Locus 80

Sequence ID Bcere.0
Location 1,861,158 – 1,861,274
Length 116
Max. P 0.999618
window452 window453 window454 window455

overview

Window 2

Location 1,861,158 – 1,861,274
Length 116
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 77.25
Mean single sequence MFE -33.77
Consensus MFE -31.02
Energy contribution -29.70
Covariance contribution -1.32
Combinations/Pair 1.22
Mean z-score -1.82
Structure conservation index 0.92
SVM decision value 2.84
SVM RNA-class probability 0.997353
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 1861158 116 + 5224283/40-160
GGUGUUUACAUGGCGAUUACAAUUCAAUUGCCGGACACUGCAGCGUCUCAUGCAAAGCCAAGUAUGGAAAUGGCGAUACUUUGCGUGAGGUAGACAAGUAAUAUACAAU----CGCCUAA
(((((((((.((((((((.......)))))))).............(((((((((((....((((....)).))....)))))))))))))))))..(((...)))...----.)))... ( -33.40)
>Banth.0 1723710 120 + 5227293/40-160
GGUGUUUAAAUGGCGAUUACAAUUCAAUUGCCGGACACUGCAGCGUCUCAUGCAAAGCCAAGUAUGGAAAUGGCGAUACUUUGCGUGAGGUAGACAAGUAAUAUACAAUUCAUCGCCAAA
((((((....((((((((.......))))))))))))))...(((.(((((((((((....((((....)).))....)))))))))))(((...........))).......))).... ( -32.40)
>Bsubt.0 2748265 114 + 4214630/40-160
GGUGAUGUAAUGGCAAGCAAGAUGAGAAUGCCAGAUUCCGCAACGUCCCAUGCAAAGCCUACUAUUGGGAAGGCGAUACUUUGCAUGGGGUAGACU--UUCUAAAAGAU----CGCCCAA
((((((.(..(((((..(.......)..)))))............(((((((((((((((.((....)).)))).....)))))))))))......--.......).))----))))... ( -35.50)
>consensus
GGUGUUUAAAUGGCGAUUACAAUUCAAUUGCCGGACACUGCAGCGUCUCAUGCAAAGCCAAGUAUGGAAAUGGCGAUACUUUGCGUGAGGUAGACAAGUAAUAUACAAU____CGCCAAA
((((......((((((((.......))))))))............(((((((((((((((..........)))).....))))))))))).......................))))... (-31.02 = -29.70 +  -1.32)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,861,158 – 1,861,274
Length 116
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 77.25
Mean single sequence MFE -31.47
Consensus MFE -23.65
Energy contribution -22.10
Covariance contribution -1.55
Combinations/Pair 1.24
Mean z-score -1.80
Structure conservation index 0.75
SVM decision value 1.39
SVM RNA-class probability 0.948813
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 1861158 116 + 5224283/40-160
UUAGGCG----AUUGUAUAUUACUUGUCUACCUCACGCAAAGUAUCGCCAUUUCCAUACUUGGCUUUGCAUGAGACGCUGCAGUGUCCGGCAAUUGAAUUGUAAUCGCCAUGUAAACACC
...((((----((((((..(((.(((((....(((.(((((.....((((..........))))))))).)))(((((....))))).))))).)))..))))))))))........... ( -33.50)
>Banth.0 1723710 120 + 5227293/40-160
UUUGGCGAUGAAUUGUAUAUUACUUGUCUACCUCACGCAAAGUAUCGCCAUUUCCAUACUUGGCUUUGCAUGAGACGCUGCAGUGUCCGGCAAUUGAAUUGUAAUCGCCAUUUAAACACC
..(((((((.....((...(((.(((((....(((.(((((.....((((..........))))))))).)))(((((....))))).))))).)))))....))))))).......... ( -29.80)
>Bsubt.0 2748265 114 + 4214630/40-160
UUGGGCG----AUCUUUUAGAA--AGUCUACCCCAUGCAAAGUAUCGCCUUCCCAAUAGUAGGCUUUGCAUGGGACGUUGCGGAAUCUGGCAUUCUCAUCUUGCUUGCCAUUACAUCACC
..(((((----((....(((..--...))).((((((((((((...((..........))..))))))))))))..)))))......(((((..(.......)..)))))........)) ( -31.10)
>consensus
UUAGGCG____AUUGUAUAUUACUUGUCUACCUCACGCAAAGUAUCGCCAUUUCCAUACUUGGCUUUGCAUGAGACGCUGCAGUGUCCGGCAAUUGAAUUGUAAUCGCCAUUUAAACACC
...((((........................((((.(((((.....((((..........))))))))).))))..((((.......))))..............))))........... (-23.65 = -22.10 +  -1.55)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,861,158 – 1,861,273
Length 115
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 78.87
Mean single sequence MFE -38.13
Consensus MFE -26.61
Energy contribution -26.73
Covariance contribution 0.12
Combinations/Pair 1.19
Mean z-score -3.86
Structure conservation index 0.70
SVM decision value 3.79
SVM RNA-class probability 0.999618
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 1861158 115 + 5224283/80-200
CAGCGUCUCAUGCAAAGCCAAGUAUGGAAAUGGCGAUACUUUGCGUGAGGUAGACAAGUAAUAUACAAU----CGCCUAAAUGAGCUCGUAUCAUUUUUUAUAUU-UGGCUUUGCACCUU
..........(((((((((((((((((((..(((((((((((....)))))).....(((...)))..)----))))..(((((.......))))))))))))))-)))))))))).... ( -38.00)
>Banth.0 1723710 119 + 5227293/80-200
CAGCGUCUCAUGCAAAGCCAAGUAUGGAAAUGGCGAUACUUUGCGUGAGGUAGACAAGUAAUAUACAAUUCAUCGCCAAAAUGAGCUCGUAUCAUUUUUUGUAUU-UGGCUUUGCACCUU
..........((((((((((((((..(((.((((((((((((....)))))).....(((...)))......)))))).(((((.......))))))))..))))-)))))))))).... ( -39.40)
>Bsubt.0 2748265 107 + 4214630/80-200
CAACGUCCCAUGCAAAGCCUACUAUUGGGAAGGCGAUACUUUGCAUGGGGUAGACU--UUCUAAAAGAU----CGCCCAAGUAAGCU-------UUUCUGAUAUAGUGGCUUUGCACCUU
..........(((((((((.(((((.((((((((..(((((......((((.((((--(.....))).)----)))))))))).)))-------)))))...)))))))))))))).... ( -37.00)
>consensus
CAGCGUCUCAUGCAAAGCCAAGUAUGGAAAUGGCGAUACUUUGCGUGAGGUAGACAAGUAAUAUACAAU____CGCCAAAAUGAGCUCGUAUCAUUUUUUAUAUU_UGGCUUUGCACCUU
..........((((((((((((((((((((.((((.((((((....)))))).....(((...))).......))))...((((.......)))))))))))))).)))))))))).... (-26.61 = -26.73 +   0.12)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,861,158 – 1,861,273
Length 115
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 78.87
Mean single sequence MFE -32.28
Consensus MFE -20.19
Energy contribution -19.31
Covariance contribution -0.88
Combinations/Pair 1.17
Mean z-score -2.59
Structure conservation index 0.63
SVM decision value 1.86
SVM RNA-class probability 0.980253
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 1861158 115 + 5224283/80-200
AAGGUGCAAAGCCA-AAUAUAAAAAAUGAUACGAGCUCAUUUAGGCG----AUUGUAUAUUACUUGUCUACCUCACGCAAAGUAUCGCCAUUUCCAUACUUGGCUUUGCAUGAGACGCUG
...(((((((((((-(.(((..(((.((((((..((.....((((((----(.((.....)).)))))))......))...))))))...)))..))).))))))))))))......... ( -31.00)
>Banth.0 1723710 119 + 5227293/80-200
AAGGUGCAAAGCCA-AAUACAAAAAAUGAUACGAGCUCAUUUUGGCGAUGAAUUGUAUAUUACUUGUCUACCUCACGCAAAGUAUCGCCAUUUCCAUACUUGGCUUUGCAUGAGACGCUG
...(((((((((((-(......(((((((.......)))))))(((((((..((((....................))))..)))))))..........))))))))))))......... ( -34.55)
>Bsubt.0 2748265 107 + 4214630/80-200
AAGGUGCAAAGCCACUAUAUCAGAAA-------AGCUUACUUGGGCG----AUCUUUUAGAA--AGUCUACCCCAUGCAAAGUAUCGCCUUCCCAAUAGUAGGCUUUGCAUGGGACGUUG
...(((((((((((((((.......(-------((....)))(((((----(((((((((..--...)))........)))).))))))).....))))).))))))))))......... ( -31.30)
>consensus
AAGGUGCAAAGCCA_AAUAUAAAAAAUGAUACGAGCUCAUUUAGGCG____AUUGUAUAUUACUUGUCUACCUCACGCAAAGUAUCGCCAUUUCCAUACUUGGCUUUGCAUGAGACGCUG
..(((.....)))....................(((.....(((((...................))))).((((.(((((.....((((..........))))))))).))))..))). (-20.19 = -19.31 +  -0.88)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 17:21:31 2006