Locus 9666

Sequence ID 3R_DroMel_CAF1
Location 25,558,207 – 25,558,339
Length 132
Max. P 0.975495
window15447 window15448

overview

Window 7

Location 25,558,207 – 25,558,300
Length 93
Sequences 4
Columns 93
Reading direction forward
Mean pairwise identity 92.83
Mean single sequence MFE -35.70
Consensus MFE -33.00
Energy contribution -33.62
Covariance contribution 0.62
Combinations/Pair 1.04
Mean z-score -2.19
Structure conservation index 0.92
SVM decision value 1.75
SVM RNA-class probability 0.975495
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25558207 93 + 27905053
CCACAACUUCAGGACGCGCUCCACAGGCACAGGGGCUGCAGCUGGAAAGCCAGGAGCAGCAGUCACUUCUGCAGCAGCAACCUCUGCAGGAGC
............((((((((((.(((.(.....).)))..(((....)))..))))).)).))).(((((((((.((....))))))))))). ( -35.60)
>DroSec_CAF1 41858 93 + 1
CCACAACUUCAGGACGCGCUCCACAGGCACAGGAGCUGCAGCUGGAAAGCCAGGAGCAGCAGUCCCUUCUGCAGCAGCAACCUCUGCAGGAGC
...........(((((((((((.........)))))(((..((((....))))..))))).))))(((((((((.((....))))))))))). ( -37.30)
>DroSim_CAF1 42838 93 + 1
CCACAACUUCAGGACGCGCUCCACAGGCACAGGAGCUGCAGCUGGAAAGCCAGGAGCAGCAGUCCCUUCUGCAGCAGCAACCUCUGCAGGAGC
...........(((((((((((.........)))))(((..((((....))))..))))).))))(((((((((.((....))))))))))). ( -37.30)
>DroYak_CAF1 45696 93 + 1
GAACAACUUCAGGUCGCGCUCUACGGGCACAGGAGCUGCAACUGGAAAGCCAGGAGCAGCAGGCACUUCUGCAGCAGUUACAUCUGCAGGAUC
...........(((((((((.....)))......(((((..((((....))))..)))))..))....((((((.(......))))))))))) ( -32.60)
>consensus
CCACAACUUCAGGACGCGCUCCACAGGCACAGGAGCUGCAGCUGGAAAGCCAGGAGCAGCAGUCACUUCUGCAGCAGCAACCUCUGCAGGAGC
...........(((((.(((.....))).)....(((((..((((....))))..))))).))))(((((((((.((....))))))))))). (-33.00 = -33.62 +   0.62)

alignment

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secondary structure

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dotplot

Postscript

Window 8

Location 25,558,238 – 25,558,339
Length 101
Sequences 4
Columns 101
Reading direction forward
Mean pairwise identity 94.88
Mean single sequence MFE -39.70
Consensus MFE -36.33
Energy contribution -37.07
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -2.44
Structure conservation index 0.91
SVM decision value 1.72
SVM RNA-class probability 0.973838
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25558238 101 + 27905053
GGGGCUGCAGCUGGAAAGCCAGGAGCAGCAGUCACUUCUGCAGCAGCAACCUCUGCAGGAGCCUCAUCUGCAGCAGCAUCGAACGAGAACAACGAGCUGCC
((((((((..((((....))))..))))).....(((((((((.((....))))))))))).))).......(((((.(((...........)))))))). ( -40.20)
>DroSec_CAF1 41889 101 + 1
GGAGCUGCAGCUGGAAAGCCAGGAGCAGCAGUCCCUUCUGCAGCAGCAACCUCUGCAGGAGCCGCAUCUGCAGCAGCAUCGAACGAGAACAACGAGCUGCC
((.(((((..((((....))))..))))).....(((((((((.((....)))))))))))))((....)).(((((.(((...........)))))))). ( -41.20)
>DroSim_CAF1 42869 101 + 1
GGAGCUGCAGCUGGAAAGCCAGGAGCAGCAGUCCCUUCUGCAGCAGCAACCUCUGCAGGAGCCGCAUCUGCAGCAGCAUCGAACGAGAACAACGAGCUGCC
((.(((((..((((....))))..))))).....(((((((((.((....)))))))))))))((....)).(((((.(((...........)))))))). ( -41.20)
>DroYak_CAF1 45727 101 + 1
GGAGCUGCAACUGGAAAGCCAGGAGCAGCAGGCACUUCUGCAGCAGUUACAUCUGCAGGAUCCGCAUCUGCAUCAGCAUCGAACGAGAACAACGAGCUGCC
((((((((..((((....))))..)))))......((((((((.(......))))))))))))((....))..((((.(((...........))))))).. ( -36.20)
>consensus
GGAGCUGCAGCUGGAAAGCCAGGAGCAGCAGUCACUUCUGCAGCAGCAACCUCUGCAGGAGCCGCAUCUGCAGCAGCAUCGAACGAGAACAACGAGCUGCC
((.(((((..((((....))))..))))).....(((((((((.((....))))))))))))).........(((((.(((...........)))))))). (-36.33 = -37.07 +   0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:39:27 2006