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
let-7a-1         AUGUU-CUCUUCACUGUGGGAU---GAG-GUAGUAGGUUGUAUAGUU---UUAGGGUC--
let-7a-3         AGACC-GACUGCCCUUUGGGGU---GAG-GUAGUAGGUUGUAUAGUU----UGGGGCU--
let-7b           CAAGGCCGGGC-CUGGCGGGGU---GAG-GUAGUAGGUUGUGUGGUU-UCAGGGCAGUG-
let-7d           AAAAA-AAUGG-GUUCCUAGGAA--GAG-GUAGUAGGUUGCAUAGUU-UUAGGGCAGGG-
let-7f-1         AAAACAUUGCU-CUAUCAGAGU---GAG-GUAGUAGAUUGUAUAGUUG-UGGGGUAGUG-
let-7f-2         GACAC-UGGUGCUCUGUGGGAU---GAG-GUAGUAGAUUGUAUAGUU---UUAGGGUC--
let-7g           CCUUUUGCCUG-AUUCCAGGCU---GAG-GUAGUAGUUUGUACAGUUUGAGGGUCUAUG-
let-7i           CCCGACACCAU-GGCCCUGGCU---GAG-GUAGUAGUUUGUGCUGUUGGUCGGGUUGUG-
mir-193b         -G-GAGG------CUGUGGUCU---CA-GAAU-CGGGGUUU--UGAGGG--C-GAGAUGA
mir-224          --AGAUAA-GG-CCCAGGGGCUUUCAAG-UCACUAGUGGUUCC----GUUU-AG-UAGA-
mir-340          -A-CCGUUU-G--UACCUGGUG---UGA--UUAUAAAGCAA--UGAGAC--UGAUUGUCA
mir-365-1        -C-------GUUACCGCAGGGA---AAA-UGAGGGACUUUUG-GGGG-CAGAUGUGUUU-
mir-365-2        CA-------AGGACAGCAAGAA---AAA-UGAGGGACUUUCA-GGGG-CAGCUGUGUUU-
mir-370          -A-GUCGGG-G--CACA-AGAC---AGAGAAG-CCAGGUCA--CGUCUC--UGCAGUUAC
mir-433          G-------------GAGAAGUA---CGG-UGAGCCU-GUCAU-UAUU-CAGAGAGGCUA-
mir-621          -UAGAUUGAGG-AAGGGGCUGA-------GUGGUAGGCGGUGCUGCU----GUGCUCUG-
mir-708          G-UGAAAUGGUA--ACUGCCCU---CAA-GGAGCUUACAAUCUA---GCUGGGGGUAAA-
mir-887          GA----GAGCCCCGGGGUGCAG-------AUCCUUGGGAGC--CCUG-UUAGACUCUGG-
mir-98           GGAUUCUGCUC-AUGCCAGGGU---GAG-GUAGUAAGUUGUAUUGUUGU-GGGGUAGGG-
CONS STRUCTURE   .........................(((.((((((((((((((((((.............

let-7a-1         ACA-CC---CACC-ACUGGGAGAUAACUAUACAAUCUACUGU--CU--U----UCCUAA-
let-7a-3         CUG-CC---CUG--CUAUGG-GAUAACUAUACAAUCUACUGU--CU--U----UCCUGA-
let-7b           AUG-UU-GCC--CCUCGGAAG-AUAACUAUACAACCUACUGC--CU--U----CCCUG--
let-7d           AUU-UU-GCCCACA---AGGAGGUAACUAUACGACCUGCUGC--CU--U----UCUUAG-
let-7f-1         AUU-UU-ACCC-UGUUCAGGAGAUAACUAUACAAUCUAUUGC--CU--U----CCCUGA-
let-7f-2         AUA-CC---C-CA-UCUUGGAGAUAACUAUACAGUCUACUGU--CU--U----UCCCAC-
let-7g           AUA-CC-ACCCGGUAC-AGGAGAUAACUGUACAGGCCACUGC--CU--U-----GCCAG-
let-7i           ACA-UU-GCCCGCUGU--GGAGAUAACUGCGCAAGCUACUGC--CU--U----GCUAGU-
mir-193b         GUUUAUGUUUU-A-UCCAACUGGCCCUCA-AAGUCCCGCUUUUGGG--G-U---CAU---
mir-224          UGAUUG-UGC-AUUGU-UUC----AAAAUGGUGCCCUAGUGA--CUACAAA---GCCCC-
mir-340          -UAUGUCGUUU---GUGGGAUCCGUCUCAGUUACUUUAUAG---CC--A-U---ACC---
mir-365-1        CCA-UU-CCA--CUAUCAUAAUGCCCCUAAAAAUCCU-UAUU--GC--U-----CUUGC-
mir-365-2        UCU-G--ACU--CAGUCAUAAUGCCCCUAAAAAUCCU-UAUU--GU--U-----CUUGC-
mir-370          -ACAGCUCACG-A-GUGCCUGCUGGGGUG-GAACCUGGUCUG--UC--U-G---UCU---
mir-433          GAU-CC-UCU--GUGUUGAGAAGGAUCAUGAUGGGCU-CCUC--GG--U-----GUUCUC
mir-621          AUG-AA-GACC-CAUG-UG--GCUAGCAACAGCGCUUACCUU--UU--GUCUCUGGGUC-
mir-708          UGA-CU-UG-CACA---UGAACACAACUAGACUGUGAGCUUC--UA--GA-----GGGC-
mir-887          AUU-UU-ACA--CUUGGAGUGAACGGGCGCCAUCCCG-AGGC--UU--U-----GCACA-
mir-98           AUAUUAGGCCC-CAAUUAGAAGAUAACUAUACAACUUACUAC--UU--U-----CCC---
CONS STRUCTURE   ........................))))))))))))))))))..))..)...........

let-7a-1         -CG----------UGA
let-7a-3         -AG-------UGGCUG
let-7b           ------------AG-G
let-7d           -GG-------------
let-7f-1         ----------------
let-7f-2         -GG-------U--GGU
let-7g           ----------------
let-7i           ----------------
mir-193b         -----UCUGGACAGCG
mir-224          -AG---------AGCC
mir-340          -----UGGUAUCUUAU
mir-365-1        -AG----UAUUCCUCG
mir-365-2        -AG----UGUGCAUCG
mir-370          -----GUCUAAC-ACC
mir-433          CAGGUAGCGGCACCAC
mir-621          -CU---------GGCC
mir-708          ---AG---GGA--CCU
mir-887          -GG----GGCAAGCUU
mir-98           ---------U------
CONS STRUCTURE   ................



Consensus
CPU time: 0.00
Average sequence ID: 0.299493165412
Average free energy: -11.8010526316
Average covariation: 0.263157894737
Average basepair probability: 0.61259666047
Canonical basepairs: NA

Sequence and structure consensus for Consensus
VAAGMCDRSKKcMYWSCRGGVWwucRARgGUAGUARGKUGUAYWGUKgYWGGGGYKKURmAUWuYYsRCCCvCWDYBAGRAGAYAACUAU AMAAYCUACUKYugCUacUwuucyCCYRMccRGrkwsbgkWmRBCB
.........................(((.((((((((((((((((((.....................................)))))) ))))))))))))..))..)...........................

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
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