Structure #6214

Summary

Genome/Assembly	hg17
Chromosome/Contig	chr1
Strand	+
Position	28,727,511 - 28,727,638
Number of sequences	6
Organisms	human, dog, mouse, rat, chicken, fugu
Mean pairwise identity	73.44
Columns	130
Mean single MFE	-43.87
Consensus MFE	-27.15
Combinations/base pair	45 / 32 = 1.41
SCI	0.62
z-score	-1.68
RNA class probability	0.923102

This structure is part of cluster 1391

Alignment

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RNAz output

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

 Sequences: 6
 Slice: 1 to 130
 Columns: 130
 Strand: +
 Mean pairwise identity:  73.44
 Mean single sequence MFE: -43.87
 Consensus MFE: -27.15
 Energy contribution: -27.55
 Covariance contribution:   0.40
 Mean z-score:  -1.68
 Structure conservation index:   0.62
 SVM decision value:   1.15
 SVM RNA-class probability: 0.923102
 Prediction: RNA

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

>hg17.chr1/28727511-28727638
UAUAGGAAAGCUGAGUGGCAGCUUGCAGGUAUUGUACUGACCUGCGCUGUCAAAGUCUUUCCAGGUUGCUCUUGCAUGCAGUUGGAGAUCCCAUGGCUAUGACCAGCCACAGCCCUUGGAAACAUGC
....((((((((...(((((((..((((((.........))))))))))))).)).)))))).(((((((((.((.....)).))))......(((((......))))))))))..((....))... ( -48.20)
>canFam1.chr2/15150030-15149904
UAUAGGAAAGGCGAGUGGCAGCUGCAGGUAUUAUGCUGACCUGUGCUGUCAAAGUCUCUCCAAGUUGCUCUCGCAUGCAGUUGGAGAUCCCAUGGCCACUACCGGCCACAGCCCUUGGAAACAUGC
....(((..(((...(((((((.((((((.........)))))))))))))..)))(((((((.((((........))))))))))))))..(((((......)))))..((...((....)).)) ( -49.80)
>mm5.chr4/23582415-23582291
UAUAGGAAAGAUGAGUGGCAGCUGCAGGCACUGUGCUGACCUGAGCUGUCAAAGUCUCUCCAUUACUCUGGCAUGCAGUUGGAGAUCCCAUGGCUACAGGCAGCCACAGCCCUUGGAAACAUGC
....(((.((((...((((((((.((((((......)).))))))))))))..)))).)))....(((..((.....))..)))....((((.(((..(((.......)))..)))...)))). ( -46.00)
>rn3.chr1/43374679-43374555
UAUAGGAGAGCUGAGUGGCAACAGCAGGCACUGUGAUAACCUGGGCUGUCAAAGUCUCUCCGUUACUCUGGCAUGCAGUUGGAGAUCCCAUGGCUAUGAGCAGCCACAGCCCUUGGAAACAUGC
....((((((((...(((((.(..((((...........)))).).))))).)).))))))(((.(((..((.....))..)))...(((.((((.((......)).))))..))).))).... ( -41.30)
>galGal2.chr23/2165876-2166000
UAUAGGAGGGGUGAGUGACAGCAACAGGCAGAAGAGGCCGAGCAGUCAAAGACCUUCCCGUUGCUCUUGCAUGUUGUUGGAGACCUGCAGCUACGUCAGAGCCACAGCUCUUGGAUUAACAUGC
....((..((((...((((.((....(((.......)))..)).))))...))))..)).........((((((((((.((((.(((..(((.(....))))..))).)))).)).)))))))) ( -41.50)
>fr1.chrUn/97369278-97369401
UGUCGGACAGCUGAGUGGCUGCUGAUGACAUGAGGCCACAGCAGUCAAAGACUGCCCUGUUUUCUUGCACGCACAUGGAGAACCCAGAACUACAGACAAGCCUGGAUCCUUAGGAUAGCAUGC
((((((.(((((...(((((((((.((.(.....).))))))))))).)).)))))(((..(((((.((......)))))))..))).......)))).((.((.((((...))))..)).)) ( -36.40)
>consensus
UAUAGGAAAGCUGAGUGGCAGC_UGCAGGCAUUGUGCUGACCUGAGCUGUCAAAGUCUCUCCA__UUGCUCUUGCAUGCAGUUGGAGAUCCCAUGGCUACGACC_AGCCACAGCCCUUGGA__AACAUGC
....((((((.(...(((((((...(((((.........))))).)))))))..).))))))...........(((((....(((.....)))(((((.......)))))...............))))) (-27.15 = -27.55 +   0.40)

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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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