Structure #3578

Summary

Genome/Assembly	hg17
Chromosome/Contig	chr1
Strand	-
Position	122,565 - 122,684
Number of sequences	4
Organisms	human, dog, mouse, rat
Mean pairwise identity	83.19
Columns	120
Mean single MFE	-58.65
Consensus MFE	-46.6
Combinations/base pair	52 / 40 = 1.30
SCI	0.79
z-score	-2.04
RNA class probability	0.913686

This structure is part of cluster 7

Alignment

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RNAz output

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

 Sequences: 4
 Slice: 1 to 120
 Columns: 120
 Strand: +
 Mean pairwise identity:  83.19
 Mean single sequence MFE: -58.65
 Consensus MFE: -46.60
 Energy contribution: -46.73
 Covariance contribution:   0.13
 Mean z-score:  -2.04
 Structure conservation index:   0.79
 SVM decision value:   1.09
 SVM RNA-class probability: 0.913686
 Prediction: RNA

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>hg17.chr1/122684-122565
GGCAGGAUCCAUUGGGAGGAAACAGGCCACCUUGGAAGGCGUCCCUGGGCCCCCAUCCCCAGGGGUUGGGGCCGUAGGGGGCCCGCUCUGCUGCGUUGACCAGACUCCUGGGCUUUGAA
((((((.((((..(((.(....)...)).)..)))).(((.((((((((((((.((((....)))).)))))).)))))))))...)))))).((..(.((((....)))).)..)).. ( -55.70)
>canFam1.chr1/459-579
CGCAGGAUCCGUUGGAAGGAACCGGGUGGCCUUGGAAGGUGUCACUGGGCCCCCAGCCCCAGGGGGUGGGGGCCGUAGUGGGCCUGCUGUGCUGCCCUGGCCUGACUCCUGGGCCUUGAA
....((.(((.......))).))(((..((..(((.((((.((((((((((((((.(((....))))))))))).)))))))))).))).))..))).(((((.......)))))..... ( -64.80)
>mm5.chr7/573-453
GGCAGAAUCCGUAGGAGGAAACCGAGUGGCCUUGGAAGGUGUUGCUGGGCCCCCGGCUCCAGGGGGUGGGGGCCGUAGUGGCACCGCUGUGCUGCCCUGACCAGACUCCUGGGUCUUAAA
(((((..(((......)))..(((((....)))))..(((((..(((((((((((.(((....))))))))))).)))..)))))......)))))..((((((....)).))))..... ( -59.80)
>rn3.chr1/573-453
GGCAGAAUCCGUAGGAAGAAACCGAGUGGCCUUGGAAGGUGUUGUUGGGCCCCCAGCUCCAGGAGGUGGGGGCCGUAGUGGCACCGCUGUGCUGCCCUGACCAGACUCCUGCGUUUUAAA
.....((..(((((((.....(((((....)))))..(((((..(((((((((((.(((...))).)))))))).)))..))))).(((..(......)..)))..)))))))..))... ( -54.30)
>consensus
GGCAGAAUCCGUAGGAAGAAACCGAGUGGCCUUGGAAGGUGUCGCUGGGCCCCCAGCCCCAGGGGGUGGGGGCCGUAGUGGCACCGCUGUGCUGCCCUGACCAGACUCCUGGGCCUUAAA
(((((..((((.(((..(........)..))))))).((((((((((((((((((.(((...))).)))))))).))))))))))......)))))..((((((....))).)))..... (-46.60 = -46.73 +   0.13)

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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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