Locus 7274

Sequence ID X_DroMel_CAF1
Location 18,117,724 – 18,117,881
Length 157
Max. P 0.787340
window11912 window11913

overview

Window 2

Location 18,117,724 – 18,117,844
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.92
Mean single sequence MFE -38.62
Consensus MFE -31.52
Energy contribution -33.24
Covariance contribution 1.72
Combinations/Pair 1.13
Mean z-score -1.58
Structure conservation index 0.82
SVM decision value 0.58
SVM RNA-class probability 0.787340
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18117724 120 + 22224390
CACCACCGCCCGACGACCUGAUGGUCCUGGAGCAGCACGCCCUCUUCACCAAACUGAAGUUUGUGCAGUAUCUCAAGAGUAUCCGCAAGAUACUCGCGAACCAGCGUAAGAGUCUGUGCA
.......(((((..((((....)))).))).)).(((((..(((((.((....(((..(((((((.(((((((...(......)...))))))))))))))))).)))))))..))))). ( -40.60)
>DroSec_CAF1 406 120 + 1
CGCCACCGCCCGACGACCUGUUGGUUCUGGAGCACCACGCCCUCUUCACCAAACUGAAGUAUGUGCAGUAUCUCAAGAGUAUCCGCAAGAUACUCGCAAACCAGCGGAAGAGUCUGUGCA
.......(((.(((...(((((((((.(((((.((..(((...(((((......)))))...)))..))..)))..((((((.(....))))))).)))))))))))....))).).)). ( -37.20)
>DroSim_CAF1 406 120 + 1
CACCACCGCCCGACGACCUGAUGGUCCUGGAGCAGCACGCCCUCUUCACCAAACUGAAGUUUGUGCAGUAUCUCAAGAGUAUCCGCAAGAUACUCGCGAACCAGCGGAAGAGUCUGUGCA
.......(((((..((((....)))).))).)).(((((..((((((......(((..(((((((.(((((((...(......)...)))))))))))))))))..))))))..))))). ( -43.40)
>DroEre_CAF1 406 119 + 1
CGGCACCGCCCGACGACCUGAUGGUCCUGGAGCAGCACGCCCUCUUCACCAAACUGAAGUUCGUGCAGUAUCUGAAGAGCAUCCGCAAGAUACUUGCCAAGCAGCGGAGGAAUCUAUGC-
.((((..(((((..((((....)))).))).)).(((((....(((((......)))))..)))))(((((((.....((....)).)))))))))))..(((..(((....))).)))- ( -39.30)
>DroYak_CAF1 406 120 + 1
UACCGCCGCCCGACAAUCUGAUGGUCCUGGAGCAGCACGCCCUCUUCACCAAACUGAAGUUCGUGCAGUAUCUGAAGGGCAUCCGCAAGAUACUCGCAAAACAGCGAAAGACUCUGUGCA
.......(((((...(((....)))..))).)).(((((....(((((......)))))..)))))(((((((...((....))...))))))).(((......(....)......))). ( -32.60)
>consensus
CACCACCGCCCGACGACCUGAUGGUCCUGGAGCAGCACGCCCUCUUCACCAAACUGAAGUUUGUGCAGUAUCUCAAGAGUAUCCGCAAGAUACUCGCAAACCAGCGGAAGAGUCUGUGCA
.......(((((..((((....)))).))).)).(((((..((((((......(((..(((((((.(((((((...(......)...)))))))))))))))))..))))))..))))). (-31.52 = -33.24 +   1.72)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,117,764 – 18,117,881
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 84.53
Mean single sequence MFE -34.65
Consensus MFE -24.10
Energy contribution -24.22
Covariance contribution 0.12
Combinations/Pair 1.07
Mean z-score -1.47
Structure conservation index 0.70
SVM decision value -0.02
SVM RNA-class probability 0.522596
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18117764 117 + 22224390
CCUCUUCACCAAACUGAAGUUUGUGCAGUAUCUCAAGAGUAUCCGCAAGAUACUCGCGAACCAGCGUAAGAGUCUGUGCAAGGCGACCACCCACGU---GCCAAAGGCGAUCCAGAAGAA
..(((((.............(((..(((...(((..((((((.(....)))))))((......))....))).)))..)))(((.((.......))---)))............))))). ( -34.10)
>DroSec_CAF1 446 117 + 1
CCUCUUCACCAAACUGAAGUAUGUGCAGUAUCUCAAGAGUAUCCGCAAGAUACUCGCAAACCAGCGGAAGAGUCUGUGCAAGGCGACCGCCCACGC---GCCGAAGGCGAUCCAGUCGAA
((((((((......)))))..((..(((...(((..((((((.(....)))))))((......))....))).)))..)))))((((((((..((.---..))..)))).....)))).. ( -35.90)
>DroSim_CAF1 446 105 + 1
CCUCUUCACCAAACUGAAGUUUGUGCAGUAUCUCAAGAGUAUCCGCAAGAUACUCGCGAACCAGCGGAAGAGUCUGUGCAAGGC---------------GCCGAAGGCGAUCCAGUCGAA
...(((((......))))).(((..(((...(((..((((((.(....)))))))((......))....))).)))..)))(((---------------(((...))))..))....... ( -33.30)
>DroYak_CAF1 446 120 + 1
CCUCUUCACCAAACUGAAGUUCGUGCAGUAUCUGAAGGGCAUCCGCAAGAUACUCGCAAAACAGCGAAAGACUCUGUGCAAGGCCACCGCCAAGGGAUCUUCGAAGGCGAUCCCCAUGAA
...(((((......)))))((((((.(((((((...((....))...))))))).(((......(....)......)))..(((....)))..((((((..(....).)))))))))))) ( -35.30)
>consensus
CCUCUUCACCAAACUGAAGUUUGUGCAGUAUCUCAAGAGUAUCCGCAAGAUACUCGCAAACCAGCGGAAGAGUCUGUGCAAGGCGACCGCCCACG____GCCGAAGGCGAUCCAGACGAA
((((((((......)))))...(..(((..(((...((((((.(....)))))))((......))...)))..)))..).)))................(((...)))............ (-24.10 = -24.22 +   0.12)

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 12:34:49 2006