Locus 10013

Sequence ID 3R_DroMel_CAF1
Location 26,798,134 – 26,798,230
Length 96
Max. P 0.938672
window15959 window15960

overview

Window 9

Location 26,798,134 – 26,798,230
Length 96
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 84.89
Mean single sequence MFE -27.69
Consensus MFE -19.01
Energy contribution -19.21
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.64
Structure conservation index 0.69
SVM decision value 1.29
SVM RNA-class probability 0.938672
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26798134 96 + 27905053
GCCCCCACCACCGCCUACUCUUCCGCCCACCAGCACUUGACGCUCUUCGAAAUGCGAAACAAAUAAACAAAGGGCAGCUAAAAGGCGGUGGCGCCU
.....(.(((((((((........((((...(((.......))).((((.....)))).............)))).......))))))))).)... ( -29.16)
>DroSec_CAF1 6905 96 + 1
GCCCCCGCCACCGCCUACUCUUCCGCCCACCAGCACUUGACGCUCUUCAAAAUGCGAAACAAAUAAACAAAGGGCAGCUAAAAGGCGGUGGCGCCU
.....(((((((((((........((((..(((...))).(((..........)))...............)))).......)))))))))))... ( -32.56)
>DroSim_CAF1 6891 96 + 1
GCCCCCGCCACCGCCUACUCUUCCGCCCACCAGCACUUGACGCUCUUCGAAAUGCGAAACAAAUAAACAAAGGGCAGCUAAAAGGCGGUGGCGCCU
.....(((((((((((........((((...(((.......))).((((.....)))).............)))).......)))))))))))... ( -34.56)
>DroEre_CAF1 9012 89 + 1
GCCUACA---CAUCCAAC----CAGCCCACCAGCACUUGACGCUCUCCGCAAUGCGAAACAAAUAAACAAAGGGCAGCUAAAAGGCGGUGGCGCCU
.......---........----..(((((((.((.(((...(((.(((.......................))).)))...)))))))))).)).. ( -21.10)
>DroYak_CAF1 9198 74 + 1
----------------------ACGCCCACCAGCACUUGACGCUCUUCGGAAUGCGAAACAAAUAAACAAAGGGCAGCUAAAAGGCGGUGGCGCCU
----------------------..(((((((.((.(((..(((((....))..))).............))).)).(((....)))))))).)).. ( -21.06)
>consensus
GCCCCCACCACCGCCUACUCUUCCGCCCACCAGCACUUGACGCUCUUCGAAAUGCGAAACAAAUAAACAAAGGGCAGCUAAAAGGCGGUGGCGCCU
........................(((((((..........((((((......................)))))).(((....)))))))).)).. (-19.01 = -19.21 +   0.20)

alignment

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secondary structure

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dotplot

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Window 0

Location 26,798,134 – 26,798,230
Length 96
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 84.89
Mean single sequence MFE -35.48
Consensus MFE -26.56
Energy contribution -30.20
Covariance contribution 3.64
Combinations/Pair 1.04
Mean z-score -2.01
Structure conservation index 0.75
SVM decision value 0.77
SVM RNA-class probability 0.846589
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26798134 96 - 27905053
AGGCGCCACCGCCUUUUAGCUGCCCUUUGUUUAUUUGUUUCGCAUUUCGAAGAGCGUCAAGUGCUGGUGGGCGGAAGAGUAGGCGGUGGUGGGGGC
...((((((((((((((..((((((......((((((...(((..........))).)))))).....))))))..))).)))))))))))..... ( -42.10)
>DroSec_CAF1 6905 96 - 1
AGGCGCCACCGCCUUUUAGCUGCCCUUUGUUUAUUUGUUUCGCAUUUUGAAGAGCGUCAAGUGCUGGUGGGCGGAAGAGUAGGCGGUGGCGGGGGC
...((((((((((((((..((((((......((((((...(((..........))).)))))).....))))))..))).)))))))))))..... ( -44.00)
>DroSim_CAF1 6891 96 - 1
AGGCGCCACCGCCUUUUAGCUGCCCUUUGUUUAUUUGUUUCGCAUUUCGAAGAGCGUCAAGUGCUGGUGGGCGGAAGAGUAGGCGGUGGCGGGGGC
...((((((((((((((..((((((......((((((...(((..........))).)))))).....))))))..))).)))))))))))..... ( -44.00)
>DroEre_CAF1 9012 89 - 1
AGGCGCCACCGCCUUUUAGCUGCCCUUUGUUUAUUUGUUUCGCAUUGCGGAGAGCGUCAAGUGCUGGUGGGCUG----GUUGGAUG---UGUAGGC
....(((..(((..(((((((((((............((((((...))))))((((.....))))...)))).)----)))))).)---))..))) ( -26.60)
>DroYak_CAF1 9198 74 - 1
AGGCGCCACCGCCUUUUAGCUGCCCUUUGUUUAUUUGUUUCGCAUUCCGAAGAGCGUCAAGUGCUGGUGGGCGU----------------------
..((.((((((((((...(((...(((((......((.....))...))))))))...))).)).)))))))..---------------------- ( -20.70)
>consensus
AGGCGCCACCGCCUUUUAGCUGCCCUUUGUUUAUUUGUUUCGCAUUUCGAAGAGCGUCAAGUGCUGGUGGGCGGAAGAGUAGGCGGUGGCGGGGGC
...(((((((((((.....((((((......((((((...(((..........))).)))))).....))))))......)))))))))))..... (-26.56 = -30.20 +   3.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:47:03 2006