Locus 1372

Sequence ID 3L_DroMel_CAF1
Location 3,990,181 – 3,990,331
Length 150
Max. P 0.841685
window2134 window2135

overview

Window 4

Location 3,990,181 – 3,990,300
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 85.97
Mean single sequence MFE -29.22
Consensus MFE -19.74
Energy contribution -20.73
Covariance contribution 1.00
Combinations/Pair 1.11
Mean z-score -2.26
Structure conservation index 0.68
SVM decision value 0.75
SVM RNA-class probability 0.841685
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3990181 119 + 23771897
-ACUGUUCCAAGGACUUUAAAAACCAUACUAAAAGGACAUGAAAACACAAUAACUUGUUUGCAGCGAAAACAGGAACUCCAUAGAAGGUCAAAUUAUUGAGUUCCUGGUUGAGCACAAAA
-..(((((...(..((((.............))))..).((.(((((........))))).)).......(((((((((.((((.........)))).)))))))))...)))))..... ( -22.52)
>DroSec_CAF1 62544 120 + 1
GACUGUUCCAAGGACUUUAAAGGCCAUGCUUAAAGGACAUGAAAACACAAUAACUUGUUUGCAGCGAAAACAGGAACUCCAUAGAAGGCCAACUUAUUGAGUUCCUGGGUGAGCAGAAAA
..(((((((..(..(((((..(((...))))))))..).((.(((((........))))).)).......(((((((((.....(((.....)))...))))))))).).)))))).... ( -31.70)
>DroEre_CAF1 64071 120 + 1
GACUUUUCCAAGGACUUUGCAAGCCUUGCUUAAAGGCCAAGAAAACACAAUAACUUGUUUGCAGCGAAAACAGGAACUGCGUUGAAUACAAACUUAUAGAGUUCCUGUGCGAGCACAAAA
.................((((((((((.....)))))((((............)))).)))))((....(((((((((.(..(((........)))..))))))))))....))...... ( -27.60)
>DroYak_CAF1 66702 120 + 1
GACUACUCCAAGGACUUUAAAAGCCUUGCUUAAAGGACAAGGGAACACAAUAACUUGUUUGCAGCGAAAACAGGAACUCCACACAAUACAAACUUAUGGAGUUCCUGUGCGAGCACAAGA
......(((..(..(((((..(((...))))))))..)...))).........(((((..((..((...((((((((((((...............)))))))))))).)).))))))). ( -35.06)
>consensus
GACUGUUCCAAGGACUUUAAAAGCCAUGCUUAAAGGACAAGAAAACACAAUAACUUGUUUGCAGCGAAAACAGGAACUCCAUAGAAGACAAACUUAUUGAGUUCCUGGGCGAGCACAAAA
...........(..(((((..(((...))))))))..)..(.(((((........))))).).((....((((((((((...................))))))))))....))...... (-19.74 = -20.73 +   1.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,990,220 – 3,990,331
Length 111
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 88.55
Mean single sequence MFE -27.17
Consensus MFE -21.56
Energy contribution -22.56
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.73
Structure conservation index 0.79
SVM decision value 0.48
SVM RNA-class probability 0.753402
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3990220 111 + 23771897
GAAAACACAAUAACUUGUUUGCAGCGAAAACAGGAACUCCAUAGAAGGUCAAAUUAUUGAGUUCCUGGUUGAGCACAAAACCUCCUGUUACUGGGCAUAGCAAAGUCGUAA
.........(..((((((((((.((..((.(((((((((.((((.........)))).))))))))).))..)).........((.......))))).))).))))..).. ( -25.60)
>DroSec_CAF1 62584 111 + 1
GAAAACACAAUAACUUGUUUGCAGCGAAAACAGGAACUCCAUAGAAGGCCAACUUAUUGAGUUCCUGGGUGAGCAGAAAACCUCCUGUUACUGGGCAUAGCAAAGUCGUAA
.........(..((((((((((........(((((((((.....(((.....)))...)))))))))(((((.(((........))))))))..))).))).))))..).. ( -28.80)
>DroEre_CAF1 64111 109 + 1
GAAAACACAAUAACUUGUUUGCAGCGAAAACAGGAACUGCGUUGAAUACAAACUUAUAGAGUUCCUGUGCGAGCACAAAAA--CCUGUUACUGGGCAUAGGAAAGUCGUAA
....((.((.((((..((((...((....(((((((((.(..(((........)))..))))))))))....))....)))--)..)))).))(((........))))).. ( -23.40)
>DroYak_CAF1 66742 109 + 1
GGGAACACAAUAACUUGUUUGCAGCGAAAACAGGAACUCCACACAAUACAAACUUAUGGAGUUCCUGUGCGAGCACAAGAA--CCUGUUACUGGGCAUAGCAAAGUCGUAA
.........(..((((((((((.((....((((((((((((...............))))))))))))....)).......--((.......))))).))).))))..).. ( -30.86)
>consensus
GAAAACACAAUAACUUGUUUGCAGCGAAAACAGGAACUCCAUAGAAGACAAACUUAUUGAGUUCCUGGGCGAGCACAAAAA__CCUGUUACUGGGCAUAGCAAAGUCGUAA
.........(..((((((((((.((....((((((((((...................))))))))))....)).........((.......))))).))).))))..).. (-21.56 = -22.56 +   1.00)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:05:52 2006