Structure #131417

Summary

Genome/Assembly	hg17
Chromosome/Contig	chr3
Strand	+
Position	159,072,905 - 159,073,002
Number of sequences	4
Organisms	human, dog, mouse, rat
Mean pairwise identity	79.97
Columns	107
Mean single MFE	-23.06
Consensus MFE	-17.76
Combinations/base pair	32 / 23 = 1.39
SCI	0.77
z-score	-3.57
RNA class probability	0.999733

This structure is part of cluster 72139

Alignment

[Download Clustal]

RNAz output

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

 Sequences: 4
 Slice: 1 to 107
 Columns: 107
 Strand: +
 Mean pairwise identity:  73.73
 Mean single sequence MFE: -23.05
 Consensus MFE: -17.76
 Energy contribution: -16.32
 Covariance contribution:  -1.44
 Mean z-score:  -3.57
 Structure conservation index:   0.77
 SVM decision value:   5.39
 SVM RNA-class probability: 0.999985
 Prediction: RNA

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

>hg17.chr3/159072905-159073002
CACAGGAAAGAAAAGCAGGAACUUUUCUUUCUUCCCUUUUUUUAAAAAACCACAGACAGAUUUUCUCUGCUUCUCUCCUUGCCACCUUGCCUGUGAC
((((((..(((.(((((((((....(((.(((....((((.....))))....))).)))..))).)))))).))).............)))))).. ( -20.86)
>canFam1.chr23/54362776-54362883
CGCAGGAAAGAAAGGCAGGAACUUUGCUUUCUUUCUUUCUUUUUUUUUUUUUUUAAAAACCACAGCCAGGGUUUCUCUGCUUGUCUCCCUCCCACCUGGCCUGCGAC
(((((((((((((((.(((((......))))).)))))))))).....................((((((........................))))))))))).. ( -30.16)
>mm5.chr3/67010886-67010980
CACAGGAAAGGAAAGCAGAAACUUUUCUUUCUUCUCUCUUUUUAAAGCCACAGACAGCUUUUCUUUGCUCUCUCCUUCCCACCCUGCCUGUGAC
((((((((((((.((.(((((......))))).)).)))))).........(((.(((........))).))).............)))))).. ( -21.50)
>rn3.chr2/156533733-156533827
CACAGGAAAAGAAAGCAGAAACUUUUCUUUCUUCUCUCUUUUUAAAGCCACAGACAGCUUUUCUCUGCUCCCUCCUUCCCACCCUGCCUGUGAC
((((((((((((.((.(((((......))))).)).)))))).(((((........))))).........................)))))).. ( -19.70)
>consensus
CACAGGAAAGAAAAGCAGAAACUUUUCUUUCUUCCCUCUUUUUA____________AAACCACAGACAGCUUUUCUCUGC_UCUCUCCUUCCCACCCUGCCUGUGAC
((((((((((((.((.(((((......))))).)).))))))........................((((.....))))....................)))))).. (-17.76 = -16.32 +  -1.44)

[Download RNAz result]

Consensus structure

Secondary structure graph

Secondary structure

[PS | PDF]

Montain plot

Secondary structure

[PS | PDF]

Dotplot

Secondary structure

[PS | PDF]