Structure #145108

Summary

Genome/Assembly	hg17
Chromosome/Contig	chr5
Strand	+
Position	40,868,515 - 40,868,594
Number of sequences	6
Organisms	human, dog, mouse, rat, chicken, fugu
Mean pairwise identity	78.66
Columns	81
Mean single MFE	-15.55
Consensus MFE	-9.38
Combinations/base pair	16 / 15 = 1.07
SCI	0.6
z-score	-2.25
RNA class probability	0.929942

This structure is part of cluster 80237

Alignment

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RNAz output

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

 Sequences: 6
 Slice: 1 to 81
 Columns: 81
 Strand: +
 Mean pairwise identity:  78.66
 Mean single sequence MFE: -15.55
 Consensus MFE:  -9.38
 Energy contribution:  -9.60
 Covariance contribution:   0.22
 Mean z-score:  -2.25
 Structure conservation index:   0.60
 SVM decision value:   1.20
 SVM RNA-class probability: 0.929942
 Prediction: RNA

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>hg17.chr5/40868515-40868594
GCUUAUCUCAGUUAAAUGCUGAAAUCAAUACUGCAUUCAUAUGUUCAGACAUUUAUUUUUACAACAUCACUGAUAAGCU
(((((..((((((((((((((((....(((.((....))))).))))).)))))).............)))))))))). ( -15.31)
>canFam1.chr4/19597005-19596926
GCUUAUCUCAGUUAAAUGCUGAAAUCAGUAUCAAAUUCAUAUGUUCAGACAUUUAUUUUUACAACAUCAUUGAUAAGCU
((((((((((((.....))))).....(((..((((....((((....))))..)))).))).........))))))). ( -16.10)
>mm5.chr15/99200129-99200049
GCUUAUCUCAGUUAAAUGCUGAAAUCAUUAUAGCAGUCAUAUGUUCAGACAUUUAUUUUUUAGGACAUCAUUGAUAAGCU
((((((((((((.....)))))..................((((((................))))))....))))))). ( -16.19)
>rn3.chr2/203989872-203989793
GCUUAUCUCAGUUAAAUGCUGAAAUCAGUAUAGCAUUCAUAUGUUCAGACAUUUACUUUUAGGACAUCAUCGAUAAGCU
(((((((...((((..(((((....)))))))))......(((((((((........))).))))))....))))))). ( -18.80)
>galGal2.chrZ/6023107-6023186
GCUUAUCUCAGUAAUGCACUGAAAUCACUAUGAAGUUCAUAUGUUCAGACAUUUUAGUAAGAAACAUCAUUGACAAGCU
((((...(((((.(((..(((((..((.((((.....)))))))))))((......))......))).))))).)))). ( -12.90)
>fr1.chrUn/290521710-290521634
GCUUACCUCAGAAUGAAUACUGAUUUCACAUUUGAUUCAUUUGUUCGGACAUUUUCCUCAUUCCAUCAUCGGUAAG
.((((((...((((((((...(((.....)))..))))))))....(((.....))).............)))))) ( -14.00)
>consensus
GCUUAUCUCAG_UUAAAUGCUGAAAUCAGUAUAGCAUUCAUAUGUUCAGACAUUUA_UUUUUACAACAUCAUUGAUAAGCU
(((((((((((........))))..................((((....))))....................))))))). ( -9.38 =  -9.60 +   0.22)

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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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