Locus 3976

Sequence ID X_DroMel_CAF1
Location 10,538,144 – 10,538,253
Length 109
Max. P 0.970225
window6537 window6538

overview

Window 7

Location 10,538,144 – 10,538,253
Length 109
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 92.46
Mean single sequence MFE -27.61
Consensus MFE -21.60
Energy contribution -22.98
Covariance contribution 1.37
Combinations/Pair 1.04
Mean z-score -2.32
Structure conservation index 0.78
SVM decision value 0.72
SVM RNA-class probability 0.832488
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10538144 109 + 22224390
CAUGUGCUUCAACUGAAGCUGUAGCUGAGUUCUCGUUUCUGCAGCUGCAGCACCACUGAUAAUGGACUGACAGCGAAAGCAAAACCAACCACCCACUCAAC---CAAACCAA
....(((((...(((..((((((((((((.........)).)))))))))).(((.......))).....)))...)))))....................---........ ( -27.20)
>DroSec_CAF1 64588 109 + 1
CAUGUGCUUCAGCUGAAGCUGAAGCUGAGUUCUCGUUUCUGCAGCUGCAGCACCACUGAUAAUGGACUGACAGUGAAAGCAAAACCAACCACCCACUCAAC---CAAACCAA
.....((((((((....))))))))(((((....((((.(((.(((((((..(((.......))).))).))))....))))))).........)))))..---........ ( -28.62)
>DroSim_CAF1 68402 109 + 1
CAUGUGCUUCAGCUGAAGCUGAAGCUGAGUUCUCGUUUCUGCAGCUGCAGCACCACUGAUAAUGGACUGACAGCGAAAGCAAAACCAACCACCCACUCAAC---CAAACCAA
.....((((((((....))))))))(((((....((((.(((.(((((((..(((.......))).))).))))....))))))).........)))))..---........ ( -30.22)
>DroYak_CAF1 66999 105 + 1
CAUGUGCUUCAGCUGAA------GCUGAGUUCCCGUUUCUGCAGCUGCAGCACCACUGAUAAUGGACUGACAGCGAAAGCAAAACCAACCACCCACCC-ACAAACCACCCAA
..((((.((((((....------)))))).....((((.(((.(((((((..(((.......))).))).))))....)))))))............)-))).......... ( -24.40)
>consensus
CAUGUGCUUCAGCUGAAGCUGAAGCUGAGUUCUCGUUUCUGCAGCUGCAGCACCACUGAUAAUGGACUGACAGCGAAAGCAAAACCAACCACCCACUCAAC___CAAACCAA
....(((((..((((..((((.(((((((.........)).))))).)))).(((.......))).....))))..)))))............................... (-21.60 = -22.98 +   1.37)

alignment

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secondary structure

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dotplot

Postscript

Window 8

Location 10,538,144 – 10,538,253
Length 109
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 92.46
Mean single sequence MFE -38.90
Consensus MFE -34.44
Energy contribution -36.12
Covariance contribution 1.69
Combinations/Pair 1.06
Mean z-score -2.31
Structure conservation index 0.89
SVM decision value 1.65
SVM RNA-class probability 0.970225
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10538144 109 - 22224390
UUGGUUUG---GUUGAGUGGGUGGUUGGUUUUGCUUUCGCUGUCAGUCCAUUAUCAGUGGUGCUGCAGCUGCAGAAACGAGAACUCAGCUACAGCUUCAGUUGAAGCACAUG
......((---(((((((...((.....((((((....((((.((((((((.....)))).)))))))).)))))).))...)))))))))..(((((....)))))..... ( -38.90)
>DroSec_CAF1 64588 109 - 1
UUGGUUUG---GUUGAGUGGGUGGUUGGUUUUGCUUUCACUGUCAGUCCAUUAUCAGUGGUGCUGCAGCUGCAGAAACGAGAACUCAGCUUCAGCUUCAGCUGAAGCACAUG
........---......(((((..(((.((((((.....(((.((((((((.....)))).)))))))..)))))).)))..)))))((((((((....))))))))..... ( -38.70)
>DroSim_CAF1 68402 109 - 1
UUGGUUUG---GUUGAGUGGGUGGUUGGUUUUGCUUUCGCUGUCAGUCCAUUAUCAGUGGUGCUGCAGCUGCAGAAACGAGAACUCAGCUUCAGCUUCAGCUGAAGCACAUG
........---......(((((..(((.((((((....((((.((((((((.....)))).)))))))).)))))).)))..)))))((((((((....))))))))..... ( -42.50)
>DroYak_CAF1 66999 105 - 1
UUGGGUGGUUUGU-GGGUGGGUGGUUGGUUUUGCUUUCGCUGUCAGUCCAUUAUCAGUGGUGCUGCAGCUGCAGAAACGGGAACUCAGC------UUCAGCUGAAGCACAUG
....(((......-...(((((..(((.((((((....((((.((((((((.....)))).)))))))).)))))).)))..)))))((------(((....))))).))). ( -35.50)
>consensus
UUGGUUUG___GUUGAGUGGGUGGUUGGUUUUGCUUUCGCUGUCAGUCCAUUAUCAGUGGUGCUGCAGCUGCAGAAACGAGAACUCAGCUUCAGCUUCAGCUGAAGCACAUG
.................(((((..(((.((((((....((((.((((((((.....)))).)))))))).)))))).)))..)))))((((((((....))))))))..... (-34.44 = -36.12 +   1.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:21 2006