Locus 41

Sequence ID pao_1
Location 3,395,191 – 3,395,313
Length 122
Max. P 0.917750
window117 window118 window119 window120

overview

Window 7

Location 3,395,191 – 3,395,308
Length 117
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 91.60
Mean single sequence MFE -48.57
Consensus MFE -45.64
Energy contribution -45.87
Covariance contribution 0.22
Combinations/Pair 1.03
Mean z-score -2.10
Structure conservation index 0.94
SVM decision value 1.12
SVM RNA-class probability 0.917750
Prediction RNA

Download alignment: ClustalW | MAF

>pao_1 3395191 117 + 1
CGGAGCGUAGCGCAGCUUGGUAGCGCGUCUCGUUCGGGACGAGAAGGUCGCUGGUUCGAAUCCAGUCGCUCCGACCAUAUCCCG---AAAAACCCGCCUCAACGGCGGGUUUUUUAUUGC
(((((((..((((.((...)).)))).(((((((...))))))).....(((((.......))))))))))))..........(---(((((((((((.....))))))))))))..... ( -51.30)
>pau_1 1 117 + 1
CGGAGCGUAGCGCAGCUUGGUAGCGCGUCUCGUUCGGGACGAGAAGGUCGCUGGUUCGAAUCCAGUCGCUCCGACCAUAUCCCG---AAAAACCCGCCUCAACGGCGGGUUUUUUAUUGC
(((((((..((((.((...)).)))).(((((((...))))))).....(((((.......))))))))))))..........(---(((((((((((.....))))))))))))..... ( -51.30)
>pel_1 1 117 + 1
CGGAGUGUAGCGCAGCCAGGUAGCGCGUCUCGUUCGGGACGAGAAGGCCGCAGGUUCGAAUCCUGUCUCUCCGACCAAAUCCCGUAAAAAAACCCGCCUCGA--GCGGGUUUUUU-UUGC
(((((.((((((.((((.(((..(.((((((....)))))).)...)))...))))))....))).).)))))..........((((((((((((((.....--))))).)))))-)))) ( -43.10)
>consensus
CGGAGCGUAGCGCAGCUUGGUAGCGCGUCUCGUUCGGGACGAGAAGGUCGCUGGUUCGAAUCCAGUCGCUCCGACCAUAUCCCG___AAAAACCCGCCUCAACGGCGGGUUUUUUAUUGC
(((((((..((((.((...)).)))).(((((((...))))))).....(((((.......)))))))))))).........((...(((((((((((.....)))))))))))...)). (-45.64 = -45.87 +   0.22)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,395,191 – 3,395,308
Length 117
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 91.60
Mean single sequence MFE -45.63
Consensus MFE -43.33
Energy contribution -43.00
Covariance contribution -0.33
Combinations/Pair 1.06
Mean z-score -1.67
Structure conservation index 0.95
SVM decision value 0.54
SVM RNA-class probability 0.773919
Prediction RNA

Download alignment: ClustalW | MAF

>pao_1 3395191 117 - 1
GCAAUAAAAAACCCGCCGUUGAGGCGGGUUUUU---CGGGAUAUGGUCGGAGCGACUGGAUUCGAACCAGCGACCUUCUCGUCCCGAACGAGACGCGCUACCAAGCUGCGCUACGCUCCG
......(((((((((((.....)))))))))))---...........(((((((.((((.......))))......((((((.....)))))).((((.........))))..))))))) ( -46.90)
>pau_1 1 117 - 1
GCAAUAAAAAACCCGCCGUUGAGGCGGGUUUUU---CGGGAUAUGGUCGGAGCGACUGGAUUCGAACCAGCGACCUUCUCGUCCCGAACGAGACGCGCUACCAAGCUGCGCUACGCUCCG
......(((((((((((.....)))))))))))---...........(((((((.((((.......))))......((((((.....)))))).((((.........))))..))))))) ( -46.90)
>pel_1 1 117 - 1
GCAA-AAAAAACCCGC--UCGAGGCGGGUUUUUUUACGGGAUUUGGUCGGAGAGACAGGAUUCGAACCUGCGGCCUUCUCGUCCCGAACGAGACGCGCUACCUGGCUGCGCUACACUCCG
...(-(((((((((((--.....)))))))))))).(((..(.(((.((.((...((((...((......))(((.((((((.....)))))).).))..)))).)).))))).)..))) ( -43.10)
>consensus
GCAAUAAAAAACCCGCCGUUGAGGCGGGUUUUU___CGGGAUAUGGUCGGAGCGACUGGAUUCGAACCAGCGACCUUCUCGUCCCGAACGAGACGCGCUACCAAGCUGCGCUACGCUCCG
......(((((((((((.....)))))))))))...((((((..(((((......((((.......))))))))).....))))))...(((..((((.........))))....))).. (-43.33 = -43.00 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,395,196 – 3,395,313
Length 117
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 91.60
Mean single sequence MFE -48.17
Consensus MFE -43.70
Energy contribution -43.37
Covariance contribution -0.33
Combinations/Pair 1.05
Mean z-score -2.16
Structure conservation index 0.91
SVM decision value 0.88
SVM RNA-class probability 0.872593
Prediction RNA

Download alignment: ClustalW | MAF

>pao_1 3395196 117 + 1
CGUAGCGCAGCUUGGUAGCGCGUCUCGUUCGGGACGAGAAGGUCGCUGGUUCGAAUCCAGUCGCUCCGACCAUAUCCCG---AAAAACCCGCCUCAACGGCGGGUUUUUUAUUGCCUGCG
(((((.((((.((((.((((((((((....))))))........(((((.......))))))))))))).).......(---(((((((((((.....))))))))))))..)))))))) ( -51.00)
>pau_1 6 117 + 1
CGUAGCGCAGCUUGGUAGCGCGUCUCGUUCGGGACGAGAAGGUCGCUGGUUCGAAUCCAGUCGCUCCGACCAUAUCCCG---AAAAACCCGCCUCAACGGCGGGUUUUUUAUUGCCUGCG
(((((.((((.((((.((((((((((....))))))........(((((.......))))))))))))).).......(---(((((((((((.....))))))))))))..)))))))) ( -51.00)
>pel_1 6 117 + 1
UGUAGCGCAGCCAGGUAGCGCGUCUCGUUCGGGACGAGAAGGCCGCAGGUUCGAAUCCUGUCUCUCCGACCAAAUCCCGUAAAAAAACCCGCCUCGA--GCGGGUUUUUU-UUGCCUGCG
.((((.(((....(((..(.((((((....)))))).)...)))(((((.......)))))...................((((((((((((.....--)))))))))))-)))))))). ( -42.50)
>consensus
CGUAGCGCAGCUUGGUAGCGCGUCUCGUUCGGGACGAGAAGGUCGCUGGUUCGAAUCCAGUCGCUCCGACCAUAUCCCG___AAAAACCCGCCUCAACGGCGGGUUUUUUAUUGCCUGCG
(((((.((((...(((..(.((((((....)))))).)..((..(((((.......)))))....)).)))...........(((((((((((.....)))))))))))..))))))))) (-43.70 = -43.37 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,395,196 – 3,395,313
Length 117
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 91.60
Mean single sequence MFE -46.90
Consensus MFE -43.92
Energy contribution -43.37
Covariance contribution -0.55
Combinations/Pair 1.09
Mean z-score -1.95
Structure conservation index 0.94
SVM decision value 0.85
SVM RNA-class probability 0.865542
Prediction RNA

Download alignment: ClustalW | MAF

>pao_1 3395196 117 - 1
CGCAGGCAAUAAAAAACCCGCCGUUGAGGCGGGUUUUU---CGGGAUAUGGUCGGAGCGACUGGAUUCGAACCAGCGACCUUCUCGUCCCGAACGAGACGCGCUACCAAGCUGCGCUACG
((((.((.....((((((((((.....))))))))))(---((((((..(((((......((((.......))))))))).....))))))).......))(((....)))))))..... ( -46.20)
>pau_1 6 117 - 1
CGCAGGCAAUAAAAAACCCGCCGUUGAGGCGGGUUUUU---CGGGAUAUGGUCGGAGCGACUGGAUUCGAACCAGCGACCUUCUCGUCCCGAACGAGACGCGCUACCAAGCUGCGCUACG
((((.((.....((((((((((.....))))))))))(---((((((..(((((......((((.......))))))))).....))))))).......))(((....)))))))..... ( -46.20)
>pel_1 6 117 - 1
CGCAGGCAA-AAAAAACCCGC--UCGAGGCGGGUUUUUUUACGGGAUUUGGUCGGAGAGACAGGAUUCGAACCUGCGGCCUUCUCGUCCCGAACGAGACGCGCUACCUGGCUGCGCUACA
((((((..(-(((((((((((--.....))))))))))))...(((((..(((.....)))..)))))...))))))....((((((.....)))))).((((.........)))).... ( -48.30)
>consensus
CGCAGGCAAUAAAAAACCCGCCGUUGAGGCGGGUUUUU___CGGGAUAUGGUCGGAGCGACUGGAUUCGAACCAGCGACCUUCUCGUCCCGAACGAGACGCGCUACCAAGCUGCGCUACG
((((.((....(((((((((((.....)))))))))))...((((((..(((((......((((.......))))))))).....))))))........))(((....)))))))..... (-43.92 = -43.37 +  -0.55)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 11:48:05 2007