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-100          UAUU-GAGGCCU----GUUG-CCACAAACCCGUAGA---UCCGAA--CUUGUG-------
mir-373          C-GAGGAGCUCAUA--CUGG-GAUAC-UCAA-AAUG---GGGGCG--CUUUCC------U
mir-516b-1       --GAAUAUCUCAGG--CUGU-GACCA-UCUG-GAGGUAAGAAGCA--CUUUCU------G
mir-516b-2       --GAAGAUCUCAUG--AUGU-GACCA-UCUG-GAGGUAAGAAGCA--CUUUGU------G
mir-517a         A-GAAGAUCUCAGG--CAGU-GACCC-UCUA-GAUG---GAAGCA--CUGUCU------G
mir-517b         A-GAAGACCUCAUG--CUGU-GACCC-UCUA-GAUG---GAAGCA--CUGUCU------G
mir-517c         A-GAAGAUCUCAGG--CAGU-GACCC-UCUA-GAUG---GAAGCA--CUGUCU------G
mir-518b         AAGAAUAUGUCAUG--CUGU-GGCCC-UCCA-GAGG---GAAGCG--CUUUCU------G
mir-518c         A-GAAGAUCUCAUG--CUGU-GACUC-UCUG-GAGG---GAAGCA--CUUUCU------G
mir-518e         --CAAGAUCUCAGG--CUGU-GACCC-UCUA-GAGG---GAAGCG--CUUUCU------G
mir-518f         --GAAGAUCUCAUG--CUGU-GACCC-UCUA-GAGG---GAAGCA--CUUUCU------C
mir-519a-1       --GAAGACCUCAGG--CUGU-GACAC-UCUA-GAGG---GAAGCG--CUUUCU------G
mir-519a-2       A-GAAGAUCUCAGG--CUGU-GUCCC-UCUA-CAGG---GAAGCG--CUUUCU------G
mir-519d         A-GAAGAUCCCAUG--CUGU-GACCC-UCCA-AAGG---GAAGCG--CUUUCUGU-----
mir-519e         GAGAAGAUCUCAUG--CAGU-CAUUC-UCCA-AAAG---GGAGCA--CUUUCU------G
mir-520b         AAGAAGAUGUCAGG--CUGU-GUCCC-UCUA-CAGG---GAAGCG--CUUUCU------G
mir-520e         AAGACUGUCUCCUG--CUGU-GACCC-UCAA-GAUG---GAAGCA--GUUUCU------G
mir-520f         --GAGGAUCUCAGG--CUGU-GACCC-UCUA-AAGG---GAAGCG--CUUUCU------G
mir-520g         ----AGAUCCCAUG--CUGU-GACCC-UCUA-GA-G---GAAGCA--CUUUCUGUUU--G
mir-520h         --GAAGAUCCCAUG--CUGU-GACCC-UCUA-GA-G---GAAGCA--CUUUCUGUUU--G
mir-521-1        A-GAAGAUCUCAGG--CUGU-GACCC-UCCA-AAGG---GAAGAA--CUUUCU------G
mir-521-2        A-GAAGGUCUCGGG--CUGU-GACUC-UCCA-AAGG---GAAGAA--UUUUCU------C
mir-522          --GAAGAUCUCAGG--CUGU-GUCCC-UCUA-GAGG---GAAGCG--CUUUCU------G
mir-523          --GAAGAUCUCAUG--CUGU-GACCC-UCUA-GAGG---GAAGCG--CUUUCU------G
mir-526a-1       --GAAGAGCUCAGG--CUGU-GACCC-UCUA-GAGG---GAAGCA--CUUUCU------G
mir-526a-2       --GAAGAUCUCGUG--CUGU-GACCC-UCUA-GAGG---GAAGCA--CUUUCU------G
mir-526b         --GAAGAUGUCAGG--CUGU-GACCC-UCUU-GAGG---GAAGCA--CUUUCU------G
mir-527          AAGAAGAUCUCAAG--CUGU-GA--C-UGCA-AAGG---GAAGCC--CUUUCU------G
mir-551b         G-AUGUGC-UCU--CCUGG-CCCAUG-AAAU-CAA-GCG--UGGGUG-AGA--CCUGGUG
mir-593          U-GUAGCCCCCAGAAUCUGUCAGGCA-CCAG-CCA-GGC--AUUGCUCAGCC-CGUU---
mir-99b          G-ACUCCUGGGUC---CUGG-CACCCACCCG-UAGA---ACCGAC--CUUGCG-------
CONS STRUCTURE   ...........................((((.((((...((((((..((((((.......

mir-100          -G--UAUUA-GUC-CGCACAAGCU--UGUAUCUAUAGGUAUGUGU-CUGUUAGGCAAUCU
mir-373          UUUU--GUCUGUA-CUGGGAAGUG--CUUCGAUUUUGGGGUGUCC-CUGUUUGAGUAGGG
mir-516b-1       UUU-UGUGAAAGA-AAAGAAAGUG--CUUCCUUUCAGAG-GGUUAC-UCUUUGAGAAAAG
mir-516b-2       U------UUUGUG-AAAGAAAGUG--CUUCCUUUCAGAG-GGUUAC-UCUUUGAGAAAAG
mir-517a         UUG-UAUAAAAGA-AAAGAUCGUG--CAUCCCUUUAGAG-UGUUAC-UGUUUGAGACAAG
mir-517b         UUG-UCUAA--GA-AAAGAUCGUG--CAUCCCUUUAGAG-UGUUAC-UGUUUGAGAAAAG
mir-517c         UUG-UCUAA--GA-AAAGAUCGUG--CAUCCUUUUAGAG-UGUUAC-UGUUUGAGAAAAU
mir-518b         UUG-UCUGAAAGA-AAACAAAGCG--CUCCCCUUUAGAG-GUUUAC-GGUUUGAGUAAAG
mir-518c         UUG-UCUGAAAGA-AAACAAAGCG--CUUCUCUUUAGAG-UGUUAC-GGUUUGAGAAAAG
mir-518e         UUG-GCUAAAAGA-AAAGAAAGCG--CUUCCCUUCAGAG-UGUUAACGCUUUGAGAAAAG
mir-518f         UUG-UCUAAAAGA-AAAGAAAGCG--CUUCUCUUUAGAG-GAUUA-CUCUUUGAGAAAAG
mir-519a-1       UUG-UCUGAAAGA-AAGGAAAGUG--CAUCCUUUUAGAG-UGUUAC-UGUUUGAGAAAAG
mir-519a-2       UUG-UCUGAAAGA-AAGGAAAGUG--CAUCCUUUUAGAG-UGUUAC-UGUUUGAGAAAAG
mir-519d         UUG-UUUUCUCUUAAA-CAAAGUG--CCUCCCUUUAGAG-UGUUA-CCGUUUGGGAAAAG
mir-519e         ----UUUGAAAGA-AAACAAAGUG--CCUCCUUUUAGAG-UGUUAC-UGUUUGAGAAAAA
mir-520b         UUG-UCUGAAAGA-AAAGAAAGUG--CUUCCUUUUAGAG-GGUUAC-CGUUUAAGAAAAG
mir-520e         UUG-UCUGAAAGG-AAAGAAAGUG--CUUCCUUUUUGAG-GGUUAC-UGUUUGAGAAAAG
mir-520f         UGG-UCAGAAAGA-AAAGCAAGUG--CUUCCUUUUAGAG-GGUUA-CCGUUUGGGAAAAG
mir-520g         UUG-UCUGA-GAAAAAACAAAGUG--CUUCCCUUUAGAG-UGUUA-CCGUUUGGGAAAAG
mir-520h         UUG-UCUGA-GAAAAAACAAAGUG--CUUCCCUUUAGAG---UUA-CUGUUUGGGAAAAG
mir-521-1        UUG-UCUAAAAGA-AAAGAACGCA--CUUCCCUUUAGAG-UGUUA-CCGUGUGAGAAAAG
mir-521-2        UUG-UCUAAAAGA-AAAGAACGCA--CUUCCCUUUAGAG-UGUUA-CCGUGUGAGAAAAG
mir-522          UUG-UCUGAAAGA-AAAGAAAAUG--GUUCCCUUUAGAG-UGUUAC-GCUUUGAGAAAAG
mir-523          UUG-UCUGAAAGA-AAAGAACGCG--CUUCCCUAUAGAG-GGUUAC-CCUUUGAGAAAAG
mir-526a-1       UUG-CUUGAAAGA-AGAGAAAGCG--CUUCCUUUUAGAG-GAUUAC-UCUUUGAGAAAAA
mir-526a-2       U-----UGAAAGA-AAAGAACAUG--CAUCCUUUCAGAG-GGUUAC-UCUUUGAGAAGAG
mir-526b         UUG-UCUGAAAGA-AGAGAAAGUG--CUUCCUUUUAGAG-GCUUAC-UGUCUGAGAAAAG
mir-527          UUG-UCUAAAAGA-AAAGAAAGUG--CUUCCCUUUGGUG-AAUUA-CGGUUUGAGAAAAG
mir-551b         CAG-AACGGGAAG-GCGA------CCCAUACUUGGUUUC-AGAGGC-UG--UGAGAAUAA
mir-593          -UC-CCUCUGGGG-GAGCAAGGAGUGGUGCUGGGUUUGU-CUCUGC------UGGGGUU-
mir-99b          -GGGCCUUCGCCG-CACACAAGCU--CGUGUCUGUG--GGUCCG---UGUCGGGGGCUCA
CONS STRUCTURE   ....((.....))...))))))))..))))))))))))......................

mir-100          CACG-G-AC
mir-373          CAUC-----
mir-516b-1       CA-------
mir-516b-2       CAGCAU--U
mir-517a         CAAC-----
mir-517b         CAACG---U
mir-517c         CAACG---U
mir-518b         CAG------
mir-518c         CAAC-----
mir-518e         CAAC-----
mir-518f         CAACG----
mir-519a-1       CAACA----
mir-519a-2       CAAC-----
mir-519d         CCA------
mir-519e         CCACG---U
mir-520b         CAA------
mir-520e         CAA------
mir-520f         CAAUG----
mir-520g         CAGU-----
mir-520h         CAGU-----
mir-521-1        CAAC-----
mir-521-2        CAAU-----
mir-522          CAUCG----
mir-523          CAGCA----
mir-526a-1       CAACA----
mir-526a-2       CAACGUUUA
mir-526b         CAACG----
mir-527          CAACG----
mir-551b         CUGC---AA
mir-593          ---U---C-
mir-99b          CCAUCG-CG
CONS STRUCTURE   .........



Consensus
CPU time: 0.00
Average sequence ID: 0.6343746226
Average free energy: -19.4119354839
Average covariation: -0.0234115347019
Average basepair probability: 0.757860729014
Canonical basepairs: NA

Sequence and structure consensus for Consensus
AaGAAGAUCUCAKGmyCUGUcGACCCaUCYAgGAGGkmmGAAGCRykCUUUCUsyuuguGUUGkUCUGAAAGAaAAASAAMGYGysCUUC CYUUUAGAGrKGUUACcYSUUUGAGAAAAGCAACrkumu
...........................((((.((((...((((((..((((((...........((.....))...))))))))..)))) ))))))))...............................

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