Locus 107

Sequence ID pao_1
Location 6,041,946 – 6,042,224
Length 278
Max. P 0.999644
window418 window419 window420 window421 window422

overview

Window 8

Location 6,041,946 – 6,042,066
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 97.44
Mean single sequence MFE -37.12
Consensus MFE -36.17
Energy contribution -35.78
Covariance contribution -0.39
Combinations/Pair 1.08
Mean z-score -1.32
Structure conservation index 0.97
SVM decision value 1.98
SVM RNA-class probability 0.984695
Prediction RNA

Download alignment: ClustalW | MAF

>pao_1 6041946 120 - 1
CGAUCUAUCCAUGAGCAGGUUGAAGGUUAGGUAACACUGACUGGAGGACCGAACCCACUCCCGUUGAAAAGGUAGGGGAUGACUUGUGGAUCGGAGUGAAAGGCUAAUCAAGCUCGGAGA
(((((((((((..((((((((...((((((......))))))....))))...(((.((.((........)).))))).)).))..))))).))).......(((.....)))))).... ( -36.80)
>pfs_1 2119 120 - 1
CGAUCUAUCCAUGGGCAGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUACCGUUGAAAAGUUAGCGGAUGACCUGUGGAUCGGAGUGAAAGGCUAAUCAAGCUCGGAGA
(((((((((((((((((((((...((((((......))))))....))))..........(((((((....))))))).)).))))))))).))).......(((.....)))))).... ( -37.10)
>ppk_1 2120 120 - 1
CGAUCUAUCCAUGGGCAGGUUGAAGGUUAGGUAACACUGACUGGAGGACCGAACCGACUACCGUUGAAAAGUUAGCGGAUGACCUGUGGAUCGGAGUGAAAGGCUAAUCAAGCUCGGAGA
(((((((((((((((((((((...((((((......))))))....))))..........(((((((....))))))).)).))))))))).))).......(((.....)))))).... ( -37.50)
>psp_1 2117 120 - 1
CGAUCUAUCCAUGGGCAGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUACCGUUGAAAAGUUAGCGGAUGACCUGUGGAUCGGAGUGAAAGGCUAAUCAAGCUCGGAGA
(((((((((((((((((((((...((((((......))))))....))))..........(((((((....))))))).)).))))))))).))).......(((.....)))))).... ( -37.10)
>pss_1 2118 120 - 1
CGAUCUAUCCAUGGGCAGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUACCGUUGAAAAGUUAGCGGAUGACCUGUGGAUCGGAGUGAAAGGCUAAUCAAGCUCGGAGA
(((((((((((((((((((((...((((((......))))))....))))..........(((((((....))))))).)).))))))))).))).......(((.....)))))).... ( -37.10)
>pst_1 2118 120 - 1
CGAUCUAUCCAUGGGCAGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUACCGUUGAAAAGUUAGCGGAUGACCUGUGGAUCGGAGUGAAAGGCUAAUCAAGCUCGGAGA
(((((((((((((((((((((...((((((......))))))....))))..........(((((((....))))))).)).))))))))).))).......(((.....)))))).... ( -37.10)
>consensus
CGAUCUAUCCAUGGGCAGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUACCGUUGAAAAGUUAGCGGAUGACCUGUGGAUCGGAGUGAAAGGCUAAUCAAGCUCGGAGA
(((((((((((((((((((((...((((((......))))))....))))..........(((((((....))))))).)).))))))))).))).......(((.....)))))).... (-36.17 = -35.78 +  -0.39)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,041,986 – 6,042,105
Length 119
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 96.31
Mean single sequence MFE -39.00
Consensus MFE -37.06
Energy contribution -37.08
Covariance contribution 0.03
Combinations/Pair 1.08
Mean z-score -1.18
Structure conservation index 0.95
SVM decision value 1.17
SVM RNA-class probability 0.925977
Prediction RNA

Download alignment: ClustalW | MAF

>pao_1 6041986 119 - 1
AUAGGGCG-UUUAGUCGCUGGGUAUAGACCCGAAACCGGGCGAUCUAUCCAUGAGCAGGUUGAAGGUUAGGUAACACUGACUGGAGGACCGAACCCACUCCCGUUGAAAAGGUAGGGGAU
....(((.-....)))(((.((.(((((((((....))))...)))))))...))).((((...((((((......))))))....))))...(((.((.((........)).))))).. ( -37.50)
>pel_1 2159 120 - 1
AUAGGGCGCUUUAGUCGCUGGGUAUAGACCCGAAACCGGGCGAUCUAUCCAUGGGCAGGUUGAAGGUUAGGUAACACUGACUGGAGGACCGAACCGACUACCGUUGAAAAGUUAGCGGAU
...........((((((((.((.(((((((((....))))...)))))))...))).((((...((((((......))))))....)))).....)))))(((((((....))))))).. ( -39.60)
>ppk_1 2160 119 - 1
AUAGGGCG-UUUAGUCGCUGGGUAUAGACCCGAAACCGGGCGAUCUAUCCAUGGGCAGGUUGAAGGUUAGGUAACACUGACUGGAGGACCGAACCGACUACCGUUGAAAAGUUAGCGGAU
........-..((((((((.((.(((((((((....))))...)))))))...))).((((...((((((......))))))....)))).....)))))(((((((....))))))).. ( -39.60)
>psp_1 2157 119 - 1
AUAGGGCG-UCUAGUCGCUGGGAAUAGACCCGAAACCGGGCGAUCUAUCCAUGGGCAGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUACCGUUGAAAAGUUAGCGGAU
........-..((((((((.(((.((((((((....))))...)))))))...))).((((...((((((......))))))....)))).....)))))(((((((....))))))).. ( -39.10)
>pss_1 2158 119 - 1
AUAGGGCG-UCUAGUCGCUGGGAAUAGACCCGAAACCGGGCGAUCUAUCCAUGGGCAGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUACCGUUGAAAAGUUAGCGGAU
........-..((((((((.(((.((((((((....))))...)))))))...))).((((...((((((......))))))....)))).....)))))(((((((....))))))).. ( -39.10)
>pst_1 2158 119 - 1
AUAGGGCG-UCUAGUCGCUGGGAAUAGACCCGAAACCGGGCGAUCUAUCCAUGGGCAGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUACCGUUGAAAAGUUAGCGGAU
........-..((((((((.(((.((((((((....))))...)))))))...))).((((...((((((......))))))....)))).....)))))(((((((....))))))).. ( -39.10)
>consensus
AUAGGGCG_UCUAGUCGCUGGGAAUAGACCCGAAACCGGGCGAUCUAUCCAUGGGCAGGUUGAAGGUUAGGUAACACUAACUGGAGGACCGAACCGACUACCGUUGAAAAGUUAGCGGAU
...........((((((((.((.(((((((((....))))...)))))))...))).((((...((((((......))))))....)))).....)))))(((((((....))))))).. (-37.06 = -37.08 +   0.03)

alignment

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secondary structure

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dotplot

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Window 0

Location 6,042,026 – 6,042,145
Length 119
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 96.87
Mean single sequence MFE -39.78
Consensus MFE -38.22
Energy contribution -38.00
Covariance contribution -0.22
Combinations/Pair 1.06
Mean z-score -1.72
Structure conservation index 0.96
SVM decision value 2.82
SVM RNA-class probability 0.997253
Prediction RNA

Download alignment: ClustalW | MAF

>pao_1 6042026 119 - 1
GCUUAACCGUAUAGGGUAGGCGUAGCGAAAGCGAGUCUUAAUAGGGCG-UUUAGUCGCUGGGUAUAGACCCGAAACCGGGCGAUCUAUCCAUGAGCAGGUUGAAGGUUAGGUAACACUGA
((((((((.....((.(((((...((....))..((((.....)))))-)))).))(((.((.(((((((((....))))...)))))))...)))........))))))))........ ( -39.60)
>pel_1 2199 120 - 1
GCUUAACCGAAUAGGGGAGGCGUAGCGAAAGCGAGUCUUAAUAGGGCGCUUUAGUCGCUGGGUAUAGACCCGAAACCGGGCGAUCUAUCCAUGGGCAGGUUGAAGGUUAGGUAACACUGA
((((((((.....(((...((.(((((((((((..(((....))).)))))...)))))).)).....))).........((((((..(....)..))))))..))))))))........ ( -40.60)
>ppk_1 2200 119 - 1
GCUUAACCGAAUAGGGGAGGCGUAGCGAAAGCGAGUCUUAAUAGGGCG-UUUAGUCGCUGGGUAUAGACCCGAAACCGGGCGAUCUAUCCAUGGGCAGGUUGAAGGUUAGGUAACACUGA
((((((((.....((.(((((...((....))..))))).....((((-......))))((((....))))....))...((((((..(....)..))))))..))))))))........ ( -40.30)
>psp_1 2197 119 - 1
GCUUAACCGAAUAGGGGAGGCGUAGCGAAAGCGAGUCUUAAUAGGGCG-UCUAGUCGCUGGGAAUAGACCCGAAACCGGGCGAUCUAUCCAUGGGCAGGUUGAAGGUUGGGUAACACUAA
((((((((.....((.(((((...((....))..))))).....((.(-((((.((.....)).)))))))....))...((((((..(....)..))))))..))))))))........ ( -39.40)
>pss_1 2198 119 - 1
GCUUAACCGAAUAGGGGAGGCGUAGCGAAAGCGAGUCUUAAUAGGGCG-UCUAGUCGCUGGGAAUAGACCCGAAACCGGGCGAUCUAUCCAUGGGCAGGUUGAAGGUUGGGUAACACUAA
((((((((.....((.(((((...((....))..))))).....((.(-((((.((.....)).)))))))....))...((((((..(....)..))))))..))))))))........ ( -39.40)
>pst_1 2198 119 - 1
GCUUAACCGAAUAGGGGAGGCGUAGCGAAAGCGAGUCUUAAUAGGGCG-UCUAGUCGCUGGGAAUAGACCCGAAACCGGGCGAUCUAUCCAUGGGCAGGUUGAAGGUUGGGUAACACUAA
((((((((.....((.(((((...((....))..))))).....((.(-((((.((.....)).)))))))....))...((((((..(....)..))))))..))))))))........ ( -39.40)
>consensus
GCUUAACCGAAUAGGGGAGGCGUAGCGAAAGCGAGUCUUAAUAGGGCG_UCUAGUCGCUGGGAAUAGACCCGAAACCGGGCGAUCUAUCCAUGGGCAGGUUGAAGGUUAGGUAACACUAA
((((((((........(((((...((....))..))))).....(((......)))(((.((.(((((((((....))))...)))))))...)))........))))))))........ (-38.22 = -38.00 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,042,066 – 6,042,185
Length 119
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 97.21
Mean single sequence MFE -40.84
Consensus MFE -40.68
Energy contribution -40.18
Covariance contribution -0.50
Combinations/Pair 1.03
Mean z-score -1.86
Structure conservation index 1.00
SVM decision value 3.83
SVM RNA-class probability 0.999644
Prediction RNA

Download alignment: ClustalW | MAF

>pao_1 6042066 119 - 1
CCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCAGUGGCAAGCUUAACCGUAUAGGGUAGGCGUAGCGAAAGCGAGUCUUAAUAGGGCG-UUUAGUCGCUGGGUAUAGACCCGAAACCGGG
............((((((.......(((((((((((((..(((((.((.....)).)))))...((....))..((((.....)))).-....)))))))))))))))))))........ ( -40.21)
>pel_1 2239 120 - 1
CCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCAGUGGCGAGCUUAACCGAAUAGGGGAGGCGUAGCGAAAGCGAGUCUUAAUAGGGCGCUUUAGUCGCUGGGUAUAGACCCGAAACCGGG
............((((((.......(((((((((((((..((((..((.....))..))))((.((....))..((((.....))))))....)))))))))))))))))))........ ( -41.21)
>pf5_1 2236 119 - 1
CCUUUUGUAUAAUGGGUCAGCGACUUAUUUUCAGUGGCAAGCUUAACCGAAUAGGGGAGGCGUAGCGAAAGCGAGUCUUAAUAGGGCG-UCUAGUCGCUGGGAAUAGACCCGAAACCGGG
............((((((.......((((..(((((((..((((..((.....))..))))...((....))((((((.....)))).-))..)))))))..))))))))))........ ( -40.91)
>ppk_1 2240 119 - 1
CCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCAGUGGCGAGCUUAACCGAAUAGGGGAGGCGUAGCGAAAGCGAGUCUUAAUAGGGCG-UUUAGUCGCUGGGUAUAGACCCGAAACCGGG
............((((((.......(((((((((((((..((((..((.....))..))))...((....))..((((.....)))).-....)))))))))))))))))))........ ( -40.91)
>pss_1 2238 119 - 1
CCUUUUGUAUAAUGGGUCAGCGACUUAUUUUCAGUGGCGAGCUUAACCGAAUAGGGGAGGCGUAGCGAAAGCGAGUCUUAAUAGGGCG-UCUAGUCGCUGGGAAUAGACCCGAAACCGGG
............((((((.......((((..(((((((..((((..((.....))..))))...((....))((((((.....)))).-))..)))))))..))))))))))........ ( -40.91)
>pst_1 2238 119 - 1
CCUUUUGUAUAAUGGGUCAGCGACUUAUUUUCAGUGGCGAGCUUAACCGAAUAGGGGAGGCGUAGCGAAAGCGAGUCUUAAUAGGGCG-UCUAGUCGCUGGGAAUAGACCCGAAACCGGG
............((((((.......((((..(((((((..((((..((.....))..))))...((....))((((((.....)))).-))..)))))))..))))))))))........ ( -40.91)
>consensus
CCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCAGUGGCGAGCUUAACCGAAUAGGGGAGGCGUAGCGAAAGCGAGUCUUAAUAGGGCG_UCUAGUCGCUGGGAAUAGACCCGAAACCGGG
............((((((.......(((((((((((((..((((..((.....))..))))...((....))..((((.....))))......)))))))))))))))))))........ (-40.68 = -40.18 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,042,105 – 6,042,224
Length 119
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 96.11
Mean single sequence MFE -36.20
Consensus MFE -36.27
Energy contribution -35.22
Covariance contribution -1.05
Combinations/Pair 1.11
Mean z-score -0.85
Structure conservation index 1.00
SVM decision value 0.95
SVM RNA-class probability 0.888144
Prediction RNA

Download alignment: ClustalW | MAF

>pao_1 6042105 119 - 1
GUACAAGCAGUGGGAGCCUAC-UUGUUAGGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCAGUGGCAAGCUUAACCGUAUAGGGUAGGCGUAGCGAAAGCGAGUCUUA
...(.((((((((....))))-.)))).)..((((((.(((((..(((((..(((((..((.(((.......))).))..)))))...)))))))))).))...((....)).))))... ( -35.60)
>pel_1 2279 120 - 1
GUACAAGCAGUGGGAGCCUACUUUGUUAGGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCAGUGGCGAGCUUAACCGAAUAGGGGAGGCGUAGCGAAAGCGAGUCUUA
(((((((..(..(..(((((......)))))..)..)......)))))))..(((((..((.(((.......))).))..))))).((.....)).(((((...((....))..))))). ( -35.70)
>pf5_1 2275 120 - 1
GUACAAGCAGUGGGAGCAGACUUUGUUCUGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUUUUCAGUGGCAAGCUUAACCGAAUAGGGGAGGCGUAGCGAAAGCGAGUCUUA
((((..(((((....(((((......))))).)))))))))...(((...((((((((...))))))))..))).(((..((((..((.....))..))))...((....))..)))... ( -35.90)
>pfo_1 2277 120 - 1
GUACAAGCAGUGGGAGCAGACUUUGUUCUGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUUUUCAGUGGCGAGCUUAACCGAAUAGGGGAGGCGUAGCGAAAGCGAGUCUUA
......((.(..(..(((((......)))))..)..)(.((((..........))))).))((((..(((((....((..((((..((.....))..))))...)))))))..))))... ( -36.10)
>ppk_1 2279 120 - 1
GUACAAGCAGUGGGAGCCUACUUUGUUAGGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCAGUGGCGAGCUUAACCGAAUAGGGGAGGCGUAGCGAAAGCGAGUCUUA
(((((((..(..(..(((((......)))))..)..)......)))))))..(((((..((.(((.......))).))..))))).((.....)).(((((...((....))..))))). ( -35.70)
>pst_1 2277 120 - 1
GUACAAGCAGUGGGAGCCCACUUUGUUGGGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUUUUCAGUGGCGAGCUUAACCGAAUAGGGGAGGCGUAGCGAAAGCGAGUCUUA
......((.(..(..(((((......)))))..)..)(.((((..........))))).))((((..(((((....((..((((..((.....))..))))...)))))))..))))... ( -38.20)
>consensus
GUACAAGCAGUGGGAGCCUACUUUGUUAGGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCAGUGGCGAGCUUAACCGAAUAGGGGAGGCGUAGCGAAAGCGAGUCUUA
......((.(..(..(((((......)))))..)..)(.((((..........))))).))(((((..............((((..((.....))..))))...((....)))))))... (-36.27 = -35.22 +  -1.05)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 11:54:49 2007