dme-mir-3643

chr2R:13653898-13653965 -

Known_mirbase
[View on miRBase] [View on UCSC Genome Browser {Cornell Mirror}]

tailed_mirtron

Legend:

   mature strand at position 13653944-13653965
   star strand at position 13653910-13653931
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

12-way Fast Statistical Aligner re-alignment (From MAFs)

Species Coordinate Alignment
dm3 chr2R:13653883-13653980 - GAATCCAAGCTGAACGTGAGTTT-A--TCTAAATATG-CCCATTTATCAATAG-TCATAC----------TTATTTA-----T-------GC-TCCTTTA--ACTCCTTGCAGAGCTTCGAAAAAGAC
droSim1 chr2R:12393703-12393800 - GAGTCCAAGCTGAACGTGGGTTT-A--TCTAGATACG-CCCATTTATCATTGG-TCATAC----------TTATTTA-----T-------GT-TCCTTTA--ACTCCTTGCAGAGCTTCGAAAAAGAC
droSec1 super_1:11152590-11152687 - GAGTCCAAGCTGAACGTGGGTTT-A--TCTATTTACG-CCCATTTATCATTGG-TCATAC----------TTATTTA-----T-------GT-TCCTTTA--ACGCCTTGCAGAGCTTCGAAAAAGAC
droYak2 chr2R:15527673-15527770 + GAATCCAAGCTGAACGTGGGTTC-A--TCTAGATACT-TCCATATATCAAAAG-CCGTAC----------TTATTTA-----T-------GT-TATTTAA--ACTGCTTGCAGAGCTTCGAAAAAGAC
droEre2 scaffold_4845:7883019-7883116 - GAATCCAAGCTGAACGTGGGTTT-T--TCTAGATACG-CCCATTTATCAATGG-CCCTAC----------TTATTTA-----T-------GC-ATTTTAA--ACTCCTTGCAGAGCTTCGAAAAAGAC
droAna3 scaffold_13266:10531972-10532067 + GAATCCAAGCTGAACGTTAGTTACT--TGTGCA-A---CTCGT------------CCAATCGGTTC-AATAACTAGA-----T-------CC-TCCTTTACATCTCCTTGTAGGGCTTCGAGAAGGAC
dp4 chr3:16466931-16467019 - GAATCCAAGCTGAACGTAAGTGC-TTAGCAA---ATG-TTCACTGAACCTTGAAT----------------CATTGCCTTTG------------------TTCTCGGTTCCAGAGCTTCGAAAAGGAC
droPer1 super_4:295271-295359 + GAATCCAAGCTGAACGTAAGTGC-TTAGCAA---ATG-TTCACTGAACCTTGAAT----------------CATTGCCTTTG------------------TTCTCGGTTCCAGAGCTTCGAAAAGGAC
droWil1 scaffold_181141:4609865-4609965 + GAATCAAAATTGAATGTAAGCTG---------A-AAA------------TTTAATTT---ATATTTTGTTTTCTCCTATTTACATACCACGTGTCCTTCA--CTCAATTACAGAGCTTCGAAAAGGAT
droVir3 scaffold_12875:16919908-16919994 - GAATCCAAACTAAATGTGAGTAT-C--TCCTAA-TCGCCTCAT------------CCAAT----------TCATTTT-----T-------GA-CCCTTTG--CCTACTTTTAGAACTTTGAAAAAGAC
droMoj3 scaffold_6496:11084070-11084155 + GAATCTAAACTAAATGTAGGTAT-A--GTAA---TAG-ATGAGTTTTTCTTTTAT----------------TTTAACC-----------------TTTGG--CCCGCTTGCAGAACTTTGAGAAGGAC
droGri2 scaffold_15245:16459236-16459327 - GAATCCAAACTAAATGTGAGATACC--TCTAAA-ACAAATCAT------------AA---AGATTTTGATGTATTGAGATTA------------------TGTACATTTGCAGAACTTTGAGAAAGAC

20-way Fast Statistical Aligner re-alignment (Top LASTZ hits)

Species Coordinate Lastz Id Alignment
dm3 chr2R:13653883-13653980 - NA GAATCCAAGCTGAACGTGAGTTTATC-TA--AATATG-CCCA-------------TTTATCAATAGTCATA--CTTATTTATG----------C--------T-----CCTTTAACTCCTTGCAGAGCTTCGAAAAAGAC
droSim1 chr2R:12393703-12393800 - 1 GAGTCCAAGCTGAACGTGGGTTTATC-TA--GATACG-CCCA-------------TTTATCATTGGTCATA--CTTATTTATG----------T--------T-----CCTTTAACTCCTTGCAGAGCTTCGAAAAAGAC
droSec1 super_1:11152590-11152687 - 1 GAGTCCAAGCTGAACGTGGGTTTATC-TA--TTTACG-CCCA-------------TTTATCATTGGTCATA--CTTATTTATG----------T--------T-----CCTTTAACGCCTTGCAGAGCTTCGAAAAAGAC
droYak2 chr2R:15527673-15527770 + 1 GAATCCAAGCTGAACGTGGGTTCATC-TA--GATACT-TCCA-------------TATATCAAAAGCCGTA--CTTATTTATG----------T--------T-----ATTTAAACTGCTTGCAGAGCTTCGAAAAAGAC
droEre2 scaffold_4845:7883019-7883116 - 1 GAATCCAAGCTGAACGTGGGTTTTTC-TA--GATACG-CCCA-------------TTTATCAATGGCCCTA--CTTATTTATG----------C--------A-----TTTTAAACTCCTTGCAGAGCTTCGAAAAAGAC
droEug1 scf7180000409672:1451984-1452077 + 1 GAATCCAAGCTGAACGTGAGTTCTTC-TA--TATACG-CCCA-------------CATGTCGGTACCTC------TTCTTATG----------C--------T-----TCCTTTACGTTTCGTAGAGTTTTGAAAAGGAC
droBia1 scf7180000301754:2921050-2921150 + 1 GAATCCAAGCTGAACGTGCGTCTCTT-AAAACACACG-CCCA-------------TTTATCTGTATCCC------TACTTACGCTC-------G--------TC---CTTTTTTACTGATTGTAGAGCTTCGAGAAGGAC
droTak1 scf7180000415313:36259-36358 + 1 GAATCCAAGCTGAACGTGGGTTCTGTCTA-ACATACG-CCGA-------------AATATATGTATCCC------TACTTATGCTA-----C-T--------C-----CTTTTGACTCCTTGCAGAGCTTCGAAAAGGAC
droEle1 scf7180000491214:594780-594873 + 2 GAATCCAAGCTAAACGTGGGTTCTCC-CA--TATACG-CCCA-------------TTTGCCTGTACCC------CTATTTATG----------C--------T-----CCATTGACTTTTTGCAGAGCTTCGAAAAGGAC
droRho1 scf7180000777956:135402-135495 + 2 GAATCCAAGCTGAACGTGGGTTCTCC-TA--TACACG-CCCA-------------TATGTCTGTACCCA------TGTTTATG----------C--------T-----CCTTTGACTCCTTGCAGAGCTTCGAAAAGGAC
droFic1 scf7180000453948:1793989-1794080 + 1 GAATCCAAGCTGAACGTATGTTTTTT-CT--CACACG-CCCA-------------TTTGT--GTATC------CCTATTTATG----------C--------T-----TCATTATCTCCTTGCAGAGCTTCGAAAAGGAC
droKik1 scf7180000302385:414803-414893 - 1 GAGTCCAAGCTGAACGTGGGTCCTTCCTA--GACACG-CCCA-------------TTTTT--------ACA--CGTATTAATA----------C--------T-----CCCTTAACTCCTTGCAGAGCTTCGAGAAGGAC
droAna3 scaffold_13266:10531972-10532067 + 1 GAATCCAAGCTGAACGTTAGTTACTT-GTGCAACTCG-TCCA-------------ATCGG---TT-C--AATAACTA--GATC----------C--------TC---CTTTACATCTCCTTGTAGGGCTTCGAGAAGGAC
droBip1 scf7180000396428:953655-953755 + 1 GAATCCAAGCTGAACGTTAGTTAATT-AC--TACACC-CCTC-------------TAAAACCTGTGCAATA--ACTA--GACC----------A--------TCCATCTTTCCATCTTCTTGTAGAGCTTCGAGAAGGAC
dp4 chr3:16466931-16467019 - 1 GAATCCAAGCTGAACGTAAGTGCTTA-G---CAAATG-TTCACTGAACCTTGAAT------------------------CAT---------TGC--------C-----TTTGTTCTCGGTTCCAGAGCTTCGAAAAGGAC
droPer1 super_4:295271-295359 + 2 GAATCCAAGCTGAACGTAAGTGCTTA-G---CAAATG-TTCACTGAACCTTGAAT------------------------CAT---------TGC--------C-----TTTGTTCTCGGTTCCAGAGCTTCGAAAAGGAC
droWil1 scaffold_181141:4609865-4609965 + 2 GAATCAAAATTGAATGTAAGCTGA----------------------AAATTTAA-TTTATATTTTGT------TTTCTCCTAT---TTACA--TACCACGTGT-----CCTTCACTCAATTACAGAGCTTCGAAAAGGAT
droVir3 scaffold_12875:16919908-16919994 - 1 GAATCCAAACTAAATGTGAGTATCTC-CT--AAT-CGCCTCA-------------TCCA-----------A--TTCATTTTTG----------A--------C-----CCTTTGCCTACTTTTAGAACTTTGAAAAAGAC
droMoj3 scaffold_6496:11084070-11084155 + 1 GAATCTAAACTAAATGTAGGTATAGT-AA--TAGATG----AGTTTTTCTTTTAT------------------------TTT---------A-A--------C-----CTTTGGCCCGCTTGCAGAACTTTGAGAAGGAC
droGri2 scaffold_15245:16459236-16459327 - 1 GAATCCAAACTAAATGTGAGATACCTCTA-AAACAAA-T-CA-------------TAAA----GATTTTGA--TGTATTGAGA--------------------------TTATGTACATTTGCAGAACTTTGAGAAAGAC

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species Alignment
dm3
GAATCCAAGCTGAACGTGAGTTT-A--TCTAAATATG-CCCATTTATCAATAG-TCATAC----------TTATTTA-----T-------GC-TCCTTTA--ACTCCTTGCAGAGCTTCGAAAAAGACSizeHit CountTotal Norm
droSim1
GAGTCCAAGCTGAACGTGGGTTT-A--TCTAGATACG-CCCATTTATCATTGG-TCATAC----------TTATTTA-----T-------GT-TCCTTTA--ACTCCTTGCAGAGCTTCGAAAAAGACSizeHit CountTotal NormV044
Embryo		M023
Head		M024
Male body		M025
Embryo
............................................................................................................TGAACAGCTTCGAAAAAGA.1911.000.001.000.000.00
droSec1
GAGTCCAAGCTGAACGTGGGTTT-A--TCTATTTACG-CCCATTTATCATTGG-TCATAC----------TTATTTA-----T-------GT-TCCTTTA--ACGCCTTGCAGAGCTTCGAAAAAGACSizeHit CountTotal NormV113
Male body		V114
Embryo		V115
Head
droYak2
GAATCCAAGCTGAACGTGGGTTC-A--TCTAGATACT-TCCATATATCAAAAG-CCGTAC----------TTATTTA-----T-------GT-TATTTAA--ACTGCTTGCAGAGCTTCGAAAAAGACSizeHit CountTotal NormV046
Embryo		V052
Head		V120
Male body		V058
Head		M026
Head
.......................................................................TATTTA-----T-------AT-TGTTTAA--AC........................1811.000.000.000.001.000.00
........GTTGGACGTGGGTTC-A--T....................................................................................................1711.000.000.000.001.000.00
........GTTGAACGTGGGTTA-A--TC...................................................................................................1811.000.000.000.001.000.00
........................................................................ATTTA-----T-------GT-TCTTGAA--ACT.......................1811.000.000.001.000.000.00
........GCTGGACGTGGGTTC-G--TC...................................................................................................1811.000.000.000.001.000.00
droEre2
GAATCCAAGCTGAACGTGGGTTT-T--TCTAGATACG-CCCATTTATCAATGG-CCCTAC----------TTATTTA-----T-------GC-ATTTTAA--ACTCCTTGCAGAGCTTCGAAAAAGACSizeHit CountTotal NormV040
Embryo		V060
Head		V047
Embryo		V108
Head
......AAGCTGAACGAGAGTTT-T--T....................................................................................................1912.002.000.000.000.00
.......AGCTGAACGAGAGTTT-T--T....................................................................................................1812.000.000.000.002.00
..ATCCAAGCTGAACGAGAG............................................................................................................1811.000.000.000.001.00
........GATGAACGTGGGTTT-G--TC...................................................................................................1811.000.000.001.000.00
....CCAAGCTGAACGTGCGCT..........................................................................................................1811.000.000.001.000.00
droAna3
GAATCCAAGCTGAACGTTAGTTACT--TGTGCA-A---CTCGT------------CCAATCGGTTC-AATAACTAGA-----T-------CC-TCCTTTACATCTCCTTGTAGGGCTTCGAGAAGGACSizeHit CountTotal NormV105
Male body		V106
Head		V055
Unknown		V039
Embryo
...............................................................................................................................T2020.500.500.000.000.00
dp4
GAATCCAAGCTGAACGTAAGTGC-TTAGCAA---ATG-TTCACTGAACCTTGAAT----------------CATTGCCTTTG------------------TTCTCGGTTCCAGAGCTTCGAAAAGGACSizeHit CountTotal NormV112
Male body		V043
Embryo		V051
Head		M022
Male body
droPer1
GAATCCAAGCTGAACGTAAGTGC-TTAGCAA---ATG-TTCACTGAACCTTGAAT----------------CATTGCCTTTG------------------TTCTCGGTTCCAGAGCTTCGAAAAGGACSizeHit CountTotal NormV111
Male body		V042
Embryo		V050
Head		V057
Head		M021
Embryo
droWil1
GAATCAAAATTGAATGTAAGCTG---------A-AAA------------TTTAATTT---ATATTTTGTTTTCTCCTATTTACATACCACGTGTCCTTCA--CTCAATTACAGAGCTTCGAAAAGGATSizeHit CountTotal NormV117
Male body		V118
Embryo		V119
Head		M020
Head
...........................................................................................................TTACAGAGxTTCGACAAGG..1811.000.001.000.000.00
....................................A------------TTCAATTT---ATxTTTTGTT..........................................................1811.000.001.000.000.00
....................................A------------TTTxATTT---ATATTTTATTT.........................................................1911.000.001.000.000.00
.............................................................................................................ACAGAGCCTCGAAAGGGA.1811.000.001.000.000.00
......................................................TTT---ATATTTTGTTTTGTT.....................................................1811.000.001.000.000.00
droVir3
GAATCCAAACTAAATGTGAGTAT-C--TCCTAA-TCGCCTCAT------------CCAAT----------TCATTTT-----T-------GA-CCCTTTG--CCTACTTTTAGAACTTTGAAAAAGACSizeHit CountTotal NormV116
Male body		V053
Unknown		V047
Embryo		M027
Male body		M028
Head
droMoj3
GAATCTAAACTAAATGTAGGTAT-A--GTAA---TAG-ATGAGTTTTTCTTTTAT----------------TTTAACC-----------------TTTGG--CCCGCTTGCAGAACTTTGAGAAGGACSizeHit CountTotal NormV110
Male body		V056
Unknown		V049
Head		V041
Embryo
...........AAATTTAGATAT-A--GTAA---T.............................................................................................1811.000.001.000.000.00
droGri2
GAATCCAAACTAAATGTGAGATACC--TCTAAA-ACAAATCAT------------AA---AGATTTTGATGTATTGAGATTA------------------TGTACATTTGCAGAACTTTGAGAAAGACSizeHit CountTotal NormV109
Male body

12-way Secondary Structure

dm3 droSim1 droSec1 droYak2 droEre2 droAna3 dp4 droPer1 droWil1 droVir3 droMoj3 droGri2
RNAfold Image
UNAFold Image

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

Generated: 04/20/2012 at 05:10:32 EDT