Results

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


T-coffee consensus alignment

BAD AVG GOOD
mir-124-1        -AGGAGAAAGGCCUCUCUCUCCGUGUUC-ACAGCGGA-CCUUGA-UUUAAAUGUCCAU-A
mir-124-2        -AGAUUAGAGGCUCUGCUCUCCGUGUUC-ACAGCGGA-CCUUGA-UUUA-AUGUC-AU-A
mir-124-3        CAGCCCUG-AGGGCCCCUCUGCGUGUUC-ACAGCGGA-CCUUGA-UUUAA-UGUCUAU-A
mir-133a-1       CAGCACUACAAUGCUUUGCUAGAGCUGGUAAAAUGGA-ACCAAA-UCGC-CUCUUCAA-U
mir-133a-2       UGGGAGCCAAAUGCUUUGCUAGAGCUGGUAAAAUGGA-ACCAAA-UCGA-CUGUCCAA-U
mir-133b         AAGAAAGAUGCC-CCCUGCUCUGGCUGGUCAAACGGA-ACCAAGUCCGU-CUUCCUGA-G
mir-215          CAGAAA-UGGUAUACAGGAAAAUGACCUAU-GAAUUG-ACAGAC-AAUA--UAGCUGA-G
mir-216b         CUUCAAAGUGGCAGACUGGA-AAAUCUCUGCAGGCAA-AUGUG-AUGU-CACUGAGGAAA
mir-452          UAUAAUUGCUAAGCACUUACAACUGUUUGCAGAGGAA-ACUGAG-ACUU-UG-UAACU-A
mir-488          AAUUUC-AGAGAAUCAUCU-CUCCCAGAUAAUGGCACUCUCAAA-CAAG--UUUCCAA-A
CONS STRUCTURE   ..........(..(........((((((..........((((((.((.............

mir-124-1        CAAUUAAGGCACGCGG-UGAAUGCCAAGAAUGGGGCUGGCUG-AGCA-C
mir-124-2        CAAUUAAGGCACGCGG-UGAAUGCCAAGAGCGGAGCCUACGGCUGCACU
mir-124-3        CAAUUAAGGCACGCGG-UGAAUGCCAAGAGAGGCGCCUCCG-CCGCUCC
mir-133a-1       GGAUUUGGUCCCCUUCAACCAGCUGUAGCUAUG-CAU-UGAUUA--CUA
mir-133a-2       GGAUUUGGUCCCCUUCAACCAGCUGUAGCUGUG-CAU-UGAUGG--CGC
mir-133b         AGGUUUGGUCCCCUUCAACCAGCUACAGCAGGG--CUGGCAA-UGCCC-
mir-215          UUUGUCUGUCAUUUCUUUAGGCCAAUAUUCUGU-AUGACUGUGCUACUU
mir-216b         UCACACACUUACCCGU-AGAGAU-UCUACAGUCUGACAUCUU-CA-AGC
mir-452          UGUCUCAGUCUCAUCUGCAAAGAAGUAAGUG-C-UUU-GCCAAGCUCCU
mir-488          UUGUUUGAAAGGCUAUU-UCUUGGUCAGAUGAC-UCUCAAUUUCUUCUG
CONS STRUCTURE   .)))))))).........))))))........)..).............



Consensus
CPU time: 0.00
Average sequence ID: 0.325605900948
Average free energy: -6.132
Average covariation: 0.654166666667
Average basepair probability: 0.81246636167
Canonical basepairs: NA

Sequence and structure consensus for Consensus
CAKMAMWRARRMGCYYYKCUMMRKSUKSUAMARSGRAuMCYWRAwUYKAmMUKUCYRWaAYRAUUHRGKCMCSYKBWWSMAKSYSHAGMW GKSsGMYDKCDUBCGYMYY
..........(..(........((((((..........((((((.((..............)))))))).........))))))...... ..)..).............

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