Structure #33720

Summary

Genome/Assembly	hg17
Chromosome/Contig	chr11
Strand	+
Position	13,693,360 - 13,693,472
Number of sequences	4
Organisms	human, dog, mouse, rat
Mean pairwise identity	78.98
Columns	119
Mean single MFE	-29.62
Consensus MFE	-17.26
Combinations/base pair	39 / 30 = 1.30
SCI	0.58
z-score	-1.94
RNA class probability	0.658656

This structure is part of cluster 16399

Alignment

[Download Clustal]

RNAz output

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

 Sequences: 4
 Slice: 1 to 119
 Columns: 119
 Strand: +
 Mean pairwise identity:  78.98
 Mean single sequence MFE: -29.62
 Consensus MFE: -17.26
 Energy contribution: -17.20
 Covariance contribution:  -0.06
 Mean z-score:  -1.94
 Structure conservation index:   0.58
 SVM decision value:   0.26
 SVM RNA-class probability: 0.658656
 Prediction: RNA

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

>hg17.chr11/13693360-13693472
UUAGAUUUACUCACCUGAUUAAUCACAAUCAGAAUGCUAGGACAUUUCUUAGAAUUUGGAGAUCUUUGGGGACACUAACUAUGGAUCACAUCGUAUUGGGUCGUUCAUCCUC
...(((..((..(((..((.........(((((...((((((....))))))..))))).(((((.(((.........))).))))).......))..))).))..)))... ( -22.00)
>canFam1.chr21/38836296-38836415
AUAGAAUUACUAACCUGAUUAAUCACAAUCACAAUCAGGAUGCUAGGACAUUUUUUAGAAAUUAAGGAUAUUUGGGGAGUCUAAUUGUGGAUCUCAUUCUUAUUGGGCCAUUGAUCCUU
.............(((((((............)))))))...((((((....)))))).....((((((...(((.(((((((....)))).)))..(((....))))))...)))))) ( -22.80)
>mm5.chr7/100824887-100825003
UUAGAAUUACUAACCCGAUGAAGUGCAAUCACAAUCAAGAUGCCAGGACAUUUCCUAGAAAUUGGAGAUGUUUGGAGGCCAAGAAUGGACCUCAUCAUAUUGGGUCAUUGAUUCUC
..(((((((.(.((((((((..(((....)))......((((((((.((((((((........))))))))))))((((((....))).))))))).)))))))).).))))))). ( -38.60)
>rn3.chr1/171543093-171543209
UUAGAAUUACUAACCUAAUUAAGUGCAAUCACAAUCAAGAUGCCAGGACAUUUCCUAGAAGUUGGAGAUGUUUGGAGGCCAAGAAUGGACCUCAUCUUAUUGGGUCAUCGAUUCUC
..((((((....(((((((...(((....)))....((((((((((.((((((((........))))))))))))((((((....))).))))))))))))))))....)))))). ( -35.10)
>consensus
UUAGAAUUACUAACCUGAUUAAGUGCAAUCACAAUCAAGAUGCCAGGACAUUUCCUAGAAAUUGGAGAUGUUUGGAG__GCCAAGAAUGGACCUCA_UCUUAUUGGGUCAUUGAUCCUC
..(((((((.(.(((((((.......................((((.((((((((........)))))))))))).....(((....)))...........))))))).).))))))). (-17.26 = -17.20 +  -0.06)

[Download RNAz result]

Consensus structure

Secondary structure graph

Secondary structure

[PS | PDF]

Montain plot

Secondary structure

[PS | PDF]

Dotplot

Secondary structure

[PS | PDF]