCTT-----------------------------------TTTTTT--TAGTT-ATAACTACGCAGGCTTTGGGAAACG------------TTTAAATTCGA------AAGGCTAAAAATCGAATTA----------------------------ACTAAAATCA-------TGAGTT-TC-GACATTCTT--------TTGTTGAATTAGTAATATTTACTAGAGTA---AAGACTTGCAGTTTGCACATTTAA------T---ATAAGTA
droEre2	TGCACTTAACGCATATTCCTAGTTC-CCAAAAGATCGTCGTTGCTCTT--------------------------------------TTT--TAGTT-ATAACTACGCAGGATTAGGTGAGCT------------TT-CAATCTGA------AA----------------G----------------------------GCTAAAAATC-------TGAGTT-TC-GACACTCTT--------TTGTTGAATTAGTAATATTTTGTAGAGTA---AAGACTTGCAGTTTGCACATTTAT------T---ATAAGTA
droEug1	GGCACTTGACT-ATA---------------GCGTTTCTTCTTGTTTAT-------------------ATATGTTTCCTAGCTTTTTACTTTTGCATGGGAACTAC------------------TATTAAGATTA-----------TTCCT------------------------------------------------------AATC-------CGTAAA-TCGGTAAAGTTTTTAAGAGAAAGTTTAGTCAGTAATATTTCGCAAAATA---ACA-CTT---GTTTGAACCTGGAT------TCGTATATATT
droBia1	--CACTTAAAGAATATTTCTAGTTTACTAGAAGGCTGTCCTAGGTCTGAAA-----------------------------------------------------------------------------------------------------------------TAATTA----------------------------ACTAAAAACATTTCTTACGATTT-AT-GACATTCTT--------CTAGTAAATTAGCAATATAAAGTAGAGTA---AAGACTTGCAGCTTGCACTTTTAA------T---ATAAGTA
droTak1	--CACTTAGAACTTATTTCTAGTTTCCCAGAAGTCTGTCGTT------------------------------------------TTAAT--TCGTTTT-----------------------------------------------CGTACA---TTTAAAAGTGTAATTA--------------------------TTTT-----TCA-------CGAGTTTTC-GACATTCTT--------TTGGTAAATTAGCCATAAAAAGTAGAGTA---AAGACTTGCAGCTTGCACTTTTAT------T---ATAAGTA
droEle1	---ATGTAAAACATATTGCC---------------------------------------------------------TAGTTTATTATT--ACGTTCGCAAGTGCG-AAGC----------TTAATTTTAATTA-----------CTCTTGA--TCTAA-AATCCATAAA--------------------------CAACTGAAAAGA-------CGA-----C-AACATTTTA--------TCACTGGTTCTATTA----TGGAAGAGTATTTGAGGCTTACGGCCTTTAAATCTTAAATAAAT---ATA-ATA
droRho1	TGCACTTAAAACATATTCCTAGTTTTCTAGAAGTCTGTCATAACTGAGAAAAGCTGTTCTCGTTTAAAAGTTTTACGA-----ACCATT--TGGATGTTA---------------------------------------------------A--ACTAAAATTGTAATTA----------------------------ACTAAAACACATGGTAAAGAGTA-AC-GACATTCTT--------TCAGTAAACTGGCAATATAAAGTAGAGTA---AAGACTTGCAGTTTGCACATTTAT------T---ATAAGTA
droFic1	TGCCCTTAAAACCTATTTCTATTTTCGAAGAGGTCTGCCATAACTCAAACA----------------------------------CATT--TGGCAGTTAAC------AGT----------T------------T---------------------------ACTCATTAAAAAATCTTAATTATATGTGTTTAACAT-------TTT-------AGAGTT-AT-GGCAGACTT--------TTAGCGAACGAACCATATATAGTAGAGTA---AAGACTTGCAGTTTGCACATTTAT------A---TTAAGTA

20-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droEug1	droBia1	droTak1	droEle1	droRho1	droFic1	droKik1	droAna3	droBip1	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image
UNAFold Image

Small RNA-seq read pileup

Species

Alignment

droSim1

TGCACTTAAAACATATT----TCTAGT----TTCCTAAAAGTCT----GTCGTTGCTCCT--------------AT---T-------------A--------TTTA------------------------GTTT--TTAA---------------CTACGCA---------------------------------------------A-----------GCT---------------------TTCTTATT-AACTAAAAACAT------------------------GAGCATCG------------------------------------------------------------GACATTCTTTTAGGGAATTAGTAATATTTGGTAGAGTAAAGACTTGCAGTTTGC--------------------------------------------ACA----------------------TT----AATATAAGTA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.......................................................................................................................................................................................................................................................................T------------------------GAGCATCG------------------------------------------------------------GACATTCTTTTAG..............................................................................................................................	22	1	22.00	0.00	19.00	3.00	0.00
....................................................................................................................................................................................................................................................................................................ATCG------------------------------------------------------------GACATTCTTTTAGGGA...........................................................................................................................	20	1	13.00	0.00	0.00	1.00	12.00
...................................TAAAAGTCT----GTCGTTGCTCCT--------------.....................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	7.00	0.00	5.00	1.00	1.00
................................................................................................................................................................................................................................................................................................GAGCATCG------------------------------------------------------------GACATTCTTTTAGG.............................................................................................................................	22	1	6.00	0.00	5.00	1.00	0.00
....................................................................................................................................................................................................................................................................................................ATCG------------------------------------------------------------GACATTCTTTTAGGGAAT.........................................................................................................................	22	1	3.00	0.00	1.00	0.00	2.00
.................................................................................................................................................................................................................................................................................................AGCATCG------------------------------------------------------------GACATTCTTTTAGGG............................................................................................................................	22	1	3.00	0.00	2.00	1.00	0.00
.................................................................................................................................................................................................................................................................................................AGCATCG------------------------------------------------------------GACATTCTTTTAGGGAATT........................................................................................................................	26	1	3.00	0.00	0.00	0.00	3.00
....................................................................................................................................................................................................................................................................................................ATCG------------------------------------------------------------GACATTCTTTTAGGGAATTAGT.....................................................................................................................	26	1	3.00	0.00	0.00	1.00	2.00
..................................................................................................................................................................................................................................................................................................GCATCG------------------------------------------------------------GACATTCTTTTAGG.............................................................................................................................	20	1	2.00	0.00	2.00	0.00	0.00
.................................................................................................................................................................................................................................................................................................AGCATCG------------------------------------------------------------GACATTCTTTTAG..............................................................................................................................	20	1	2.00	0.00	1.00	1.00	0.00
....................................................................................................................................................................................................................................................................................................ATCG------------------------------------------------------------GACATTCTTTTAGGGAA..........................................................................................................................	21	1	2.00	0.00	0.00	0.00	2.00
......................................................................................................................................................................................................................................................................AT------------------------GAGCATCG------------------------------------------------------------GACATTCTTTTAGGGAA..........................................................................................................................	27	1	2.00	0.00	0.00	0.00	2.00
....................................AAAAGTCT----GTCGTTGCTCC....................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
..................................................................................................................................................................................................................................................................AAACAT------------------------GAGCATCG------------------------------------------------------------GACATTCTTT.................................................................................................................................	24	1	1.00	0.00	0.00	0.00	1.00
.......................................................................................................................................................................................................................................................TATT-AACTAAAAACAT------------------------GAGCATCG------------------------------------------------------------GAC........................................................................................................................................	27	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................................................................................................................................................................................................ATCG------------------------------------------------------------GACATTCTTTTAGGGAATTAGG.....................................................................................................................	26	1	1.00	0.00	0.00	0.00	1.00
.......................................................................................................................................................................................................................................................................................................................................................................................AGTAATATTTGGTAGAGTAAAGACTTG.............................................................................................	27	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................................................................................................................................................ATCG------------------------------------------------------------GACATTCTTTTAGGGAATT........................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................................................................................................................................................................................................................................................................................................................ATTTGGTAGAGTAAAGACTTGC............................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
.......................................................................................................................................................................................................................................................................T------------------------GAGCATCG------------------------------------------------------------GACATTCTTTTAGGGAAT.........................................................................................................................	27	1	1.00	0.00	0.00	1.00	0.00
.......................................................................................................................................................................................................................................................................T------------------------GAGCGTCG------------------------------------------------------------GACATTCTTTT................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
.......................................................................................................................................................................................................................................................................T------------------------GAGCATCG------------------------------------------------------------GACATTCTTTTA...............................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
.........................GT----TTCCTAAAAGTCT----GTCGTTGCTCCT--------------.....................................................................................................................................................................................................................................................................................................................................................................................................................................	27	1	1.00	0.00	1.00	0.00	0.00
......................................................................................................................................................................................................................................................................AT------------------------GAGCATCG------------------------------------------------------------GACATTCTTTT................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
...................................................................................................................................................................................................................................................................................................CATCG------------------------------------------------------------GACATTCTTTTAGGGG...........................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................................................................................................................................................................................................ATCG------------------------------------------------------------GACATTCTTTTAGGG............................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
........................................................................................................................................................................................................................................................................................................................................................................................GTAATATTTGGTAGAGTAAAGAC................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
...............................TTCCTAAAAGTCT----GTCGTTGCTCCT--------------.....................................................................................................................................................................................................................................................................................................................................................................................................................................	25	1	1.00	0.00	1.00	0.00	0.00
......................................AAGTCT----GTCGTTGCTCCT--------------.....................................................................................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...............TT----TCTAGT----TTCCTAAAAGTCT----GTCGTT.........................................................................................................................................................................................................................................................................................................................................................................................................................................................	27	1	1.00	0.00	0.00	0.00	1.00
...............................TTCCTAAAAGTCT----GTCGTTGCTCT....................................................................................................................................................................................................................................................................................................................................................................................................................................................	24	1	1.00	0.00	0.00	1.00	0.00
..................................CTAAAAGTCT----GTCGTTGCTC.....................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
..........................................................................................................................................................................................................................................................................................................................................................................................AATATTTGGTAGAGTAAAGA.................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
.................................................................................................................................................................................................................................................................................................AGCATCG------------------------------------------------------------GACATTCTTTTAGG.............................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
......................................................................................................................................................................................................................................................................AT------------------------GAGCATCG------------------------------------------------------------GACATTCTTTTA...............................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................................................................................................................................................ATCG------------------------------------------------------------GACATTCTTTTAGGGAATTAGTA....................................................................................................................	27	1	1.00	0.00	0.00	0.00	1.00
.......................................................................................................................................................................................................................................................................T------------------------GAGCATCG------------------------------------------------------------GACATTGTTTTAG..............................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.....................................................................................................................................................................................................................................................................CAT------------------------GAGCATCG------------------------------------------------------------GACATTCTTTTAGGGA...........................................................................................................................	27	1	1.00	0.00	0.00	0.00	1.00
....CTTAAAACATATT----TTTTGT----................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	2	0.50	0.00	0.00	0.00	0.50
................................................................................................................................................................................................................................................................................................GAGCATCG------------------------------------------------------------GACATTCTTTTAG..............................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
...................................................................................................................................................................................................................................................................AACAT------------------------GAGCATCG------------------------------------------------------------GACATTCTTTTAG..............................................................................................................................	26	1	1.00	0.00	0.00	0.00	1.00
...................................TAAAAGTCT----GTCGTTGCTC.....................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...................................TAAAAGTCT----GTCGTTGCTCC....................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
.....................................AAAGTCT----GTCGTTGCTCC....................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
..................................................................................................................................................................................................................................................................................................GCATCG------------------------------------------------------------GACATTCTTTTAGGG............................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
...................................TAAAAGTCT----GTCGTTGCTCCT--------------G....................................................................................................................................................................................................................................................................................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
...............................TTCCTAAAAGTCT----GTCGTTGCTCC....................................................................................................................................................................................................................................................................................................................................................................................................................................................	24	1	1.00	0.00	0.00	0.00	1.00
.........................GT----TTCCTAAAAGTCT----GTCGTTGCT......................................................................................................................................................................................................................................................................................................................................................................................................................................................	24	1	1.00	0.00	1.00	0.00	0.00
.......................................................................................................................................................................................................................................................................T------------------------GAGCATCG------------------------------------------------------------GACATTCTTTTAGTT............................................................................................................................	24	1	1.00	0.00	0.00	0.00	1.00

droSec1

TGCACTTAAAACATATT----T-TAGT----TTCCTAAAAGTCT----GTCGTTGCTCCT--------------AT---T-------------A--------TTTA------------------------GTTT--TTAA---------------CTACGCA---------------------------------------------A-----------GCT---------------------TTCTTATT-AACTAAAAATAT------------------------GAGCTTCG------------------------------------------------------------GACATTCTTTTAGGGAATTAGTAATATTTGGTAGAGTAAAGACTTGCAGTTTGC--------------------------------------------ACA----------------------TA----TATATAAGTA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.......................................................................................................................................................................................................................................................................................................................................................................................................GTAAAGACTTGCAGTTTGC--------------------------------------------.........................................	19	1	2.00	0.00	2.00	0.00
..........................T----TTCCTAAAAGTCT----GTCGTTGCT......................................................................................................................................................................................................................................................................................................................................................................................................................................................	23	1	2.00	0.00	2.00	0.00
.............................................................................................................................................................................................................................................................................................................................................................................................ATTTGGTAGAGTAAAGACTTGC............................................................................................	22	1	1.00	0.00	1.00	0.00
....................................................................................................................................................................................................................................................................................................................................................................................ATTAGTAATATTTGGTAGAGTAAA...................................................................................................	24	1	1.00	0.00	1.00	0.00
.................................CCTAAAAATCT----GTCGTTGCTC.....................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	0.00	0.00	1.00
................................................................................................................................................................................................................................................................................................GAGCTTCG------------------------------------------------------------GACATTCTTTTAGGG............................................................................................................................	23	1	1.00	1.00	0.00	0.00
........................................................................................................................................................................................................................................................ATT-AACTAAAAATAT------------------------GAG............................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00
..................................................................................................................................................................................................................................................................................................GCTTCG------------------------------------------------------------GACATTCTTTTAGGG............................................................................................................................	21	1	1.00	0.00	0.00	1.00
.......................................................................................................................................................................................................................................................................................................................................................................................AGTAATATTTGGTAGAGT......................................................................................................	18	1	1.00	0.00	1.00	0.00
..............................................................................................................................................................CGCA---------------------------------------------A-----------GCT---------------------TTCTTATT-AACT...............................................................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00
.............................................................................................................................................................................................................................................................................................................................................................................................ATTTGGTAGAGTAAAGACTTGCAGT.........................................................................................	25	1	1.00	0.00	1.00	0.00
.................................................................................................................................................................................................................................................................................................AGCTTCG------------------------------------------------------------GACATTCTTTTAGGGT...........................................................................................................................	23	1	1.00	0.00	0.00	1.00
...................................................................................................................................................................................................................................................................................................CTTCG------------------------------------------------------------GACATTTTTTTAGGGA...........................................................................................................................	21	1	1.00	0.00	1.00	0.00
................................TCCTAAAAGTCT----GTCGTTGCTC.....................................................................................................................................................................................................................................................................................................................................................................................................................................................	22	1	1.00	0.00	0.00	1.00
...............................TTCCTAAAAGTCT----GTCGTTGCTTT....................................................................................................................................................................................................................................................................................................................................................................................................................................................	24	1	1.00	0.00	0.00	1.00
....................................AAAAGTCT----GTCGTTGCTCCT--------------.....................................................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00
......................................................................................................................................................................................................................................................................................................................................................................................TAGTAATATTTGGTAGAGTAAAGACT...............................................................................................	26	1	1.00	0.00	1.00	0.00
.........................GT----TTCCTAAAAGTCT----GTC............................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00
....................................................................................................................................................................................................................................................................................................................................................................................ATTAGTAATATTTGGTAGA........................................................................................................	19	1	1.00	0.00	1.00	0.00
..................................................................................................................................................................................................................................................................................................GCTTCG------------------------------------------------------------GACATTCTTTTAGGGAATT........................................................................................................................	25	1	1.00	0.00	1.00	0.00
.................................................................................................................................................................................................................................................................................................AGCTTCG------------------------------------------------------------GACATTCTTTTAGGGAATT........................................................................................................................	26	1	1.00	0.00	0.00	1.00
........................AGT----TTCCTAAAAGTCT----GTCGTTGCTC.....................................................................................................................................................................................................................................................................................................................................................................................................................................................	26	1	1.00	1.00	0.00	0.00
....................................................................................................................................TT--TTAA---------------CTACGCA---------------------------------------------A-----------GCT---------------------TTCT........................................................................................................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00
....................................................................................................................................................................................................................................................................................................................................................................................ATTAGTAATATTTGGTAGAGT......................................................................................................	21	1	1.00	0.00	1.00	0.00
..................................CTAAAAGTCT----GTCGTTGCTCT....................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	0.00	0.00	1.00
...................................................................................................................................................................................................................................................................................................CTTCG------------------------------------------------------------GACATTCTTTTAGGGAATTAGTAA...................................................................................................................	29	1	1.00	1.00	0.00	0.00
.......................................................................................................................................................................................................................................................................T------------------------GAGCTTCG------------------------------------------------------------GACACTCTTTT................................................................................................................................	20	1	1.00	1.00	0.00	0.00
...................................................................................................................................................................................................................................................................................................CTTCG------------------------------------------------------------GACATTCTTTTAGGGA...........................................................................................................................	21	1	1.00	0.00	1.00	0.00
.............................................................................................................................................................................................................................................................................................................................................................................................ATTTGGTAGAGTAAAGACTTGCAGTT........................................................................................	26	1	1.00	0.00	1.00	0.00
.........................................................................................................................................................................................................................................................................................................................................................................................................AAAGACTTGCAGTTTGC--------------------------------------------ACA----------------------T...............	21	1	1.00	0.00	1.00	0.00
..................................................................................................................................................................................................................................................................................................GCTTCG------------------------------------------------------------GACATTCTTTTAG..............................................................................................................................	19	1	1.00	0.00	0.00	1.00
.......................................................................................................................................................................................................................................................................................................................................................................................................GTAAAGACTTGCAGTTTGC--------------------------------------------A........................................	20	1	1.00	0.00	1.00	0.00
..................................................................................................................................................................................................................................................................................................GCTTCG------------------------------------------------------------GACATTCTTTTAGGGA...........................................................................................................................	22	1	1.00	0.00	1.00	0.00
....................................................................................................................................................................................................................................................................................................TTCG------------------------------------------------------------GACATTCTTTTAGGGA...........................................................................................................................	20	1	1.00	0.00	1.00	0.00
....................................................................................................................................................................................................................................................................................................................................................................................................AGAGTAAAGACTTGCAGT.........................................................................................	18	1	1.00	0.00	1.00	0.00

droYak2

TGCACTTAAAACATATT----CTTAGT----TCTCTAAAAGACT----GTCGTTACTCTT--------------TT---T-------------T--------TTTA------------------------GTT---ATAA---------------CTACGCAGGCTTTGGGA-----------------------------------A-----------ACGTTTAAATTCGAAAGGCTAAAAATCGAATT-AACTAAAATCAT------------------------GAGTTTC-------------------------------------------------------------GACATTCTTTTGTTGAATTAGTAATATTTACTAGAGTAAAGACTTGCAGTTTGC--------------------------------------------ACA----------------------TT---TAATATAAGTA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
....................................................................................................................................T---ATAA---------------CTACGCAGGCTTTGGGA-----------------------------------................................................................................................................................................................................................................................................................................................	22	2	1.50	1.00	0.00	0.50	0.00	0.00
........................................................................................................................................ATAA---------------CTACGCAGGCTTTGGGA-----------------------------------................................................................................................................................................................................................................................................................................................	21	2	1.00	0.50	0.00	0.50	0.00	0.00
...........................................................................................................................................A---------------CTACGCAGGCTTTGGGA-----------------------------------................................................................................................................................................................................................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50	0.00
.......................................................................................................................................................................................................................................................................................................................................................................................................GTAAAGACTTGCAGTTTGC--------------------------------------------A........................................	20	2	0.50	0.50	0.00	0.00	0.00	0.00

droEre2

TGCACTTAACGCATATT----CCTAGT----T-CCCAAAAGATC----GTCGTTGCTCTT---------------------------------T--------TTTA------------------------GTT---ATAA---------------CTACGCAGGATTAGGTG-----------------------------------A-----------GCTTTC-AATCTGAA----------------A-GGCTAAAAATCT------------------------GAGTTTC-------------------------------------------------------------GACACTCTTTTGTTGAATTAGTAATATTTTGTAGAGTAAAGACTTGCAGTTTGC--------------------------------------------ACA----------------------TT---TATTATAAGTA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
........................................................................................................................................................................................................................................................................................................................................................................................................................................................................A----------------------TT---TATTATATGCA	19	2	0.50	0.50	0.00	0.00	0.00
.........................................................................................................................................................................................................................................................................................................................................................................................................AAAGACTTGCAGTTTGC--------------------------------------------ACA----------------------T...............	21	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................CGCAGGATTAGGTG-----------------------------------A-----------GCTTT...............................................................................................................................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................................................................................ACGCAGGATTAGGTG-----------------------------------A-----------GCTTT...............................................................................................................................................................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00

droEug1

GGCACTTGACTATAGCG----TTTCTTCTTGTTTATATATGT------TTCCTAGCTTTT--------------T----A-------------CTT------TTGC------A--TGGGAACTACTATTA-------AGATTATTCCT---------------------------------------------------------------------------------------------------------------AATCC------------------------GTAAATCGG--------------TAA-----------------------------------AGT----------TTTTAAGAGAAA------------GTTTAGTCAGT------A------ATATTTCGCAAAATAACACTTGTTTGA-----------------ACC----------------------TGGATTCGTATATATT

Size

Hit Count

Total Norm

droBia1

CA--CTTAAAGAATATT----TCTAGT----TTACTAGAAGGCT----GTCCTAGGTCTG--------------A----------------------------------------------------------------------------------------------------------AA---------------------------------------------------------------TAATT-AACTAAAAACATT-----------------TCTTACGATTTAT-------------------------------------------------------------GACATTCTTCTAGTAAATTAGCAATATAAAGTAGAGTAAAGACTTGCAGCTTGC--------------------------------------------ACT----------------------TT---TAATATAAGTA

Size

Hit Count

Total Norm

droTak1

CA--CTTAGAACTTATT----TCTAGT----TTCCCAGAAGTCT----GTCGTTT------------------------T-------------A--------ATTC------------------------GTTT--T---------------------CGTA----------------------------C--------------------------------------------------------------------ATTT---------------------------AAAA-------------------------------------GTGTAATTATTTTTCACGAGTTTTCGACATTCTTTTGGTAAATTAGCCATAAAAAGTAGAGTAAAGACTTGCAGCTTGC--------------------------------------------ACT----------------------TT---TATTATAAGTA

Size

Hit Count

Total Norm

droEle1

AT---GTAAAACATATTG---CCTAGT----TTATTA-----------------------------------------------------------------TTACGTTCGCAAGTGCGAAGCTTAATTT-------TAATTACTCTT---------------------------------------------------------------------------------------------------------------GATC---------------------------TAAA-------------------------------------ATCCATAAACAACTGAAAAGACGACAACATTTTATCACTGGTTCTATTAT----GGAAGAGTAT------TTG------------------------------------------AGGCTTACGGCCTT----------TAAATCT--TAAATAAATAT-AATA

Size

Hit Count

Total Norm

droRho1

TGCACTTAAAACATATT----CCTAGT----TTTCTAGAAGTCT----GTCATAACTGAGAAAAGCTGTTCTCGTTTAAAAGTTTTACGAACCA--------TTTG--------------------G---ATGT--TAAA---------------CTA----------------------------------------------------------------------------------AAATTGTAATT-AACTAAAACACAT-----------------GGTAAAGAGTAAC-------------------------------------------------------------GACATTCTTTCAGTAAACTGGCAATATAAAGTAGAGTAAAGACTTGCAGTTTGC--------------------------------------------ACA----------------------TT---TATTATAAGTA

Size

Hit Count

Total Norm

droFic1

TGCCCTTAAAACCTATT----TCTATT----TTCGAAGAGGTCT----GCCATAACTCAA--------------A----------------------------------------------------------------------------------------------------------CACATTTGGC---------AGTTAACA-----------GTT---------------------TACTCATT-A---AAAAATCTTAATTATATGTGTTTAACATTTTAGAGTTAT-------------------------------------------------------------GGCAGACTTTTAGCGAACGAACCATATATAGTAGAGTAAAGACTTGCAGTTTGC--------------------------------------------ACA----------------------TT---TATATTAAGTA

Size

Hit Count

Total Norm

droKik1

TTTAGTCA---TGTTCG----TCCATG----TTCTTAAAGGCTT----AACGGC--TACT---------------T---A-------------ATTTGGTTACATA------------------------GTT----GCA---------------CCACGCC---------------------------------------------A-----------A--------------------------CTATG-AGCCAAAATCAT------------------------GGGATTTGAATGTCCA----------------------------------------------------------CTGATATCGAATAATAAGTCCTTAGTGAAGG---TACTCTTA------------------------------------------ACGTTTGAGC--------------TAAATCA--A-AAGATAAATGAGTA

Size

Hit Count

Total Norm

droAna3

TTCATTTAAAAGGAATT----TTTATT----CTTATCGAAAACAATATATCGTTC----C--------------AA---T-------------T--------CTTA------------------------GTTT--CCGA---------------TTTAAGG-------------------------------------------------------------------------------------------------------------------------------------------------------G-----------------------------------AATTTTTGAAGTAATTTTATTGAATTTATTATAGGTGGTTAAACAATA-------------------------------TTTTCTTCAATTAAATTGGAGTTTTTAATCTC------------------------ATATTTTCAAA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...............................................................................................................................................................................................................................................................................................................................................................................ATTGAATTTATTATAGGTGGT...........................................................................................................	21	1	5.00	0.00	5.00	0.00	0.00
.......................................................................................................................................................................................................................................................................................................................................................................................................................................................TAAATTTGAGTTTTTAATCT....................................	20	2	1.00	0.00	1.00	0.00	0.00
..............................................................................................................................................................................................................................................................................................................................................................................TATTGAATTTATTATAGGTGGT...........................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
...........................................................................................................................................................................................................................................................................................................................................................................................................TA-------------------------------TTTTCGTCAATTAAATTTGA...............................................	22	2	0.50	0.00	0.50	0.00	0.00
...........................................................................................................................................................................................................................................................................................................................................................................................................TA-------------------------------TTTTCGTCAATTAAATTGG................................................	21	2	0.50	0.00	0.50	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................................................................TGAATTTATTATAGGGGGTTAGACAA....................................................................................................	26	1	1.00	1.00	0.00	0.00	0.00
......................................................................................................................................................................................................................................................................................................................................................................................TTATTATAGGTGGTTAAACAA....................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
......................................................................................................................................................................................................................................................................................................................................................................................................................................................TTGAATTGGAGTTTTTAATCT....................................	21	3	0.33	0.33	0.00	0.00	0.00
..................................................................................................................................................................................................................................................................................................................................................................................................................................................TCAATTAAATTGGAGTTTTTA........................................	21	2	0.50	0.50	0.00	0.00	0.00
..........................................................................................................................................................................................................................................................................................................................................................................................TATAGGTGGTTAAACAATA-------------------------------TTTTCGT............................................................	26	2	0.50	0.50	0.00	0.00	0.00
........................................................................................................................................................................................................................................................................................................................................................................................................CAATA-------------------------------TTTTCGTCAATTAAATTGTAG..............................................	26	1	1.00	0.00	0.00	0.00	1.00
............................................................................................................................................................................................................................................................................................................................................................................TTTATTGAATTTATTGTAGGTGGT...........................................................................................................	24	1	1.00	1.00	0.00	0.00	0.00
............................................................................................................................................................................................................................................................................................................................................................................TTTATTGAAATTATTATAGGTGTTT..........................................................................................................	25	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................................................................................................................................................................................................................................................................................................TAAACAATA-------------------------------TTTTCGTCAATT.......................................................	21	2	0.50	0.50	0.00	0.00	0.00
................................................................................................................................................................................................................................................................................................................................................................................TTGAATTTAATATAGGTGGTT..........................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................................................................................................................................................................TATTGAATTTAATATAGGCGG............................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.....................................................................................................................................................................................................................................................................................................................................................................................................................................................ATTAAATGGGAGTTTTTAAT......................................	20	2	0.50	0.50	0.00	0.00	0.00
...............................................................................................................................................................................................................................................................................................................................................................................GTTGAATCTATTATAGGTGGT...........................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................................................................................................................................................................................................................................................................................................................................................TTTCGTCAATTACATTGGAGT.............................................	21	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................................................................................................................................................................................................................................................................ATTGAATTTAATATAGGTGGT...........................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
................................................................................................................................................................................................................................................................................................................................................................................TTGAATTTATTATAGGTGGTT..........................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................................................................................................................................................................................................................................................ATTTTGxAGTAATTTTATTGAA..........................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................................................................................................................................................................................................................................TTCGTCAATTAGATTGGAGT.............................................	20	1	1.00	1.00	0.00	0.00	0.00
............................................................................................................................................................................................................................................................................................................................................................................................................................................TTTTCGTCAATTAAATTGGA...............................................	20	2	0.50	0.00	0.50	0.00	0.00
............................................................................................................................................................................................................................................................................................................................................................................................................................................TTTTCGTCAATTAAATTGGAG..............................................	21	2	0.50	0.50	0.00	0.00	0.00
............................................................................................................................................................................................................................................................................................................................................................................................TAGGTGGTTAAACAATA-------------------------------TTTTCGTCAAT........................................................	28	2	0.50	0.00	0.00	0.00	0.50
..............................................................................................................................................................................................................................................................................................................................................................................................................................................TTCGTCAATTAAATTGGAGTT............................................	21	2	0.50	0.00	0.50	0.00	0.00
...............................................................................................................................................................................................................................................................................................................................................................................ATTCAATTTATTATGGGT..............................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
.......................................................................................................................................................................................................................................................................................................................................................................................TATTATAGGTGGTTAAACA.....................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...................................................................................................................................................................................................................................................................................................................................................................................................................................................CAATTAAATTGGAGTTTTTA........................................	20	2	0.50	0.50	0.00	0.00	0.00
................................................................................................................................................................................................................................................................................................................................................................................TTGAATTTATTATAGGTGGT...........................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................................................................................................................................................................................................................................................................................GTGGTTAAACAATA-------------------------------TTTTCGT............................................................	21	2	0.50	0.00	0.00	0.50	0.00
..........................................................................................................................................................................................................................................................................................................................................................................................................ATA-------------------------------TTTTCGTCAATTAAATTGG................................................	22	2	0.50	0.50	0.00	0.00	0.00
................................................................................................................................................................................................................................................................................................................................................................................TTGAATTTATTATAGGGGGTTT.........................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00

droBip1

AAAACATA---CGTTTT--------TT----TCGCTCAGTGA-A----TTCTCTGCTCTC--------------AT---T-------------G--------TTT--------------------------TTC--TCTG---------------CTACGCA---------------------------------------------C-----------ACA---------------------CTCAAATT-TTAAACATGTGT------------------------TAGTTT-----------------------------------------------------------------TGCCCACCACTGGTTTAGATATACTCTCTCGAGTATAT----------------------------------------------CAAACACACAAAATATAATCTTCCGAAATAATCATACT---AATCCATAATA

Size

Hit Count

Total Norm

dp4

CATT--TTAAATATATT----TTAAAT----CTGAATTCAGTCT----GG------ACCT--------------AT---C-------------A--------CTTA---------------CTTCTTTCA-------AGTCTATTCCG------------AA----------------------------TATATCTTCAATCCGACACCTTTTTGAAACCGTCTTGAATCGAAATTTT--TTTTTTTTTT-AATAAAAAAAAT------------------------TGGATTC----------------------------------------------------------------ATT-TTTTAG-------------------------------------TGCC--------------------------------------------ATT----------------------TT-----------TAT	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.............................................................................................................................................................................................................................GTCTTxAAACGAAATTTT--TTT...........................................................................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
..................................................................................................................................................................................................................................GAAGTGAAATTTT--TTTTTT........................................................................................................................................................................................................................................................	19	2	0.50	0.00	0.50	0.00	0.00
..................................................................................................................................................................................................................................GAAGCGAAATTTT--GTTTT.........................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00

droPer1

ATTTCTAA---TCTG-----------T----TTCCGATAAG--T----GACGATCCATAT--------------AA---T-------------A--------TTGCACACTGACTTACGG-GCACTGTTG-------TA------------------------------------------------------------------------------------------------------------------AGTACATACAA------------------------ACGTAAT-------------------------------------CGCATTTACATATGGAAATAT---GTACCTCATT----------------TATAGTAT------------------------ATAGTATATTCATAGAAGTTTGC-----------------ACA----------------------TAAATATATATATATA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.................................................................................................................................................................................................................................................................................................................................................TTACATATGGATGTAT---GT.........................................................................................................................................	18	9	0.11	0.00	0.11	0.00	0.00	0.00

droWil1

AAATCAAA---T----T----TACATT----CTTTTTCCAACTT----GGGCTTTTTCTT--------------TT---T-------------T--------TTTT------------------------GTTC--TTAC---------------CTACGCAAAAGTAATAAGAGGTTCGATT--------------------------------------------------------------------------------------------------------------------ATCGCAATATATCGCATTTTCCGTCTGACATT-----------GTTCACAATTTTGTGTCAGTATTA-AGTTAATTTGCAATGCAACACAAAT-------------------------------------------------------------------------------------------------GAAATA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.................................................GGCAATTTCTT--------------TT---T-------------T--------TTT......................................................................................................................................................................................................................................................................................................................................................................................................	18	4	0.25	0.00	0.25	0.00	0.00
.......................................................................................................................................................................................................................................................................................................................................CACT-----------GTTCACAAATTTGT...........................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droVir3

TCCAATTAAAACAGTTA----T--TTC----CTCATAACAGTCA----TTCT---CTTTG--------------AC---C-------------G-C------TTTC------------------------GTG---AGCA---------------CTATCCA---------------------------------------------A-----------ACT---------------------ATTTTATTAAGTTAGAGTCGT------------------------TAGTTTTA-------------------------------AGTT-----------GCTTACAATTAATCGGGCATATATCGGGAATTTAGC--------------TAAACAAT---------------------------------------------------------------------------TATTTT---ATATATAAGCA	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
......................................................................................................TTTC------------------------GTG---AGCG---------------CTATCCA---------------------------------------------A-----------AC..................................................................................................................................................................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
...........................................................................................................................................................................................................................................................................................................................................................CAATTAGTCGGGCATATGTCGG..............................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
........................TTC----CTCATAACAGTTA----TTCT---ATTTG--------------AC---................................................................................................................................................................................................................................................................................................................................................................................................................................	27	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................................................................................................................................................................................................................................................................................................................................TTACAATTAATCGGGCATA....................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................................................................................................................................................................................................................................................................................................................................TTACAATTAATCGGGCATATGTCGG..............................................................................................................................	25	1	1.00	1.00	0.00	0.00	0.00	0.00
........................TTC----CTCATAACAGTCA----TTxT---TTTTG--------------A....................................................................................................................................................................................................................................................................................................................................................................................................................................	25	1	1.00	1.00	0.00	0.00	0.00	0.00
............................................................................................................................................................................................................................................................................................................................................................................GTCGGGAATTTAGC--------------TAAACAAT---------------------------------------------------------------------------TAT.................	25	1	1.00	0.00	0.00	0.00	1.00	0.00

droMoj3

GGCAAGCTTTGGAGCAT-ACAAGTTGT-----GCATAACTGACT----ATCATTGAACAT--------------AT---T-------------T--------TTTC------------------------CTATTCTTTC------CTATTA---TGTCGT--------------------------------------------------------------------------------------------ACAAATAATAT------------------------GTATTTTGT--------------GCA-----------------------------------AGC--------TTCCAAAAGGCATTCAACCCTATTTTGTAATAAAAAAAT----ATTTTTC--------------------------------------------AAA----------------------TA----AAAAATATAG	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
........................................................................................................................................................................................................................................................................................................T--------------GCA-----------------------------------CGC--------TTCCAAAAGTCA...........................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00

droGri2

TATGTGTA---TATATT----T--------------GAATATTT----AATTTC--TTTT---------------T---T-------------ATTTACTTATTTA------------------------ATG---TCAACTAAAGTC----AGTCTTCGCAAAAATTGCAAAAAGTCAGAAA----------------------------------------------------AACTTGAAATTAAATT-AAATGTAATATA-----------------CAATTTAAAATTAT-----------------------------------------------------------------------------------------------------------------AT--------------------------------------------ATA-------------TAAA----------TTACAAAATAA

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:35:16 EDT

sblock109902

chr3L:21200899-21201043 +

Candidate

three_prime_UTR

20-way Fast Statistical Aligner (FSA) re-alignment

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup