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-1-1          -----------------GCAGACUGCCUGCUUGGG--AAAC-AU-ACUUCUUUAUAUGCC
mir-1-2          -----------------UAGUAAUACCUACUCAGA--GUAC-AU-ACUUCUUUAUGUACC
mir-122          -GAG--------------UUUCCUUAG----CAG---AGCU-GU-GGAGUGUGACAAUGG
mir-135b         CCCUC-----------------CACUCUGCUGUGG--CCUA-UG-GCUUUUCAUUCCUAU
mir-136          -GU--------------UGGAUGAGCCCUCGG--------AGGA-CUCCAUUUGUUUUGA
mir-137          -GG--------------UCCUCUGACUCUCUUCGG--UGAC-GG-GUAUUCUUGG--GUG
mir-144          -CCC--------------CAGUGGGGCCCUGGCUG--GGAU------AUCAUCAUAUACU
mir-153-1        CUCUC-CC--------U-C-A-----CAGCUGCCA--GUG--UC-AUUUUUGUGAUCUGC
mir-153-2        -GCUA-AU--------UAGCG------GUGGCCAG--UGU--CA-UUUUUGUGAUGUUGC
mir-155          UUGC------------UGUAGGCUGUAUGCUGUUA--AUGC-UA-AUCGUG----AUAGG
mir-186          UUUC-------------AUUGCUUGU-AACU------UUCC-AA-AGAAUUCUCCUUUUG
mir-194-1        UGUUUAAU-------------GGUG-U--------UAUCAAG-U-GUAACAGCAACUCCA
mir-194-2        UCCA--AUU------------GGUUCC--------CGCCCCC-U-GUAACAGCAACUCCA
mir-196a-2       -CGCUCAG------------CUG----AU-C-UGU--GGCU-UA-GGUAGUUUCAUGUUG
mir-203          -GGG---------------GACUCGCGCGCUGG--GUCCAGU-G-GUUCUUAACAGUUCA
mir-205          CAAUCCA----------UGUGCUUCUCUUGUCC------------UUCAUUCCA-CCGGA
mir-206          -AUG---------------ACACUGCUUCCCGAGG--CCAC-AU-GCUUCUUUAUAUCCC
mir-22           ------------------UCACCUGGCUGAGCCGC--AGUA-GU-UCUUCAG-UGGCAAG
mir-27b          UGACCUCU----------CUAACAAGG----UGCA--GAGC-UU-AGCUGAUUGGUGAAC
mir-31           -GUA--AC---------UUGGAACUGG--------AGAGGAG-G-CAAGAUGCU-GGCAU
mir-32           UCUGC-----------UUGCUCUGGUGGAGAUAUU--GCAC-AUUACUA------AGUUG
mir-335          UG----AUU---------UGUUUUGAGCGGGGGUC--AAGA---G-----CAAU-AACGA
mir-33a          -CCU--------------CCUGGCGGGCAGCUGUG--GUGC-AU-UGUA---GUUGCAUU
mir-345          -GAG-------------ACCCAAACCCUAGGUCUG--CU--------GACUCCUAGUCCA
mir-367          -GU--------------UCUUGGCUA-CAGG----CCAUUAC-U-GUUGCUAAUAUGCAA
mir-424          UCA---------------UUGACUCC--GAGGGGA---UACA-G-CAGCAAUUCAUGUUU
mir-451          GGC--------------ACUUGGGAAUGGCAA---GGAAACCGU-UACCAUUACU-GAGU
mir-493          UCAUUC-U----------GGCCUCCAGGGCUUUGU--ACAU-G-GUA-----GG-CUUUC
mir-498          AAGUGAAG--CUCAGGCUGUGAUUUCAAG---------------C-----C-AGGGGGCG
mir-505          UAA---AU--------UGAUGCACCCAGUGGGGG-----------AGCCAGGAA-GUAUU
mir-549          AGACAUGCAAC-----UCAAGAAUAUAUUGAGAGC--UC-----A-----UCCAUAGUUG
mir-552          -AAC--------------CAUUCAAAUAUACCACA--GUU--UG-UUUAACCUUUUGCCU
mir-558          GUGUGUGUG--------UGUGUGUGUG--------UGGUUAU-U-UUGGUAUAGUAGCUC
mir-559          -GAUG-AG---------CUCCAGUAACAUCUUAAA----------GUAAAUAUGCACCAA
mir-561          UUCAU-------------CCACCAGUCCUCC----AGGAACA-U-CAAGGAUCUUAAACU
mir-577          ------------------GUAUUUGGGGGAGUGAA--GAGU-AG---AUAAAAUAUUGGU
mir-578          AGAU----------------AAAUCUAUAGA-C--AAAAUAC-A-AUCCCGGACAACAAG
mir-579          AUUA----------------GGUUAAUGCAA-A--AGUAAUC-G-CGGUUUGUG-CCAGA
mir-580          -----------------UAAAAUUUCCAAUUGG--AACCUAA-U-GAUUCAUCAGACUCA
mir-581          -AAAA-AG--------------UUAUG-UGAAGGU--AUUC-U--UGUGUUCUCUAGAUC
mir-585          UGUGG-----------GGUGUCUGUGCUAUGGCAG--CCCU-AG-CACACAGAUA--CGC
mir-586          -AAG-------------ACAUGGGGUAAAACCAUU--AUGC---A-----UUGUAUUUUU
mir-587          UGCCCCUCCUAU--GCACCCUCUUUCCAUA---------------GGUGAUGAGUCACAG
mir-605          -CUC----------------UAGCCCUAG---C--UUGGUUC-U-AAAUCCCAUGGUGCC
mir-606          --------------------UGUAUCCUUGGUUUU--UAGU-A-G-----UUUUACUAUG
mir-607          ----------------UUGCCUAAAGUCACACAGG--UUAU-AG-AUCUGGAUUGGAACC
mir-609          -----------------CAUGCUGCUCGGCUGUUCCUAGGGU-G-UUUCUCUCAUCUCUG
mir-610          -AUUUG-U---------CUAUUUGUCUUAGGU--------GA-G-CUAAAUGUGUGCUGG
mir-617          -----------------UAAGCCAUCAUAAGG-------AGCCU-A-GACUUCCCAUUUG
mir-624          UAUAUAA--------------UGCUGU--------UUCAAGG-U-AGUACCAGUACCUUG
mir-625          GUGGU-------------AAGGGUAGAGGGAUGAG----------GGGGAAAGUUCUAUA
mir-627          ------------------UGAAUUACUUAUUACUG--GUAG-UG-AGUCUCUAAGAAAAG
mir-629          -CCC---U----------UUCCCAGGG---GAGGG--GCUG-GG-UUUACGUUG-GGAGA
mir-641          CAGGC-----------UGGGUGAAAGGAAGGAAAG--ACAU-AG---GAUAGAGUCACCU
mir-642          -AGU---------------UUAUCUGAG----U--UGGGAGG-G-UCCCUCUCCAAAUGU
mir-643          -CCA-------------AGUGAUAUUCAUUGUCUA--CCUG-AG-CUAGAAU---ACAAG
mir-651          ACAG----------------AAAUCUAUCAC-U--GCUUUUU-A-GGAUAAGCUUGACUU
mir-652          -ACGA------------AUGGCUAUGCAC---U--GCACAAC-C-CUAGGAGAGGGUGCC
mir-653          UCUA---------------AUUUUUCAUUCCUUCA--GUGU----UGAAACAAUCUCUAC
mir-934          -A---------------ACUUGAGAAAUAAGGCUU--CUGU------CUACUACUGGAGA
mir-942          CAGCAA----------------ACAUUAGGAGAGU--AUCU-UC-UCUGUUUUGGCCAUG
mir-944          ------AUU---------UAUGUUCCAGACACAUC--UC------AUCUGAUAUACAAUA
mir-95           UUGUG-AC--------ACCCAACACAGUGGGCACU--CAAU---A-----AAUGUCUGUU
CONS STRUCTURE   ....................................................((.(((((

mir-1-1          CAUAUGGACCU-GC-UAAGC-UAUGG-AA---UGUAAAGAAGUAUGU-AUCUCAGGCCGG
mir-1-2          CAUAUGAACAU-AC-AAUGC-UAUGG-AA---UGUAAAGAAGUAUGU-AUUUUUGGUAGG
mir-122          UGUUUGUGUCUAAA-CUAUCAAACGC--C-AUUAUCACACUAAAUAG-CUACUGCUA-GG
mir-135b         GUGAUUGCUGUC-C-CAAAC-UCAUGUA---GG-GCUAAAAGCCAUG-GGCUACAGUGAG
mir-136          UGAUGGAUUCUUAU-GCUCC-AUCAUCG--UCU-CAAAUGAGUCUUC-AGAGGGUUC---
mir-137          GAUAAUAC-GG-AU-UACGU-UGUUAUUG---CUUAAGAAUACGCGU-AGUCGAGGAGAG
mir-144          GUAAGUUU-GCGAU-GAGACACUACAGU---AU-AGAUGAUGUACUA-GUCCGGGCACCC
mir-153-1        AGCUAGUAU-UC-U-CACUCCAGUUGCAU--AGUCACAAAAGUGAUC-AUUGGCAGG-U-
mir-153-2        AGCUAGUA--AUAU-GAGCCCAGUUGCAU-AG--UCACAAAAGUGAU-CAUUGGAAA-CU
mir-155          GGUUUUU-GCC-UC-CAACU-GACU-------CCUA--CAUAUUAGC-AUUAACAGUGUA
mir-186          GGCUUUCUGGUUUU-AUUUUAAGCCCAA---AG-GUGAAUUUUUUGG-GAAGUU-UG-AG
mir-194-1        UGUGGACUGUGUAC-CAAUUUC-CA-GUGG-AGAUGCUGUUACUUU-UGAUGGUUAC---
mir-194-2        UGUGGAAGUGCCCA-CUGGUUCCAGUG--G-GGCUGCUGUUAUCUG-GGGCGAGGGC---
mir-196a-2       UUGGGAUU-GAGUU-UUGAACUCGGCAA---CAAGAAACUGCCUGAG-UUACAUCAG-UC
mir-203          ACAGUUCUG-UAGC-GCAA--UUGU-GA--AAU-GUUUAGGACCACU-AGACCCGGC---
mir-205          GUCUGUCUC-AUAC-CCAACCAGAUUUC---AG-UGGAGUGAAGUU-CAGGAGGCAU---
mir-206          CAUAUGGA-UU-AC-UUUGC-UAUGG-AA---UGUAAGGAAGUGUGU-GGUUUCGGCAAG
mir-22           CUUUAUGUCCUGAC-CCAGCUAAAGCU----GCCAGUUGAAGAACUG-UUGC-CCUCUGC
mir-27b          AGUGAUUG-GU--U-----UCCGCUUUGU-UCA-CAG-UGGCUAAGU-UCUGCACCUGAA
mir-31           AGCUGUUGA-ACUG-GGAACCUGCU--------AUGCCAACAUAUU-GCCAUCUUUC---
mir-32           CAUGUUGU-CA-CG-GCCUC-AAUGC---------AAUUUAGUGUGU-GUGAUAUUUUCA
mir-335          AAAAUGUUUGUCAU-AAACCGUUUUUC---AUU-AUUGCUCCUGACC-UCCUCUCA----
mir-33a          GCAUGUUCUGG-UG-GUACCCAUGCAA------UGUUUCCACAGUGC-AUCACAGAGGCC
mir-345          GGGCUCGUGAUGGC-UGGUGGGCCCUGA---ACGAGGGGUCUGGAGG-CCU-GGGUUUGA
mir-367          CUCUGUUGA-AUAU-AAA-UUGGAAUU--G-CACUUUAGCAAUGGU-GAUGGAUUGU---
mir-424          UGAAGUGUU-C--U-AAAUGGUUCAAAA---CGUGAGGCGCUGCUAUACCCCCUCGU---
mir-451          UUAGUAAUGGUAAU-GGUUCUCUUGCUAU-ACCCAGAAAA--C-GU--GCCA--GG----
mir-493          AUUCAUUC-GUUUG-CACAUUCGGUGAA---GG-UCUACUGUGUGC--CAGGCCCU----
mir-498          UUUUUCUAU-AACU-GGAUGAAAAGC-A--CCUCCAGAGCUUGAAGC-UCACAGUUU-GA
mir-505          GAUGUUUCUGCCAG-UUUA-GCGUCAA---CAC-UUGCUGGUUUCCU-CUCUGGAGCAUC
mir-549          UCACUGUCUCAAAU---CA--GUGACAA---CUAUGGAUGAGCUCUU-A--------AUA
mir-552          GUUGGUUGA-AGAU-GCCUUUCAACAGG---UGACUGGUUAGACAAA-CUGUGGUAU-AU
mir-558          UAGACUCU---AUU-A-UA-GUUUCCUG------AGCUGCUGUACC-AAAAUACCAC---
mir-559          AAUUACUUUUGG-U-AAAUACAGUUUUG---GUGCAUAUUUACUUU-----AGGAUG---
mir-561          UUGCCA---GAGCU-ACAAAGGCAAAG--U-UUAAGAUCCUUGAAG-UUCCUGGGGG---
mir-577          ACCUGAUGAA-UCU-GAGGCCAGGU-U-U-CAAUACUUUAUCUGCUC-UUCAUUUCC--C
mir-578          AAGCUCCUAUAGCU-CCUGUAGCUUCUU---GUGCUCUAGGAUUGUA-UUUUGUUUA---
mir-579          UGACGAUUUGAAUU-AAUAAAUUCAUU--U-GG-UAUAAACCGCGAU-UAUUUUUGC---
mir-580          GAUAUUUA--AGUU-AACA-GUAUUUGA---GAAUGAUGAAUCAUUA-GGUUCCGGU---
mir-581          AGUGCUUUUAGAA--AAUUUGUG-UGAU---CUAAAGAACACAAAGA-AUACCUACA-CA
mir-585          CCAGAGAAAGC-CU-GAACG-UUGGG--C---GUAUCUGUAUGCUAG-GGCUGCUGUAAC
mir-586          AGGUCCCAAUACAU-GUGG-GCCCUAAA---AAUACAAUGCAUAAUG-GUUUUUCA----
mir-587          G-GCUCAGGGAA-U-GUGUCUGCACCUG---UGACUCAUCACCAGUG-GAAAGC--CC-A
mir-605          UUCUCCUUG-GGAA-AAACAGAGAAGGC---ACUAUGAGAUUUAGAA-UCAAGUUAG---
mir-606          AUGAGGUGUGCCAU-CCACCC-CAUCAU---AGUAA-ACUAC------UGAAAAUCAAAG
mir-607          CAGG-----GAGCC-AGACUGCCUGGGU---UCAAAUCCAGAUCUAU-AACUUGUGUGAC
mir-609          GUCUAU----AA-U-GGG-UUAAAUAGUAG-AGAUGAGGGCAACAC-CCUAGGAACA---
mir-610          GACACAUUU-GAGC-CAAA--UGUCCCA---GCACACAUUUAGCUCA-CAUAAGAAA---
mir-617          AAGGUGGCCAUUUC-CUACCACCUUCAA---AUGGUAAGUCCAGGCU-CCUUCUGAU---
mir-624          UGUUCAGUGGAACC-AAGGUAAACACAAGG-UAUUGGUAUUACCUU-GAGAUAGCAU---
mir-625          GUCCUGUA--AUUAGAUCUCAGGACUAU---AGAACUUUCCCCCUC-AUCCCUCUGC---
mir-627          AGGAGGUG-GUUGU-UUU-CCUCCUCUU---UUCUUUGAGACUCACU-ACCAAUAAU-AA
mir-629          ACUUUUACGGUGA--ACCAGGAGGUUCU---CC-CAACGUAAGCCCA-GCCCCUCCC-CU
mir-641          CUGUCCUCUGUCCU-CUACCUAUAGAGG---UGAC--UGUCCUAUGU-CUUUCCUUC-C-
mir-642          GUCUUGGG-GUGGG-GGAUCAAGACACA---UUUGGAGAGGGAACCU-CCCAACUCG---
mir-643          UAGUUGGC-GU-CU-UCAGAGAC-AC------UUGUAUGCUAGCUCA-GGUAGAUAUUGA
mir-651          UUGUUC----AAAU-AAAAAUGCAAAAG-GAA--AGUGUAUCCUAAA-AGGCAAUGA---
mir-652          AUUCACAUA-GACU-AUAAUUGAAUGGC---GCC----ACUAGGGUU-GUGCAGUGC---
mir-653          UGAACCAGCUUCAA-ACAA-GUUCACUG---GAGUUUGUUUCAAUAU-UGCAAG-AA-UG
mir-934          CACUGGUAGUAUA--AAACCCAGAGUCU---CCAGUAAUGGACGGGA-GCCUUAUUUCUA
mir-942          UGUGUACUC-ACAG-CCCCU-CACACAU---GGCCGAAACAGAGAAG-UUACUUUCC-UA
mir-944          UUUUCUUAAAUUGU-AUAAAGAGAAAUUA-UUGUACAUCGGAUGAGC-UGUGUCUGG-G-
mir-95           GAAUUGAA--AUGC-GUUAC-AUUCAAC---GGGUAUUUAUUGAGCA-CCCACUCU----
CONS STRUCTURE   ((((.................)))))))...)).))........................

mir-1-1          GACCUCUC------UC----------
mir-1-2          CAAUAAAC------CA----------
mir-122          CA----AU------CC-----UUCCC
mir-135b         G-----GG------CG-----AGCUC
mir-136          ---UAU--C-A-UUUC-----GUCGG
mir-137          UACCAGCG------GC----------
mir-144          CC----AG------CU-----CUGGA
mir-153-1        GU----GG-------C-----UGCUG
mir-153-2        GU----GA-------C-----UGUAC
mir-155          UGAUGCCU------GU-----UACUA
mir-186          --CUAA--------AU-----UCCUU
mir-194-1        ----CA--A-C-UUGCUACA-----A
mir-194-2        ----CA--G-U-ACCCACGAA-----
mir-196a-2       GG----UU------UU-----CGUCG
mir-203          ----GG--G-C-GCGG-----CGACA
mir-205          ---GGA--G-C-UGAC-----AACCA
mir-206          UGCCUCCU------CG----------
mir-22           CC----CU------GG-----CUUCG
mir-27b          GA----GA------AG-----GUGAG
mir-31           ----CU--G-U-CUGACAGCAGCCAU
mir-32           CAUGAGUG------CA-----UGCAC
mir-335          --UUUGC---U-AUAU-----UCAAU
mir-33a          UGCCUGG--------------CCCUC
mir-345          AU----AU------CG-----ACAGC
mir-367          ---UAA--G-C-CAA-U----GACA-
mir-424          ----GG--G-G-AAGGUAGA-----A
mir-451          ----AA--G-A-GAAC-----UCAGG
mir-493          GUGCCA-------GGC-----AUCGU
mir-498          GA----GC------AA-----UCGUC
mir-505          GC----CA------AG-----UUCGU
mir-549          UAUCCCAGGC---A-C------U-GU
mir-552          AC-----------ACA-----GG-A-
mir-558          ----AA--A-C-GGGCUGGCU-U-A-
mir-559          ----UU--A-C-UGGAGCU--CCCA-
mir-561          ----AA--C-C-AUGGAUG-------
mir-577          CAUAUCUA-------------CUUAC
mir-578          ----UA----U--AUA-----UUU-U
mir-579          ----A---U-C-AACU-----UACUA
mir-580          ---C-A--G-A-AAUU-----UUUCA
mir-581          GA----AC------CA-----CCUGC
mir-585          AAUGUAC-------------------
mir-586          --CUCUU---U-AUCU-----UCUUA
mir-587          UC------------CC-----AU-AU
mir-605          ---GAC--U-G-CAGA-----UACAG
mir-606          AUACAAGUGCCUGACC----ACUUCU
mir-607          UU----UG------GG-----CGAGU
mir-609          ----GC--A-G-AGGA-----ACC-C
mir-610          ----AA--U-G-GACU-----CUAGU
mir-617          --UCAA--U-A-AAUG-----AGGAG
mir-624          ----UA--C-A-CCUAAGU-------
mir-625          ----CC--U-C-UACC-----AACUG
mir-627          GA----AA------UA-----CUACU
mir-629          CU----GC------CU-----GCCUC
mir-641          -U------------CU-----UAC-C
mir-642          ---GCC--U-C-UGCC-----AUCAU
mir-643          AUGAAAAA-------------UCUAC
mir-651          ---CAG--U-U-UAAU-----GUGUU
mir-652          ---ACA--A-C-CUAC-----ACAAC
mir-653          AU----------AAGA-----UGGA-
mir-934          UC----AC------UC-----AGUGU
mir-942          AU-----A------UU-----UGC-C
mir-944          --AUUA-A-------------GU-AU
mir-95           --GUGCCAGA-----------CGC-U
CONS STRUCTURE   ..........................



Consensus
CPU time: 0.00
Average sequence ID: 0.191483139987
Average free energy: -4.2446031746
Average covariation: 0.720930503189
Average basepair probability: 0.722515027555
Canonical basepairs: NA

Sequence and structure consensus for Consensus
uVMBcmayuwmucagsuuBHKMYUGSSWRSGBVKRrgRYRYsdKrRKHWHWKHKWVYHBSDDKUKKUUKGWRMYgVMAMCSASMUCDAwg mRKAWRAWRWWMYVWBUrVBCHSBYRYrRVGWyyMMvrgmcuaaSCwvgmaYBCAY
....................................................((.(((((((((.................))))))).. .)).))..................................................

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