Structure #4873

Summary

Genome/Assembly hg17
Chromosome/Contig chr1
Strand +
Position 18,733,577 - 18,733,696
Number of sequences 4
Organisms human, mouse, rat, dog
Mean pairwise identity 79.94
Columns 120
Mean single MFE -49.68
Consensus MFE -34.45
Combinations/base pair 33 / 27 = 1.22
SCI 0.69
z-score -1.68
RNA class probability 0.663136

This structure is part of cluster 776

Alignment

Alignment

[Download Clustal]

RNAz output

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

 Sequences: 4
 Slice: 1 to 120
 Columns: 120
 Strand: +
 Mean pairwise identity:  79.94
 Mean single sequence MFE: -49.67
 Consensus MFE: -34.45
 Energy contribution: -34.83
 Covariance contribution:   0.37
 Mean z-score:  -1.68
 Structure conservation index:   0.69
 SVM decision value:   0.27
 SVM RNA-class probability: 0.663136
 Prediction: RNA

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

>hg17.chr1/18733577-18733696
AUUAUGGCAAUUAAUUACCCAGGGACAAUGGAGCACAGCCCUGCCCUCUGCCCGCGCCUUCCAGUGACAGGGGGUGGGCGGAGGGCGCCGGGAGGGGGAAGUUAAGCGGCUGCCUGUUU
.....((((.((((((.(((((((....((.....)).))))(((((((((((((.((((........)))).))))))))))))).((....))))).)))))).....))))..... ( -58.00)
>mm5.chr4/15880951-15880838
AUUACCACAAUUAAUCACCCAGGGACAAUGGUGCUGUCAUGCCCUCAGCCUGGCCUUCAAGGGGCAGGGGUGGGUGGAGGGCACACGAGGGGGGUUUAAGCAGCUGCCCAUUU
..............................(((((.((.(((((.(..((((.(((....))).)))).).))))))).)))))....(((.((((.....)))).))).... ( -40.10)
>rn3.chr5/14478653-14478538
AUUACCACAAUUAAUCACCCAGGGACAAUGACGCUGUCAUGCCCUCAGCCUGGCCUUCAAGGGGAAGGGAGUGGGUGGAGGGCAUCCGAGGGGGGGGUUAAGCAGCUGCCCAUUU
.................((..((((((.......))))((((((((.(((((.(((((.....)))))...))))).))))))))))..))(((.((((....)))).))).... ( -42.40)
>canFam1.chr2/7158703-7158584
AUUACCGCAAUUAAUUACCCGGGACAAUGGCUCUCAGCCCUGCCCUCUGCCCGCGCCUCCGAGUGGCAGGGGGUGGGCGGAGGGCACCGGGAGGAGGGAGGUGAAGCGGCUGCCUGUUU
....((((..........(((......)))(((((..(((((((((((((((((.(((((....))..))).))))))))))))))..)))..))))).......)))).......... ( -58.20)
>consensus
AUUACCACAAUUAAUCACCCAGGGACAAUGGCG__CAGCCAUGCCCUCAGCCCG_GCCUUCAAGGGGCAGGGGGUGGGCGGAGGGCACCCGAAGGGGG__GGUUAAGCAGCUGCCCAUUU
.....................(((.((.((...........((((((((((((((.((((........)))).))))))))))))))((....))............))..))))).... (-34.45 = -34.83 +   0.37) 

	

[Download RNAz result]

Consensus structure

Secondary structure graph

Secondary structure

[PS | PDF]

Montain plot

Secondary structure

[PS | PDF]

Dotplot

Secondary structure

[PS | PDF]