Locus 107

Sequence ID Bcere.0
Location 3,647,243 – 3,647,360
Length 117
Max. P 0.998780
window735 window736 window737 window738

overview

Window 5

Location 3,647,243 – 3,647,360
Length 117
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 75.57
Mean single sequence MFE -35.50
Consensus MFE -17.31
Energy contribution -17.76
Covariance contribution 0.45
Combinations/Pair 1.15
Mean z-score -4.57
Structure conservation index 0.49
SVM decision value 2.44
SVM RNA-class probability 0.994018
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 3647243 117 - 5224283
CUCUCUCCUUUUCCAUCGAUCAUCUCAUGGAAAGUGGAAAGGUUCUGCUAUGCCUACUUUUUCAUAGAACGAAAAAACCCUUUGUGUUUUACACAAAGGGAGAAUUUA-AGGCACAUC
.(((.(((((((((((.((.....)))))))))).))).)))........(((((..((((((.......)))))).(((((((((.....)))))))))........-))))).... ( -36.70)
>Banth.0 3804432 116 - 5227293
CUCUCUCCUUUUCCAUCGAUCAUCUCAUGGAAAGUGGAAAGGUUCUGCUAUGCCUA-UUUUUCAUAGAACGAAAAAACCCUUUGUGUUUUACACAAAGGGAGAAUUUA-AGGCACAUC
.(((.(((((((((((.((.....)))))))))).))).)))........(((((.-((((((.......)))))).(((((((((.....)))))))))........-))))).... ( -36.90)
>Blich.0 2381057 107 + 4222334
CUCUCUCCUUUUCGAUCA--CAUCUCACGAAAAGAGGAAUGGUUCU--UUCCCCUG-----UCCUAAAC--AAAAAACCCGCUUUAUUGAAAAAGCGGGGCUGUUUUACAGACAGGUC
...((..(((((((....--.......)))))))..))..((....--..))((((-----((..((((--(.....((((((((......))))))))..)))))....)))))).. ( -32.90)
>consensus
CUCUCUCCUUUUCCAUCGAUCAUCUCAUGGAAAGUGGAAAGGUUCUGCUAUGCCUA_UUUUUCAUAGAACGAAAAAACCCUUUGUGUUUUACACAAAGGGAGAAUUUA_AGGCACAUC
...((..((((((...............))))))..))..(((........))).......................(((((((((.....))))))))).................. (-17.31 = -17.76 +   0.45)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,647,243 – 3,647,360
Length 117
Sequences 3
Columns 118
Reading direction reverse
Mean pairwise identity 75.57
Mean single sequence MFE -40.03
Consensus MFE -21.14
Energy contribution -24.60
Covariance contribution 3.46
Combinations/Pair 1.16
Mean z-score -4.49
Structure conservation index 0.53
SVM decision value 3.22
SVM RNA-class probability 0.998780
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 3647243 117 - 5224283
GAUGUGCCU-UAAAUUCUCCCUUUGUGUAAAACACAAAGGGUUUUUUCGUUCUAUGAAAAAGUAGGCAUAGCAGAACCUUUCCACUUUCCAUGAGAUGAUCGAUGGAAAAGGAGAGAG
..(((((((-........(((((((((.....)))))))))(((((((((...))))))))).))))))).......((((((..(((((((((.....)).))))))).)))))).. ( -41.50)
>Banth.0 3804432 116 - 5227293
GAUGUGCCU-UAAAUUCUCCCUUUGUGUAAAACACAAAGGGUUUUUUCGUUCUAUGAAAAA-UAGGCAUAGCAGAACCUUUCCACUUUCCAUGAGAUGAUCGAUGGAAAAGGAGAGAG
..(((((((-........(((((((((.....))))))))).((((((((...))))))))-.))))))).......((((((..(((((((((.....)).))))))).)))))).. ( -40.90)
>Blich.0 2381057 107 + 4222334
GACCUGUCUGUAAAACAGCCCCGCUUUUUCAAUAAAGCGGGUUUUUU--GUUUAGGA-----CAGGGGAA--AGAACCAUUCCUCUUUUCGUGAGAUG--UGAUCGAAAAGGAGAGAG
..(((((((...((((((.((((((((......))))))))....))--)))).)))-----))))((..--....)).(((..(((((((.......--....)))))))..))).. ( -37.70)
>consensus
GAUGUGCCU_UAAAUUCUCCCUUUGUGUAAAACACAAAGGGUUUUUUCGUUCUAUGAAAAA_UAGGCAUAGCAGAACCUUUCCACUUUCCAUGAGAUGAUCGAUGGAAAAGGAGAGAG
..(((((((.........(((((((((.....)))))))))..((((((.....))))))...))))))).......((((((..(((((((((.....)).))))))).)))))).. (-21.14 = -24.60 +   3.46)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,647,243 – 3,647,360
Length 117
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 75.57
Mean single sequence MFE -35.50
Consensus MFE -17.31
Energy contribution -17.76
Covariance contribution 0.45
Combinations/Pair 1.15
Mean z-score -4.57
Structure conservation index 0.49
SVM decision value 2.44
SVM RNA-class probability 0.994018
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 3647243 117 - 5224283/0-118
CUCUCUCCUUUUCCAUCGAUCAUCUCAUGGAAAGUGGAAAGGUUCUGCUAUGCCUACUUUUUCAUAGAACGAAAAAACCCUUUGUGUUUUACACAAAGGGAGAAUUUA-AGGCACAUC
.(((.(((((((((((.((.....)))))))))).))).)))........(((((..((((((.......)))))).(((((((((.....)))))))))........-))))).... ( -36.70)
>Banth.0 3804432 116 - 5227293/0-118
CUCUCUCCUUUUCCAUCGAUCAUCUCAUGGAAAGUGGAAAGGUUCUGCUAUGCCUA-UUUUUCAUAGAACGAAAAAACCCUUUGUGUUUUACACAAAGGGAGAAUUUA-AGGCACAUC
.(((.(((((((((((.((.....)))))))))).))).)))........(((((.-((((((.......)))))).(((((((((.....)))))))))........-))))).... ( -36.90)
>Blich.0 2381057 107 + 4222334/0-118
CUCUCUCCUUUUCGAUCA--CAUCUCACGAAAAGAGGAAUGGUUCU--UUCCCCUG-----UCCUAAAC--AAAAAACCCGCUUUAUUGAAAAAGCGGGGCUGUUUUACAGACAGGUC
...((..(((((((....--.......)))))))..))..((....--..))((((-----((..((((--(.....((((((((......))))))))..)))))....)))))).. ( -32.90)
>consensus
CUCUCUCCUUUUCCAUCGAUCAUCUCAUGGAAAGUGGAAAGGUUCUGCUAUGCCUA_UUUUUCAUAGAACGAAAAAACCCUUUGUGUUUUACACAAAGGGAGAAUUUA_AGGCACAUC
...((..((((((...............))))))..))..(((........))).......................(((((((((.....))))))))).................. (-17.31 = -17.76 +   0.45)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 8

Location 3,647,243 – 3,647,360
Length 117
Sequences 3
Columns 118
Reading direction reverse
Mean pairwise identity 75.57
Mean single sequence MFE -40.03
Consensus MFE -21.14
Energy contribution -24.60
Covariance contribution 3.46
Combinations/Pair 1.16
Mean z-score -4.49
Structure conservation index 0.53
SVM decision value 3.22
SVM RNA-class probability 0.998780
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 3647243 117 - 5224283/0-118
GAUGUGCCU-UAAAUUCUCCCUUUGUGUAAAACACAAAGGGUUUUUUCGUUCUAUGAAAAAGUAGGCAUAGCAGAACCUUUCCACUUUCCAUGAGAUGAUCGAUGGAAAAGGAGAGAG
..(((((((-........(((((((((.....)))))))))(((((((((...))))))))).))))))).......((((((..(((((((((.....)).))))))).)))))).. ( -41.50)
>Banth.0 3804432 116 - 5227293/0-118
GAUGUGCCU-UAAAUUCUCCCUUUGUGUAAAACACAAAGGGUUUUUUCGUUCUAUGAAAAA-UAGGCAUAGCAGAACCUUUCCACUUUCCAUGAGAUGAUCGAUGGAAAAGGAGAGAG
..(((((((-........(((((((((.....))))))))).((((((((...))))))))-.))))))).......((((((..(((((((((.....)).))))))).)))))).. ( -40.90)
>Blich.0 2381057 107 + 4222334/0-118
GACCUGUCUGUAAAACAGCCCCGCUUUUUCAAUAAAGCGGGUUUUUU--GUUUAGGA-----CAGGGGAA--AGAACCAUUCCUCUUUUCGUGAGAUG--UGAUCGAAAAGGAGAGAG
..(((((((...((((((.((((((((......))))))))....))--)))).)))-----))))((..--....)).(((..(((((((.......--....)))))))..))).. ( -37.70)
>consensus
GAUGUGCCU_UAAAUUCUCCCUUUGUGUAAAACACAAAGGGUUUUUUCGUUCUAUGAAAAA_UAGGCAUAGCAGAACCUUUCCACUUUCCAUGAGAUGAUCGAUGGAAAAGGAGAGAG
..(((((((.........(((((((((.....)))))))))..((((((.....))))))...))))))).......((((((..(((((((((.....)).))))))).)))))).. (-21.14 = -24.60 +   3.46)

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 17:25:15 2006