Structure #140500

Summary

Genome/Assembly	hg17
Chromosome/Contig	chr4
Strand	+
Position	135,577,131 - 135,577,246
Number of sequences	4
Organisms	human, dog, mouse, rat
Mean pairwise identity	80.2
Columns	120
Mean single MFE	-25.05
Consensus MFE	-17.92
Combinations/base pair	49 / 35 = 1.40
SCI	0.72
z-score	-1.84
RNA class probability	0.82482

This structure is part of cluster 77493

Alignment

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RNAz output

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

 Sequences: 4
 Slice: 1 to 120
 Columns: 120
 Strand: +
 Mean pairwise identity:  80.20
 Mean single sequence MFE: -25.05
 Consensus MFE: -17.92
 Energy contribution: -18.55
 Covariance contribution:   0.63
 Mean z-score:  -1.84
 Structure conservation index:   0.72
 SVM decision value:   0.69
 SVM RNA-class probability: 0.824820
 Prediction: RNA

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

>hg17.chr4/135577131-135577246
UUUUAAUAAAAAUUUGUAUAGGGACUUGUUUAUAAGCACAAUAAACUAUUCUGUGUGUGAAUUAUGGGGUAACAAUUCACACCUUGUGCAUUAAAUGGAGCUCAGUAUGAUCUUA
.............(..(((.(((..(..((((...((((((...((......))((((((((..((......)))))))))).))))))..))))..)..))).)))..)..... ( -25.40)
>canFam1.chr19/46120445-46120330
UUUUAAUAAAAAACAUAUAGGGGCUUAUUUAUAAGCAUAAUAAACCAUUUUAUGGUGUGAAAUAUAGGGUAAUAUUUCACACCUUGUGCAUUAAAUGAAGCUCAGUACAGUCUUA
....................(((((((((((...((((((((((....)))))((((((((((((......)))))))))))).)))))..)))))).)))))............ ( -30.20)
>mm5.chr3/46524327-46524447
UUUUAAUAAAAAAAUAUUUGUGUAGGGACUUGUUUAUAAGCACAGUAAAGCACUCCAUGCUGUGAGUUAUGGAAUAAUAAUCAACACCUCCUGCACUAAAUAGUGCUCUGUACAGCCUUA
..............(((((((((((((...((((......(((((((..........))))))).(((((......))))).))))..)))))))).)))))((((...))))....... ( -24.20)
>rn3.chr2/134205709-134205828
UUUUAAUAAAAAAUAUUUGUAUACGGGCUUGUUUAUAAGUACAAUAAACUACUUCAUGCUGUGAAUUAUGGGAUAAUAAUCAACACCUUGUGCACUAAAUAGUGCUCAGUACAGCCUUA
.............((((((((.(((....))).))))))))................((((((.(((((......))))).......(((.(((((....))))).))))))))).... ( -20.40)
>consensus
UUUUAAUAAAA_AAUAUUUGUAUAGGGACUUGUUUAUAAGCACAAUAAACCACUCCAUGCUGUGAAUUAUGGGAUAAUAAUCAACACCUUGUGCACUAAAUAGAGCUCAGUACAGCCUUA
.................((((((.(((..(((((((...((((((...((((.....))))(((((((((......)))))))))...))))))..)))))))..))).))))))..... (-17.92 = -18.55 +   0.63)

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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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