Locus 1136

Sequence ID X_DroMel_CAF1
Location 3,366,969 – 3,367,110
Length 141
Max. P 0.908036
window1825 window1826

overview

Window 5

Location 3,366,969 – 3,367,087
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 87.78
Mean single sequence MFE -44.05
Consensus MFE -33.71
Energy contribution -35.27
Covariance contribution 1.56
Combinations/Pair 1.06
Mean z-score -2.63
Structure conservation index 0.77
SVM decision value 0.73
SVM RNA-class probability 0.834076
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3366969 118 + 22224390
GCCGAACAAACAAACUCUCUAAGCUAGCCGAUGCAAUUCGAAGCGAGCAGAGCGCAGGAAAACCGUUCGUCACAUCUGGCGCCCAACGUGGGCGUUAGCAUGGAAGAGCUUUUCCUGU--
................((((..(((.(((((......)))..)).))))))).(((((((((..((((.((.((((((((((((.....))))))))).))))).)))))))))))))-- ( -43.70)
>DroSec_CAF1 14326 120 + 1
GACGAACGAACAAACUGGCUGAGCUAGUCGUUGCAAUUCGAAGCGAGCAGAAGGCUGGAAAACAGUUCGUCACAGCUGGCGCCCAACGUGGGCGUUAGCAGAGCAGAGCCUUUCCUGCAA
(((((((.......(..(((...((..(((((.........)))))..))..)))..)......)))))))...((((((((((.....))))))))))...((((........)))).. ( -49.22)
>DroSim_CAF1 14300 119 + 1
GACGAACAAACAAACUGGCUGAGCUAGUCGUUGCAAUUCGAAGCGAGCAGAAGGCAGGAAAACAGUUUGUCACAGCUGGCGCCCAACGUGGGCGG-AGCAGAGCAGAGCCUUUCCUGCAA
(((((((.......(((.((..(((..(((........)))....)))...)).))).......)))))))...(((..(((((.....))))).-)))...((((........)))).. ( -39.24)
>consensus
GACGAACAAACAAACUGGCUGAGCUAGUCGUUGCAAUUCGAAGCGAGCAGAAGGCAGGAAAACAGUUCGUCACAGCUGGCGCCCAACGUGGGCGUUAGCAGAGCAGAGCCUUUCCUGCAA
..............(((.((..(((..(((........)))))).)))))...((((((((...((((......((((((((((.....))))))))))......)))).)))))))).. (-33.71 = -35.27 +   1.56)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,367,009 – 3,367,110
Length 101
Sequences 3
Columns 107
Reading direction forward
Mean pairwise identity 87.54
Mean single sequence MFE -37.00
Consensus MFE -31.01
Energy contribution -32.57
Covariance contribution 1.56
Combinations/Pair 1.08
Mean z-score -2.55
Structure conservation index 0.84
SVM decision value 1.06
SVM RNA-class probability 0.908036
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3367009 101 + 22224390
AAGCGAGCAGAGCGCAGGAAAACCGUUCGUCACAUCUGGCGCCCAACGUGGGCGUUAGCAUGGAAGAGCUUUUCCUGU------AGCAACAUGAGAAGGCCGACAAA
..(((.((...(((((((((((..((((.((.((((((((((((.....))))))))).))))).)))))))))))))------.))..(....)...)))).)... ( -38.90)
>DroSec_CAF1 14366 107 + 1
AAGCGAGCAGAAGGCUGGAAAACAGUUCGUCACAGCUGGCGCCCAACGUGGGCGUUAGCAGAGCAGAGCCUUUCCUGCAACAUGAGCAACAUGAGAAGCCCGACAAA
..((..(((((((((((.....).((((......((((((((((.....)))))))))).))))..))))))..))))..((((.....))))....))........ ( -38.50)
>DroSim_CAF1 14340 106 + 1
AAGCGAGCAGAAGGCAGGAAAACAGUUUGUCACAGCUGGCGCCCAACGUGGGCGG-AGCAGAGCAGAGCCUUUCCUGCAACAUGAGCAACAUGAGAAGCCCGACAAA
..(((.((.....((((((((....(((((....(((..(((((.....))))).-)))...)))))...))))))))..((((.....))))....)).)).)... ( -33.60)
>consensus
AAGCGAGCAGAAGGCAGGAAAACAGUUCGUCACAGCUGGCGCCCAACGUGGGCGUUAGCAGAGCAGAGCCUUUCCUGCAACAUGAGCAACAUGAGAAGCCCGACAAA
..((...((....((((((((...((((......((((((((((.....))))))))))......)))).))))))))....)).)).................... (-31.01 = -32.57 +   1.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:13 2006