Locus 6886

Sequence ID 3R_DroMel_CAF1
Location 18,195,434 – 18,195,554
Length 120
Max. P 0.749751
window11179 window11180

overview

Window 9

Location 18,195,434 – 18,195,554
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.75
Mean single sequence MFE -44.23
Consensus MFE -37.37
Energy contribution -38.56
Covariance contribution 1.19
Combinations/Pair 1.09
Mean z-score -1.63
Structure conservation index 0.85
SVM decision value 0.47
SVM RNA-class probability 0.749751
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18195434 120 + 27905053
GAGAAAAUUCUGUCGGUCGCGGUCGGCAGAACUGACCUUCGGCGGUGCAGAUGUGCAGCGCUGCCGGUGUCGGCUUCGCUGCACACUUUUCUUCCGCCUGCUGCUUUCUCUCUGCCACUC
((((((.(((((((((......))))))))).........(((((...((((((((((((..((((....))))..)))))))))....))).)))))......)))))).......... ( -51.70)
>DroSec_CAF1 3540 120 + 1
GAGAAAAUUCUGUCGGUCGCGGUCGGCAGAACUGACCUUCGGCGGUGCAGCUGUGCAGCGCUGCCGGCGCCGACUUCGCUGCACACUUUUCUUCCGCCUGCUGCAUUCUCUCUGCCCUUC
(((((......(((((.(((((((((.....))))))..(((((((((.((...)).)))))))))))))))))...((.(((..(.........)..))).)).))))).......... ( -49.20)
>DroEre_CAF1 3743 112 + 1
AAGAAAAUUCUGUCGGUCGCGGUCGACAGAACUGACCUUCGGCGGUG--------CAGCGCUGCCGGCGUCGAAUUCGCUGCACAGGUUUCUUCCGCCUGCUGCUUUCUCUCUGCCACUC
.(((((.(((((((((......))))))))).((((..(((((((((--------...))))))))).))))........((((((((.......))))).))))))))........... ( -37.90)
>DroYak_CAF1 3638 112 + 1
GAGAAAAUUCUGUCGGUCGCGGUCGGCACAACUGACCUUCGGCGGUG--------CAGCGCUGCCGGCGUCGAAUUCGCUGCACACUUUUCUUCCGCCUGCUGCUUUCUCUCUGGCACUC
((((((......((((.(((((((((.....))))))..((((((((--------...)))))))))))))))....((.(((..(.........)..))).)))))))).......... ( -38.10)
>consensus
GAGAAAAUUCUGUCGGUCGCGGUCGGCAGAACUGACCUUCGGCGGUG________CAGCGCUGCCGGCGUCGAAUUCGCUGCACACUUUUCUUCCGCCUGCUGCUUUCUCUCUGCCACUC
((((((.....(((((.(((((((((.....))))))..(((((((((.........)))))))))))))))))...((.(((...............))).)))))))).......... (-37.37 = -38.56 +   1.19)

alignment

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secondary structure

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dotplot

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Window 0

Location 18,195,434 – 18,195,554
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.75
Mean single sequence MFE -44.65
Consensus MFE -34.33
Energy contribution -36.27
Covariance contribution 1.94
Combinations/Pair 1.09
Mean z-score -1.59
Structure conservation index 0.77
SVM decision value 0.17
SVM RNA-class probability 0.616441
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18195434 120 - 27905053
GAGUGGCAGAGAGAAAGCAGCAGGCGGAAGAAAAGUGUGCAGCGAAGCCGACACCGGCAGCGCUGCACAUCUGCACCGCCGAAGGUCAGUUCUGCCGACCGCGACCGACAGAAUUUUCUC
........(((((((.((.(..(((((((.....((((((((((..((((....))))..))))))))))(((.(((......)))))))))))))..).))...(....)..))))))) ( -50.10)
>DroSec_CAF1 3540 120 - 1
GAAGGGCAGAGAGAAUGCAGCAGGCGGAAGAAAAGUGUGCAGCGAAGUCGGCGCCGGCAGCGCUGCACAGCUGCACCGCCGAAGGUCAGUUCUGCCGACCGCGACCGACAGAAUUUUCUC
........((((((((((.(..((((((.......(((((((((..((((....))))..)))))))))((((.(((......)))))))))))))..).))...(....).)))))))) ( -49.60)
>DroEre_CAF1 3743 112 - 1
GAGUGGCAGAGAGAAAGCAGCAGGCGGAAGAAACCUGUGCAGCGAAUUCGACGCCGGCAGCGCUG--------CACCGCCGAAGGUCAGUUCUGUCGACCGCGACCGACAGAAUUUUCUU
...((((............((((((....)...)))))((((((...(((....)))...)))))--------)...)))).(((..((((((((((........))))))))))..))) ( -40.00)
>DroYak_CAF1 3638 112 - 1
GAGUGCCAGAGAGAAAGCAGCAGGCGGAAGAAAAGUGUGCAGCGAAUUCGACGCCGGCAGCGCUG--------CACCGCCGAAGGUCAGUUGUGCCGACCGCGACCGACAGAAUUUUCUC
........(((((((..(....(((((..........(((((((...(((....)))...)))))--------)))))))....(((.((((((.....)))))).))).)..))))))) ( -38.90)
>consensus
GAGUGGCAGAGAGAAAGCAGCAGGCGGAAGAAAAGUGUGCAGCGAAGUCGACGCCGGCAGCGCUG________CACCGCCGAAGGUCAGUUCUGCCGACCGCGACCGACAGAAUUUUCUC
........(((((((....((.(((((........(((((((((..((((....))))..)))))))))......)))))...((((.(.....).))))))...(....)..))))))) (-34.33 = -36.27 +   1.94)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:32:30 2006