Webserver for Aligning structural RNAs

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-198          AUUCUGU----GGUU-CUGAUCA---UUGGUCC-----AGAGGG-GAGAUA-GG-U-UCC
mir-220c         G-GCAUUGUAACACUGG---GACCACACAGGG--CUGUUGU--GAAGACUC-AGUG--AG
mir-453          GGCUGUGCAG-AAGAUGCAG----GAAUG-CUGCGA-GCAGU-GCCAC---CUCAUG-GU
mir-484          -CUCGCGGCCCUGCAGCCUCGUC---AGGCUCAGUCCCCUCCCGAU---AA-AC-CCCUA
mir-565          CAGUGGCGCAA---UGGAUAACG---CGUCUGACU-ACGGAUCAG-AAGAU-UCUAGGUU
mir-566          AAUUAGCUAG-GCGUGGU-GGCGGG--CGCCU--GUGAUCC--CAACUACU-CAG-G-AG
mir-571          CCUCAGUAAGACCAAGCUCA------GUGUGCCAU-----UUCC-UUGUCU-GU-AGCCA
mir-591          -GGGAGUCUUAUCAAUGAGG--U---AGACCAUGGG--UUCUCAUUGUAAU-AG--UGUA
mir-596          AAGCGAGCAC-G-GCCUCUCCGAAGCCUGC----CCGGCUCC-UCGGG---AACCUG-CC
mir-601          A-AAAGUGCAUGAGUUCGU-CUU---GGUCUAGGAUUGUUGGAG-GAGU---CAGAAAAA
mir-604          GGAGAGCAUCGUGCUUGA-CCUUCCAC--GCU--CUCG-UG--UCCACUAG-CAGG--CA
mir-608          CCACUGGGCC-AAGGUGGG-CCAGGGGUGGUGU-----UGGG-ACAGCU-CCGUUUA-AA
mir-611          GGAUUAGCCU-UCGCGGG-GCAAAAUGGU-GA--GAGCGUU--GAGGGGAG-UUCC--AG
mir-630          ACUUAACAUCAUGCUACCUC--U---UUGUAUCAU---AUUUUG-UUAUUC-UG-G-UCA
mir-637          CUAAGGUGUU-GGCUCG---GGCUCCCCACUG--CAGUUAC--CCUCCCCU-CGGC--GU
mir-646          GAGAUCAGGA---GUC--UGCCA---GUGGAGUCAGCACACCUGCUUUUCA-CC-UGUGA
mir-648          AGAUGAUCAC-A-GACAC--CUCCAAGUGUGC--A-GGGCA--CUGGUGGGGGCCG--GG
mir-658          GGUUGC-CGU-GGUUGCGGG----CCCUGCCCGCCCGCCAGC--UCGCU--GACAGC-AC
mir-744          GCACACUGGGUUGGGCAA-GGUGCG--GGGCU--AGGG-CU--AACAGCAGUCUUA--CU
mir-765          CUGAUGAAAG--UGGAGU-UCAGUAGACA-GC--CCUUUUC--AAGCCCUA-CGAG--AA
mir-801          UGGCA-CACGUAGGGCAA-CUCGAUUGC-UCU--GCGUGCG--GAA-UCGA-CAUCA-AG
mir-921          AGAAAAGGGCA-GUGCCACAACU---AGUGAGGGA-CAGAAC--CAGGAUU-CAG--ACU
mir-922          GGAUGG-CGUUUUCCCUCUCCCU---GUCCUGGAC-UGGGGUCA--GACUG-UGC-CCCG
mir-941-1        CACACCC-GG---CUGUGU-GGACAUGUGCCCAGGGCCCGGG--ACAG---CGCCAC-GG
mir-941-2        CGCACCC-GG---CUGUGU-GCACAUGUGCCCAGGGCCCGGG--ACAG---CGCCAC-GG
mir-941-3        CGCACCC-GG---CUGUGU-GCACAUGUGCCCAGGGCCCGGG--ACAG---CGCCAC-GG
CONS STRUCTURE   ............................................................

mir-198          UGUGAUUUUUCCUUCUUCUCUAUAGAAU-AAAUGAAA--UCU-UGU-UACUAGAACAAGA
mir-220c         CUCAUCCC---C--ACACAG-CCUUCAGCA-CAGGG-CC-UGGCUCAGGGCAGAUG--CU
mir-453          ACUCGGAG---GG-AGGUUGUCCGUGGUGAGUUCGCAU-U--AUUUA-AUGAUGC--CCA
mir-484          AAUAG--GGACUUUCCCGGGGGG-UGAC-CCUGGCUU--UU--UUG-G--C-GAA-AACC
mir-565          CGACU--CCUG---GCUGGCUCG-CGAU-GUCUGUUU--UGC-CAC-ACUUGAC--CCAU
mir-566          GCUGGGGC---A--GCAGAA-UCGCUUGAACCCGGGAGGC-GAAG-GUU-GCAGUG--AG
mir-571          UGUCUAUGGGCUC-UUGAGUUGG-CCAU-CUGAG--UGAGGG-CCU-GCUUAUUCUAAAU
mir-591          GAAUGUUG---GUUAACUGUGGA---CU-CCCUGGCUCUGUC-UCA-AAUCUACUG--AU
mir-596          UCCCGCAU---GGCAGCUGCUGCCCUUCGGAGG--CCG-A--CCCGA-CCCAUCC-CUGG
mir-601          CUACCCC--A-GGGAUCC-UGAAG-UCC-UUUGG---GUGGA-AAG-GGGGAGGCC--CC
mir-604          GGUUUUCU---G--ACACAG-GCUGCGGAAUUCAGGACAGUGCAUCAUG-G-A-GA--AA
mir-608          AAGGCAUC---UCCAAGAGCUUCCA-UCAAAGGCUG---C--CUCUU-GGUGCAG-CA-C
mir-611          ACGGAGAU---G--CGAGGA-CCCCUCGGGGUCUGA-CC-CACACCGC-GCUUAUC--UC
mir-630          CAGAAUG--ACCU-AGUAUUC--UGUAC-CAGGGAAGGUAGU-UCU-UAACUAUAUUGUA
mir-637          UACUGAGC---A--CUGGGG-GCUUUCGGGCUCUGCGUC-UGCA-CAG-AUACUUC--GA
mir-646          UCC-----CAGGAGAGGAAGCAG-CUGC-CUCUGAGG--CCU-CAG-GCUCAGUG-GCCU
mir-648          GCAGGCCC---A--GCGAAA-GUGCA-GGACCUGGCACU-UAGUC--G-GAAGUGAGGGU
mir-658          GACUCAGG---GCG-GAGGG-AAGUAGGUCCGUUGGUC-G--GUCGG-GA-ACGA-GGCU
mir-744          GAAGGUUU---C--CUGGAA-ACCA-CGCACAUGCUGU--UGCCACUAACCUC---AACC
mir-765          ACUGGGGU---U--UCUGGA-GGAGAA-GGAAGGUG-AU-GAAG-GAU-CUGUUCUCGUG
mir-801          AGAUUUCG---G--AAGCAUAAUUUUUUGGUAUUUGG----GCAGCUGG-UGAUCG--UU
mir-921          CAGGUCCAU--GG-GCCUG-G--AUCAC-UGGCUA--AUUCU-GUG-GGUCAGGGCUGGA
mir-922          AGG-----AGAAGCAGCAGA---GAAUA-GGACUAC--GUCA-UGG-GCAUUUCGUCCAC
mir-941-1        AAGAGGAC---GC-ACCCGGCUGUGUGCACAUGUGCCC-A--GGGCC-C--GGGA-CAGC
mir-941-2        AAGAGGAC---GC-ACCCGGCUGUGUGCACAUGUGCCC-A--GGGCC-C--GGGA-CAGC
mir-941-3        AAGAGGAC---GC-ACCCGGCUGUGUGCACAUGUGCCC-A--GGGCC-C--GGGA-CAGC
CONS STRUCTURE   ............................................................

mir-198          AAU
mir-220c         CAG
mir-453          AUA
mir-484          CCC
mir-565          GUA
mir-566          CCA
mir-571          AA-
mir-591          UCA
mir-596          GU-
mir-601          CAU
mir-604          CAU
mir-608          AGG
mir-611          CU-
mir-630          C--
mir-637          GUC
mir-646          AUC
mir-648          GCA
mir-658          CAG
mir-744          UUA
mir-765          AGC
mir-801          GGU
mir-921          G-G
mir-922          UUA
mir-941-1        GCC
mir-941-2        GCC
mir-941-3        GCC
CONS STRUCTURE   ...




 
 Consensus 


 CPU time:
 0.00
 

Average sequence ID:
 0.202148932199
 

Average free energy:
 0.0
 

Average covariation:
 0.0
 

Average basepair probability:
 0.0
 

Canonical basepairs:
 NA
 

Sequence and structure consensus for Consensus 
VGWHRSYVRSwKGSUSSAUVSYWMRHRUGCYYRVSBSSYKSByRMYRGYWWcCCYWSyMRAMDRKKHYywcGBbACSVRRYRSUYWABRM
HUKKRSWCUWYDSWCSAKVUYADKAYMAVHVHM

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The alignment colored using colorrna.pl of the Vienna package 

Cluster tree of the methods Tree

Table