Locus 53

Sequence ID Bcere.0
Location 1,781 – 824,640
Length 822859
Max. P 0.999785
window339 window340 window341 window342 window343

overview

Window 9

Location 824,595 – 824,640
Length 45
Sequences 3
Columns 45
Reading direction forward
Mean pairwise identity 71.85
Mean single sequence MFE -12.50
Consensus MFE -9.25
Energy contribution -9.03
Covariance contribution -0.21
Combinations/Pair 1.42
Mean z-score -0.97
Structure conservation index 0.74
SVM decision value -0.02
SVM RNA-class probability 0.523562
Prediction RNA
WARNING Sequence 1 too short.
WARNING Sequence 2 too short.
WARNING Sequence 3 too short.

Download alignment: ClustalW | MAF

>Bcere.0 824595 45 + 5224283
AUAAGCGUGAGGUCGAUGGUUCGAGUCCAUUUAGGCCCACCAUAU
....(.(((.(((((((((.......)))))..)))))))).... ( -12.60)
>Banth.0 747899 45 + 5227293
AUAAGCGUGAGGUCGAUGGUUCGAGUCCAUUUAGACCCACCAUAU
....(.(((.(((((((((.......)))))..)))))))).... ( -13.20)
>Bclau.0 3447146 45 + 4303871
CUAAGCUGAGGGUUGCAGGUUCAAUUCCUGCUAGGCGCGUCCUCU
.......((((((.(((((.......)))))...))....)))). ( -11.70)
>consensus
AUAAGCGUGAGGUCGAUGGUUCGAGUCCAUUUAGGCCCACCAUAU
......(((.(((((((((.......)))))..)))))))..... ( -9.25 =  -9.03 +  -0.21)

alignment

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secondary structure

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dotplot

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Window 0

Location 1,781 – 1,880
Length 99
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 76.03
Mean single sequence MFE -19.50
Consensus MFE -13.44
Energy contribution -14.24
Covariance contribution 0.80
Combinations/Pair 1.17
Mean z-score -3.57
Structure conservation index 0.69
SVM decision value 4.07
SVM RNA-class probability 0.999785
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 1781 99 + 5224283
ACGCACAGUCUAUCCACAUGUAGAUAGACUGUUUUUACAUCCUUUAACGGG-GUUAUCCACAUAUCCACAAGCCCUAUUACUAUUACUACUAUUUUUUAU
....((((((((((........))))))))))............(((..((-(((...............)))))..))).................... ( -19.76)
>Banth.0 1780 99 + 5227293
ACGCACAGUCUAUCCACAUGUAGAUAGACUGUUUUUACAUCUUUCAACGGG-GUUAUCCACAUAUCCACAAGCCCUAUUACUAUUACUACUAUUUUUUAU
....((((((((((........))))))))))................(((-(((...............))))))........................ ( -19.06)
>Bsubt.0 1798 100 + 4214630
AUACACAGUCUGUCCACAUGUGGAUAGGCUGUGUUUCCUGUCUUUUUCACAACUUAUCCACAAAUCCACAGGCCCUACUAUUACUUCUACUAUUUUUUAU
..((((((((((((((....))))))))))))))..(((((..........................)))))............................ ( -25.47)
>Blich.0 1885 98 + 4222334
UUACACAGUCUGUCCACAUGUGGAUAGGCUGUGUUUCCGUUCUUUUUUACA-CUUAUCCACAAAUCCACAGCCCCUACUAGUACUUCUGCUAUUUUU-AU
..((((((((((((((....)))))))))))))).................-..........................(((((....))))).....-.. ( -24.40)
>Bclau.0 1569 100 + 4303871
AUCCACAAACUACCCACAUGUGAAUAGGCUGUCUCUUUACGCAUUUUGCUUACUUAUCCACAAAUACACAAGCCCUAGUACUAUUACUACGACAUUUAAA
..................((((.(((((..((......))((.....))...))))).)))).........(.(.(((((....))))).).)....... (  -8.80)
>consensus
AUACACAGUCUAUCCACAUGUGGAUAGGCUGUGUUUACAUCCUUUUUCACA_CUUAUCCACAAAUCCACAAGCCCUACUACUAUUACUACUAUUUUUUAU
....((((((((((((....)))))))))))).................................................................... (-13.44 = -14.24 +   0.80)

alignment

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secondary structure

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dotplot

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Window 1

Location 1,781 – 1,880
Length 99
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 76.03
Mean single sequence MFE -23.86
Consensus MFE -12.04
Energy contribution -11.72
Covariance contribution -0.32
Combinations/Pair 1.36
Mean z-score -2.40
Structure conservation index 0.50
SVM decision value 2.00
SVM RNA-class probability 0.985233
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 1781 99 + 5224283
AUAAAAAAUAGUAGUAAUAGUAAUAGGGCUUGUGGAUAUGUGGAUAAC-CCCGUUAAAGGAUGUAAAAACAGUCUAUCUACAUGUGGAUAGACUGUGCGU
.............((.....(((..(((.((((..........)))))-))..)))............((((((((((((....)))))))))))))).. ( -23.30)
>Banth.0 1780 99 + 5227293
AUAAAAAAUAGUAGUAAUAGUAAUAGGGCUUGUGGAUAUGUGGAUAAC-CCCGUUGAAAGAUGUAAAAACAGUCUAUCUACAUGUGGAUAGACUGUGCGU
........((.((....)).))...(((.((((..........)))))-))((((....)))).....((((((((((((....)))))))))))).... ( -23.70)
>Bsubt.0 1798 100 + 4214630
AUAAAAAAUAGUAGAAGUAAUAGUAGGGCCUGUGGAUUUGUGGAUAAGUUGUGAAAAAGACAGGAAACACAGCCUAUCCACAUGUGGACAGACUGUGUAU
.......................((.((.((((..((.((((((((.((((((..............)))))).)))))))).))..)))).)).))... ( -25.14)
>Blich.0 1885 98 + 4222334
AU-AAAAAUAGCAGAAGUACUAGUAGGGGCUGUGGAUUUGUGGAUAAG-UGUAAAAAAGAACGGAAACACAGCCUAUCCACAUGUGGACAGACUGUGUAA
..-.......((((............((((((((..(((((.......-...........)))))..)))))))).((((....))))....)))).... ( -25.67)
>Bclau.0 1569 100 + 4303871
UUUAAAUGUCGUAGUAAUAGUACUAGGGCUUGUGUAUUUGUGGAUAAGUAAGCAAAAUGCGUAAAGAGACAGCCUAUUCACAUGUGGGUAGUUUGUGGAU
.......(((.(((((....))))).)))((((.((((((....)))))).)))).........(.((((.((((((......)))))).)))).).... ( -21.50)
>consensus
AUAAAAAAUAGUAGUAAUAGUAAUAGGGCUUGUGGAUUUGUGGAUAAG_CCCGAAAAAGAAUGGAAAAACAGCCUAUCCACAUGUGGAUAGACUGUGCAU
....................................................................((((.(((((((....))))))).)))).... (-12.04 = -11.72 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 2

Location 1,781 – 1,880
Length 99
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 76.03
Mean single sequence MFE -19.50
Consensus MFE -13.44
Energy contribution -14.24
Covariance contribution 0.80
Combinations/Pair 1.17
Mean z-score -3.57
Structure conservation index 0.69
SVM decision value 4.07
SVM RNA-class probability 0.999785
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 1781 99 + 5224283/0-100
ACGCACAGUCUAUCCACAUGUAGAUAGACUGUUUUUACAUCCUUUAACGGG-GUUAUCCACAUAUCCACAAGCCCUAUUACUAUUACUACUAUUUUUUAU
....((((((((((........))))))))))............(((..((-(((...............)))))..))).................... ( -19.76)
>Banth.0 1780 99 + 5227293/0-100
ACGCACAGUCUAUCCACAUGUAGAUAGACUGUUUUUACAUCUUUCAACGGG-GUUAUCCACAUAUCCACAAGCCCUAUUACUAUUACUACUAUUUUUUAU
....((((((((((........))))))))))................(((-(((...............))))))........................ ( -19.06)
>Bsubt.0 1798 100 + 4214630/0-100
AUACACAGUCUGUCCACAUGUGGAUAGGCUGUGUUUCCUGUCUUUUUCACAACUUAUCCACAAAUCCACAGGCCCUACUAUUACUUCUACUAUUUUUUAU
..((((((((((((((....))))))))))))))..(((((..........................)))))............................ ( -25.47)
>Blich.0 1885 98 + 4222334/0-100
UUACACAGUCUGUCCACAUGUGGAUAGGCUGUGUUUCCGUUCUUUUUUACA-CUUAUCCACAAAUCCACAGCCCCUACUAGUACUUCUGCUAUUUUU-AU
..((((((((((((((....)))))))))))))).................-..........................(((((....))))).....-.. ( -24.40)
>Bclau.0 1569 100 + 4303871/0-100
AUCCACAAACUACCCACAUGUGAAUAGGCUGUCUCUUUACGCAUUUUGCUUACUUAUCCACAAAUACACAAGCCCUAGUACUAUUACUACGACAUUUAAA
..................((((.(((((..((......))((.....))...))))).)))).........(.(.(((((....))))).).)....... (  -8.80)
>consensus
AUACACAGUCUAUCCACAUGUGGAUAGGCUGUGUUUACAUCCUUUUUCACA_CUUAUCCACAAAUCCACAAGCCCUACUACUAUUACUACUAUUUUUUAU
....((((((((((((....)))))))))))).................................................................... (-13.44 = -14.24 +   0.80)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,781 – 1,880
Length 99
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 76.03
Mean single sequence MFE -23.86
Consensus MFE -12.04
Energy contribution -11.72
Covariance contribution -0.32
Combinations/Pair 1.36
Mean z-score -2.40
Structure conservation index 0.50
SVM decision value 2.00
SVM RNA-class probability 0.985233
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 1781 99 + 5224283/0-100
AUAAAAAAUAGUAGUAAUAGUAAUAGGGCUUGUGGAUAUGUGGAUAAC-CCCGUUAAAGGAUGUAAAAACAGUCUAUCUACAUGUGGAUAGACUGUGCGU
.............((.....(((..(((.((((..........)))))-))..)))............((((((((((((....)))))))))))))).. ( -23.30)
>Banth.0 1780 99 + 5227293/0-100
AUAAAAAAUAGUAGUAAUAGUAAUAGGGCUUGUGGAUAUGUGGAUAAC-CCCGUUGAAAGAUGUAAAAACAGUCUAUCUACAUGUGGAUAGACUGUGCGU
........((.((....)).))...(((.((((..........)))))-))((((....)))).....((((((((((((....)))))))))))).... ( -23.70)
>Bsubt.0 1798 100 + 4214630/0-100
AUAAAAAAUAGUAGAAGUAAUAGUAGGGCCUGUGGAUUUGUGGAUAAGUUGUGAAAAAGACAGGAAACACAGCCUAUCCACAUGUGGACAGACUGUGUAU
.......................((.((.((((..((.((((((((.((((((..............)))))).)))))))).))..)))).)).))... ( -25.14)
>Blich.0 1885 98 + 4222334/0-100
AU-AAAAAUAGCAGAAGUACUAGUAGGGGCUGUGGAUUUGUGGAUAAG-UGUAAAAAAGAACGGAAACACAGCCUAUCCACAUGUGGACAGACUGUGUAA
..-.......((((............((((((((..(((((.......-...........)))))..)))))))).((((....))))....)))).... ( -25.67)
>Bclau.0 1569 100 + 4303871/0-100
UUUAAAUGUCGUAGUAAUAGUACUAGGGCUUGUGUAUUUGUGGAUAAGUAAGCAAAAUGCGUAAAGAGACAGCCUAUUCACAUGUGGGUAGUUUGUGGAU
.......(((.(((((....))))).)))((((.((((((....)))))).)))).........(.((((.((((((......)))))).)))).).... ( -21.50)
>consensus
AUAAAAAAUAGUAGUAAUAGUAAUAGGGCUUGUGGAUUUGUGGAUAAG_CCCGAAAAAGAAUGGAAAAACAGCCUAUCCACAUGUGGAUAGACUGUGCAU
....................................................................((((.(((((((....))))))).)))).... (-12.04 = -11.72 +  -0.32)

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 17:20:09 2006