Locus 103

Sequence ID Bcere.0
Location 3,798,782 – 3,798,894
Length 112
Max. P 0.988988
window722 window723 window724

overview

Window 2

Location 3,798,782 – 3,798,894
Length 112
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 81.82
Mean single sequence MFE -29.94
Consensus MFE -23.86
Energy contribution -22.36
Covariance contribution -1.49
Combinations/Pair 1.15
Mean z-score -1.48
Structure conservation index 0.80
SVM decision value 0.13
SVM RNA-class probability 0.595786
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 3798782 112 - 5224283/0-120
CCAAAGGGGAGUAGCGUCCAAGAAUAUUUCUUGGAAACAAAGUCGUCAUUACGUAGAACUUAGUUCUUCCGGCUUUGUUGGCAU-UUUCAUUACAU-------AUGUCUAGCAAGACCUU
......(..(((.((.(((((((.....)))))))((((((((((.........(((((...)))))..)))))))))).))))-)..).......-------..((((....))))... ( -29.10)
>Banth.0 3958133 112 - 5227293/0-120
CCAAAGGGGAGUAGCGUCCAAGAAUAUUUCUUGGAAACAAAGUCGUCAUUACGUAGAACUUAGUUCUUCCGGCUUUGUUGGCAU-UUUCAUUACAU-------AUGUCUAGCAAGACCUU
......(..(((.((.(((((((.....)))))))((((((((((.........(((((...)))))..)))))))))).))))-)..).......-------..((((....))))... ( -29.10)
>Blich.0 1470567 118 + 4222334/0-120
CCAAAGGGGAGUAGCGUCCGGAUGU-UUAACCGGAAACAAAGUCGUCAGUUCAUGGAUCUUCAUCCAUC-GGCUUUGUUGGCAUGUUUUAAUUAAUGAUAACCAUGUCUAGCAAGACCUU
....((((.....((.(((((....-....)))))((((((((((.......((((((....)))))))-)))))))))((((((.((...........)).))))))..))....)))) ( -31.61)
>consensus
CCAAAGGGGAGUAGCGUCCAAGAAUAUUUCUUGGAAACAAAGUCGUCAUUACGUAGAACUUAGUUCUUCCGGCUUUGUUGGCAU_UUUCAUUACAU_______AUGUCUAGCAAGACCUU
....((((.....((.((((((((...))))))))((((((((((......)...(((........))).)))))))))((((((.................))))))..))....)))) (-23.86 = -22.36 +  -1.49)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 3,798,782 – 3,798,894
Length 112
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 83.52
Mean single sequence MFE -37.20
Consensus MFE -31.06
Energy contribution -30.56
Covariance contribution -0.50
Combinations/Pair 1.06
Mean z-score -4.47
Structure conservation index 0.83
SVM decision value 2.14
SVM RNA-class probability 0.988988
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 3798782 112 - 5224283/33-153
GAAACAAAGUCGUCAUUACGUAGAACUUAGUUCUUCCGGCUUUGUUGGCAU-UUUCAUUACAU-------AUGUCUAGCAAGACCUUUGCCUAUUAACGGCAGAGGUCUUUUUUGCAUCC
..((((((((((.........(((((...)))))..))))))))))(((((-...........-------)))))..((((((((((((((.......)))))))))))....))).... ( -36.00)
>Banth.0 3958133 112 - 5227293/33-153
GAAACAAAGUCGUCAUUACGUAGAACUUAGUUCUUCCGGCUUUGUUGGCAU-UUUCAUUACAU-------AUGUCUAGCAAGACCUUUGCCUAUUAACGGCAGAGGUCUUUUUUGCAUUC
..((((((((((.........(((((...)))))..))))))))))(((((-...........-------)))))..((((((((((((((.......)))))))))))....))).... ( -36.00)
>Blich.0 1470567 119 + 4222334/33-153
GAAACAAAGUCGUCAGUUCAUGGAUCUUCAUCCAUC-GGCUUUGUUGGCAUGUUUUAAUUAAUGAUAACCAUGUCUAGCAAGACCUUUGCCUAAUGUUGGCAGAGGUCUUUUUUGUUUUC
..((((((((((.......((((((....)))))))-)))))))))((((((.((...........)).))))))....((((((((((((.......)))))))))))).......... ( -39.61)
>consensus
GAAACAAAGUCGUCAUUACGUAGAACUUAGUUCUUCCGGCUUUGUUGGCAU_UUUCAUUACAU_______AUGUCUAGCAAGACCUUUGCCUAUUAACGGCAGAGGUCUUUUUUGCAUUC
..((((((((((......)...(((........))).)))))))))((((((.................))))))..((((((((((((((.......)))))))))))....))).... (-31.06 = -30.56 +  -0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 3,798,782 – 3,798,894
Length 112
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 83.52
Mean single sequence MFE -28.63
Consensus MFE -21.56
Energy contribution -21.23
Covariance contribution -0.33
Combinations/Pair 1.08
Mean z-score -2.36
Structure conservation index 0.75
SVM decision value 1.01
SVM RNA-class probability 0.900461
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 3798782 112 - 5224283/33-153
GGAUGCAAAAAAGACCUCUGCCGUUAAUAGGCAAAGGUCUUGCUAGACAU-------AUGUAAUGAAA-AUGCCAACAAAGCCGGAAGAACUAAGUUCUACGUAAUGACGACUUUGUUUC
((..(((....((((((.((((.......)))).)))))))))....(((-------.....)))...-...))(((((((.....(((((...))))).(((....))).))))))).. ( -27.90)
>Banth.0 3958133 112 - 5227293/33-153
GAAUGCAAAAAAGACCUCUGCCGUUAAUAGGCAAAGGUCUUGCUAGACAU-------AUGUAAUGAAA-AUGCCAACAAAGCCGGAAGAACUAAGUUCUACGUAAUGACGACUUUGUUUC
....(((...(((((((.((((.......)))).)))))))......(((-------.....)))...-.))).(((((((.....(((((...))))).(((....))).))))))).. ( -27.80)
>Blich.0 1470567 119 + 4222334/33-153
GAAAACAAAAAAGACCUCUGCCAACAUUAGGCAAAGGUCUUGCUAGACAUGGUUAUCAUUAAUUAAAACAUGCCAACAAAGCC-GAUGGAUGAAGAUCCAUGAACUGACGACUUUGUUUC
..........(((((((.((((.......)))).)))))))...(((((.(((..(((.............((.......)).-.((((((....))))))....)))..))).))))). ( -30.20)
>consensus
GAAUGCAAAAAAGACCUCUGCCGUUAAUAGGCAAAGGUCUUGCUAGACAU_______AUGUAAUGAAA_AUGCCAACAAAGCCGGAAGAACUAAGUUCUACGUAAUGACGACUUUGUUUC
..........(((((((.((((.......)))).))))))).................................(((((((..((((........)))).((......)).))))))).. (-21.56 = -21.23 +  -0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 17:25:05 2006