dme-mir-4917- Best orthologs

dme-mir-4917	chrX:14093578-14093654 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	mirtron

Legend:

   mature strand at position 14093578-14093602
   star strand at position 14093632-14093653
   mutations
   read mismatches

Notes: droVir3 and droGri2 orthologs are reported in two pieces by LASTZ suggesting that the orthologous intron is too long to span. droBip1 ortholog looks incorrected; splice sites are difficult to determine.

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chrX:14093563-14093669 +		1	GAGAGCCCCAGCAGAGTGAGTAGCGATGGGGGTCAGATG----GCCGTGGAAGA---------------------------------------------------------------------TATGT-----------------GACGATT---------------------GC--CC-----CCTTACTACTAT-----------------------------------------------CGTCTG--C-T----CAACAGGAAAGCA----A----------ACTACAT
droSim1	chrX_random:3764305-3764407 +	LASTZ	5	GAGAGCCCCA---GAGTGAGTAGCGATGGGGGTCAGATGGATGGCCGTGGATGA---------------------------------------------------------------------TATGT-----------------GACGATT---------------------GC---------CCTTACT---AC-----------------------------------------------GCTCTG--C-C----CAACAGGAAAGCA----A----------GCTACAT
droSec1	super_20:697977-698075 +	LASTZ	5	GAGAGCCCCA---GAGTGAGTAGCGATGGGGGTCAGATG----GCCGTGGATGA---------------------------------------------------------------------TATGT-----------------GACGATT---------------------GC---------CCTTACT---AC-----------------------------------------------GCTCTG--C-C----CAACAGGAAAGCA----A----------GCTACAT
droYak2	chrX:8347469-8347564 +	LASTZ	5	GAGAGCCCCA---GAGTAAGTAGCCAGGGGGATCAGGAG----GCCGCGGAAGG---------------------------------------------------------------------TATGT-----------------GATGATT---------------------CC---------CATT------AC-----------------------------------------------CCTCCG--A-T----CCACAGGAAAGCA----A----------CCTACAT
droEre2	scaffold_4690:12836867-12836962 -	LASTZ	5	GAGAGCCCCA---GAGTGAGTACGCAGTCGGGTCAGAAG----GCCGCGGAAGA---------------------------------------------------------------------TATGT-----------------GATGATT---------------------CC---------CATT------CC-----------------------------------------------CCTCCG--A-T----CAACAGGAAAGCA----A----------CCTACAC
droEug1	scf7180000409008:504391-504474 +	LASTZ	5	GAAAGCCCCA---GAGTGAGTAGAAGTGGGGGCGAGAAA----TCTACGGAAGA---------------------------------------------------------------------GATATGATCC--------A---TATGATT------------------------------------------------------------------------------------------------------------ACAGGAAAGCA----A----------CCTACAC
droBia1	scf7180000302041:1138735-1138821 +	LASTZ	5	GAAAGTCCTA---GGGTGAGTAGCGCCGC----CAT------------------------------------------------------------------------------------------ATGATCCATGACGCAC---GATGATT---------------------AC---------CCTA-------------------------------------------------------CCTCCG--A-T----CAGCAGGAAAGCA----A----------CCTACAC
droTak1	scf7180000415667:540030-540111 -	LASTZ	5	GAGAGCCCCA---GAGTGAGTAGTTTATA--TTT--------------------------------------------------------------------------------------------AAGATTC--------AAGAGATGATT---------------------TT---------TATA-------------------------------------------------------AATTTG--G-T----TAGCAGGAAAGCA----A----------CCTACAC
droEle1	scf7180000491011:415435-415552 -	LASTZ	5	GAGAGCCCCA---GAGTGAGTGAATGCATGGA----------------GAAAGC---------------------------------------------------------------------TACACGATCC--------C---AATGATA---------------------AC---------CATC--------CATCCAAC-----TATCCA--------TCCAACCAACCATCCG----GCGCCG--C-A----CAACAGGAGAGCA----G----------CCTACAG
droRho1	scf7180000776513:33442-33533 +	LASTZ	5	GAGAGCCCCA---GAGTGAGTAGTAGTGGTAGTAGA--G----ATCACCAATGA---------------------------------------------------------------------TTACC-----------------AATGATA---------------------AC---------CTTA-------------------------------------------------------CCTCCG--C-C----CAACAGGAAAACA----G----------CCTACAC
droFic1	scf7180000454073:905651-905737 -	LASTZ	5	GAGAGCCCCA---GAGTGAGTAGCGGGGA----------------------GAA---------------------------------------------------------------------TATGTGATCC--------A---ATTGATT---------------------GC---------CCTA-------------------------------------------------------ACTCCGTAC-C----AAGCAGGAAAGCAGCC-A----------CCTACAC
droKik1	scf7180000302517:390473-390554 -	LASTZ	5	GAAAGCCCCA---GAGTAAGTTTTAATTT-------------------------------------------------------------------------------------------------------------------------------------------------C---------TC-----------TCTAAAAAGCAATTTTTAAAG-------------------------CTTTTT--C-T----TTACAGGCAAGCAGCA-A----------CCTACAG
droAna3	scaffold_13047:1616598-1616749 +	LASTZ	5	GATACCCCGA---GAGTGAGTTAAATAGGTAGACT----------------------GGGTTTTACGGGTTTTGG-GGATTAGGGTTAAGGGGTTTAAGGATCAGGGACTTGGCTAGAAGGACCAAAGGACTT--------A---AGAACTA---------------------AC---------AAAA------AT-----------------------------------------------TCACCA--T-T----CCACAGGCAAGCA----C----------GGTACAC
droBip1	scf7180000396740:414605-414756 +	LASTZ	0	GATACCCCGA---GAGTGAGTTAAATAGGTAGAATT--T----ATCGTAA--CCTATGGGGTTTACGGGTTTTTGGG--------GCAAAGGGCTTAAGGGTTA----------------------AAGATTA--------AA--ATCAAAA---------------------AC---------TTTA-------------------------------------------------------ATAACTTAA-C----GGGTTAAAAGTCAGACAATCGAACGGATGGATCTT
dp4	chrXL_group1e:6144259-6144391 -	LASTZ	5	GAAAACTCCA---GAGTGAGTTGAGTGAG--GTT--------------------------------------------------------------------------------------------GAGAGCCGGGGTGCTC-G-GAAGACCATCCTCACTGATCCTATTCTAAT---------CTTC--------CCCTCTTT-----CGTCTATATCTCTCTC------------------TCTCTC--G-T----CCGCAGGCAAGCG----A----------ACTATAC
droPer1	super_21:1109353-1109492 -	LASTZ	5	GAAAACTCCA---GAGTGAGTGGTTGAGA--GCCGGG---------------------------------------------------------------------------------------------------GTGCTC-GCAA-GACCTTCCTCACTGATCCTATTCTAAT---------CTTC--------CCCTCTTT-----CGTCTATATCTCTCTCTCTCTCTCTCTCTC----GCTCTC--G-T----CCGCAGGCAAGCG----A----------ACTATAC
droWil1	scaffold_180702:2428501-2428590 +	LASTZ	5	GAGAACACAA---GGGTGAGTGGGAGGAGAGATGAGAGG----AGAATGGAC---------------------------------------------------------------------------------------------TTTAACC---------------------GC---------CATTATT----------------------------------------------------TCTTTC--T-T----CCACAGGGAAGTG----A----------ACTACAA
droVir3	scaffold_12932:1910954-1911056 +	LASTZ	5	AGGAACGGCA---GCAGCAGCGGCAGCGGCGGCGGCGCC----ACC---GTCAG---------------------------------------------------------------------TTGGT-----------------GCTGCGC---------------------CC---------GCTG-------------------------CACAG------------------CC-----GCCGCC--CTCGGCAGGCGAAGCAGCCG----C----------TAAATCC
droMoj3	scaffold_6359:2739408-2739517 -	LASTZ	5	GAAAACACAA---GAGTGAGTGACAAGATTTATATATAT----TTA-------------------------------------------------------------------------------TAGGAATA--------T---AATACTA---------------------ATTCTTATCTACGT--------------------------TATTC------------------CCGTCTCACTCAA--T-C----AATTAGTCGAGCC----G----------AATACAT
droGri2	scaffold_15081:1312788-1312809 -	LASTZ	5	T-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAACAGTCGAGCG----A----------AATACAG

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	GAGAGCCCCAGCAGAGTGAGTAGCGAT-------------------------------------------------------------------GGGGGTCAGATG----GCCGTGGAAGATATGT----------------GACGATT---------------------GC--CC-----CCTTACTACTA------------------------------------TCGT--CTGCTCAAC-----AGGAAAGCA---AACTACAT
droSim1	GAGAGCCCCA---GAGTGAGTAGCGAT-------------------------------------------------------------------GGGGGTCAGATGGATGGCCGTGGATGATATGT----------------GACGATT---------------------GC---------CCTTACT---A------------------------------------CGCT--CTGCCCAAC-----AGGAAAGCA---AGCTACAT
droSec1	GAGAGCCCCA---GAGTGAGTAGCGAT-------------------------------------------------------------------GGGGGTCAGATG----GCCGTGGATGATATGT----------------GACGATT---------------------GC---------CCTTACT---A------------------------------------CGCT--CTGCCCAAC-----AGGAAAGCA---AGCTACAT
droYak2	GAGAGCCCCA---GAGTAAGTAGCCAG-------------------------------------------------------------------GGGGATCAGGAG----GCCGCGGAAGGTATGT----------------GATGATT---------------------CC---------CATT------A------------------------------------CCCT--CCGATCCAC-----AGGAAAGCA---ACCTACAT
droEre2	GAGAGCCCCA---GAGTGAGTACGCAG-------------------------------------------------------------------TCGGGTCAGAAG----GCCGCGGAAGATATGT----------------GATGATT---------------------CC---------CATT------C------------------------------------CCCT--CCGATCAAC-----AGGAAAGCA---ACCTACAC
droEug1	GAAAGCCCCA---GAGTGAGTAGAAGT-------------------------------------------------------------------GGGGGCGAGAAA----TCTACGGAAGAGATATGATCCA----------TATGATT--------------------------------------------------------------------------------------------AC-----AGGAAAGCA---ACCTACAC
droBia1	GAAAGTCCTA---GGGTGAGTAGCGCC-------------------------------------------------------------------G----CCATA---------------------TGATCCATGACGCAC--GATGATT---------------------AC---------CCTA------C--------------------------------------CT--CCGATCAGC-----AGGAAAGCA---ACCTACAC
droTak1	GAGAGCCCCA---GAGTGAGTAGTTTA-------------------------------------------------------------------T--ATT----------------TA-------AGATTCAAG-------AGATGATT---------------------TT---------TATA------A--------------------------------------AT--TTGGTTAGC-----AGGAAAGCA---ACCTACAC
droEle1	GAGAGCCCCA---GAGTGAGTGAATGC-------------------------------------------------------------------ATGGA----------------GAAAGCTACACGATCCC----------AATGATA---------------------AC---------CATC------CATCCAACTAT--------CCATCCAACCAACCATCCGGCG--CCGCACAAC-----AGGAGAGCA---GCCTACAG
droRho1	GAGAGCCCCA---GAGTGAGTAGTAGT-------------------------------------------------------------------GGTAGTAGA--G----ATCACCAATGATTACC----------------AATGATA---------------------AC---------CTTA------C--------------------------------------CT--CCGCCCAAC-----AGGAAAACA---GCCTACAC
droFic1	GAGAGCCCCA---GAGTGAGTAGCGGG-------------------------------------------------------------------G----------------------AGAATATGTGATCCA----------ATTGATT---------------------GC---------CCTA------A--------------------------------------CTCCGTACCAAGC-----AGGAAAGCAGCCACCTACAC
droKik1	GAAAGCCCCA---GAGTAAGTTTTAAT-------------------------------------------------------------------TTCTCTC---------------TA-------AAAAG--------------CAATT---------------------TT-------------------------------TAAAG---------------------CTT--TTTCTTTAC-----AGGCAAGCAGCAACCTACAG
droAna3	GATACCCCGA---GAGTGAGTTAAATAGGTAGACTGGGTTTTACGGGTTTTGGGGATTAGGGTTAAGGGGTTTAAGGATCAGGGACTTGGCTAGAAGGACCAAA---------------------GGACTTA----------AGAACTA---------------------AC---------AAAA------A------------------------------------TTCA--CCATTCCAC-----AGGCAAGCA---CGGTACAC
dp4	GAAAACTCCA---GAGTGAGTTGAGTG-------------------------------------------------------------------A-GGTTG------------------------AGAGCCGGGGTGCTCG-GAAGACCATCCTCACTGATCCTATTCTAAT---------CTTC------CCCTCTTTCGTCTATATCTCTCT--------------CTCT--CTCGTCCGC-----AGGCAAGCG---AACTATAC
droPer1	GAAAACTCCA---GAGTGAGTGGTTGA-------------------------------------------------------------------G--AGCCGGG------------------------------GTGCTCGCAA-GACCTTCCTCACTGATCCTATTCTAAT---------CTTC------CCCTCTTTCGTCTATATCTCTCTCTCTCTCTCTCTCTCGCT--CTCGTCCGC-----AGGCAAGCG---AACTATAC
droWil1	GAGAACACAA---GGGTGAGTGGGAGG-------------------------------------------------------------------AGAGATGAGAGG----AGAATGGAC-----------------------TTTAACC---------------------GC---------CATTATT---T--------------------------------------CT--TTCTTCCAC-----AGGGAAGTG---AACTACAA
droVir3	AGGAACGGCA---GCAGCAGCGGCAGC-------------------------------------------------------------------GGCGGCGGCGCC----ACC---GTCAGTTGGT----------------GCTGCGC---------------------CC---------GCTG------------------CACAGCC-------------------GCC--GCCCTCGGCAGGCGAAGCAGCCG---CTAAATCC
droMoj3	GAAAACACAA---GAGTGAGTGACAAG-------------------------------------------------------------------ATTTATATATAT----TTA---TA-------GGAATAT----------AATACTA---------------------ATTCTTATCTACGTTATT---C----------------CCGTCT--------------CACT--CAATCAATT-----AGTCGAGCC---GAATACAT
droGri2	T----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAAC-----AGTCGAGCG---AAATACAG

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																				None

Small RNA-seq read pileup

Species

Alignment

droSim1

GAGAGCCCCA---GAGTGAGTAGCGATGGGGGTCAGATGGATGGCCGTGGATGA---------------------------------------------------------------------TATGT-----------------GACGATT---------------------GC---------CCTTACT---AC-----------------------------------------------GCTCTG--C-C----CAACAGGAAAGCA----A----------GCTACAT

Size

Hit Count

Total Norm

V044
Embryo

M023
Head

M024
Male body

M025
Embryo

droSec1

GAGAGCCCCA---GAGTGAGTAGCGATGGGGGTCAGATG----GCCGTGGATGA---------------------------------------------------------------------TATGT-----------------GACGATT---------------------GC---------CCTTACT---AC-----------------------------------------------GCTCTG--C-C----CAACAGGAAAGCA----A----------GCTACAT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.........A---GAGTGAGTAGCCATGGAG......................................................................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00
..................AGTAGCGATGCTGGTCAG.................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00

droYak2

GAGAGCCCCA---GAGTAAGTAGCCAGGGGGATCAGGAG----GCCGCGGAAGG---------------------------------------------------------------------TATGT-----------------GATGATT---------------------CC---------CATT------AC-----------------------------------------------CCTCCG--A-T----CCACAGGAAAGCA----A----------CCTACAT

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

GAGAGCCCCA---GAGTGAGTACGCAGTCGGGTCAGAAG----GCCGCGGAAGA---------------------------------------------------------------------TATGT-----------------GATGATT---------------------CC---------CATT------CC-----------------------------------------------CCTCCG--A-T----CAACAGGAAAGCA----A----------CCTACAC

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droEug1

GAAAGCCCCA---GAGTGAGTAGAAGTGGGGGCGAGAAA----TCTACGGAAGA---------------------------------------------------------------------GATATGATCC--------A---TATGATT------------------------------------------------------------------------------------------------------------ACAGGAAAGCA----A----------CCTACAC

Size

Hit Count

Total Norm

droBia1

GAAAGTCCTA---GGGTGAGTAGCGCCGC----CAT------------------------------------------------------------------------------------------ATGATCCATGACGCAC---GATGATT---------------------AC---------CCTA-------------------------------------------------------CCTCCG--A-T----CAGCAGGAAAGCA----A----------CCTACAC

Size

Hit Count

Total Norm

droTak1

GAGAGCCCCA---GAGTGAGTAGTTTATA--TTT--------------------------------------------------------------------------------------------AAGATTC--------AAGAGATGATT---------------------TT---------TATA-------------------------------------------------------AATTTG--G-T----TAGCAGGAAAGCA----A----------CCTACAC

Size

Hit Count

Total Norm

droEle1

GAGAGCCCCA---GAGTGAGTGAATGCATGGA----------------GAAAGC---------------------------------------------------------------------TACACGATCC--------C---AATGATA---------------------AC---------CATC--------CATCCAAC-----TATCCA--------TCCAACCAACCATCCG----GCGCCG--C-A----CAACAGGAGAGCA----G----------CCTACAG

Size

Hit Count

Total Norm

droRho1

GAGAGCCCCA---GAGTGAGTAGTAGTGGTAGTAGA--G----ATCACCAATGA---------------------------------------------------------------------TTACC-----------------AATGATA---------------------AC---------CTTA-------------------------------------------------------CCTCCG--C-C----CAACAGGAAAACA----G----------CCTACAC

Size

Hit Count

Total Norm

droFic1

GAGAGCCCCA---GAGTGAGTAGCGGGGA----------------------GAA---------------------------------------------------------------------TATGTGATCC--------A---ATTGATT---------------------GC---------CCTA-------------------------------------------------------ACTCCGTAC-C----AAGCAGGAAAGCAGCC-A----------CCTACAC

Size

Hit Count

Total Norm

droKik1

GAAAGCCCCA---GAGTAAGTTTTAATTT-------------------------------------------------------------------------------------------------------------------------------------------------C---------TC-----------TCTAAAAAGCAATTTTTAAAG-------------------------CTTTTT--C-T----TTACAGGCAAGCAGCA-A----------CCTACAG

Size

Hit Count

Total Norm

droAna3

GATACCCCGA---GAGTGAGTTAAATAGGTAGACT----------------------GGGTTTTACGGGTTTTGG-GGATTAGGGTTAAGGGGTTTAAGGATCAGGGACTTGGCTAGAAGGACCAAAGGACTT--------A---AGAACTA---------------------AC---------AAAA------AT-----------------------------------------------TCACCA--T-T----CCACAGGCAAGCA----C----------GGTACAC	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
..............................AGCCT----------------------GGGTTTTACGCG................................................................................................................................................................................................................................	17	1	1.00	0.00	0.00	1.00	0.00
.......................................................................................................................................................A---------------------AC---------AAAA------AT-----------------------------------------------TCGTCA--T-T----CC.................................	19	1	1.00	0.00	0.00	0.00	1.00
..................................T----------------------GGGTTTTGCGGATTTTG...........................................................................................................................................................................................................................	18	2	0.50	0.00	0.00	0.50	0.00
..............................................................TTACGGGTTATGG-GGATG....................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00

droBip1

GATACCCCGA---GAGTGAGTTAAATAGGTAGAATT--T----ATCGTAA--CCTATGGGGTTTACGGGTTTTTGGG--------GCAAAGGGCTTAAGGGTTA----------------------AAGATTA--------AA--ATCAAAA---------------------AC---------TTTA-------------------------------------------------------ATAACTTAA-C----GGGTTAAAAGTCAGACAATCGAACGGATGGATCTT

Size

Hit Count

Total Norm

dp4

GAAAACTCCA---GAGTGAGTTGAGTGAG--GTT--------------------------------------------------------------------------------------------GAGAGCCGGGGTGCTC-G-GAAGACCATCCTCACTGATCCTATTCTAAT---------CTTC--------CCCTCTTT-----CGTCTATATCTCTCTC------------------TCTCTC--G-T----CCGCAGGCAAGCG----A----------ACTATAC

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

GAAAACTCCA---GAGTGAGTGGTTGAGA--GCCGGG---------------------------------------------------------------------------------------------------GTGCTC-GCAA-GACCTTCCTCACTGATCCTATTCTAAT---------CTTC--------CCCTCTTT-----CGTCTATATCTCTCTCTCTCTCTCTCTCTC----GCTCTC--G-T----CCGCAGGCAAGCG----A----------ACTATAC	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
..............................................................................................................................................................................................................................CTCTCTCTCTCTGTCGC----GC................................................	19	12	0.17	0.00	0.00	0.00	0.00	0.17
................................................................................................................................................................................................................................CTCTCTCTCTCTGTC----GCGC..............................................	19	12	0.17	0.00	0.00	0.00	0.00	0.17
............................................................................................................................................................................................................................................ATC----GCTCTC--G-T----ACGCAGG............................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
.................................................................................................................................................................................................................................TCTCTCTCTCTCTC----GCTG..............................................	18	17	0.06	0.00	0.00	0.00	0.00	0.06
............................................................................................................................................................................................................................CGCTCTGTCTCTCTCTCTC----GCT...............................................	22	7	0.14	0.00	0.00	0.00	0.00	0.14
......................................................................................................................................................................................................................ATAGCTCTCTCTCTCTCCCTCT.........................................................	22	3	0.33	0.00	0.33	0.00	0.00	0.00
..................................................................................................................................................................................................................................CTCTCTCTCTCGC----GCACT.............................................	18	14	0.07	0.00	0.00	0.00	0.00	0.07

droWil1

GAGAACACAA---GGGTGAGTGGGAGGAGAGATGAGAGG----AGAATGGAC---------------------------------------------------------------------------------------------TTTAACC---------------------GC---------CATTATT----------------------------------------------------TCTTTC--T-T----CCACAGGGAAGTG----A----------ACTACAA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
........AA---GGGTGGGTxGGAGGAGA.......................................................................................................................................................................................................................................................................	18	1	2.00	0.00	2.00	0.00	0.00
.........................AGAGAGATGAGAGA----AGAA......................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
....ACACAA---GGGGGAGAGGGA............................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
........................AGAAGAGATGAGATG----AGA.......................................................................................................................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
...................GTCGGTGGAGAGATGAGA................................................................................................................................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
............................AAGAGGAGAGG----AGAATGGA..................................................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
............................GAGATGAGAxG----AGAATGAA..................................................................................................................................................................................................................................................	18	12	0.08	0.00	0.00	0.08	0.00

droVir3

AGGAACGGCA---GCAGCAGCGGCAGCGGCGGCGGCGCC----ACC---GTCAG---------------------------------------------------------------------TTGGT-----------------GCTGCGC---------------------CC---------GCTG-------------------------CACAG------------------CC-----GCCGCC--CTCGGCAGGCGAAGCAGCCG----C----------TAAATCC	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.................CAGCGGCAGTGGCGGCGGCG................................................................................................................................................................................................................................................................	20	19	0.05	0.05	0.00	0.00	0.00	0.00
................GCAGTGGCAGCCGCGGCGGCG................................................................................................................................................................................................................................................................	21	2	0.50	0.00	0.50	0.00	0.00	0.00
.......GCA---GCAGCAGCGGCGGCGGCGTC....................................................................................................................................................................................................................................................................	23	42	0.02	0.02	0.00	0.00	0.00	0.00
...............AGCAGCGGCAGCGGCGCCGGC.................................................................................................................................................................................................................................................................	21	33	0.03	0.00	0.00	0.03	0.00	0.00
................GCAGCAGCAGCGGCGGCGGCGTC----..........................................................................................................................................................................................................................................................	23	42	0.02	0.02	0.00	0.00	0.00	0.00
........CA---GCAGCAGCGGCGGCGGCGG.....................................................................................................................................................................................................................................................................	21	45	0.02	0.02	0.00	0.00	0.00	0.00
...............AGCAGCGGCGGCGGCGGAGGC.................................................................................................................................................................................................................................................................	21	24	0.04	0.04	0.00	0.00	0.00	0.00
.......GCA---GCAGCATTGGCAGCGGC.......................................................................................................................................................................................................................................................................	20	42	0.02	0.00	0.00	0.02	0.00	0.00
.........A---GCAGCAGCGGCAGAGGGG......................................................................................................................................................................................................................................................................	19	10	0.10	0.10	0.00	0.00	0.00	0.00
...............AGCAGCGGCACCGGCGGCGG..................................................................................................................................................................................................................................................................	20	34	0.03	0.03	0.00	0.00	0.00	0.00
........GA---GCAGCAGCGGCAGAGGC.......................................................................................................................................................................................................................................................................	19	46	0.02	0.00	0.00	0.02	0.00	0.00
..............CAGCAGCGGCAGCGGCGGCGG..................................................................................................................................................................................................................................................................	21	31	0.03	0.03	0.00	0.00	0.00	0.00
.........A---GTAGCAGCGGCAGCGGCC......................................................................................................................................................................................................................................................................	19	30	0.03	0.00	0.00	0.03	0.00	0.00
...................GCGGCAGCGGCGGCGGCGGC----C.........................................................................................................................................................................................................................................................	21	38	0.03	0.00	0.00	0.03	0.00	0.00
..................AGTGGCAGCGGCGGCGGCGG...............................................................................................................................................................................................................................................................	20	22	0.05	0.05	0.00	0.00	0.00	0.00

droMoj3

GAAAACACAA---GAGTGAGTGACAAGATTTATATATAT----TTA-------------------------------------------------------------------------------TAGGAATA--------T---AATACTA---------------------ATTCTTATCTACGT--------------------------TATTC------------------CCGTCTCACTCAA--T-C----AATTAGTCGAGCC----G----------AATACAT	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
...........................................TGA-------------------------------------------------------------------------------TAGGAATA--------T---TATACT..............................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00

droGri2

T-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAACAGTCGAGCG----A----------AATACAG

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:33:52 EDT

dme-mir-4917

chrX:14093578-14093654 +

Known_mirbase

mirtron

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