Locus 109

Sequence ID Bcere.0
Location 3,365,488 – 4,806,405
Length 1440917
Max. P 0.999998
window741 window742 window743 window744 window745

overview

Window 1

Location 4,806,285 – 4,806,405
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 68.33
Mean single sequence MFE -29.48
Consensus MFE -18.54
Energy contribution -19.00
Covariance contribution 0.46
Combinations/Pair 1.29
Mean z-score -2.99
Structure conservation index 0.63
SVM decision value 6.40
SVM RNA-class probability 0.999998
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 4806285 120 + 5224283/8-128
GGUACUAAAAAGUGCCUAUGUUACUUUUUGGUACCUAUCGUACUUUUAAGUGCGUUCUUCAAAAAAAGAGCGAAGCCAUUCAUAAUAGCAUAUAUGAGCAAUAAAGUUAUUUUUGUAGAA
((((((((((((((.......))))))))))))))...((((((....))))))((((.((((((...(((.......((((((........)))))).......))).)))))).)))) ( -31.64)
>Banth.0 4814425 119 + 5227293/8-128
GGUACUGAAAAGUGACUAUGUUACUUUUUGGUGCCUAUCGUACUUUAAAGCGCGUUCUUCAAAAAAAGAAUGAAACCAUUCAUAAUAGCAUUUGUAGAGAUUAAAUAUAUUUUU-UAGAA
(((((..(((((((((...)))))))))..)))))...((..((....))..))....((.(((((((((((....))))).((((..(.......)..))))......)))))-).)). ( -27.70)
>Blich.0 2724962 120 + 4222334/8-128
GGUACCGAAAAGUACCUAUCUCACUUUUUGGUUCCUAUCACACUUAAAAGUGCGUACUUUUUUUCGCAGAUGAUAUGUACCAUAAUAUCAUUAGCCGGCAGCCAUUUGCUAUACCUUAAA
(((((((((((((((......(((((((.(((.........))).))))))).))))))))....((.((((((((........)))))))).))))).(((.....))).))))..... ( -29.10)
>consensus
GGUACUGAAAAGUGCCUAUGUUACUUUUUGGUACCUAUCGUACUUUAAAGUGCGUUCUUCAAAAAAAGAAUGAAACCAUUCAUAAUAGCAUUUGUAGGCAAUAAAUUUAUUUUU_UAGAA
((((((((((((((.......)))))))))))))).................(((((((......)))))))................................................ (-18.54 = -19.00 +   0.46)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,365,488 – 3,365,548
Length 60
Sequences 4
Columns 60
Reading direction forward
Mean pairwise identity 85.56
Mean single sequence MFE -18.78
Consensus MFE -17.60
Energy contribution -17.60
Covariance contribution -0.00
Combinations/Pair 1.08
Mean z-score -4.43
Structure conservation index 0.94
SVM decision value 3.12
SVM RNA-class probability 0.998487
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 3365488 60 - 5224283
AUAAAAAACGUCCCUACGCAAAUACGUAGGGACGAUAAAUUAUCGCGGUACCACCCUAGU
........((((((((((......))))))))))............((.....))..... ( -19.60)
>Banth.0 3505951 60 - 5227293
AUAAAAAACGUCCCUACGUAAAUACGUAGGGACGAUAAAUUAUCGCGGUACCACCCUAGU
........(((((((((((....)))))))))))............((.....))..... ( -21.00)
>Bsubt.0 3036937 60 + 4214630
AUAAAAAACGCCCCUUCGUUUACACGAAGGGACGAUUGAUUAUCGCGGUACCACCCUACU
........(((((((((((....))))))))..(((.....))))))............. ( -17.30)
>Blich.0 3000788 59 + 4222334
AAAUAAAACGCCCCUUCGCAAAAACGAAGGGACGAUAAAA-AUCGCGGUACCACCCUGCU
........((.(((((((......))))))).))......-...((((.......)))). ( -17.20)
>consensus
AUAAAAAACGCCCCUACGCAAAUACGAAGGGACGAUAAAUUAUCGCGGUACCACCCUACU
........((((((((((......))))))))))............((.....))..... (-17.60 = -17.60 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 3,365,488 – 3,365,548
Length 60
Sequences 4
Columns 60
Reading direction reverse
Mean pairwise identity 85.56
Mean single sequence MFE -22.90
Consensus MFE -23.35
Energy contribution -22.35
Covariance contribution -1.00
Combinations/Pair 1.21
Mean z-score -4.10
Structure conservation index 1.02
SVM decision value 3.44
SVM RNA-class probability 0.999214
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 3365488 60 - 5224283
ACUAGGGUGGUACCGCGAUAAUUUAUCGUCCCUACGUAUUUGCGUAGGGACGUUUUUUAU
......(((....))).((((.....(((((((((((....)))))))))))....)))) ( -22.90)
>Banth.0 3505951 60 - 5227293
ACUAGGGUGGUACCGCGAUAAUUUAUCGUCCCUACGUAUUUACGUAGGGACGUUUUUUAU
......(((....))).((((.....(((((((((((....)))))))))))....)))) ( -22.60)
>Bsubt.0 3036937 60 + 4214630
AGUAGGGUGGUACCGCGAUAAUCAAUCGUCCCUUCGUGUAAACGAAGGGGCGUUUUUUAU
......(((....))).((((.....(((((((((((....)))))))))))....)))) ( -22.70)
>Blich.0 3000788 59 + 4222334
AGCAGGGUGGUACCGCGAU-UUUUAUCGUCCCUUCGUUUUUGCGAAGGGGCGUUUUAUUU
.((.((......))))...-......(((((((((((....)))))))))))........ ( -23.40)
>consensus
ACUAGGGUGGUACCGCGAUAAUUUAUCGUCCCUACGUAUUUACGAAGGGACGUUUUUUAU
......(((....)))..........(((((((((((....)))))))))))........ (-23.35 = -22.35 +  -1.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,365,488 – 3,365,548
Length 60
Sequences 4
Columns 60
Reading direction forward
Mean pairwise identity 85.56
Mean single sequence MFE -18.78
Consensus MFE -17.60
Energy contribution -17.60
Covariance contribution -0.00
Combinations/Pair 1.08
Mean z-score -4.43
Structure conservation index 0.94
SVM decision value 3.12
SVM RNA-class probability 0.998487
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 3365488 60 - 5224283/0-60
AUAAAAAACGUCCCUACGCAAAUACGUAGGGACGAUAAAUUAUCGCGGUACCACCCUAGU
........((((((((((......))))))))))............((.....))..... ( -19.60)
>Banth.0 3505951 60 - 5227293/0-60
AUAAAAAACGUCCCUACGUAAAUACGUAGGGACGAUAAAUUAUCGCGGUACCACCCUAGU
........(((((((((((....)))))))))))............((.....))..... ( -21.00)
>Bsubt.0 3036937 60 + 4214630/0-60
AUAAAAAACGCCCCUUCGUUUACACGAAGGGACGAUUGAUUAUCGCGGUACCACCCUACU
........(((((((((((....))))))))..(((.....))))))............. ( -17.30)
>Blich.0 3000788 59 + 4222334/0-60
AAAUAAAACGCCCCUUCGCAAAAACGAAGGGACGAUAAAA-AUCGCGGUACCACCCUGCU
........((.(((((((......))))))).))......-...((((.......)))). ( -17.20)
>consensus
AUAAAAAACGCCCCUACGCAAAUACGAAGGGACGAUAAAUUAUCGCGGUACCACCCUACU
........((((((((((......))))))))))............((.....))..... (-17.60 = -17.60 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,365,488 – 3,365,548
Length 60
Sequences 4
Columns 60
Reading direction reverse
Mean pairwise identity 85.56
Mean single sequence MFE -22.90
Consensus MFE -23.35
Energy contribution -22.35
Covariance contribution -1.00
Combinations/Pair 1.21
Mean z-score -4.10
Structure conservation index 1.02
SVM decision value 3.44
SVM RNA-class probability 0.999214
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 3365488 60 - 5224283/0-60
ACUAGGGUGGUACCGCGAUAAUUUAUCGUCCCUACGUAUUUGCGUAGGGACGUUUUUUAU
......(((....))).((((.....(((((((((((....)))))))))))....)))) ( -22.90)
>Banth.0 3505951 60 - 5227293/0-60
ACUAGGGUGGUACCGCGAUAAUUUAUCGUCCCUACGUAUUUACGUAGGGACGUUUUUUAU
......(((....))).((((.....(((((((((((....)))))))))))....)))) ( -22.60)
>Bsubt.0 3036937 60 + 4214630/0-60
AGUAGGGUGGUACCGCGAUAAUCAAUCGUCCCUUCGUGUAAACGAAGGGGCGUUUUUUAU
......(((....))).((((.....(((((((((((....)))))))))))....)))) ( -22.70)
>Blich.0 3000788 59 + 4222334/0-60
AGCAGGGUGGUACCGCGAU-UUUUAUCGUCCCUUCGUUUUUGCGAAGGGGCGUUUUAUUU
.((.((......))))...-......(((((((((((....)))))))))))........ ( -23.40)
>consensus
ACUAGGGUGGUACCGCGAUAAUUUAUCGUCCCUACGUAUUUACGAAGGGACGUUUUUUAU
......(((....)))..........(((((((((((....)))))))))))........ (-23.35 = -22.35 +  -1.00)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 17:25:19 2006