Index >

Results for CNB 134270_43-rev

Input Alignment

CLUSTAL W(1.81) multiple sequence alignment


134270_ENSDARG00000020961_ZEBRAFISH_5965_8474/1-2687 AGCACCCCACTGCATTTCAATGTTTAA-ATTTTA-ATGAACCCTTTAAAAATGTCTCAAG
134270_ENSG00000164853_HUMAN_5374_7839/1-2687        --C--CGCGCCGC-GGCGGCTCCGTGC-GTCCCA-ATG--C---T--CGCATTTC-AATC
134270_SINFRUG00000149320_FUGU_3315_5852/1-2687      AGCAGCCCTCTGTATTTCAGCGCGTGCAGCCCCACATT--C---TAACGAACTCCTCACA
134270_ENSRNOG00000001284_RAT_5040_7483/1-2687       --CCGTGCGCCGCAGCCGGCTCCACGC-ATCTCA-ATG--C---G--ACCATTTC-AATC
134270_ENSMUSG00000029546_MOUSE_5013_7498/1-2687     --CCGCGCGCTGCAGCCGGCTCCACGC-ATCTCA-ATG--C---G--ACCATTTC-AATC
                                                       *    * * *                     * **   *         *   *  *  


134270_ENSDARG00000020961_ZEBRAFISH_5965_8474/1-2687 ATGTAGCCTTTTAT--CCCTCTATCTTACAAAAAGTGCTTTTAGAAGTTTG--GGAATCT
134270_ENSG00000164853_HUMAN_5374_7839/1-2687        GCCCTGTGTTTT-TCATGCTGTCGGGCCGGCT-CGCGCTCCGA-AAACCTCCTCGAGTGT
134270_SINFRUG00000149320_FUGU_3315_5852/1-2687      AATCTGCCTTAT-TCATCCTTCCTCCTCTTTTAAGCGCTT--C-TTTCTTC--GGATTT-
134270_ENSRNOG00000001284_RAT_5040_7483/1-2687       GCCCAGTGGCNN-N--NNNNNNNNNNNNNNNN-NNNNCTC--A--------------TG-
134270_ENSMUSG00000029546_MOUSE_5013_7498/1-2687     GCCCAGTGGCTT-T--TTNNNNNNNNNNNNNN-NNNNNNNNNN-NNNNNNNNNNNNNNNN
                                                          *                                                      


134270_ENSDARG00000020961_ZEBRAFISH_5965_8474/1-2687 TTGAATGTTTTTTTCTTTGTGTCTTAAACTTAT--TTTAT-----CATACTGTACACAAG
134270_ENSG00000164853_HUMAN_5374_7839/1-2687        TTGAGAGGGGCCTTTAATGACGGTGGGGGCGGCCGGGACGACCCCCGC--CCGGCTCGAG
134270_SINFRUG00000149320_FUGU_3315_5852/1-2687      -TGAGGGCGATCTG--ATGAATAATTGCCCCTC--TCTCG-----GTC--TCTTTTTGAA
134270_ENSRNOG00000001284_RAT_5040_7483/1-2687       -TGCTCGGGACCCT--NNNNNNNNNNNNNNNTC--TCAAG-----CGT--TGGAGTGGGG
134270_ENSMUSG00000029546_MOUSE_5013_7498/1-2687     GTGCCCGGGACCCTNNNNNNNNNNNNNNNNNNC--TCAAG-----CGT--TGGAGTGGGG
                                                      **   *                                                     


134270_ENSDARG00000020961_ZEBRAFISH_5965_8474/1-2687 TATGAATAATTCGGTTTATCCAGATCCCCCTTTTGAACATCAGAATTCTATAATTGCAGC
134270_ENSG00000164853_HUMAN_5374_7839/1-2687        AGCTCTTCAGAGGCCCTCGGC-TGCGGCGGCGCCGCGGGGAGTCGCTCGGCTTCTGCTCT
134270_SINFRUG00000149320_FUGU_3315_5852/1-2687      CATCTAAAATTCAGTGATTGCTTTTGGTCATTTTCAGGCACGACTCCAACCNNNNNNNNN
134270_ENSRNOG00000001284_RAT_5040_7483/1-2687       GACTTTAATGACGGTGGGGGT-GGCCGAGTCGACCCCGCCCGGCTCGAGAGCTCTTCAGA
134270_ENSMUSG00000029546_MOUSE_5013_7498/1-2687     GACTTTAATGACAGTGGGGGT-GGCCGAGACGACCCCGCCCGTCTCGAGAGCTCTTCAGA
                                                                                                                 


134270_ENSDARG00000020961_ZEBRAFISH_5965_8474/1-2687 TTTGACAGTTCAGGGCGCGGTCTCGTCCTGGCGCGATCTTAGCTCAATGAAAAGC-AGCC
134270_ENSG00000164853_HUMAN_5374_7839/1-2687        CGGNNNNNNNN-NNNNNNNNNNNNNNNNNATTTTCAACATCAAAATTTCATAATCGCCTC
134270_SINFRUG00000149320_FUGU_3315_5852/1-2687      NNNNNNNNNNN-NNNNNNNNNNNNNNNNNNNNNNN-NNNNNNNNNNNNNNNNNNNNNGTG
134270_ENSRNOG00000001284_RAT_5040_7483/1-2687       GGCCCTCGGGC-TGGCGGTGGCGCGGCGGGGAGTC-ACTTGGCTCCAACTGGAGCGCGCA
134270_ENSMUSG00000029546_MOUSE_5013_7498/1-2687     GGCCCTCGGGC-TGGCAGTGGCGCGGCGGGGAGTC-ACTTGGCTCCAACTGGAGCGCGCA

134270_43-rev.aln

RNAz output


############################  RNAz 0.1  ##############################

 Sequences: 5
 Columns: 300
 Mean pairwise identity:  35.02
 Mean single sequence MFE: -80.91
 Consensus MFE:  -8.17
 Energy contribution:  -9.70
 Covariance contribution:   1.53
 Mean z-score:  -0.66
 Structure conservation index:   0.10
 SVM decision value:   0.06
 SVM RNA-class probability: 0.561898
 Prediction: RNA

######################################################################

>134270_ENSDARG00000020961_ZEBRAFISH_5965_8474/1-2687
AGCACCCCACUGCAUUUCAAUGUUUAAAUUUUAAUGAACCCUUUAAAAAUGUCUCAAGAUGUAGCCUUUUAUCCCUCUAUCUUACAAAAAGUGCUUUUAGAAGUUUGGGAAUCUUUGAAUGUUUUUUUCUUUGUGUCUUAAACUUAUUUUAUCAUACUGUACACAAGUAUGAAUAAUUCGGUUUAUCCAGAUCCCCCUUUUGAACAUCAGAAUUCUAUAAUUGCAGCUUUGACAGUUCAGGGCGCGGUCUCGUCCUGGCGCGAUCUUAGCUCAAUGAAAAGCAGCC
.........((((.((((.((((((((((((..(((((((..(((((((((((....))))).(((((((................))))).))))))))((((((((((......(((.......)))......))))))))))......(((((((.......))))))).......)))))))..)))).......))))))))............((((.((((..((..((((((((((......)))))))).))..))..)))))))))))).)))).. ( -63.70)
>134270_ENSG00000164853_HUMAN_5374_7839/1-2687
CCGCGCCGCGGCGGCUCCGUGCGUCCCAAUGCUCGCAUUUCAAUCGCCCUGUGUUUUUCAUGCUGUCGGGCCGGCUCGCGCUCCGAAAACCUCCUCGAGUGUUUGAGAGGGGCCUUUAAUGACGGUGGGGGCGGCCGGGACGACCCCCGCCCGGCUCGAGAGCUCUUCAGAGGCCCUCGGCUGCGGCGGCGCCGCGGGGAGUCGCUCGGCUUCUGCUCUCGGNNNNNNNNNNNNNNNNNNNNNNNNNAUUUUCAACAUCAAAAUUUCAUAAUCGCCUC
..((((((.(((((((((.((((((((((((....))))....((((((((((.....)))(((((((((((..(((((((((.((........))))))))..)))...))))).....)))))).)))))))..))))).....(((((((((.((((.((((....)).)).)))))))).)))))....))).)))))))))))))..(((....)))...................................................))... ( -106.30)
>134270_SINFRUG00000149320_FUGU_3315_5852/1-2687
AGCAGCCCUCUGUAUUUCAGCGCGUGCAGCCCCACAUUCUAACGAACUCCUCACAAAUCUGCCUUAUUCAUCCUUCCUCCUCUUUUAAGCGCUUCUUUCUUCGGAUUUUGAGGGCGAUCUGAUGAAUAAUUGCCCCUCUCUCGGUCUCUUUUUGAACAUCUAAAAUUCAGUGAUUGCUUUUGGUCAUUUUCAGGCACGACUCCAACCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGUG
.((.((((((........((((((((......))).(((....)))..........................................)))))....((....))....))))))...(((((((((....(((........))).((.....)).........)))))((((((......))))))..))))))............................................................................... ( -38.60)
>134270_ENSRNOG00000001284_RAT_5040_7483/1-2687
CCGUGCGCCGCAGCCGGCUCCACGCAUCUCAAUGCGACCAUUUCAAUCGCCCAGUGGCNNNNNNNNNNNNNNNNNNNNNNNCUCAUGUGCUCGGGACCCUNNNNNNNNNNNNNNNUCUCAAGCGUUGGAGUGGGGGACUUUAAUGACGGUGGGGGUGGCCGAGUCGACCCCGCCCGGCUCGAGAGCUCUUCAGAGGCCCUCGGGCUGGCGGUGGCGCGGCGGGGAGUCACUUGGCUCCAACUGGAGCGCGCA
...(((((....((((.((((((((((....))))..((((((((((.(((....)))..............................(((.((((...................)))).)))))))))))))...............)))))).))))(((((.((((((((((((((((((.((((....)).)).)))))))))(((....))))))))))..)))))))(((((....)))))))))) ( -100.31)
>134270_ENSMUSG00000029546_MOUSE_5013_7498/1-2687
CCGCGCGCUGCAGCCGGCUCCACGCAUCUCAAUGCGACCAUUUCAAUCGCCCAGUGGCUUUUUNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGUGCCCGGGACCCUNNNNNNNNNNNNNNNNNNCUCAAGCGUUGGAGUGGGGGACUUUAAUGACAGUGGGGGUGGCCGAGACGACCCCGCCCGUCUCGAGAGCUCUUCAGAGGCCCUCGGGCUGGCAGUGGCGCGGCGGGGAGUCACUUGGCUCCAACUGGAGCGCGCA
..(((((((.((((((.(.((((((((....))))(.(((........(((....)))...............................................((((((((((((....................((..(((((((((.....)))))))))....)))))))((((((((((........))))))(((.....)))...))))))))))))))).)))).)))))..((((((....))))))...)).))))))). ( -95.65)
>consensus
__CAGCGCGCUGCAGCCGGCUCCAUGC_AUCUCA_AUG__C___U__ACCAUUUC_AAUCGCCCAGUGUUUU_U__UCCU______________G_GCUC__A______U____GA_UG__UGAGCGGGACCUU___UG____________UC__UCAAG_____CGU__UGGACUCGAGGACUUUAAAGACGGUGGGGGC_GGCCGAGACGACCCCGCCCGGCUCGAGACCUCUGCAGAGGC____G__C__GGC___G_C_CG_C__GGAGUC_ACUUGGCUCCAACAGAAGCGCGCA
....((((((...................................................................................................................((((((.............................................((....)).........((((((..............))))))..))))))..........................................(((((.......))))).......)))))). ( -8.17 =  -9.70 +   1.53)

134270_43-rev.rnaz

RNAalifold consensus structure

Secondary Structure Dot Plot
PS | PDF PS | PDF
Stefan Washietl
Last modified: Thu Aug 12 14:35:44 CEST 2004