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
hsa-mir-143      CGCC--CUGUCUCCC-A-GC-CUG-AGGUGCAGUG--CUGCAUCUCUGG-UCAGUUGGGA
hsa-mir-297      CAUACUUUAUGAACAUAUGUAUGU-AUGUGUGCAU---GUGCAUGUAUG-UGUA-UAUAC
hsa-mir-302a     CCAAGACUGGGCUCCC-C-ACCAC-UUAAACGUGG--AUGUACUUGCUU-UGAAACUAAA
hsa-mir-302b     UGUUGGG--UGGGCUCCC-UUCAA-CUUUAACAUG--GAAGUGCUUUCUGUGACUU-UAA
hsa-mir-302c     UUUGAAG--GGAUCCC-C-U-UUG-CUUUAACAUG--GGGGUACCUGCUGUGUGAAACAA
hsa-mir-302d     UCUG--UUAAGGGGCCCCCUCUAC-UUUAACAUGG--AGGCACUUGCU-GUGACAUGACA
hsa-mir-372      AUGGAGCUGCUCACCCUG-UGGGC-CUCAAAUGU---GGAGCACUAUUCUGAUGUCCAAG
hsa-mir-374a     AAGAAAUUUUACAUC-GG-CCAUU-AU-AAUACAA--CCUGAUAAGUGU-U-A------U
hsa-mir-374b     AAGAAA-U-CCUAC--UC-GGAUG-GAUAUAAUAC--AACCUGCUAAGUGU-CC-U--AG
hsa-mir-378      GGUGACAGAGCCACCCAG-GGCUC-CU-GACUCCA--GGUCCUGUGU-GUU-ACCUAGAA
hsa-mir-421      CCUAAUCCGGUGCAC-AUUGUAGG-CCUCAUUAAA--UGUUUGUUGAAUGAAAAAAUGAA
hsa-mir-544      CUAAGAUUUUCAUCACCUAGGGAU-CUUGUUAAAAA---GCAGAUUCUGAUUCAG-GGAC
hsa-mir-553      ---------ACAUUC-UUCAAUUU-UAUUUUAAAACGGUGAGAUUUUG--UUUUG--UCU
hsa-mir-563      -UU---UUUACAGGAAGCAAA-G-----AAGUGUG--UUGCC-CUCUAGGAAAUGUGUGU
hsa-mir-600      GUCACGUGCUGUGGCUCCAGCUUCAUAGGAAGGCU--CUUGUCUGUCAGGCAGUGGAGUU
hsa-mir-616      UUACCUUAGGUAAUUCCU-CCACU-CAAAACCCUU--CAGUGACUUCCA-UGACAUGAAA
hsa-mir-633      CCUCU-CUUAGCCUCUGUUUCUUU-AUUGCGGUAG--AUACUAUUAACC-UAAAAUGAGA
hsa-mir-659      ACCGACCCUCGAUUUGGU-UCAGG-ACCUUCCCUG--AACCAAGGAAGAGUCACA--G-U
hsa-mir-802      CUCGU-UCUGUUAUU-UG-CAGUC-AGUAACAAAG--AUUCAUCCUUGUGUCCAUCAUGC
hsa-mir-873      -GAAUAAGUUUGUG--UGCA-UUU-GCAGGAACUU--GUGAGUCUCCUAUUGAAAAUGAA
CONS STRUCTURE   ............................(((((((..((((((((((((...........

hsa-mir-143      GUCUGAGAUGAAGC--ACUGUAGC--------------UCAGGA--AGAGAGAAGUUGUU
hsa-mir-297      AUAUAUAUGUAUUA--UGUACUCA-UAUAUCAAG---------G-AGAUUUCAUU-----
hsa-mir-302a     GAAGUAAGUGCUUC--CAUGUUU-UGGUGA--UG------------GUAAGUCUU-----
hsa-mir-302b     AAGUAAGUGCUUCC--AUGUUUUA-GUAG---------G----AGUGAAUCCAAU-----
hsa-mir-302c     AAGUAAGUGCUUCC--AUGUUUCA-GUGG--------------AGGUGUCUCCAA-----
hsa-mir-302d     AAAAUAAGUGCUUC--CAUGUUUG-AGUG-------------UG--GUGGUUCCU-----
hsa-mir-372      UGGAAAGUGCUGCG--ACAUUUGAGCGUC----------------ACCGGUGACG-----
hsa-mir-374a     AGCACUUAUCAGAU--UGUAUU-G-UAAU---------UGUCUG---UGUAUAUG--CCU
hsa-mir-374b     CACUUAGCAGGUUG--UAUUAUCA-UUGUC--CG--------UG--UCUAUGGCU----C
hsa-mir-378      AUAGCACUGGACUU--GGAGUC-A-GAAGG--------CCUGA-----GUGGAG-U----
hsa-mir-421      UCAUCAACAGACAU--UAAUUGGG----C---------GCCUGC-UCUGUGAUCU-----
hsa-mir-544      CAAGAUUCUGCA--UUUUUAGCAA-GUUC-----------UCA---AGUGAUGCU-----
hsa-mir-553      GAGAAAAUCUCGCUGUUUUAGACU-GAGG-----------C-AGUGUGUUAUGAU-----
hsa-mir-563      UGCUCUGAUGUAAU--UAGGUUGACAUA-C--GUUUCCCUGGUA-GCCAAUAU-------
hsa-mir-600      ACUUACAGACAAGA--GCCUU------------------GCUCAGGCCAGCCC-U---GC
hsa-mir-616      UAGGAAGUCAUUGG--AGGGUU-U-GAGCA--GAGGA----------A-UGACCU-G---
hsa-mir-633      AGGCUAAUAGUAUC--UACCACAA----------------UAAA-A-UUGUUGUG---AG
hsa-mir-659      CUCUUCCUUGGUUC--AGGGAGGG-UCCCC--AACAA------------UGUCCU-----
hsa-mir-802      AACAAGGA-GAAUC--UUUGUCACUUAGU---GU---------A-AUUAAUAGCU-----
hsa-mir-873      -CAGGAGACUGAUG--AGUUCC---CGGGA--AC--------AC---CCACAAAU-----
CONS STRUCTURE   .)))))))))))))..))))))......................................

hsa-mir-143      C---UGCAG------CC
hsa-mir-297      ------------UCUAU
hsa-mir-302a     ----CCUUU---UA-CA
hsa-mir-302b     ------UUA--CUUCUC
hsa-mir-302c     ----GCCAG--CACACC
hsa-mir-302d     A---CCUAA----UCAG
hsa-mir-372      -----CCCA---UAUCA
hsa-mir-374a     GUC-UCUCU---UCCUG
hsa-mir-374b     U---CGUCU--ACCAGA
hsa-mir-378      C------AC-CUUCCCC
hsa-mir-421      --CC--A-------UGG
hsa-mir-544      ------AAUA---CCGC
hsa-mir-553      A---GAGAGCACUAAAC
hsa-mir-563      ------AAG----GAAU
hsa-mir-600      --CC--------CUGCC
hsa-mir-616      U---UUUAA-------A
hsa-mir-633      --GAU-A-----AAAAA
hsa-mir-659      C---AUGGU----CCUU
hsa-mir-802      ------GG---ACCUUG
hsa-mir-873      -----CUUCCUACUCAU
CONS STRUCTURE   .................



Consensus
CPU time: 0.00
Average sequence ID: 0.224725859436
Average free energy: -19.726
Average covariation: 0.838296398892
Average basepair probability: 0.799869747939
Canonical basepairs: NA

Sequence and structure consensus for Consensus
CYURAAYUKKSMACCCCBMKSWKBaMUURAMAMWRmgVKGSAAYUKYKKGURAMRURRAAAAVKAARUKSAWUCkuWRKKUYSRbKDKSm cargbdmcbsysWRgRSYDKKUVMUukssycusmYCUADmhmYCMMC
............................(((((((..((((((((((((............)))))))))))))..))))))........ ...............................................

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