Results

You can download the results in the following formats: fasta clustal stockholm col
The consensus is based on:
CMfinder   FoldalignM   LaRA   MASTR   RNAalifold   RNAforester   RNASampler  


T-coffee consensus alignment

BAD AVG GOOD
mir-130a         ------UGCUG---CUGGCCAGAGCUCUUUUC---ACAUUGUGCU---ACUGUCUGCACC
mir-184          UU----GCCG-GC-CAGUCACGUCCCCUUAUCA--CUUUUCCAGC--CCAGCUUUGUGAC
mir-19b-1        CU---GAACAC---UGUUCUAUGGUUAGUUUU-GCAGGUUUGCAU--CCAGCUGUGUGAU
mir-19b-2        AG---ACAUUG---CUACUUACAAUUAGUUUUGCAGGUUUGCAUUU-CAGCGUAUAUAUG
mir-29b-1        U-CAUAAAGCU--UCUUCAGGAAGCUGGUUUCA-U-AUGGUGGUU-UAGAUUUAAAUAGU
mir-29b-2        A-GAUCCUCUU--C-UUCUGGAAGCUGGUUUCA---CAUGGUGGC--UUAGAUUUUUCCA
mir-504          UUGAAUCAGCU--G----CUGUUGGGAGACCCU-G-GUCUGCACU--CUAUCUGUAUUCU
mir-551a         G---GGGACUG---CCGGGUGACCCUGGAAAUC-CAGAGUGGGUGGGGCCAGUCUG-ACC
mir-599          C----AAAGACAUGCUGUCCACAGUGUGUUUGA-UAAGCUGACAUG-GGACAGGGAUUCU
CONS STRUCTURE   ...................(((((((((((((............................

mir-130a         UGUCACUAG-CAGUGCAAUG--U----UAAAAGGGCAUUGG--CCGUGUAGUGCUACCCA
mir-184          UGUAAGUGU-UGGACGGAG--AAC--UGAUAAGGGUAGGUG----AU-UG-ACACUCACA
mir-19b-1        AUUC--UGC-UGUGCAAAUCCAUG--CAAAACUGACUGUGG---------------UAGU
mir-19b-2        UAUAUGUGG-CUGUGCAAAU-CCAUGCAAAACUGAUUGUGA-----------------UA
mir-29b-1        G---AUUGUC-UAGCACCAU--U---UGAAAUCAGUGUUCUUGGGGG-AG-A----CCAG
mir-29b-2        UCUUUGUAUCUAGCACCAUU------UGAAAUCAGUGUUU-UAGGA----------GUAA
mir-504          UACUGAAGGG-AGUGCAGGG--C---AGGGUUUCCCA----UACAG----------AGGG
mir-551a         GUUUCUAGG-CGACCCACUC--UU--GGUUUCCAGGG----UUGC-----------CCUG
mir-599          UUUCACUGU-UGUGUCAGUU--UAU-CAAACCCAUACUUGG----AU-------GACAGU
CONS STRUCTURE   ...........................)))))))))))))....................

mir-130a         G-------CGCU
mir-184          G---------C-
mir-19b-1        G--AAAAGUCUG
mir-19b-2        A-----UGUGUG
mir-29b-1        C------U----
mir-29b-2        G-A---AUUGC-
mir-504          C-ACAGACUACC
mir-551a         GAA---ACCACA
mir-599          C----------A
CONS STRUCTURE   ............



Consensus
CPU time: 0.00
Average sequence ID: 0.267653482165
Average free energy: -8.59555555556
Average covariation: 0.619658119658
Average basepair probability: 0.740080679733
Canonical basepairs: NA

Sequence and structure consensus for Consensus
HusawRMASYBrysCUKYCYRMASYUVGUUUYAsYASWYUGSVYYkkCCMBSUSURUACYUWUHASUGKsYRGBSCMMUYcmYAugYRAA AYYRGYRKUGGuaSSRugwrgwsmbwCMSRSaamarABYRCR
...................(((((((((((((.......................................................))) ))))))))))................................

The alignment colored using colorrna.pl of the Vienna package

Cluster tree of the methods














Please send any comments or report bugs to Elfar Torarinsson or Stinus Lindgreen
Table