Structure #3577

Summary

Genome/Assembly	hg17
Chromosome/Contig	chr1
Strand	+
Position	122,565 - 122,684
Number of sequences	4
Organisms	human, dog, mouse, rat
Mean pairwise identity	83.19
Columns	120
Mean single MFE	-48.82
Consensus MFE	-33.43
Combinations/base pair	44 / 34 = 1.29
SCI	0.68
z-score	-1.62
RNA class probability	0.59369

This structure is part of cluster 7

Alignment

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RNAz output

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

 Sequences: 4
 Slice: 1 to 120
 Columns: 120
 Strand: +
 Mean pairwise identity:  83.19
 Mean single sequence MFE: -48.82
 Consensus MFE: -33.43
 Energy contribution: -33.37
 Covariance contribution:  -0.06
 Mean z-score:  -1.62
 Structure conservation index:   0.68
 SVM decision value:   0.12
 SVM RNA-class probability: 0.593690
 Prediction: RNA

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>hg17.chr1/122565-122684
UUCAAAGCCCAGGAGUCUGGUCAACGCAGCAGAGCGGGCCCCCUACGGCCCCAACCCCUGGGGAUGGGGGCCCAGGGACGCCUUCCAAGGUGGCCUGUUUCCUCCCAAUGGAUCCUGCC
......(.((((....)))).)...(((((((.((((((((((.....(((((.....)))))..)))))))).....(((((....))))))))))..(((.......)))..)))). ( -52.50)
>canFam1.chr1/579-459
UUCAAGGCCCAGGAGUCAGGCCAGGGCAGCACAGCAGGCCCACUACGGCCCCCACCCCCUGGGGCUGGGGGCCCAGUGACACCUUCCAAGGCCACCCGGUUCCUUCCAACGGAUCCUGCG
.....((((..((((...((((...((......)).))))((((..(((((((((((....))).)))))))).)))).....))))..))))....((.(((.......))).)).... ( -55.60)
>mm5.chr7/453-573
UUUAAGACCCAGGAGUCUGGUCAGGGCAGCACAGCGGUGCCACUACGGCCCCCACCCCCUGGAGCCGGGGGCCCAGCAACACCUUCCAAGGCCACUCGGUUUCCUCCUACGGAUUCUGCC
...........((((((((..(((((..((...))((.(((.....))))).....)))))((((((((((((................)))).)))))))).......))))))))... ( -41.69)
>rn3.chr1/453-573
UUUAAAACGCAGGAGUCUGGUCAGGGCAGCACAGCGGUGCCACUACGGCCCCCACCUCCUGGAGCUGGGGGCCCAACAACACCUUCCAAGGCCACUCGGUUUCUUCCUACGGAUUCUGCC
........((((.(((((((((((((((.(.....).)))).))..((((((((.(((...))).))))))))................))))....((......))...))))))))). ( -45.50)
>consensus
UUCAAAACCCAGGAGUCUGGUCAGGGCAGCACAGCGGGCCCACUACGGCCCCCACCCCCUGGAGCUGGGGGCCCAGCAACACCUUCCAAGGCCACCCGGUUCCUUCCAACGGAUCCUGCC
.........(((((.((((...((((..((...))((((((.....))))))....))))(((((((((((((................)))).)))))))))......))))))))).. (-33.43 = -33.37 +  -0.06)

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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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