Locus 4783

Sequence ID X_DroMel_CAF1
Location 12,425,241 – 12,425,399
Length 158
Max. P 0.918810
window7827 window7828

overview

Window 7

Location 12,425,241 – 12,425,359
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 86.31
Mean single sequence MFE -40.43
Consensus MFE -33.10
Energy contribution -33.67
Covariance contribution 0.56
Combinations/Pair 1.11
Mean z-score -2.60
Structure conservation index 0.82
SVM decision value 1.12
SVM RNA-class probability 0.918810
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12425241 118 - 22224390
GUUAAAGUAAAAGUUCAAUGGGUUAAGCAGGUGAUUAAAGGCACAUUAACCCCUAAUGGAGCUUGGACUGCACUUAACGCACGGCUCACAUGU--GACCACUGUGCGCGCGUGCAAGUGU
.....(((..((((((...(((((((....(((........))).)))))))......))))))..)))((((((...(((((((.((((.((--....)))))).)).))))))))))) ( -41.20)
>DroSim_CAF1 4108 120 - 1
GCUAAAGUAAAAGUUCAAGGGGUUAAGCAGGUGAUUAAAGGCACAUUAACCCCUAAUGGAGCUUGGACUGCACUUAACGCACGGCUCACAUGUGUGCCCACUGUGCGCGCGUGCAAGUGU
.....(((..((((((.(((((((((....(((........))).)))))))))....))))))..)))((((((...(((((((.((((.(((....))))))).)).))))))))))) ( -48.40)
>DroYak_CAF1 4253 116 - 1
--UAAAGUAAAUGCCUAAUGGGUUAAGCAGGUGAUCAAAAGCACAUUAACCUCCAUUGUUGCAUAGGCUGCAAUUAGCGCACCGCUCAAAUGU--GCCCACUGUGCGCGCGUGCAAGUGU
--...(((..((((.(((((((((((....(((........))).)))))..))))))..))))..)))(((....(((((((((......))--)......))))))...)))...... ( -31.70)
>consensus
G_UAAAGUAAAAGUUCAAUGGGUUAAGCAGGUGAUUAAAGGCACAUUAACCCCUAAUGGAGCUUGGACUGCACUUAACGCACGGCUCACAUGU__GCCCACUGUGCGCGCGUGCAAGUGU
.....(((..((((((...(((((((....(((........))).)))))))......))))))..)))((((((...(((((((.((((.((......)))))).)).))))))))))) (-33.10 = -33.67 +   0.56)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 8

Location 12,425,279 – 12,425,399
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 75.84
Mean single sequence MFE -28.67
Consensus MFE -20.09
Energy contribution -20.43
Covariance contribution 0.34
Combinations/Pair 1.19
Mean z-score -1.51
Structure conservation index 0.70
SVM decision value 0.66
SVM RNA-class probability 0.815491
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12425279 120 - 22224390
AAUCUCUUCAAAGCAAAAUCACAGCACUGUGAUAUGGUUGGUUAAAGUAAAAGUUCAAUGGGUUAAGCAGGUGAUUAAAGGCACAUUAACCCCUAAUGGAGCUUGGACUGCACUUAACGC
............((...((((((....))))))...(((((....(((..((((((...(((((((....(((........))).)))))))......))))))..)))....))))))) ( -30.10)
>DroSim_CAF1 4148 116 - 1
AUUCUCUUCACAUCAAAAUCACAGCACUGUGA----GUUGGCUAAAGUAAAAGUUCAAGGGGUUAAGCAGGUGAUUAAAGGCACAUUAACCCCUAAUGGAGCUUGGACUGCACUUAACGC
..................(((((....)))))----(((((....(((..((((((.(((((((((....(((........))).)))))))))....))))))..)))....))))).. ( -33.60)
>DroYak_CAF1 4291 105 - 1
AGUUUUCUUACUGCAAAUUCG-----CUGUGA----------UAAAGUAAAUGCCUAAUGGGUUAAGCAGGUGAUCAAAAGCACAUUAACCUCCAUUGUUGCAUAGGCUGCAAUUAGCGC
...................((-----(((...----------...(((..((((.(((((((((((....(((........))).)))))..))))))..))))..))).....))))). ( -22.30)
>consensus
AAUCUCUUCACAGCAAAAUCACAGCACUGUGA____GUUGG_UAAAGUAAAAGUUCAAUGGGUUAAGCAGGUGAUUAAAGGCACAUUAACCCCUAAUGGAGCUUGGACUGCACUUAACGC
............((....(((((....))))).............(((..((((((...(((((((....(((........))).)))))))......))))))..)))))......... (-20.09 = -20.43 +   0.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:33:02 2006