Structure #140513

Summary

Genome/Assembly	hg17
Chromosome/Contig	chr4
Strand	-
Position	135,577,246 - 135,577,328
Number of sequences	4
Organisms	human, dog, mouse, rat
Mean pairwise identity	85.57
Columns	82
Mean single MFE	-15.88
Consensus MFE	-12.39
Combinations/base pair	15 / 13 = 1.15
SCI	0.78
z-score	-2.09
RNA class probability	0.90496

This structure is part of cluster 77493

Alignment

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RNAz output

	  
###########################  RNAz 0.1.1  #############################

 Sequences: 4
 Slice: 1 to 82
 Columns: 82
 Strand: +
 Mean pairwise identity:  85.57
 Mean single sequence MFE: -15.87
 Consensus MFE: -12.39
 Energy contribution: -13.57
 Covariance contribution:   1.19
 Mean z-score:  -2.09
 Structure conservation index:   0.78
 SVM decision value:   1.04
 SVM RNA-class probability: 0.904960
 Prediction: RNA

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>hg17.chr4/135577328-135577246
CAAAAAGAUGAUAUUUAAGAAGCACAACACAACAGGAUGUGAAUGAUGAUGUAAUAAUUCACAUCCUUUGCAUGGGUAGACA
.....................((.((...(((.(((((((((((.((......)).))))))))))))))..)).))..... ( -16.90)
>canFam1.chr19/46120445-46120527
CAAAAAGAUGAUAUUUAAGAAGCACAACACAACAGGAUGUGAAUUAUGAUGUAAUAAUUCAUACCCUUUGCAUUGUUAGAUG
...........(((((((.(((((.........(((.((((((((((......)))))))))).))).))).)).))))))) ( -16.70)
>mm5.chr3/46524529-46524447
CAAAAUGAUGAUUUUUAAGAAACAUAGCACAACAGGGUAUGAAUUAUGAUGUAAUAAUUCACACCCAUUGCAUUGUUAGAUA
....................((((..(((.....((((.((((((((......)))))))).))))..)))..))))..... ( -17.80)
>rn3.chr2/134205910-134205828
CAAAAUGAUGAUUUUUAAGAAACAUAAGAAAUCACGGUAUGAAAUAUGAUGUAAUAAUUCACACCCAUUGCAUUGUUAAAUG
...((((.((((((((..........)))))))).(((.((((.(((......))).)))).))))))).((((....)))) ( -12.10)
>consensus
CAAAAAGAUGAUAUUUAAGAAACACAACACAACAGGAUAUGAAUUAUGAUGUAAUAAUUCACACCCAUUGCAUUGUUAGAUA
..................................(((((((((((((......)))))))))))))................ (-12.39 = -13.57 +   1.19)

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Consensus structure

Secondary structure graph

Secondary structure

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Montain plot

Secondary structure

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Dotplot

Secondary structure

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