Locus 2

Sequence ID Banth.0
Location 4,131,099 – 4,131,150
Length 51
Max. P 0.974993
window3 window4 window5 window6

overview

Window 3

Location 4,131,099 – 4,131,150
Length 51
Sequences 6
Columns 51
Reading direction forward
Mean pairwise identity 76.34
Mean single sequence MFE -13.77
Consensus MFE -11.87
Energy contribution -11.87
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -4.41
Structure conservation index 0.86
SVM decision value 1.29
SVM RNA-class probability 0.938118
Prediction RNA

Download alignment: ClustalW | MAF

>Banth.0 4131099 51 + 5227293
CUGUUAGCACUCUUUGUCUUCGAGUGCUAAAUCUAUUAAUAACUUACCAAA
...(((((((((.........)))))))))..................... ( -12.00)
>Bcere.0 4079729 51 + 5224283
CUGUUAGCACUCUUUGUCUUCGAGUGCUAAAUCUAUUAAUAACUUACCAAA
...(((((((((.........)))))))))..................... ( -12.00)
>Bhalo.0 2773051 51 - 4202352
CUGUUAGCACUCUCAUAGUUCGAGUGCUAAAUCUAUUGCUAACUUAUCAAA
...(((((((((.........)))))))))..................... ( -12.00)
>Bclau.0 2517408 51 - 4303871
CUGUUAGCACUCAAAUGCAACGAGUGCUAAUACUAUUGAUACACUAUCAAA
.(((((((((((.........)))))))))))...((((((...)))))). ( -16.30)
>Bsubt.0 2628871 51 + 4214630
CUGUUAGCACUCUCAAUAAGCGAGUGCUAAUUCUAUAACAAAAGUAUCAAA
..((((((((((.(.....).)))))))))).................... ( -13.60)
>Blich.0 2636880 51 + 4222334
CUGUUAGCACUCGGCACAACUGAGUGCUAAUUGUAUAUCAAAAUUACCAAA
..((((((((((((.....)))))))))))).................... ( -16.70)
>consensus
CUGUUAGCACUCUCAAUCAUCGAGUGCUAAAUCUAUUAAUAAAUUACCAAA
...(((((((((.........)))))))))..................... (-11.87 = -11.87 +  -0.00) 

alignment

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secondary structure

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dotplot

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Window 4

Location 4,131,099 – 4,131,150
Length 51
Sequences 6
Columns 51
Reading direction reverse
Mean pairwise identity 76.34
Mean single sequence MFE -13.18
Consensus MFE -12.25
Energy contribution -12.25
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.89
Structure conservation index 0.93
SVM decision value 1.74
SVM RNA-class probability 0.974993
Prediction RNA

Download alignment: ClustalW | MAF

>Banth.0 4131099 51 + 5227293
UUUGGUAAGUUAUUAAUAGAUUUAGCACUCGAAGACAAAGAGUGCUAACAG
.....................(((((((((.........)))))))))... ( -12.50)
>Bcere.0 4079729 51 + 5224283
UUUGGUAAGUUAUUAAUAGAUUUAGCACUCGAAGACAAAGAGUGCUAACAG
.....................(((((((((.........)))))))))... ( -12.50)
>Bhalo.0 2773051 51 - 4202352
UUUGAUAAGUUAGCAAUAGAUUUAGCACUCGAACUAUGAGAGUGCUAACAG
.....................(((((((((.........)))))))))... ( -12.50)
>Bclau.0 2517408 51 - 4303871
UUUGAUAGUGUAUCAAUAGUAUUAGCACUCGUUGCAUUUGAGUGCUAACAG
.((((((...)))))).....((((((((((.......))))))))))... ( -15.30)
>Bsubt.0 2628871 51 + 4214630
UUUGAUACUUUUGUUAUAGAAUUAGCACUCGCUUAUUGAGAGUGCUAACAG
.....................(((((((((.(.....).)))))))))... ( -13.30)
>Blich.0 2636880 51 + 4222334
UUUGGUAAUUUUGAUAUACAAUUAGCACUCAGUUGUGCCGAGUGCUAACAG
.....................(((((((((.(.....).)))))))))... ( -13.00)
>consensus
UUUGAUAAGUUAGUAAUAGAAUUAGCACUCGAAGAAUAAGAGUGCUAACAG
.....................(((((((((.........)))))))))... (-12.25 = -12.25 +   0.00) 

alignment

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secondary structure

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dotplot

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Window 5

Location 4,131,099 – 4,131,150
Length 51
Sequences 6
Columns 51
Reading direction forward
Mean pairwise identity 76.34
Mean single sequence MFE -13.77
Consensus MFE -11.87
Energy contribution -11.87
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -4.41
Structure conservation index 0.86
SVM decision value 1.29
SVM RNA-class probability 0.938118
Prediction RNA

Download alignment: ClustalW | MAF

>Banth.0 4131099 51 + 5227293/0-51
CUGUUAGCACUCUUUGUCUUCGAGUGCUAAAUCUAUUAAUAACUUACCAAA
...(((((((((.........)))))))))..................... ( -12.00)
>Bcere.0 4079729 51 + 5224283/0-51
CUGUUAGCACUCUUUGUCUUCGAGUGCUAAAUCUAUUAAUAACUUACCAAA
...(((((((((.........)))))))))..................... ( -12.00)
>Bhalo.0 2773051 51 - 4202352/0-51
CUGUUAGCACUCUCAUAGUUCGAGUGCUAAAUCUAUUGCUAACUUAUCAAA
...(((((((((.........)))))))))..................... ( -12.00)
>Bclau.0 2517408 51 - 4303871/0-51
CUGUUAGCACUCAAAUGCAACGAGUGCUAAUACUAUUGAUACACUAUCAAA
.(((((((((((.........)))))))))))...((((((...)))))). ( -16.30)
>Bsubt.0 2628871 51 + 4214630/0-51
CUGUUAGCACUCUCAAUAAGCGAGUGCUAAUUCUAUAACAAAAGUAUCAAA
..((((((((((.(.....).)))))))))).................... ( -13.60)
>Blich.0 2636880 51 + 4222334/0-51
CUGUUAGCACUCGGCACAACUGAGUGCUAAUUGUAUAUCAAAAUUACCAAA
..((((((((((((.....)))))))))))).................... ( -16.70)
>consensus
CUGUUAGCACUCUCAAUCAUCGAGUGCUAAAUCUAUUAAUAAAUUACCAAA
...(((((((((.........)))))))))..................... (-11.87 = -11.87 +  -0.00) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 4,131,099 – 4,131,150
Length 51
Sequences 6
Columns 51
Reading direction reverse
Mean pairwise identity 76.34
Mean single sequence MFE -13.18
Consensus MFE -12.25
Energy contribution -12.25
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.89
Structure conservation index 0.93
SVM decision value 1.74
SVM RNA-class probability 0.974993
Prediction RNA

Download alignment: ClustalW | MAF

>Banth.0 4131099 51 + 5227293/0-51
UUUGGUAAGUUAUUAAUAGAUUUAGCACUCGAAGACAAAGAGUGCUAACAG
.....................(((((((((.........)))))))))... ( -12.50)
>Bcere.0 4079729 51 + 5224283/0-51
UUUGGUAAGUUAUUAAUAGAUUUAGCACUCGAAGACAAAGAGUGCUAACAG
.....................(((((((((.........)))))))))... ( -12.50)
>Bhalo.0 2773051 51 - 4202352/0-51
UUUGAUAAGUUAGCAAUAGAUUUAGCACUCGAACUAUGAGAGUGCUAACAG
.....................(((((((((.........)))))))))... ( -12.50)
>Bclau.0 2517408 51 - 4303871/0-51
UUUGAUAGUGUAUCAAUAGUAUUAGCACUCGUUGCAUUUGAGUGCUAACAG
.((((((...)))))).....((((((((((.......))))))))))... ( -15.30)
>Bsubt.0 2628871 51 + 4214630/0-51
UUUGAUACUUUUGUUAUAGAAUUAGCACUCGCUUAUUGAGAGUGCUAACAG
.....................(((((((((.(.....).)))))))))... ( -13.30)
>Blich.0 2636880 51 + 4222334/0-51
UUUGGUAAUUUUGAUAUACAAUUAGCACUCAGUUGUGCCGAGUGCUAACAG
.....................(((((((((.(.....).)))))))))... ( -13.00)
>consensus
UUUGAUAAGUUAGUAAUAGAAUUAGCACUCGAAGAAUAAGAGUGCUAACAG
.....................(((((((((.........)))))))))... (-12.25 = -12.25 +   0.00) 

alignment

Postscript

secondary structure

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dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 17:14:52 2006