Locus 137

Sequence ID sp_mu.0
Location 1,930,502 – 1,930,622
Length 120
Max. P 0.816172
window844 window845 window846

overview

Window 4

Location 1,930,502 – 1,930,622
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 85.83
Mean single sequence MFE -29.77
Consensus MFE -28.31
Energy contribution -27.87
Covariance contribution -0.44
Combinations/Pair 1.05
Mean z-score -1.20
Structure conservation index 0.95
SVM decision value 0.66
SVM RNA-class probability 0.816172
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1930502 120 - 2030921/0-120
UUUGCGGAGAGAGGGACUUGAACCCUCACGACCAAAAGCGGUCACAAGAUCCUUAGUCUUGCGCGUCUGCCAAUUCCGCCAUCCCCGCGUAGCAACUUUUUAAAUUAUAUCAACUAACAA
.((((((((((((((.......)))))..((((......)))).((((((.....))))))....))).)).....(((.......)))..))))......................... ( -28.10)
>sp_ag.0 2041574 120 - 2160267/0-120
UCUGCGGAGAGAGGGACUUGAACCCUCACGACCAAAAGCGGUCACAAGAUCCUUAGUCUUGCGCGUCUGCCAAUUCCGCCAUCCCCGCUUAACAACAUAAUAAAUUAUAUCAACUUAUCA
...((((.(((((((.......)))))..((((......)))).((((((.....)))))).(((...........)))..)).))))................................ ( -27.50)
>sp_pn.0 1421991 120 + 2038615/0-120
UAUGCGGAGAGAGGGACUUGAACCCUCACGACCUAAAGCGGUCACAGGAUCCUUAGUCCUGCACGUCUGCCAAUUCCGCCAUCCCCGCGUCGAUUACUUUACUAGUAUAUCAACUUUUGG
.((((((.(((((((.......)))))..((((......)))).((((((.....))))))....................)).)))))).(((((((.....)))).)))......... ( -33.70)
>consensus
UAUGCGGAGAGAGGGACUUGAACCCUCACGACCAAAAGCGGUCACAAGAUCCUUAGUCUUGCGCGUCUGCCAAUUCCGCCAUCCCCGCGUAGCAACAUUUUAAAUUAUAUCAACUUAUAA
...((((((.(((((.......)))))..((((......)))).((((((.....))))))............))))))......................................... (-28.31 = -27.87 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,930,502 – 1,930,622
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 85.83
Mean single sequence MFE -39.73
Consensus MFE -35.43
Energy contribution -34.77
Covariance contribution -0.66
Combinations/Pair 1.08
Mean z-score -1.71
Structure conservation index 0.89
SVM decision value 0.63
SVM RNA-class probability 0.804621
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1930502 120 - 2030921/0-120
UUGUUAGUUGAUAUAAUUUAAAAAGUUGCUACGCGGGGAUGGCGGAAUUGGCAGACGCGCAAGACUAAGGAUCUUGUGACCGCUUUUGGUCGUGAGGGUUCAAGUCCCUCUCUCCGCAAA
................................(((((((((((.(((..(((.(...((((((((....).))))))).).)))))).)))))(((((.......))))).))))))... ( -35.50)
>sp_ag.0 2041574 120 - 2160267/0-120
UGAUAAGUUGAUAUAAUUUAUUAUGUUGUUAAGCGGGGAUGGCGGAAUUGGCAGACGCGCAAGACUAAGGAUCUUGUGACCGCUUUUGGUCGUGAGGGUUCAAGUCCCUCUCUCCGCAGA
((((((..(((((.....)))))..)))))).(((((((((((.(((..(((.(...((((((((....).))))))).).)))))).)))))(((((.......))))).))))))... ( -39.50)
>sp_pn.0 1421991 120 + 2038615/0-120
CCAAAAGUUGAUAUACUAGUAAAGUAAUCGACGCGGGGAUGGCGGAAUUGGCAGACGUGCAGGACUAAGGAUCCUGUGACCGCUUUAGGUCGUGAGGGUUCAAGUCCCUCUCUCCGCAUA
......((((((.((((.....))))))))))(((((((.((........(((....))).(((((..(((((((((((((......)))))).))))))).))))))).)))))))... ( -44.20)
>consensus
UCAUAAGUUGAUAUAAUUUAAAAAGUUGCUACGCGGGGAUGGCGGAAUUGGCAGACGCGCAAGACUAAGGAUCUUGUGACCGCUUUUGGUCGUGAGGGUUCAAGUCCCUCUCUCCGCAAA
................................(((((((.(((((.....((....))(((((((....).))))))..))))).........(((((.......))))))))))))... (-35.43 = -34.77 +  -0.66) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,930,502 – 1,930,622
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 82.78
Mean single sequence MFE -37.64
Consensus MFE -25.61
Energy contribution -25.17
Covariance contribution -0.44
Combinations/Pair 1.08
Mean z-score -1.73
Structure conservation index 0.68
SVM decision value 0.00
SVM RNA-class probability 0.535486
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1930502 120 - 2030921/12-132
UUGACACUAUCUUUGUUAGUUGAUAUAAUUUAAAAAGUUGCUACGCGGGGAUGGCGGAAUUGGCAGACGCGCAAGACUAAGGAUCUUGUGACCGCUUUUGGUCGUGAGGGUUCAAGUCCC
....(.((((((((((((((...................)))).)))))))))).)...(((((....)).)))((((..((((((..((((((....))))))..).))))).)))).. ( -30.81)
>sp_ag.0 2041574 120 - 2160267/12-132
UUGACAACAAUAUGAUAAGUUGAUAUAAUUUAUUAUGUUGUUAAGCGGGGAUGGCGGAAUUGGCAGACGCGCAAGACUAAGGAUCUUGUGACCGCUUUUGGUCGUGAGGGUUCAAGUCCC
.....(((((((((((((((((...)))))))))))))))))..(((.(..((.((....)).))..).)))..((((..((((((..((((((....))))))..).))))).)))).. ( -40.20)
>sp_pn.0 1421991 120 + 2038615/12-132
UUGACAAGCAUCCCAAAAGUUGAUAUACUAGUAAAGUAAUCGACGCGGGGAUGGCGGAAUUGGCAGACGUGCAGGACUAAGGAUCCUGUGACCGCUUUAGGUCGUGAGGGUUCAAGUCCC
........((((((....((((((.((((.....))))))))))...)))))).........(((....))).(((((..(((((((((((((......)))))).))))))).))))). ( -41.90)
>consensus
UUGACAACAAUAUCAUAAGUUGAUAUAAUUUAAAAAGUUGCUACGCGGGGAUGGCGGAAUUGGCAGACGCGCAAGACUAAGGAUCUUGUGACCGCUUUUGGUCGUGAGGGUUCAAGUCCC
..(((.......................................(((.(..((.((....)).))..).)))........(((((((((((((......)))))).)))))))..))).. (-25.61 = -25.17 +  -0.44) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 19:02:21 2006