Structure #192506

Summary

Genome/Assembly	hg17
Chromosome/Contig	chr9
Strand	+
Position	125,537,265 - 125,537,384
Number of sequences	5
Organisms	human, dog, mouse, rat, chicken
Mean pairwise identity	88.94
Columns	120
Mean single MFE	-30.64
Consensus MFE	-20.88
Combinations/base pair	39 / 31 = 1.26
SCI	0.68
z-score	-2.38
RNA class probability	0.687655

This structure is part of cluster 107113

Alignment

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RNAz output

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

 Sequences: 5
 Slice: 1 to 120
 Columns: 120
 Strand: +
 Mean pairwise identity:  88.94
 Mean single sequence MFE: -30.64
 Consensus MFE: -20.88
 Energy contribution: -19.72
 Covariance contribution:  -1.16
 Mean z-score:  -2.38
 Structure conservation index:   0.68
 SVM decision value:   0.32
 SVM RNA-class probability: 0.687655
 Prediction: RNA

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

>hg17.chr9/125537265-125537384
CAGCUGUCAUUGCAAAGAGUGCAAUAUCAAUUUGAACAGAUGACAAAGUGCUGUCAUUUUUCAUUCUGAUAAUAUACAGAAUGCUUUGGACAGAAGUAGUUUACAAAAGAAACAUCUUG
...(((((((((((.....))))))..(((...(((.((((((((......)))))))))))((((((........))))))...))))))))(((..((((.......))))..))). ( -26.50)
>canFam1.chr9/3624458-3624338
CAGCUGUCAUUGCAUAGAGUGCAAUAUCAAUUUGAACAGAUGACAAAGUGCUGUCAUUUUUCAUUCUGAUAAUAUACAGAAUGCUUUGGACAGAAGCAGUUUACAAAAAGAAACAUCUUG
...((((..((((((...))))))(((((...((((.((((((((......))))))))))))...)))))....))))..((((((.....))))))((((........))))...... ( -27.70)
>mm5.chr2/147310461-147310343
CAGCUGUCAUCCUGAAGAGUGCAGUAUCAAUUUGAGCAGAUGACAAAGUGCUGUCAUUUUUCAUUCUGAUAAUACACAGAAUGCUUUGGACAGAGCAGUUUACAAAGGAAACAAGUUG
(((((....((((.....(((...(((((...((((.((((((((......))))))))))))...)))))...)))(((.((((((....)))))).)))....))))....))))) ( -32.50)
>rn3.chr3/157625449-157625331
CAGCUGUCAUCCUGAAGAGUGCAGUAUCAAUUUGAGCGGAUGACAAAGUGCUGUCAUUUUUCAUUCUGAUAAUACACAGAAUGCUUUGGACAAAGCAGUUUACAAAGGAAACAACUUG
.....(((((((....((((.........))))....)))))))(((.(((((((......(((((((........))))))).....)))..)))).))).....(....)...... ( -29.10)
>galGal2.chr17/9903381-9903262
CAGCUGUCACUGCAAAGAGUGCAAUAUCAAUUUGAACAGAUGACAAAGUGUUGUCAUUUUUCAUUCUGAUAUUGCACUGAAUGGUUUGGAAAGAAACAGUUUAGAAAAGCUGCAUCUUG
(((((.((.........((((((((((((...((((.(((((((((....)))))))))))))...))))))))))))((((.((((......)))).)))).))..)))))....... ( -37.40)
>consensus
CAGCUGUCAUUGCAAAGAGUGCAAUAUCAAUUUGAACAGAUGACAAAGUGCUGUCAUUUUUCAUUCUGAUAAUACACAGAAUGCUUUGGACAGAAGCAGUUUAC_AAAAGAAACAUCUUG
....(((..((.......(((...(((((...((((.((((((((......))))))))))))...)))))...)))....((((((.....))))))..........))..)))..... (-20.88 = -19.72 +  -1.16) 

	

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Consensus structure

Secondary structure graph

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Montain plot

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Dotplot

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