Structure #140501

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	-24.18
Consensus MFE	-13.27
Combinations/base pair	34 / 26 = 1.31
SCI	0.55
z-score	-2.16
RNA class probability	0.654646

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: +
HÖ?x
 Mean pairwise identity:  80.20
 Mean single sequence MFE: -24.17
 Consensus MFE: -13.27
 Energy contribution: -12.65
 Covariance contribution:  -0.62
 Mean z-score:  -2.16
 Structure conservation index:   0.55
 SVM decision value:   0.25
 SVM RNA-class probability: 0.654646
 Prediction: RNA

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

>hg17.chr4/135577246-135577131
UAAGAUCAUACUGAGCUCCAUUUAAUGCACAAGGUGUGAAUUGUUACCCCAUAAUUCACACACAGAAUAGUUUAUUGUGCUUAUAAACAAGUCCCUAUACAAAUUUUUAUUAAAA
..........(((.((..........)).....(((((((((((......))))))))))).))).((((....((((........))))....))))................. ( -20.40)
>canFam1.chr19/46120330-46120445
UAAGACUGUACUGAGCUUCAUUUAAUGCACAAGGUGUGAAAUAUUACCCUAUAUUUCACACCAUAAAAUGGUUUAUUAUGCUUAUAAAUAAGCCCCUAUAUGUUUUUUAUUAAAA
.(((((((((..(.((((.(((((..(((...((((((((((((......))))))))))))(((((....)))))..)))...))))))))))..)))).)))))......... ( -27.20)
>mm5.chr3/46524447-46524327
UAAGGCUGUACAGAGCACUAUUUAGUGCAGGAGGUGUUGAUUAUUAUUCCAUAACUCACAGCAUGGAGUGCUUUACUGUGCUUAUAAACAAGUCCCUACACAAAUAUUUUUUUAUUAAAA
...((((((((((((((((.....((((..(((.(((.((.......)).))).)))...))))..))))))...)))))).........)))).......................... ( -25.00)
>rn3.chr2/134205828-134205709
UAAGGCUGUACUGAGCACUAUUUAGUGCACAAGGUGUUGAUUAUUAUCCCAUAAUUCACAGCAUGAAGUAGUUUAUUGUACUUAUAAACAAGCCCGUAUACAAAUAUUUUUUAUUAAAA
...((((.((((..(((((....))))).((.(.(((.((((((......)))))).))).).)).))))((((((.......)))))).))))......................... ( -24.10)
>consensus
UAAGACUGUACUGAGCACCAUUUAAUGCACAAGGUGUGAAUUAUUACCCCAUAAUUCACAGCAUAAAAUAGUUUAUUGUGCUUAUAAACAAGCCCCUAUACAAAUAUU_UUUUAUUAAAA
....................(((((((.....(.((((((((((......)))))))))).).....((((....((((........))))....)))).............))))))). (-13.27 = -12.65 +  -0.62)

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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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