Structure #115226

Summary

Genome/Assembly	hg17
Chromosome/Contig	chr20
Strand	+
Position	1,222,054 - 1,222,171
Number of sequences	4
Organisms	human, mouse, rat, dog
Mean pairwise identity	74.72
Columns	120
Mean single MFE	-44.17
Consensus MFE	-29.89
Combinations/base pair	38 / 28 = 1.36
SCI	0.68
z-score	-1.9
RNA class probability	0.951903

This structure is part of cluster 61099

Alignment

[Download Clustal]

RNAz output

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

 Sequences: 4
 Slice: 1 to 120
 Columns: 120
 Strand: +
 Mean pairwise identity:  74.72
 Mean single sequence MFE: -44.17
 Consensus MFE: -29.89
 Energy contribution: -29.57
 Covariance contribution:  -0.31
 Mean z-score:  -1.90
 Structure conservation index:   0.68
 SVM decision value:   1.40
 SVM RNA-class probability: 0.951903
 Prediction: RNA

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

>hg17.chr20/1222054-1222171
AGGGUUUUCUUUCUACCUUCCUUUCCAAGUGGCAGCCUCUGGCCACCUGGGGAGAGGCCUGCGGGACUCCAGGCUAAGCAGGUGGCAUGGUGACAAACACCAUGGCAACCUGCCUCC
(((((.........))))).((..(((.(((((........))))).)))..)).((((((........))))))..(((((((.(((((((.....))))))).).)))))).... ( -51.80)
>mm5.chr2/30019198-30019082
AGGGUUUCCUUUCACCUUCUAUUCCAAGUGGCUGCCUCCAGCUGCCUGGGGACAGGCCUGUGGGACUCCAGGCUGAACAGGCAACGUGGCAAUAAAUGCCAUGGCAACAUGCCUCC
...(((.((((((((((....(((((...(((((....)))))(((((....)))))...)))))....))).)))).))).)))((((((.....))))))(((.....)))... ( -44.10)
>rn3.chr3/29130136-29130020
AGGGUUUCCUUUCACCUUCUAUUCCAAGUGGCUGCCUCCAGCUGCCUGGGGACAGGCCUGUGGGACUCCAGGCCGAACAGGCCACAUGACAGAGAAUGCCAUGGCAACAUGCCUCC
..((((((((.(((..............(((...((..(((..(((((....))))))))..))...)))((((.....))))...))).)).))).)))..(((.....)))... ( -42.30)
>canFam1.chr24/28100891-28100786
AGGGUUUCCUUCCACCUUCCAUUCUGGCUGCCUGGGCAAAGGGCUGUGGGACUCCAGGGGAGAAGGCAGGUGGCAUAGUGACAUAGACUAUGGCAACCUGUCUCC
.(((......)))..(((((..(((.((.((((.......)))).)).)))......))))).(((((((((.((((((.......)))))).).)))))))).. ( -38.50)
>consensus
AGGGUUUCCUUUC_ACCUUCCAUUCCAAGUGGCUGCCUCCAGCUGCCUGGGGACAGGCCUGUGGGACUCCAGGCU___AAACAGGCGACAUGGCAACAAAUACCAUGGCAACAUGCCUCC
(((((.........)))))......................((((((((......((((((........))))))......))))))))((((((.....))))))(((.....)))... (-29.89 = -29.57 +  -0.31)

[Download RNAz result]

Consensus structure

Secondary structure graph

Secondary structure

[PS | PDF]

Montain plot

Secondary structure

[PS | PDF]

Dotplot

Secondary structure

[PS | PDF]