Locus 6122

Sequence ID 2R_DroMel_CAF1
Location 19,254,790 – 19,254,943
Length 153
Max. P 0.692230
window9804 window9805

overview

Window 4

Location 19,254,790 – 19,254,903
Length 113
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 86.87
Mean single sequence MFE -26.17
Consensus MFE -18.25
Energy contribution -19.50
Covariance contribution 1.25
Combinations/Pair 1.12
Mean z-score -1.80
Structure conservation index 0.70
SVM decision value 0.33
SVM RNA-class probability 0.692230
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19254790 113 + 20766785
UUAUACAUCCUUCAAAAUCUCUAUGAACCAAACACGCAUCUGUUUUGCGGUUAUUUAAAUAAGGCCGAGUGCUAAAGCACUGCUAGAAUGGCUGAAUAGCUAUUCAGUAGAAC
...................(((((......(((.((((.......)))))))..........(((..(((((....)))))))).((((((((....)))))))).))))).. ( -27.40)
>DroSec_CAF1 45471 113 + 1
UCAUACAUCCUUCAAAAUCUCUUUGAGCCAAACACGCAUCUGUUUUGCGGUUAUUUAAAUAAGGCCGAGUGCUAAAGCACUGAUAGAAUGGCUGAAUAGCUAUUCAGUAGAAC
((.((((((..(((((.....)))))(((.....((((.......)))).((((....)))))))..(((((....)))))))).((((((((....)))))))).))))).. ( -27.70)
>DroSim_CAF1 44509 113 + 1
UCAUACAUCCUUCUAAAUCUCUUUGAGCCAAACACGCAUCUGUUUUGCGGUUAUUUAAAUAAGGCCGAGUGCUAAGGCACUGAUAGAAUGGCUGAAUAGCUAUUCAGCAGAAC
........(.(((((........((.(((.....((((.......)))).((((....)))))))))(((((....)))))..))))).)(((((((....)))))))..... ( -27.00)
>DroYak_CAF1 45773 108 + 1
UGGAACAUCCUUCAAAAUAUCUAAGUGCCACAUACGCAUCUGUU-----GCUAUGUAAAUAAGGCAAAGUGUUAAAGCACUGAAAGAAUGGCUGAAUAGCUAUAGAAAAGAAC
.((.....))(((......(((...(((((((((.(((.....)-----)))))))......)))).(((((....)))))...)))((((((....)))))).)))...... ( -22.60)
>consensus
UCAUACAUCCUUCAAAAUCUCUAUGAGCCAAACACGCAUCUGUUUUGCGGUUAUUUAAAUAAGGCCGAGUGCUAAAGCACUGAUAGAAUGGCUGAAUAGCUAUUCAGUAGAAC
.........................................(((((((((((..........)))).(((((....)))))....((((((((....)))))))).))))))) (-18.25 = -19.50 +   1.25)

alignment

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secondary structure

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dotplot

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Window 5

Location 19,254,823 – 19,254,943
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.83
Mean single sequence MFE -31.35
Consensus MFE -25.38
Energy contribution -26.62
Covariance contribution 1.25
Combinations/Pair 1.10
Mean z-score -1.48
Structure conservation index 0.81
SVM decision value 0.06
SVM RNA-class probability 0.561712
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19254823 120 + 20766785
ACGCAUCUGUUUUGCGGUUAUUUAAAUAAGGCCGAGUGCUAAAGCACUGCUAGAAUGGCUGAAUAGCUAUUCAGUAGAACUCAAAACAAUACCCGAGCUGCCUGUGUUUGCACACUUGCU
..(((..((((((..((((..........))))((((((....)).(((((.((((((((....))))))))))))).))))))))))..............((((....))))..))). ( -32.40)
>DroSec_CAF1 45504 120 + 1
ACGCAUCUGUUUUGCGGUUAUUUAAAUAAGGCCGAGUGCUAAAGCACUGAUAGAAUGGCUGAAUAGCUAUUCAGUAGAACUGAAAACAAUACCCGAGCUGCCUGUGUUUGCACACUUGCU
..(((((.(((((((((((..........)))).(((((....)))))....((((((((....)))))))).))))))).))...................((((....))))..))). ( -32.10)
>DroSim_CAF1 44542 120 + 1
ACGCAUCUGUUUUGCGGUUAUUUAAAUAAGGCCGAGUGCUAAGGCACUGAUAGAAUGGCUGAAUAGCUAUUCAGCAGAACUGAAAACAAUACCCGAGCUGCCUGUGUUUGCACACUUGCU
..(((((.(((((((((((..........)))).(((((....)))))....((((((((....)))))))).))))))).))...................((((....))))..))). ( -34.20)
>DroYak_CAF1 45806 115 + 1
ACGCAUCUGUU-----GCUAUGUAAAUAAGGCAAAGUGUUAAAGCACUGAAAGAAUGGCUGAAUAGCUAUAGAAAAGAACACAAAACAAUAUCCGAGUUGCCUGUGUUUGCACACUUGCU
..(((..(((.-----.....((((((((((((((((((....)))))......((((((....))))))...........................)))))).))))))))))..))). ( -26.70)
>consensus
ACGCAUCUGUUUUGCGGUUAUUUAAAUAAGGCCGAGUGCUAAAGCACUGAUAGAAUGGCUGAAUAGCUAUUCAGUAGAACUCAAAACAAUACCCGAGCUGCCUGUGUUUGCACACUUGCU
..(((...(((((((((((..........)))).(((((....)))))....((((((((....)))))))).)))))))......................((((....))))..))). (-25.38 = -26.62 +   1.25)

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 12:03:20 2006