dme-mir-2497

chr2L:16678250-16678317 +

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

mirtron

Legend:

   mature strand at position 16678250-16678274
   star strand at position 16678297-16678317
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species Coordinate Alignment
dm3 chr2L:16678235-16678332 + GATAAGCACGTCATCGTAAGCATTGCAAAATG--TAGTTGTTAAA-------TTCGC--------------TCTTCAATCATTA-ACAACATTT-----ACAATGTTTGCAGGCTGTCAACGTTGAT
droSim1 chr2L:16366233-16366322 + GATAAGCACGTCATCGTAAGCATTGCAAAATA--TAGTTGTTAAA-------TTCGC--------------TCTTCAATTATTT---------A-----CTATTGATTGCAGGCTGTCAACGTTGAT
droSec1 super_7:325110-325199 + GATAAGCATGTTATCGTAAGCATTGCAAAATA--TAGTTCTTAAA-------TTCGC--------------TCTTCAATTATTT---------A-----CTATTGATTGCAGGCTGTCAACGTTGAT
droYak2 chr2R:4424626-4424717 - GATAAGCACGTCATCGTAAGCTTTGCTATATATGTAGATGTGAAT-------TTCGA--------------GCTTCAATTCTTT---------T-----CTATTCTCTTCAGGCTGTCAATGTTAAT
droEre2 scaffold_4845:19748460-19748547 + GATAAGCACGTTATTGTAAGCTGCGCC--ATA--TAGTTCGTAAA-------TTCGA--------------GCTTCAATTATGT---------T-----CTATTCTCTCCAGGCTGTCAATGTTAAT
droAna3 scaffold_12916:15881689-15881781 - GAAAAGCAAGTGATTGTAAGA--TGTAAAC---------------TCTTAGACCCTCCTAACTGCTACAA---GCTAATACTTT---------T-----GCTTTGAATCCAGGCTGTTAACGTGAAC
dp4 chr4_group3:8422191-8422279 + CAAAAGCAGCTGATAGTGAGTACTGGAAGC---------------ATTTATAT---------CTCTGGAAAGCACTAATTCTTT---------T-----TTTAATCTTCTAGGCTGTCGAATTAAAT
droPer1 super_1:9873274-9873362 + CAAAAGCAGCTGATAGTGAGTACTGGAAGC---------------ATTTATAT---------CTCTGGAAAGCACTAATTCTTT---------T-----TTGAATCTTCTAGGCTGTCGAATTAAAT
droWil1 scaffold_181132:892502-892596 - GACAAAGAAGTGATTGTAGGTGTCAATGA---------------T-------TTCA----------AACTAACATCAATTTTTTATTAACGTCTTTATTTTTTCCTATTCAGGCTATCAATGTCAAT
droVir3 Unknown -------------------------------------------------------------------------------------------------------------------------------
droMoj3 Unknown -------------------------------------------------------------------------------------------------------------------------------
droGri2 Unknown -------------------------------------------------------------------------------------------------------------------------------

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

Species Coordinate Lastz Id Alignment
dm3 chr2L:16678235-16678332 + NA GATAAGCACGTC-ATCGTAAG----CATTGCAAAATGT-A-----------G--------------------------------------------TT------------------------------------------------------------GTT-AAATTCGCTCTTCAATCAT--TAACA----AC---A----TTT-A---CAATGTTTGCAGGCTGTCAACGTTGAT
droSim1 chr2L:16366233-16366322 + 100 GATAAGCACGTC-ATCGTAAG----CATTGCAAAATAT-A-----------G--------------------------------------------TT------------------------------------------------------------GTT-AAATTCGCTCTTC---------AA-----TTA---T----TTA-C---TATTGATTGCAGGCTGTCAACGTTGAT
droSec1 super_7:325110-325199 + 97 GATAAGCATGTT-ATCGTAAG----CATTGCAAAATAT-A-----------G--------------------------------------------TT------------------------------------------------------------CTT-AAATTCGCTCTTC---------AA-----TTA---T----TTA-C---TATTGATTGCAGGCTGTCAACGTTGAT
droYak2 chr2R:4424626-4424717 - 5555 GATAAGCACGTC-ATCGTAAG----CTTTGCTATATA------------------------------------------------TGTAG------AT------------------------------------------------------------GTG-AATTTCGAGCTT---------CAA-----TTC---T----TTT-C---TATTCTCTTCAGGCTGTCAATGTTAAT
droEre2 scaffold_4845:19748460-19748547 + 997 GATAAGCACGTT-ATTGTAAG----CTGCGCCA--TAT-A-----------G--------------------------------------------TT------------------------------------------------------------CGT-AAATTCGAGCTT---------CAA-----TTA---T----GTT-C---TATTCTCTCCAGGCTGTCAATGTTAAT
droEug1 scf7180000408961:253912-254004 + 21 AATAAGCAACTT-ATTGTAGG----CAACATAATTTAA-T-----------A--------------------------------------------AT------------------------------------------------------------GTTGAATCTCAGATTC---------TAA-----TCC---T----ACT-T-TTACTTCCTTTTAGGCAGTCAATATGGAT
droBia1 scf7180000301468:836914-837003 + 87 GATAAGCAAGTC-ATTGTAAG----CTACTAAACT------------------G---------CCTGTT--------------TATATCCAA-ATT-------------------------------------------------------------------------------------ACTGA-----CTAT--A----ATT-C---TCGTCCAACCAGGCTGTCAATGTAAAT
droTak1 scf7180000415914:402900-403000 + 1900 GATAAGCAAGTT-ATTGTAAG----CTACACATTTTA--------------TCT---------TTTGCA--------------AC----CAA---------------------------------------------------------------------------AGAGA---------GCCTA-----TTCTAATACTCTATTCCA-CGCAACCCACAGGCAGTCAATGTGAAT
droEle1 scf7180000490579:668430-668616 - 40 AATAAACAAGTT-ATTGTGAG----TCC---AAAT-TTAAGGCTTTTTTAAGTACGAAAACTATCATCA-TTAATCCGTTACATTTTTGACA----TGGGCTAGCTTTAACTAGGCTGAAAATTGAATATTATTACGATTACTAATATATATACTAATAC------------------------GA-----ACT---TACTTTGT-C---TTTTCTCCTCAGGCGGTCAACGTGAAC
droRho1 scf7180000764921:3062-3132 + 262 TAATCAAAACC---------------ATGGGAAATAGT-A-----------G--------------------------------------------TC------------------------------------------------------------ATT-AAATTCGTTACAAAATTTC--GAA-----CAA---------------------ATTGGA-ATTTA-----CAACG
droFic1 scf7180000449814:1574-1709 - 2 AACAAACAAGTC-ATCGTAAG----TAATCAAGG--------CTTTCTTCATCAGAAAGGTTATTTTTAGCCAAAATACAGGATTTTTGGAT-TAA-------------------------------------------------------------------------------------ACTAATAATATTTTTACATTTTGTACT--GCTTGTCCCCAGGCTGTTAATGTAAAT
droKik1 scf7180000302382:508886-508975 + 2 GACAAGCAAGTG-ATTGTAAG----TTAAGCGAATTCA-A-----------GAT---------TTTCTA--------------GC----------------------------------------------------------------------------------CCTAGTAC---------GA-----CCC---T----TCT-C---GTTTCTGACCAGGCTGTCAACGTGAAT
droAna3 scaffold_12916:15881689-15881781 - 2 GAAAAGCAAGTG-ATTGTAAG----ATGT--AAACTCTTAGACCCTCCTAACTGCT--------------------------------ACAA-----------------------------------------------------------------------------------------GCTAA-----TAC---T----TTT-G---CTTTGAATCCAGGCTGTTAACGTGAAC
droBip1 scf7180000396717:120661-120753 - 9 GAAAAGCAAGTG-ATTGTAAG----TTTCGAA--CTCTAAGACCCAAGTAGGTGCC--------------------------------ACAA-ACT-------------------------------------------------------------------------------------ATAA--------G---T----TTT-G---CTTTCAATCCAGGCTGTTAACGTGAAC
dp4 chr4_group3:8422191-8422279 + 4 CAAAAGCAGCTG-ATAGTGAG----TACTGGAAG------------------CA---------TTTATA--------------TCTCTGGAA-AGC-------------------------------------------------------------------------------------ACTAA-----TTC---T----TTT-T---TTAATCTTCTAGGCTGTCGAATTAAAT
droPer1 super_1:9873274-9873362 + 2 CAAAAGCAGCTG-ATAGTGAG----TACTGGAAG------------------CA---------TTTATA--------------TCTCTGGAA-AGC-------------------------------------------------------------------------------------ACTAA-----TTC---T----TTT-T---TGAATCTTCTAGGCTGTCGAATTAAAT
droWil1 scaffold_181132:892732-892841 - 2 GAGAAGAAGAGC-TGGAATATCAATCACTAGACG------------------AT---------TTAATT--------------GAAGTAGAAG---TG------------------------------------------------------------ATA-CAATCCGATCCCGAACCGG--AGACA---------------GA-G---CCACAAAATGAGGAATTTGAATTTGAT
droVir3 scaffold_12970:9784026-9784116 - 3 TGCAGGCAACGGCAGCAGCAACAG-CAGCGCAG-------------------CAACGAACGCTTTTCCA--------------GC---------------------------------------------------------------------------------------CG---------CAG-----CAG---C----AGC-T---GTTGCCGTTGCAGCCGTTGCCGCTAGC
droMoj3 scaffold_6359:887596-887673 - 9 CAGAAGCAACTGCAGCAACAGCAA---TTGCA-------------------GCA---------ACAGCA--------------AC------------T------------------------------------------------------------GCA-GCACCAGCT---------------------------------------ACTGCAGCAACAGCAACAGC--AACAA
droGri2 Unknown NA ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species Alignment
dm3
GATAAGCACGTCATCGTAAGCATTGCAAAATG--TAGTTGTTAAA-------TTCGC--------------TCTTCAATCATTA-ACAACATTT-----ACAATGTTTGCAGGCTGTCAACGTTGATSizeHit CountTotal Norm
droSim1
GATAAGCACGTCATCGTAAGCATTGCAAAATA--TAGTTGTTAAA-------TTCGC--------------TCTTCAATTATTT---------A-----CTATTGATTGCAGGCTGTCAACGTTGATSizeHit CountTotal NormV044
Embryo		M023
Head		M024
Male body		M025
Embryo
..TAACCAGGTCATCGTAAGC..........................................................................................................1911.000.000.000.001.00
droSec1
GATAAGCATGTTATCGTAAGCATTGCAAAATA--TAGTTCTTAAA-------TTCGC--------------TCTTCAATTATTT---------A-----CTATTGATTGCAGGCTGTCAACGTTGATSizeHit CountTotal NormV113
Male body		V114
Embryo		V115
Head
....................................................................................................TATTGATTGCAGGAGGTC.........1812.000.002.000.00
............................................................................ATTTATTT---------A-----CTTTTGATT...................1811.000.001.000.00
droYak2
GATAAGCACGTCATCGTAAGCTTTGCTATATATGTAGATGTGAAT-------TTCGA--------------GCTTCAATTCTTT---------T-----CTATTCTCTTCAGGCTGTCAATGTTAATSizeHit CountTotal NormV046
Embryo		V052
Head		V120
Male body		V058
Head		M026
Head
droEre2
GATAAGCACGTTATTGTAAGCTGCGCC--ATA--TAGTTCGTAAA-------TTCGA--------------GCTTCAATTATGT---------T-----CTATTCTCTCCAGGCTGTCAATGTTAATSizeHit CountTotal NormV040
Embryo		V060
Head		V047
Embryo		V108
Head
..................................................................................GT---------T-----CGATTCCCTCCAGGC.............1811.000.000.001.000.00
droAna3
GAAAAGCAAGTGATTGTAAGA--TGTAAAC---------------TCTTAGACCCTCCTAACTGCTACAA---GCTAATACTTT---------T-----GCTTTGAATCCAGGCTGTTAACGTGAACSizeHit CountTotal NormV105
Male body		V106
Head		V055
Unknown		V039
Embryo
........AGTGATTGAAAGA--TGAAAA..................................................................................................1914.003.001.000.000.00
.................AAGG--TxTAAAC---------------TCTTAGACC.........................................................................1911.000.000.000.001.00
.ATAAGCAAGTGAATGTA.............................................................................................................1711.000.000.001.000.00
....AGCAAGCGATAGTAAGA--T.......................................................................................................1811.000.000.001.000.00
........AGTGATGGTAAGA--TGAAA...................................................................................................1811.000.001.000.000.00
.GAAAGCAAGTGATGGTAA............................................................................................................1811.000.001.000.000.00
dp4
CAAAAGCAGCTGATAGTGAGTACTGGAAGC---------------ATTTATAT---------CTCTGGAAAGCACTAATTCTTT---------T-----TTTAATCTTCTAGGCTGTCGAATTAAATSizeHit CountTotal NormV112
Male body		V043
Embryo		V051
Head		M022
Male body
.........CTGAAAGTAAGTACTGGA....................................................................................................1811.000.001.000.000.00
droPer1
CAAAAGCAGCTGATAGTGAGTACTGGAAGC---------------ATTTATAT---------CTCTGGAAAGCACTAATTCTTT---------T-----TTGAATCTTCTAGGCTGTCGAATTAAATSizeHit CountTotal NormV111
Male body		V042
Embryo		V050
Head		V057
Head		M021
Embryo
........GCTGGGAGTGAGTACTGG.....................................................................................................1811.000.000.000.001.000.00
droWil1
GACAAAGAAGTGATTGTAGGTGTCAATGA---------------T-------TTCA----------AACTAACATCAATTTTTTATTAACGTCTTTATTTTTTCCTATTCAGGCTATCAATGTCAATSizeHit CountTotal NormV117
Male body		V118
Embryo		V119
Head		M020
Head
.......AACTGATTGTTGGTGTCA......................................................................................................1812.000.001.000.001.00
......................................................AA----------AACGAACATCAATTTTTT...........................................2011.000.001.000.000.00
droVir3
-------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormV116
Male body		V053
Unknown		V047
Embryo		M027
Male body		M028
Head
droMoj3
-------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormV110
Male body		V056
Unknown		V049
Head		V041
Embryo
droGri2
-------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormV109
Male body

12-way Secondary Structure

dm3 droSim1 droSec1 droYak2 droEre2 droAna3 dp4 droPer1 droWil1 droVir3 droMoj3 droGri2
RNAfold Image None None None
UNAFold Image None None None

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 None
UNAFold Image None

Generated: 04/20/2012 at 05:23:57 EDT