Locus 127

Sequence ID sp_mu.0
Location 353,096 – 353,190
Length 94
Max. P 0.998633
window811 window812 window813 window814

overview

Window 1

Location 353,096 – 353,187
Length 91
Sequences 2
Columns 96
Reading direction forward
Mean pairwise identity 76.04
Mean single sequence MFE -37.85
Consensus MFE -31.15
Energy contribution -32.90
Covariance contribution 1.75
Combinations/Pair 1.14
Mean z-score -4.57
Structure conservation index 0.82
SVM decision value 3.17
SVM RNA-class probability 0.998633
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 353096 91 - 2030921/120-240
AAAAUGAGUUGCGGGUCUAGCC---CGAAACUGGGUGGUACCGCGGAGAUCAUAGAAUGACAUUCGUCCCUGUC--AAUUGGCAGGGACGGUUUUU
...((((.((((((..(((.((---((....)))))))..))))))...))))..........(((((((((((--....)))))))))))..... ( -39.10)
>sp_ag.0 456464 93 + 2160267/120-240
AAAACGAGUUGCGGAUGUUAUCAUCCGAAUUUGGGUGGUACCGCGGAAAUCGUAACACGAAAUUCGUCCCUGUCAGAAUUGACAGGGA---UUUUU
...((((.((((((....(((((((((....)))))))))))))))...))))............(((((((((......))))))))---).... ( -36.60)
>consensus
AAAACGAGUUGCGGAUCUAACC___CGAAACUGGGUGGUACCGCGGAAAUCAUAAAACGAAAUUCGUCCCUGUC__AAUUGACAGGGA___UUUUU
...((((.((((((....(((((((((....)))))))))))))))...))))...........((((((((((......))))))))))...... (-31.15 = -32.90 +   1.75)

alignment

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secondary structure

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dotplot

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Window 2

Location 353,096 – 353,187
Length 91
Sequences 2
Columns 96
Reading direction reverse
Mean pairwise identity 76.04
Mean single sequence MFE -27.30
Consensus MFE -18.47
Energy contribution -19.47
Covariance contribution 1.00
Combinations/Pair 1.06
Mean z-score -3.14
Structure conservation index 0.68
SVM decision value 2.92
SVM RNA-class probability 0.997717
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 353096 91 - 2030921/120-240
AAAAACCGUCCCUGCCAAUU--GACAGGGACGAAUGUCAUUCUAUGAUCUCCGCGGUACCACCCAGUUUCG---GGCUAGACCCGCAACUCAUUUU
......((((((((.(....--).))))))))...(((((...)))))....((((..(..(((......)---))...)..)))).......... ( -26.30)
>sp_ag.0 456464 93 + 2160267/120-240
AAAAA---UCCCUGUCAAUUCUGACAGGGACGAAUUUCGUGUUACGAUUUCCGCGGUACCACCCAAAUUCGGAUGAUAACAUCCGCAACUCGUUUU
.....---(((((((((....)))))))))(((...(((.....))).....((((......))......(((((....)))))))...))).... ( -28.30)
>consensus
AAAAA___UCCCUGCCAAUU__GACAGGGACGAAUGUCAUGCUACGAUCUCCGCGGUACCACCCAAAUUCG___GACAACACCCGCAACUCAUUUU
......((((((((((......))))))))))....(((.....))).....((((..........................)))).......... (-18.47 = -19.47 +   1.00) 
# Strand winner: forward (1.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 353,096 – 353,190
Length 94
Sequences 2
Columns 99
Reading direction forward
Mean pairwise identity 75.76
Mean single sequence MFE -39.95
Consensus MFE -31.75
Energy contribution -34.25
Covariance contribution 2.50
Combinations/Pair 1.14
Mean z-score -4.82
Structure conservation index 0.79
SVM decision value 2.92
SVM RNA-class probability 0.997745
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 353096 94 - 2030921/124-244
AAAUGAGUUGCGGGUCUAGCC---CGAAACUGGGUGGUACCGCGGAGAUCAUAGAAUGACAUUCGUCCCUGUC--AAUUGGCAGGGACGGUUUUUGGUA
..((((.((((((..(((.((---((....)))))))..))))))...)))).......((.(((((((((((--....)))))))))))....))... ( -39.40)
>sp_ag.0 456464 96 + 2160267/124-244
AAACGAGUUGCGGAUGUUAUCAUCCGAAUUUGGGUGGUACCGCGGAAAUCGUAACACGAAAUUCGUCCCUGUCAGAAUUGACAGGGA---UUUUUUGUA
..((((.((((((....(((((((((....)))))))))))))))...))))...((((((...(((((((((......))))))))---).)))))). ( -40.50)
>consensus
AAACGAGUUGCGGAUCUAACC___CGAAACUGGGUGGUACCGCGGAAAUCAUAAAACGAAAUUCGUCCCUGUC__AAUUGACAGGGA___UUUUUGGUA
..((((.((((((....(((((((((....)))))))))))))))...))))...((((((..((((((((((......))))))))))...)))))). (-31.75 = -34.25 +   2.50)

alignment

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secondary structure

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dotplot

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Window 4

Location 353,096 – 353,190
Length 94
Sequences 2
Columns 99
Reading direction reverse
Mean pairwise identity 75.76
Mean single sequence MFE -28.30
Consensus MFE -18.47
Energy contribution -19.47
Covariance contribution 1.00
Combinations/Pair 1.06
Mean z-score -3.45
Structure conservation index 0.65
SVM decision value 2.99
SVM RNA-class probability 0.998034
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 353096 94 - 2030921/124-244
UACCAAAAACCGUCCCUGCCAAUU--GACAGGGACGAAUGUCAUUCUAUGAUCUCCGCGGUACCACCCAGUUUCG---GGCUAGACCCGCAACUCAUUU
((((......((((((((.(....--).))))))))...(((((...)))))......))))......((((.((---((.....)))).))))..... ( -28.30)
>sp_ag.0 456464 96 + 2160267/124-244
UACAAAAAA---UCCCUGUCAAUUCUGACAGGGACGAAUUUCGUGUUACGAUUUCCGCGGUACCACCCAAAUUCGGAUGAUAACAUCCGCAACUCGUUU
.........---(((((((((....)))))))))(((...(((.....))).....((((......))......(((((....)))))))...)))... ( -28.30)
>consensus
UACAAAAAA___UCCCUGCCAAUU__GACAGGGACGAAUGUCAUGCUACGAUCUCCGCGGUACCACCCAAAUUCG___GACAACACCCGCAACUCAUUU
..........((((((((((......))))))))))....(((.....))).....((((..........................))))......... (-18.47 = -19.47 +   1.00) 
# Strand winner: forward (1.00)

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 19:01:56 2006