Locus 20

Sequence ID Bhalo.0
Location 3,177,403 – 3,177,521
Length 118
Max. P 0.997708
window129 window130 window131

overview

Window 9

Location 3,177,403 – 3,177,509
Length 106
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 61.04
Mean single sequence MFE -29.85
Consensus MFE -20.89
Energy contribution -19.64
Covariance contribution -1.25
Combinations/Pair 1.33
Mean z-score -2.26
Structure conservation index 0.70
SVM decision value 2.91
SVM RNA-class probability 0.997708
Prediction RNA

Download alignment: ClustalW | MAF

>Bhalo.0 3177403 106 - 4202352/40-160
AGUCGCCACACUGA----------AAUGAU--AAAUUGGCAGGGGCAGUAGGAAUCGAACCCACA-CCGGAGGUUUUGGAGACCUCUGUUCUACCG-UUAAACUAUGCCCCUAUGAAAAU
....((((......----------......--....))))(((((((((.((........)))).-.((((((((.....))))))))........-........)))))))........ ( -30.29)
>Bclau.0 2856206 118 - 4303871/40-160
AACCGCCAUAUUGAUACAUGCUUAAACGAUUCAAGUUGGCAGGGGCAGUAGGAAUCGAACCCACA-CUGGAGGUUUUGGAGACCUCUGUUCUACCG-UUAAACUAUGCCCCUAUGAAAAU
....((((..((((................))))..))))(((((((.(((.(((.((((.....-..(((((((.....)))))))))))....)-))...))))))))))........ ( -32.70)
>Bcere.0 4650670 96 + 5224283/40-160
AACCGCCAUAAUUU---------------------CUGGUGCCGACUAGAGGACUUGAACCCCCAACCUACUGAUUACAAGUCAGUUGCUCUACCAAUUGAGCUAAGUC---GGCUAAAU
....(((.....((---------------------(((((....)))))))((((((............((((((.....)))))).((((........))))))))))---)))..... ( -28.20)
>Banth.0 4651692 96 + 5227293/40-160
AACCGCCAUGAUUU---------------------CUGGUGCCGACUAGAGGACUUGAACCCCCAACCUACUGAUUACAAGUCAGUUGCUCUCCCAAUUGAGCUAAGUC---GGCUAAAU
....(((.....((---------------------(((((....)))))))((((((............((((((.....)))))).((((........))))))))))---)))..... ( -28.20)
>consensus
AACCGCCAUAAUGA_____________________CUGGCACCGACAAGAGGAAUCGAACCCACA_CCGAAGGAUUACAAGACAGCUGCUCUACCA_UUAAACUAAGCC___AGCAAAAU
....((((............................))))(((((((...((........))......(((((((.....)))))))((((........))))..)))))))........ (-20.89 = -19.64 +  -1.25)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,177,403 – 3,177,509
Length 106
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 61.04
Mean single sequence MFE -29.83
Consensus MFE -24.64
Energy contribution -21.39
Covariance contribution -3.25
Combinations/Pair 1.44
Mean z-score -1.12
Structure conservation index 0.83
SVM decision value 1.20
SVM RNA-class probability 0.930124
Prediction RNA

Download alignment: ClustalW | MAF

>Bhalo.0 3177403 106 - 4202352/40-160
AUUUUCAUAGGGGCAUAGUUUAA-CGGUAGAACAGAGGUCUCCAAAACCUCCGG-UGUGGGUUCGAUUCCUACUGCCCCUGCCAAUUU--AUCAUU----------UCAGUGUGGCGACU
........(((((((..((((..-.....)))).(((((.......)))))...-.(((((.......))))))))))))((((....--..(((.----------...))))))).... ( -28.80)
>Bclau.0 2856206 118 - 4303871/40-160
AUUUUCAUAGGGGCAUAGUUUAA-CGGUAGAACAGAGGUCUCCAAAACCUCCAG-UGUGGGUUCGAUUCCUACUGCCCCUGCCAACUUGAAUCGUUUAAGCAUGUAUCAAUAUGGCGGUU
........(((((((..((((..-.....)))).(((((.......)))))...-.(((((.......))))))))))))((((..((((..(((......)))..))))..)))).... ( -32.90)
>Bcere.0 4650670 96 + 5224283/40-160
AUUUAGCC---GACUUAGCUCAAUUGGUAGAGCAACUGACUUGUAAUCAGUAGGUUGGGGGUUCAAGUCCUCUAGUCGGCACCAG---------------------AAAUUAUGGCGGUU
.....(((---(((...((((........)))).(((((.......)))))....((((((.......)))))))))))).(((.---------------------......)))..... ( -28.80)
>Banth.0 4651692 96 + 5227293/40-160
AUUUAGCC---GACUUAGCUCAAUUGGGAGAGCAACUGACUUGUAAUCAGUAGGUUGGGGGUUCAAGUCCUCUAGUCGGCACCAG---------------------AAAUCAUGGCGGUU
.....(((---((((.((.......((((((((..(..(((((.......)))))..)..))))...))))))))))))).(((.---------------------......)))..... ( -28.81)
>consensus
AUUUACAC___GACAUAGCUCAA_CGGUAGAACAAAGGACUCCAAAACAGCAGG_UGGGGGUUCAAGUCCUACAGCCCCCACCAA_____________________AAAUUAUGGCGGUU
.........((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))(((((............................)))))... (-24.64 = -21.39 +  -3.25)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,177,403 – 3,177,521
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 72.97
Mean single sequence MFE -37.95
Consensus MFE -34.75
Energy contribution -31.00
Covariance contribution -3.75
Combinations/Pair 1.41
Mean z-score -0.98
Structure conservation index 0.92
SVM decision value 1.66
SVM RNA-class probability 0.970392
Prediction RNA

Download alignment: ClustalW | MAF

>Bhalo.0 3177403 118 - 4202352/77-197
GGGUUCGGCGGUUCGAAUCCGUCCCCCUCCACCAUUUAUUUUCAUAGGGGCAUAGUUUAA-CGGUAGAACAGAGGUCUCCAAAACCUCCGG-UGUGGGUUCGAUUCCUACUGCCCCUGCC
(((...(((((.......))))).))).................((((((((..((((..-.....)))).(((((.......)))))...-.(((((.......))))))))))))).. ( -36.00)
>Bclau.0 2856206 114 - 4303871/77-197
GGGUUCGGCGGUUCGAAUCCGUCCCCCUCCACC----AUUUUCAUAGGGGCAUAGUUUAA-CGGUAGAACAGAGGUCUCCAAAACCUCCAG-UGUGGGUUCGAUUCCUACUGCCCCUGCC
(((...(((((.......))))).)))......----.......((((((((..((((..-.....)))).(((((.......)))))...-.(((((.......))))))))))))).. ( -36.00)
>Bcere.0 4650670 113 + 5224283/77-197
GGGGUCGGCGGUUCGAUCCCGUCAUCCUCCACC----AUUUAGCC---GACUUAGCUCAAUUGGUAGAGCAACUGACUUGUAAUCAGUAGGUUGGGGGUUCAAGUCCUCUAGUCGGCACC
((((..(((((.......)))))..)).))...----.....(((---(((...((((........)))).(((((.......)))))....((((((.......))))))))))))... ( -39.90)
>Banth.0 4651692 113 + 5227293/77-197
GGGGUCGGCGGUUCGAUCCCGUCAUCCUCCACC----AUUUAGCC---GACUUAGCUCAAUUGGGAGAGCAACUGACUUGUAAUCAGUAGGUUGGGGGUUCAAGUCCUCUAGUCGGCACC
((((..(((((.......)))))..)).))...----.....(((---((((.((.......((((((((..(..(((((.......)))))..)..))))...)))))))))))))... ( -39.91)
>consensus
GGGGUCGGCGGUUCGAACCCGUCACCCUCCACC____AUUUACAC___GACAUAGCUCAA_CGGUAGAACAAAGGACUCCAAAACAGCAGG_UGGGGGUUCAAGUCCUACAGCCCCCACC
((((((((....)))))))).........................(((((((..((((........)))).(((((.......))))).....(((((.......))))))))))))... (-34.75 = -31.00 +  -3.75)

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 17:17:08 2006