Structure #140509

Summary

Genome/Assembly	hg17
Chromosome/Contig	chr4
Strand	-
Position	135,577,206 - 135,577,326
Number of sequences	4
Organisms	human, dog, mouse, rat
Mean pairwise identity	83.89
Columns	120
Mean single MFE	-27.53
Consensus MFE	-20.64
Combinations/base pair	40 / 31 = 1.29
SCI	0.75
z-score	-2.13
RNA class probability	0.914654

This structure is part of cluster 77493

Alignment

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RNAz output

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

 Sequences: 4
 Slice: 1 to 120
 Columns: 120
 Strand: +
 Mean pairwise identity:  83.89
 Mean single sequence MFE: -27.52
 Consensus MFE: -20.64
 Energy contribution: -21.70
 Covariance contribution:   1.06
 Mean z-score:  -2.13
 Structure conservation index:   0.75
 SVM decision value:   1.10
 SVM RNA-class probability: 0.914654
 Prediction: RNA

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

>hg17.chr4/135577326-135577206
AAAAGAUGAUAUUUAAGAAGCACAACACAACAGGAUGUGAAUGAUGAUGUAAUAAUUCACAUCCUUUGCAUGGGUAGACAUAAGAUCAUACUGAGCUCCAUUUAAUGCACAAGGUGUGAA
...................((((........(((((((((((.((......)).))))))))))).(((((.((.((.....((......))...)))).....)))))....))))... ( -25.80)
>canFam1.chr19/46120405-46120525
AAAAGAUGAUAUUUAAGAAGCACAACACAACAGGAUGUGAAUUAUGAUGUAAUAAUUCAUACCCUUUGCAUUGUUAGAUGUAAGACUGUACUGAGCUUCAUUUAAUGCACAAGGUGUGAA
................(((((.((..(((..(((.((((((((((......)))))))))).)))(((((((....)))))))...)))..)).)))))........(((.....))).. ( -28.70)
>mm5.chr3/46524527-46524407
AAAUGAUGAUUUUUAAGAAACAUAGCACAACAGGGUAUGAAUUAUGAUGUAAUAAUUCACACCCAUUGCAUUGUUAGAUAUAAGGCUGUACAGAGCACUAUUUAGUGCAGGAGGUGUUGA
......................((((((..(.((((.((((((((......)))))))).)))).((((((...((((((....(((......)))..)))))))))))))..)))))). ( -30.70)
>rn3.chr2/134205908-134205788
AAAUGAUGAUUUUUAAGAAACAUAAGAAAUCACGGUAUGAAAUAUGAUGUAAUAAUUCACACCCAUUGCAUUGUUAAAUGUAAGGCUGUACUGAGCACUAUUUAGUGCACAAGGUGUUGA
......((((((((..........))))))))(((((((((.(((......))).))))((.((.(((((((....))))))))).))))))).(((((....)))))............ ( -24.90)
>consensus
AAAAGAUGAUAUUUAAGAAACACAACACAACAGGAUAUGAAUUAUGAUGUAAUAAUUCACACCCAUUGCAUUGUUAGAUAUAAGACUGUACUGAGCACCAUUUAAUGCACAAGGUGUGAA
...................((((.........(((((((((((((......)))))))))))))..(((((...((((((....(((......)))..)))))))))))....))))... (-20.64 = -21.70 +   1.06)

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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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