Structure #99271

Summary

Genome/Assembly	hg17
Chromosome/Contig	chr2
Strand	+
Position	29,920,030 - 29,920,150
Number of sequences	4
Organisms	human, mouse, rat, dog
Mean pairwise identity	84.03
Columns	120
Mean single MFE	-28.54
Consensus MFE	-24.88
Combinations/base pair	40 / 30 = 1.33
SCI	0.87
z-score	-1.4
RNA class probability	0.575041

This structure is part of cluster 52140

Alignment

[Download Clustal]

RNAz output

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

 Sequences: 4
 Slice: 1 to 120
 Columns: 120
 Strand: +
 Mean pairwise identity:  84.03
 Mean single sequence MFE: -28.54
 Consensus MFE: -24.88
 Energy contribution: -24.63
 Covariance contribution:  -0.25
 Mean z-score:  -1.40
 Structure conservation index:   0.87
 SVM decision value:   0.08
 SVM RNA-class probability: 0.575041
 Prediction: RNA

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

>hg17.chr2/29920030-29920150
UGAUUCGAUUUACAAAAGUUCCAUUUGUCCACAACCUUUCACACAACCUUGCAUUAACAGAGGUGAGUUACAUGGGCAUAAGUCCAUGUGACUUGCAAAAAUGCGUAAAACAAGAAGCAA
((.(((..(((((...........(((....)))................(((((.......(..((((((((((((....))))))))))))..)...))))))))))....))).)). ( -30.50)
>mm5.chr17/70902927-70903046
UGAUUAGAUUUACAAAAGUCCCAUUUGCCUGUAACCUUUCACACCGCCUUGCAUUAAGAGAGGAGAGUUACACGGGUAGGGGCUCAUGUGACUUGGAAAAUGUGUAAAACAAGAAGGAA
.........(((((..((((((...(((((((..((((((.....((...)).....)))))).(.....))))))))))))))..)))))((((..............))))...... ( -28.04)
>rn3.chr6/124492664-124492545
UGAUUAGAUUUACAAAAGUUCCAUUUGUCUGUAACCUUUCACACCACCUUGCAUUAAGAGAGGAGAGUUACACAGGUAGGGGCUGAUGUGACUCGGAAAAAUGUGUAAAACAAGAAGGA
......(.((((((....((((............((((((.................)))))).(((((((((((.......))).)))))))))))).....)))))).)........ ( -29.13)
>canFam1.chr17/26412320-26412440
UGAUUAGAUUUACAAAAGUUCCGUUUGUCCACAACCUUUCACACAGCCUUGCACUAACAAAGGAGUGUUAUAUGGGUAUGAGUCCAUGUGAUAUGGGAAAAUGUGUAAAGCAAGAAGCAA
........((((((....((((............(((((......((...))......))))).((((((((((((......)))))))))))).))))....))))))((.....)).. ( -26.50)
>consensus
UGAUUAGAUUUACAAAAGUUCCAUUUGUCCACAACCUUUCACACAACCUUGCAUUAACAGAGGAGAGUUACACGGGUAGGAGCCCAUGUGACUUGGAAAAAUGUGUAAAACAAGAAGCAA
......(.((((((....((((............((((((.................)))))).(((((((((((((....))))))))))))))))).....)))))).)......... (-24.88 = -24.63 +  -0.25) 

	

[Download RNAz result]

Consensus structure

Secondary structure graph

[PS | PDF]

Montain plot

[PS | PDF]

Dotplot

[PS | PDF]