Locus 13

Sequence ID pao_1
Location 724,128 – 724,328
Length 200
Max. P 0.999999
window27 window28 window29 window30

overview

Window 7

Location 724,128 – 724,248
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 94.28
Mean single sequence MFE -40.17
Consensus MFE -38.60
Energy contribution -37.43
Covariance contribution -1.16
Combinations/Pair 1.12
Mean z-score -1.19
Structure conservation index 0.96
SVM decision value 1.28
SVM RNA-class probability 0.939725
Prediction RNA

Download alignment: ClustalW | MAF

>pao_1 724128 120 + 1
GGAUGCCUUGGCAGUCAGAGGCGAUGAAAGACGUGGUAGCCUGCGAAAAGCUUCGGGGAGUCGGCAAACAGACUUUGAUCCGGAGAUCUCUGAAUGGGGGAACCCACCUAGGAUAACCUA
((.(((((.((...(((((((..........((..(....)..)).....((((((((((((........)))))...))))))).))))))).((((....)))))).))).)).)).. ( -40.70)
>pel_1 81 120 + 1
GGAUGCCUUGGCAGUCAGAGGCGAUGAAAGACGUGGUAGCCUGCGAUAAGCUUUGGGGAGUCGGCAAACAGACUGUGAUCCAGAGAUCUCUGAAUGGGGGAACCCACUCAGCAUAAGCUG
...(((....))).(((((((..........((..(....)..)).....(((((((.((((........))))....))))))).))))))).((((....))))..((((....)))) ( -38.80)
>pf5_1 79 120 + 1
GGAUGCCUUGGCAGUCAGAGGCGAUGAAAGACGUGGUAGCCUGCGAUAAGCUUCGGGGAGUCGGCAAACAGACUUUGAUCCGGAGAUCUCUGAAUGGGGGAACCCAGCCAUCAUAAGAUG
..(((...((((..(((((((..........((..(....)..)).....((((((((((((........)))))...))))))).))))))).((((....)))))))).)))...... ( -41.20)
>pfs_1 81 120 + 1
GGAUGCCUUGGCAGUCAGAGGCGAUGAAAGACGUGGUAGCCUGCGAAAAGCUUCGGGGAGUCGGCAAACAGACUUUGAUCCGGAGAUGUCUGAAUGGGGGAACCCAGCCAUCAUAAGAUG
....(((((........)))))((((..(((((..(....)..)......((((((((((((........)))))...)))))))..))))...((((....))))..))))........ ( -38.90)
>ppk_1 81 120 + 1
GGAUGCCUUGGCAGUCAGAGGCGAUGAAAGACGUGGUAGCCUGCGAUAAGCUUUGGGGAGUCGGCAAACAGACUGUGAUCCAGAGAUCUCUGAAUGGGGGAACCCAGCCAGCACAAGCUG
...(((..((((..(((((((..........((..(....)..)).....(((((((.((((........))))....))))))).))))))).((((....)))))))))))....... ( -40.70)
>pst_1 76 120 + 1
GGAUGCCUCGGCAGUCAGAGGCGAUGAAAGACGUGGUAGCCUGCGAAAAGCUUCGGGGAGUCGGCAAACAGACUGUGAUCCGGAGAUGUCUGAAUGGGGGAACCCAGCCAUCAUAAGAUG
....(((((........)))))((((..(((((..(....)..)......(((((((.((((........))))....)))))))..))))...((((....))))..))))........ ( -40.70)
>consensus
GGAUGCCUUGGCAGUCAGAGGCGAUGAAAGACGUGGUAGCCUGCGAAAAGCUUCGGGGAGUCGGCAAACAGACUGUGAUCCGGAGAUCUCUGAAUGGGGGAACCCAGCCAGCAUAAGAUG
...(((....))).(((((((..........((..(....)..)).....(((((((.((((........))))....))))))).))))))).((((....))))..((((....)))) (-38.60 = -37.43 +  -1.16)

alignment

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secondary structure

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dotplot

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Window 8

Location 724,168 – 724,288
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 91.33
Mean single sequence MFE -41.67
Consensus MFE -44.51
Energy contribution -41.18
Covariance contribution -3.33
Combinations/Pair 1.29
Mean z-score -2.71
Structure conservation index 1.07
SVM decision value 6.04
SVM RNA-class probability 0.999996
Prediction RNA

Download alignment: ClustalW | MAF

>pao_1 724168 120 + 1
CUGCGAAAAGCUUCGGGGAGUCGGCAAACAGACUUUGAUCCGGAGAUCUCUGAAUGGGGGAACCCACCUAGGAUAACCUAGGUAUCUUGUACUGAAUCCAUAGGUGCAAGAGGCGAACCA
..((.....))((((((((.((((((((.....))))..))))...)))))))).(((....)))(((((((....))))))).(((((((((.........)))))))))((....)). ( -43.10)
>pel_1 121 120 + 1
CUGCGAUAAGCUUUGGGGAGUCGGCAAACAGACUGUGAUCCAGAGAUCUCUGAAUGGGGGAACCCACUCAGCAUAAGCUGAGUAUCUUGUACUGAAUACAUAGGUGCAAGAGGCGAACCA
..((.....))....((...(((.(...((((....((((....))))))))...(((....)))(((((((....))))))).(((((((((.........)))))))))).))).)). ( -41.40)
>pf5_1 119 120 + 1
CUGCGAUAAGCUUCGGGGAGUCGGCAAACAGACUUUGAUCCGGAGAUCUCUGAAUGGGGGAACCCAGCCAUCAUAAGAUGGUUAUCUUGUACUGAAUACAUAGGUGCAAGAGGCGAACCA
..((.....))((((((((.((((((((.....))))..))))...)))))))).(((....)))(((((((....))))))).(((((((((.........)))))))))((....)). ( -41.20)
>pfs_1 121 120 + 1
CUGCGAAAAGCUUCGGGGAGUCGGCAAACAGACUUUGAUCCGGAGAUGUCUGAAUGGGGGAACCCAGCCAUCAUAAGAUGGUUAUCUUAAGCUGAAUACAUAGGCUUAAGAGGCGAACCA
.(((((....((((((((((((........)))))...)))))))...)).....(((....)))(((((((....))))))).(((((((((.........))))))))).)))..... ( -41.90)
>ppk_1 121 120 + 1
CUGCGAUAAGCUUUGGGGAGUCGGCAAACAGACUGUGAUCCAGAGAUCUCUGAAUGGGGGAACCCAGCCAGCACAAGCUGGUUAUCUUGUACUGAAUACAUAGGUGCAAGAGGCGAACCA
..((.....))....((...(((.(...((((....((((....))))))))...(((....)))(((((((....))))))).(((((((((.........)))))))))).))).)). ( -41.10)
>pst_1 116 120 + 1
CUGCGAAAAGCUUCGGGGAGUCGGCAAACAGACUGUGAUCCGGAGAUGUCUGAAUGGGGGAACCCAGCCAUCAUAAGAUGGUUAUCUUACACUGAAUACAUAGGUGUAAGAGGCGAACCA
.(((((....(((((((.((((........))))....)))))))...)).....(((....)))(((((((....))))))).(((((((((.........))))))))).)))..... ( -41.30)
>consensus
CUGCGAAAAGCUUCGGGGAGUCGGCAAACAGACUGUGAUCCGGAGAUCUCUGAAUGGGGGAACCCAGCCAGCAUAAGAUGGUUAUCUUGUACUGAAUACAUAGGUGCAAGAGGCGAACCA
.(((((....(((((((.((((........))))....)))))))...)).....(((....)))(((((((....))))))).(((((((((.........))))))))).)))..... (-44.51 = -41.18 +  -3.33)

alignment

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secondary structure

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dotplot

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Window 9

Location 724,208 – 724,328
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 92.78
Mean single sequence MFE -38.98
Consensus MFE -41.82
Energy contribution -38.72
Covariance contribution -3.10
Combinations/Pair 1.31
Mean z-score -3.51
Structure conservation index 1.07
SVM decision value 6.71
SVM RNA-class probability 0.999999
Prediction RNA

Download alignment: ClustalW | MAF

>pao_1 724208 120 + 1
CGGAGAUCUCUGAAUGGGGGAACCCACCUAGGAUAACCUAGGUAUCUUGUACUGAAUCCAUAGGUGCAAGAGGCGAACCAGGGGAACUGAAACAUCUAAGUACCCUGAGGAAAAGAAAUC
((((....))))...(((....)))(((((((....))))))).(((((((((.........)))))))))......((.((((.(((..........))).))))..)).......... ( -39.70)
>pel_1 161 120 + 1
CAGAGAUCUCUGAAUGGGGGAACCCACUCAGCAUAAGCUGAGUAUCUUGUACUGAAUACAUAGGUGCAAGAGGCGAACCAGGGGAACUGAAACAUCUAAGUACCCUGAGGAAAAGAAAUC
((((....))))...(((....)))(((((((....))))))).(((((((((.........)))))))))......((.((((.(((..........))).))))..)).......... ( -40.80)
>pf5_1 159 120 + 1
CGGAGAUCUCUGAAUGGGGGAACCCAGCCAUCAUAAGAUGGUUAUCUUGUACUGAAUACAUAGGUGCAAGAGGCGAACCAGGGGAACUGAAACAUCUAAGUACCCUGAGGAAAAGAAAUC
((((....))))...(((....)))(((((((....))))))).(((((((((.........)))))))))......((.((((.(((..........))).))))..)).......... ( -37.80)
>pfs_1 161 120 + 1
CGGAGAUGUCUGAAUGGGGGAACCCAGCCAUCAUAAGAUGGUUAUCUUAAGCUGAAUACAUAGGCUUAAGAGGCGAACCAGGGGAACUGAAACAUCUAAGUACCCUGAGGAAAAGAAAUC
......((((.....(((....)))(((((((....))))))).(((((((((.........)))))))))))))..((.((((.(((..........))).))))..)).......... ( -37.50)
>ppk_1 161 120 + 1
CAGAGAUCUCUGAAUGGGGGAACCCAGCCAGCACAAGCUGGUUAUCUUGUACUGAAUACAUAGGUGCAAGAGGCGAACCAGGGGAACUGAAACAUCUAAGUACCCUGAGGAAAAGAAAUC
((((....))))...(((....)))(((((((....))))))).(((((((((.........)))))))))......((.((((.(((..........))).))))..)).......... ( -40.50)
>pst_1 156 120 + 1
CGGAGAUGUCUGAAUGGGGGAACCCAGCCAUCAUAAGAUGGUUAUCUUACACUGAAUACAUAGGUGUAAGAGGCGAACCAGGGGAACUGAAACAUCUAAGUACCCUGAGGAAAAGAAAUC
......((((.....(((....)))(((((((....))))))).(((((((((.........)))))))))))))..((.((((.(((..........))).))))..)).......... ( -37.60)
>consensus
CGGAGAUCUCUGAAUGGGGGAACCCAGCCAGCAUAAGAUGGUUAUCUUGUACUGAAUACAUAGGUGCAAGAGGCGAACCAGGGGAACUGAAACAUCUAAGUACCCUGAGGAAAAGAAAUC
((((....))))...(((....)))(((((((....))))))).(((((((((.........)))))))))......((.((((.(((..........))).))))..)).......... (-41.82 = -38.72 +  -3.10)

alignment

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secondary structure

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dotplot

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Window 0

Location 724,208 – 724,328
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 92.78
Mean single sequence MFE -31.25
Consensus MFE -29.60
Energy contribution -27.88
Covariance contribution -1.72
Combinations/Pair 1.18
Mean z-score -1.84
Structure conservation index 0.95
SVM decision value 2.60
SVM RNA-class probability 0.995648
Prediction RNA

Download alignment: ClustalW | MAF

>pao_1 724208 120 - 1
GAUUUCUUUUCCUCAGGGUACUUAGAUGUUUCAGUUCCCCUGGUUCGCCUCUUGCACCUAUGGAUUCAGUACAAGAUACCUAGGUUAUCCUAGGUGGGUUCCCCCAUUCAGAGAUCUCCG
(((((((..(((..((((((...((.((..((((.....))))..)).))..))).)))..)))..........((.(((((((....)))))))(((....)))..))))))))).... ( -33.70)
>pel_1 161 120 - 1
GAUUUCUUUUCCUCAGGGUACUUAGAUGUUUCAGUUCCCCUGGUUCGCCUCUUGCACCUAUGUAUUCAGUACAAGAUACUCAGCUUAUGCUGAGUGGGUUCCCCCAUUCAGAGAUCUCUG
(((((((.....((((((.(((..((....)))))..))))))...((((((((.((...........)).)))))((((((((....)))))))))))..........))))))).... ( -33.10)
>pf5_1 159 120 - 1
GAUUUCUUUUCCUCAGGGUACUUAGAUGUUUCAGUUCCCCUGGUUCGCCUCUUGCACCUAUGUAUUCAGUACAAGAUAACCAUCUUAUGAUGGCUGGGUUCCCCCAUUCAGAGAUCUCCG
(((((((........(((.((((((..(..((((.....))))..)...(((((.((...........)).)))))...(((((....))))))))))).)))......))))))).... ( -28.44)
>pfs_1 161 120 - 1
GAUUUCUUUUCCUCAGGGUACUUAGAUGUUUCAGUUCCCCUGGUUCGCCUCUUAAGCCUAUGUAUUCAGCUUAAGAUAACCAUCUUAUGAUGGCUGGGUUCCCCCAUUCAGACAUCUCCG
(((.(((........(((.((((((..(..((((.....))))..)...((((((((...........))))))))...(((((....))))))))))).)))......))).))).... ( -29.34)
>ppk_1 161 120 - 1
GAUUUCUUUUCCUCAGGGUACUUAGAUGUUUCAGUUCCCCUGGUUCGCCUCUUGCACCUAUGUAUUCAGUACAAGAUAACCAGCUUGUGCUGGCUGGGUUCCCCCAUUCAGAGAUCUCUG
(((((((.....((((((.(((..((....)))))..))))))...(((...((((....))))...((((((((........)))))))))))((((....))))...))))))).... ( -33.50)
>pst_1 156 120 - 1
GAUUUCUUUUCCUCAGGGUACUUAGAUGUUUCAGUUCCCCUGGUUCGCCUCUUACACCUAUGUAUUCAGUGUAAGAUAACCAUCUUAUGAUGGCUGGGUUCCCCCAUUCAGACAUCUCCG
(((.(((........(((.((((((..(..((((.....))))..)...((((((((...........))))))))...(((((....))))))))))).)))......))).))).... ( -29.44)
>consensus
GAUUUCUUUUCCUCAGGGUACUUAGAUGUUUCAGUUCCCCUGGUUCGCCUCUUGCACCUAUGUAUUCAGUACAAGAUAACCAGCUUAUGAUGGCUGGGUUCCCCCAUUCAGAGAUCUCCG
(((((((.....((((((.(((..((....)))))..))))))......(((((.((...........)).)))))...(((((....))))).((((....))))...))))))).... (-29.60 = -27.88 +  -1.72)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 11:46:06 2007