Locus 121

Sequence ID pao.3167
Location 5,991,667 – 5,991,864
Length 197
Max. P 0.798239
window580 window581 window582

overview

Window 0

Location 5,991,667 – 5,991,784
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 78.89
Mean single sequence MFE -61.60
Consensus MFE -38.33
Energy contribution -40.83
Covariance contribution 2.50
Combinations/Pair 1.29
Mean z-score -1.96
Structure conservation index 0.62
SVM decision value 0.61
SVM RNA-class probability 0.798239
Prediction RNA

Download alignment: ClustalW | MAF

>pao.3167 5991667 117 + 6264404
CGCCGAAGCCUACAAGGUCGGCCAGCGCUGGUUGCUGUACAGCGCCGCGCCGGUGCG---CGGCGCCGACCAGAGCCUGCAAGGCACGCUGCUGCUGGCGGUCGACCUGCAACGGCUGCU
.((((..((.....((((((((((((((((((((.......(((((((((....)))---))))))))))))).(((.....))).))))((.....)))))))))))))..)))).... ( -65.21)
>pss.139 5859568 120 - 6093698
CCCGGAGGCGCGCAAGGUCGGCGAGCGCUGGUUGAUCUACAGCGCUGCGCCGGUGCGUGCCGCUGCCAGUCAGCCGGUGGUGGGUACGCUGCUGCUGGUCUUUGACCUGCAGCGCUUGCU
......((((((((...(((((((((((((.........))))))).))))))))))))))(((((..(((((((((..(..(.....)..)..)))))...))))..)))))....... ( -67.50)
>psp.123 5683355 120 - 5928787
CCCGGAGGCUCGCAAGGUGGGCGAGCGCUGGUUGAUCUACAGUGCUGCGCCGGUACGUGCCGCGCCAACUCAGCCGGUGGUGGGCACAUUGCUGCUGGCCUUUGACCUGCAGCGCUUGCU
...........(((((...(((((((((((.........))))))).)))).....(((((.(((((.((.....))))))))))))...(((((.((.......)).))))).))))). ( -53.10)
>pst.49 6291270 120 - 6397126
CCCGGAGGCUCGCAAGGUCGGUGAGCGCUGGCUGAUCUACAGCGCAGCGCCGGUACGUGCGGGCGCAGAUCAGCCGGUUCUGGGUACAUUGCUGCUGGCCUUCGACAUGCAGCGCUUGCU
((((((.((((((.......))))))((((((((((((...((((.((((......))))..))))))))))))))))))))))......(((((((........)).)))))....... ( -60.60)
>consensus
CCCGGAGGCUCGCAAGGUCGGCGAGCGCUGGUUGAUCUACAGCGCUGCGCCGGUACGUGCCGCCGCAAAUCAGCCGGUGCUGGGCACACUGCUGCUGGCCUUCGACCUGCAGCGCUUGCU
..((((((((.(((.(((((((((((((((.........))))))).)))))((((.((((((((.........)))))))).)))))))..))).))))))))....(((.....))). (-38.33 = -40.83 +   2.50)

alignment

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secondary structure

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dotplot

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Window 1

Location 5,991,667 – 5,991,784
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 78.89
Mean single sequence MFE -55.62
Consensus MFE -33.06
Energy contribution -35.12
Covariance contribution 2.06
Combinations/Pair 1.26
Mean z-score -1.85
Structure conservation index 0.59
SVM decision value 0.15
SVM RNA-class probability 0.608714
Prediction RNA

Download alignment: ClustalW | MAF

>pao.3167 5991667 117 - 6264404
AGCAGCCGUUGCAGGUCGACCGCCAGCAGCAGCGUGCCUUGCAGGCUCUGGUCGGCGCCG---CGCACCGGCGCGGCGCUGUACAGCAACCAGCGCUGGCCGACCUUGUAGGCUUCGGCG
....((((((((((((((...((((((.(((((.(((...))).)))(((..((((((((---(((....)))))))))))..)))......))))))))))))).)))))....)))). ( -66.10)
>pss.139 5859568 120 + 6093698
AGCAAGCGCUGCAGGUCAAAGACCAGCAGCAGCGUACCCACCACCGGCUGACUGGCAGCGGCACGCACCGGCGCAGCGCUGUAGAUCAACCAGCGCUCGCCGACCUUGCGCGCCUCCGGG
.....(((((((.((((...)))).))))).))..........(((((((.....))))(((.((((.(((((.(((((((.........))))))))))))....)))).)))..))). ( -58.20)
>psp.123 5683355 120 + 5928787
AGCAAGCGCUGCAGGUCAAAGGCCAGCAGCAAUGUGCCCACCACCGGCUGAGUUGGCGCGGCACGUACCGGCGCAGCACUGUAGAUCAACCAGCGCUCGCCCACCUUGCGAGCCUCCGGG
.(((((.(((((.(((.....))).))))).((((((((.(((.(......).))).).)))))))...((((.(((.(((.........))).)))))))...)))))........... ( -48.70)
>pst.49 6291270 120 + 6397126
AGCAAGCGCUGCAUGUCGAAGGCCAGCAGCAAUGUACCCAGAACCGGCUGAUCUGCGCCCGCACGUACCGGCGCUGCGCUGUAGAUCAGCCAGCGCUCACCGACCUUGCGAGCCUCCGGG
.(((...(((((.((.(....).)))))))..))).(((.((...((((((((((((..(((((((....))).)))).))))))))))))...((((.(.......).)))).)).))) ( -49.50)
>consensus
AGCAAGCGCUGCAGGUCAAAGGCCAGCAGCAACGUACCCACCACCGGCUGAUCGGCGCCGGCACGCACCGGCGCAGCGCUGUAGAUCAACCAGCGCUCGCCGACCUUGCGAGCCUCCGGG
.......(((((.(((.....))).))))).............(((((((.....))))(((.((((.(((((.(((((((.........))))))))))))....)))).)))..))). (-33.06 = -35.12 +   2.06)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,991,744 – 5,991,864
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 76.81
Mean single sequence MFE -53.17
Consensus MFE -38.09
Energy contribution -38.15
Covariance contribution 0.06
Combinations/Pair 1.32
Mean z-score -1.43
Structure conservation index 0.72
SVM decision value -0.04
SVM RNA-class probability 0.510976
Prediction RNA

Download alignment: ClustalW | MAF

>pao.3167 5991744 120 - 6264404
GCACCUGGGCCGGUGCGCCGGAGAACUGCUGGACCAGUUGUACCUGGCCGGCAUCGCCCGGCAAGGGCGGCAGGGCGCGCAGCAGCCGUUGCAGGUCGACCGCCAGCAGCAGCGUGCCUU
......((((((.((((((((.((..((((((.((((......))))))))))))..)))))...(((((..((.(..(((((....))))).).))..)))))....))).)).)))). ( -62.60)
>pss.139 5859648 120 + 6093698
ACACCUGAGCAGGUCCGCUGCCGAAUUGCUGGCUGAGCACCACUUGCCCGGCGUCGGCAGGCAGCGCCGGCAAGGCAUUGAGCAAGCGCUGCAGGUCAAAGACCAGCAGCAGCGUACCCA
...........(((.((((((.....(((((((((.(((.....))).))))((((((..(((((((..((..........))..)))))))..)))...)))))))))))))).))).. ( -51.60)
>psp.123 5683435 120 + 5928787
AAACCUGUGCAGGUCCGUUGCCAAACUGCUGGCUGAGCACCACCUGCCCGGCCUCGGCAGGCAGUGCCGGCAAGGCAUUGAGCAAGCGCUGCAGGUCAAAGGCCAGCAGCAAUGUGCCCA
...........((..((((((.....((((((((....(((.((((((.......))))))(((((((.....))))))).(((.....))).)))....))))))))))))))..)).. ( -52.40)
>pst.49 6291350 120 + 6397126
AAACCUGCGCAGGUCCGCUGCCGAACUGCUGACUGAGGACGAUUUGCCCAGCCUCGGCCGGCAGCACGGGCAAGGCAUCGAGCAAGCGCUGCAUGUCGAAGGCCAGCAGCAAUGUACCCA
..((((....))))..(((((((..((((((.((((((.(..........))))))).))))))..))(((..(((((..(((....)))..)))))....))).))))).......... ( -46.10)
>consensus
AAACCUGAGCAGGUCCGCUGCCGAACUGCUGGCUGAGCACCACCUGCCCGGCCUCGGCAGGCAGCGCCGGCAAGGCAUUGAGCAAGCGCUGCAGGUCAAAGGCCAGCAGCAACGUACCCA
...........(((.(((((.....(((((((((....(((..(((((.......)))))(((((((..((..........))..))))))).)))....)))))))))))))).))).. (-38.09 = -38.15 +   0.06)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 21:13:47 2007