Structure #118835

Summary

Genome/Assembly hg17
Chromosome/Contig chr20
Strand +
Position 44,330,320 - 44,330,425
Number of sequences 4
Organisms human, dog, mouse, rat
Mean pairwise identity 74.75
Columns 120
Mean single MFE -47.05
Consensus MFE -28.7
Combinations/base pair 41 / 32 = 1.28
SCI 0.61
z-score -1.77
RNA class probability 0.774982

This structure is part of cluster 63001

Alignment

Alignment

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RNAz output

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

 Sequences: 4
 Slice: 1 to 120
 Columns: 120
 Strand: +
 Mean pairwise identity:  74.75
 Mean single sequence MFE: -47.05
 Consensus MFE: -28.70
 Energy contribution: -31.45
 Covariance contribution:   2.75
 Mean z-score:  -1.77
 Structure conservation index:   0.61
 SVM decision value:   0.54
 SVM RNA-class probability: 0.774982
 Prediction: RNA

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>hg17.chr20/44330320-44330425
CCCCGCUCCGAGGGUCUGUCGCUUGCUGUGAUCACAGCAGGAUCAGUGCCCCAGAUCUUGCUUAAAGCCUGGCGGCCACCGCCUGCCUCGCAGCUCAUCUCCCGC
....(((.(((((..(((...((((((((....))))))))..))).(((((((..(((.....))).)))).))).........))))).)))........... ( -38.70)
>canFam1.chr24/36422519-36422637
CCCAGCUCUGAGCCCCGCUACCUUGCGUCCACCGCCUGCCGUGUUCACGGCGGGAUCAGAGCCCUGGAGCUCGCUCACAGCCUGGCCGCCACCUCCUGCCUGGUGGCUCAUCUCCCGU
.((((((.(((((..(((......))).......((((((((....))))))))....((((......))))))))).)).))))..((((((........))))))........... ( -50.20)
>mm5.chr2/165258872-165258989
CCAUCCGCAGAGGAGGGAGCCCCGGGUCUGCCGCCUGCUGUGCUCACAGCGGGAUCAGCGCCCCAGAUCUCUCUCAAAGCCAGGCCGCCACCGCUGGCCUCGCGGCUCAUCUCCCGC
......((.(.((((((((((..(((((((...((((((((....))))))))..))).))))...............((.(((((((....)).))))).))))))).)))))))) ( -53.80)
>rn3.chr3/156141508-156141625
CCAGCCGCAGAGGAGGGAGCCCCAGGCCUGCCGCCUGCUGUGCUCACAGCGGGAUCAGCGCCCCAGAUCUCUCUCAAAGCCAGGCCGCCGCCACUGGCCUCACAGCUCAUCUCCCGC
..(((.(..((((((((((.....((((((...((((((((....))))))))..))).)))......)))))))...(((((((....)))..))))))).).))).......... ( -45.50)
>consensus
CCAACCGCAGAGGAGGGA_GCCCCGGGUCUGCCGCCUGCUGUGCUCACAGCGGGAUCAGCGCCCCAGAUCUCGCUCAAA_GCCAGGCCG_CCACCGCCGGCCUCGCAGCUCAUCUCCCGC
.........(((((((((......(((((((...((((((((....))))))))..))).))))......))))))....((.((((((........)))))).))..)))......... (-28.70 = -31.45 +   2.75) 

	

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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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